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University of Split
Faculty of Natural Sciences, Mathematics and Kinesiology
PROPOSAL FOR THE POSTGRADUATE DEGREE PROGRAMME
Ph.D. programme in biophysics
Split, May, 2007

P O S T G R A D U A T E D E G R E E P R O G R A M M E I N B I O P H Y S I C S
DEGREE PROGRAMME
Postgraduate Degree Programme: Ph. D. Programme in

biophysics
Faculty of Natural Sciences, Mathematics and Kineziology

Nikole Tesle 12, HR-21000 Split
Phone: + 385 21 385 133
Fax: + 385 21 385 431
dekanat@pmfst.hr
http: //www.pmfst.hr
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Contents
1. INTRODUCTION............................................................................................................................................ 2
1.1. REASONS FOR ESTABLISHING THIS STUDY PROGRAMME ................................................................................................ 2
1.2. PREVIOUS EXPERIENCE IN THE IMPLEMENTATION OF SIMILAR PROGRAMMES .......................................................... 9
1.3. STUDENT MOBILITY SCHEME ............................................................................................................................................ 10
1.4. INTERNATIONAL PARTNERS / JOINT STUDY .................................................................................................................. 10
1.5. OTHER ELEMENTS AND NECESSARY INFORMATION ..................................................................................................... 11
2. GENERAL DESCRIPTION .......................................................................................................................... 13
3. DEGREE PROGRAMME .............................................................................................................................. 15
3.1. TYPE OF PROGRAMME ....................................................................................................................................................... 15
3.1.1. Arguments for organizing interdisciplinary PhD programme at the University of Split.............................................................. 16
3.2. PROGRAMME STRUCTURE .................................................................................................................................................. 18
3.3. COMPULSORY AND OPTIONAL ACTIVITIES ..................................................................................................................... 22
3.4. COURSE INFORMATION ..................................................................................................................................................... 24
3.4.1. Obligatory courses:............................................................................................................................................................................ 24
3.4.2. Elective courses: ............................................................................................................................................................................... 35
3.5. PROGRAMME REQUIREMENTS (DEGREE PLAN) ............................................................................................................. 69
3.6. THESIS SUPERVISION AND ACADEMIC ADVISING........................................................................................................... 70
3.7. TRANSFERABLE COURSES AND MODULES ....................................................................................................................... 71
3.8. COURSES AND MODULES OFFERED IN FOREIGN LANGUAGES..................................................................................... 72
3.9. ECTS RECOGNITION ......................................................................................................................................................... 72
3.10. ADMISSION TO DISSERTATION DEFENSE ....................................................................................................................... 73
3.11. CONTINUATION OF STUDIES ............................................................................................................................................ 73
3.12. CERTIFICATES REQUIREMENTS FOR LIFE-LONG EDUCATION ..................................................................................... 73
3.13. TAUGHT DOCTORATE COURSE REQUIREMENTS / NON-TAUGHT DOCTORATE ...................................................... 73
3.14. MAXIMUM DURATION OF STUDY...................................................................................................................................... 73
4. INSTITUTIONAL INFORMATION ........................................................................................................... 75
4.1. LOCATION ........................................................................................................................................................................... 75
4.2. PREMISES AND EQUIPMENT .............................................................................................................................................. 75
4.3. RESEARCH AND DEVELOPMENT PROJECTS RELATIVE TO THE PROGRAMME ............................................................ 76
4.4. INSTITUTIONAL SUPERVISION .......................................................................................................................................... 83
4.5. CONTRACTUAL ASPECTS (STUDENT – INSTITUTION) .................................................................................................... 84
4.6. LECTURERS .......................................................................................................................................................................... 85
4.7. FIELD WORK AND PROFESSIONAL PRACTICE (RESEARCH BASES AND PRACTICE SITES)......................................... 181
4.8. OPTIMAL NUMBER OF STUDENTS ................................................................................................................................... 181
4.9. COST ASSESSMENT (PER STUDENT) ................................................................................................................................ 181
4.10. FINANCIAL ASPECTS ......................................................................................................................................................... 181
4.11. QUALITY ASSESSMENT METHODS .................................................................................................................................. 183
5. ADDITIONAL REMARKS ...........................................................................................................................184
5.1. APPENDIX I: SUPPLEMENTARY COURSES ..................................................................................................................... 184
5.2. APPENDIX II: LIST OF ABBREVIATIONS ........................................................................................................................ 187
5.3. APPENDIX III: OFFICIAL LETTERS OF INTENTION TO PARTICIPATE IN THE EXECUTION OF THIS PROGRAMME
FROM THE RUĐER BOŠKOVIĆ INSTITUTE IN ZAGREB, FROM THE MEDITERRANEAN INSTITUTE FOR LIFE SCIENCES IN
SPLIT AND FROM THE UNIVERSITY OF SPLIT MEDICAL SCHOOL ............................................................................................ 188
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1. Introduction
Reasons for establishing this study programme
• Interdisciplinary sciences such as the biophysics have increasingly important role in

the development of science and society
An important conceptual role of science in human society is to provide rational answers to

complex challenges of modern time. Interdisciplinary sciences such as biophysics,
bioinformatics, bioenergetics, medical physics, mathematical biology, functional genomics,
system biology, nanobiology, ecology … are increasingly used to achieve such goal. Indeed,
this thesis is clearly illustrated by recent European University Association (EUA) report :
http://www.eua.be/eua/jsp/en/upload/Doctoral_Programmes_Project_Report.1129278878120.pdf
about need for new EU doctoral programmes where the word interdisciplinary appears on
almost every page. For that reason it is not surprising that many foreign universities offer
graduate studies of interdisciplinary sciences. Also, biotechnological and pharmaceutical
companies exhibit increasing demand for such expert profiles.
The Croatia has been slow in exiting from traditional division of natural sciences among
physics, chemistry and biology (dating from 19-th century), toward introduction of
interdisciplinary sciences that are gaining in importance and should have good perspective in
Croatia too. Molecular biophysics has similar subject study as biochemistry, the study of
biomacromolecules and their interactions, but it approaches this study in a different way,
bearing upon it the full power of physical principles, experimental methods, mathematical
modeling methods, and a characteristic mode of thinking developed by physicists for problem
solving in physics. It is only to be expected that biophysicists are fine tuning a set of tools
developed by physicists in order to make them more suitable for biological and medical
research. This happened in medical physics with spectroscopic methods such as the nuclear
magnetic resonance (NMR), ultrasound and X-rays for organ imaging, but also in molecular
biophysics with applications of NMR and X-ray spectroscopy for solving the structure of
biomacromolecles. Present biotechnological revolution would be impossible without experts
from the field of biophysics with facility in using sophisticated physical instrumentation. Such
experts are also uniquely capable of creating mathematical models which are the best
compromise between reality simplification and uncovering cause and effect relationships in
biology.
In countries with strongly developed life sciences the usual practice is that students with
excellent grades and B.Sc. or M.Sc. from different natural sciences (physics, chemistry,
biochemistry, biology, medicine) can enroll into the graduate programme in biophysics. Such
practice ensures that interdisciplinarity is achieved among student body too, because
physicists, biochemists, molecular biologists, electrical engineers, computer scientists and
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medical doctors can all be admitted into the Ph.D. biophysics programme. In addition, current
research and educational practice is geared toward removing the barriers among classical
scientific disciplines and younger interdisciplinary sciences. For instance, present day PhD
students of biophysics need to know fundamentals of structural bioinformatics as well. They
should also become able and ready to transfer quickly between one and another
interdisciplinary science, depending on changes in their scientific interest or requirements of
their scientific problem.
Interdisciplinary graduate studies have not been stimulated enough in Croatia. This is true
for bioinformatics, which was not introduced until recently as the graduate study orientation in
Croatia, probably due to its very recent origin about 15 years ago, but it is also true for
biophysics, which is present in Croatia for 35 years, however, only as the branch of physics. In
practice, students with degree in biochemistry, molecular biology or medicine have not been
allowed to enter the graduate programme in biophysics. Clearly, such boxing in of biophysics
into only physics can largely destroy the interdisciplinary character of biophysics. The analysis
of biological systems and phenomena by physicists using physical principles and methods is
biophysics of course, but research workers educated through present graduate programme in
physics often do not have enough respect toward achievements and methods developed in
biochemistry, or have difficulties in understanding the complexity of biological and medical
aspects of biophysics. Some are even afraid of attacking biological problems.
The USA and EU practice that physicists, molecular biologists and medical doctors have
equal opportunity to enroll into the Ph.D. programme in biophysics should be established in
Croatia too. Of course, supplementary courses from biology and chemistry for physicists or
from mathematics and general physics for biologists and medical doctors should be completed,
preferably before enrolling into the Ph.D. study programme in biophysics. We have in-built
this idea in the present proposal for interdisciplinary Ph. D. programme in biophysics. The
stimulation of interdisciplinary graduate studies is in the long term national interest of Croatia.
It is indeed important to anticipate such long-term national and global educational priorities,
because high quality graduate programmes are built to last not only 3-5 years, but much
longer. The long term national interests of Croatia are connected with biotechnological
revolution, with biomedicine, and with the preservation of our present genetic richness of
animal and plant species throughout ever faster global and local changes in natural
environment. Our study programme aims to educate experts capable of using interdisciplinary
methods and principles required to confront these challenges.
Courses offered by our Ph.D. programme are a combination of focused interdisciplinary

lectures leading directly toward thesis research and of courses offering fundamental
interdisciplinary biophysical background expected of biophysicists. The choice of courses will
depend on international recognition of course leaders. We have given priority to those research
workers who have developed vibrant international collaborations and ambitious and realistic
research programmes. The interdisciplinarity of offered courses and of the whole study
programme is also expressed through creative connections among physics, chemistry, biology,
ecology, mathematics, informatics and medicine, with the same goal of better understanding of
biological structures and processes at all levels, from biologically important small molecules,
to biomacromolecules, biochemical networks, organelles, cells, organs, organisms, species,
ecological networks and even biosphere.
• Interdisciplinary study programme in biophysics as the part of state initiative to

connect Croatian scientists from abroad and in the country and to ensure more
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uniform development of scientific research by strengthening the study of life sciences

in the southern Croatian region around Split (Dalmatia).
The proposed graduate study is the study of the Faculty of Natural Sciences, Mathematics
and Kinesiology from the University of Split (PMFST) with equally important participation in
its execution by the Bošković Institute in Zagreb (IRB) with collaboration of the University of
Dubrovnik. Other scientific institutions from Split, Zagreb, and from abroad also participate in
proposed study programme, which is necessary due to interdisciplinary character of this study.
For instance, in addition to the IRB, the Mediterranean Institute for Life Sciences (MedILS)
has also agreed to participate in the execution of this programme (Appendix III). The courses
will be mostly held at the University of Split and at the Ruđer Bošković Institute in Zagreb.
Interdisciplinary seminars, summer schools, get-together workshops of course leaders and
students looking for advisers and similar activities involving foreign experts, will take place
outside Split and Zagreb as well, for instance in Dubrovnik, Zadar and Rovinj at the Adriatic
coast, in collaboration with academic institutions which cooperate with the University of Split
Ruđer Bošković Institute and MedILS. Students will have opportunity to perform a part of
their research work at foreign institutions collaborating with us through this study programme.
We consider the proposed study as the scientific and educational nucleus of the broad state
initiative to connect natural scientists from Croatia with natural scientists living abroad (The
PKHZ initiative from November 2004: www.mzos.hr/pkhz). This initiative noticed that almost
all research in natural sciences in Croatia is concentrated in Zagreb (the capital of Croatia) and
recommended that the study and research from life sciences should be strengthened in Split
(the second largest city in Croatia located at the Adriatic coast about 400 km from Zagreb).
Well meaning advices of our colleagues from abroad are very important and we took them into
account during the construction of this interdisciplinary study programme. Such advices will
be very valuable too during writing grant proposals to international institutions such as the EU,
EMBO, and NIH. In addition to taking their advices, well established research workers from
abroad, working in the field of biophysics, nanophysics, statistical physics, molecular physics,
quantum chemistry, molecular dynamics, environmental physics, and neuroscience, have been
included directly into our study programme through elective or obligatory courses, through
planned seminars and workshops, through guiding research efforts of our students in their
laboratories and through mentoring of Ph.D. research topics offered to our students. In short,
we decided to offer original study programme which will emphasize interdisciplinarity and
stimulate better connections among scientists interested in biophysics, both at home and
abroad.
Since Split region has already good starting position to develop different life sciences
(Mediterranean Institute of Life Sciences, Oceanographic Research Institute, Medical School,
B.Sc. and M.Sc. study of natural sciences at different University of Split institutions, large
hospitals with in-house research departments) there is no doubt in our mind that proposed
Ph.D. study, will, if accepted, open the door for other such interdisciplinary graduate studies as
well. Our offered vision of biophysics specialization up to the M.Sc. degree level in Split has
already received a broad support of scientists from Croatia, from abroad, and of foreign
biophysicists of well known stature. That study programme (3 years of physics plus 2
additional years of biophysics specialization) has been approved, because it received excellent
referee marks. Even broader support of well known biophysicists from abroad and from
Croatia has been gathered for the present proposal of the Ph.D. study programme in
biophysics.
Research workers from different life-science fields from Split (medical physics,
biophysics, neuroscience, human genetics, ecology, microbiology, biomechanics,
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mathematical physics, chemical physics, biochemistry and molecular biology) are already
included in our study programme. Our desire was to include in this study programme several
different research and academic institutions from Split. Indeed, our course leaders are not only
from our Faculty of natural sciences, but also from the MedILS Institute, from the Medical
School and from the Institute of Oceanography and Fisheries in Split. Our scientific colleagues
from the Mediterranean Institute for Life Sciences in Split, such as Bojan Žagrović, Miroslav
Radman and Ivan Đikić, are also willing to help the excellence of this Ph.D. programme.
Miroslav Radman has agreed to serve in the Study Committee. We expect from them too a
fruitful collaboration.
The development of such interdisciplinary graduate studies in the Split region will serve as
the strong stimulus for technological development too, will keep talented students inside our
country (diminishing the brain drain) and will decrease expenses of students from Split
desiring to achieve high quality undergraduate and graduate education. It is important to point
out that brain drain is also present among different Croatian regions mostly in favor of the
Zagreb region. For instance, out of 100 high school students that excel in Split in natural
sciences and mathematics, less than 10 per year are choosing some academic institution from
the University of Split to continue their studies.
• Present plans of constructing new buildings at the University Campus, where

research laboratories and student workshops from different fields of natural sciences
will be located, are not to a satisfactory degree accompanied with research and
educational study projects which will be taking place in these new facilities.
The Ph.D. study initiative in biophysics is closely connected with plans to build up new
University Campus building, which will house the Departments of Physics, Chemistry,
Biology and Mathematics. The laboratories for biophysics, bioinformatics, environmental
physics, modeling physics, ...will also be located in this new facility. With financial resources
needed for building construction already ensured it is much more difficult goal to define
exactly what modern instruments will be necessary to ensure productive research in these
laboratories for students, and research workers. Even if building construction is finished not
two (as presently promised) but four years from now, it is already wise to start planning
research and educational projects that will be taking place in new larger facilities. As a rule
needed instrumentation for interdisciplinary research in life-sciences is less expensive than the
experimental set up for the research in pure physics. However, planning the acquisition of
financial resources and experimental facilities can be best done by experts in charge of specific
projects with clear, ambitious and realistic research and educational programme geared toward
international collaboration.
Planned interdisciplinary graduate study of biophysics has anticipated this need by

proposing regular workshops in Split about novel challenges in life sciences which need input
from creative collaboration of physicists and molecular biologists. These workshops (twice per
year for about one week) will be lead by well known senior scientists from abroad (mainly of
Croatian origin) with a goal to jump-start the development of interdisciplinary life sciences in
the Split region of Croatia (central Dalmatia). We are certain that planned collaboration of
foreign and in situ scientists will produce high quality, competitive and productive research
programmes, which will be able to return initial investment in the experimental facilities of
new laboratories. In addition, as mentioned earlier, our students will be able to perform a part
of their Ph. D. research programme in foreign laboratories led by top experts in the field.
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• Competitive research from the field of biophysics will stimulate the society
development based on knowledge acquisition and application.
The focus of this study programme is the biophysics of cells and macromolecules found in
living cells. However, we have also rich offering of elective courses from the field of medical
physics and biomedicine for those students (for instance students with medical degree) who
are interested in medical applications of biophysics. The research from the fields of cell
biophysics and biophysics of macromolecules is the next important step stimulated by the
successful outcome of the international decoding projects involving not only the human
genome but also the genomes of many other species. The knowledge of amino acid order in
protein sequences coded by known genes is not enough for modern applications in
biotechnology and medicine. It is also necessary to determine or calculate probable 3D protein
structure, which emerges in the cell either spontaneously or with the help of chaperones, but in
either case as directed by the protein folding rules popularly known as the «second half of the
genetic code». These rules are still under active investigation and researchers are still unable to
predict accurately how the protein will fold into its final, biologically functional, 3D structure.
Investigating protein folding rules is very competitive and extremely important goal. Modeling
structure and function of soluble and membrane proteins and drug interactions with proteins is
of extraordinary interest for a wide area of possible applications. For membrane proteins,
predicting their structure and modeling their function is not only necessary complementary
research to experiments, but also very often the best possibility for rational planning and
execution of experiments. It is well known that membrane proteins are biochemical targets for
more than 50% of all drugs.
The Croatia should have secure entrance to such original competitive research goals. The
proposed study programme anticipates such a need through planned interdisciplinary
collaborations and through planned seminars about new challenges in life sciences. With wise
investment in interdisciplinary life sciences Croatia can become the exporter of intellectual
services from that area, which would sooner or latter have positive influence on local plans for
development of biotechnology, pharmacology, and medicine. One such example, already eight
years in existence, is the web server SPLIT from the University of Split for predicting the
topology of integral membrane proteins based on their sequence. It daily receives many
requests for sequence analysis from renewed laboratories all over the world (up to now from
52 different countries and 309 foreign universities including all best universities in the world)
and returns (exports) its predictions automatically in seconds (a total of 11768 analysis during
three years, from March 2004.). The popularity of this web server increased even more
recently after comparative evaluation and analysis of transmembrane helix predictors has been
published (Cuthbertson i suradnici, Protein Engineering, Design & Selection vol. 18 no. 6 pp.
295–308, 2005), which selected the SPLIT 4.0 performance as the best in the world.
During their study our students will have excellent opportunities to combine theoretical
and experimental work. Students will be able to perform experiments in laboratories of
biophysicists who accepted the collaboration on this study programme. These are colleagues
from the Ruđer Bošković Institute in Zagreb (V. Svetličić, D. Vikić-Topić, K. Pavelić, I.
Weber, A. Ambriović-Ristov, D. Ražem, and others), from the MedILS Institute in Split (B.
Žagrović), from the Oceanographic Institute in Split (N. Krstulović), from the Medical School
in Split (D. Eterović, Z. Đogaš and J. Terzić), from University of Trieste, Italy (A. Tossi),
from University of Maribor, Slovenia (M. Brumen), from University of Ljubljana, Slovenia
(R. Podgornik), from University of Queensland, Australia (B. Martinac), from University of
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Melbourne, Australia (F. Šeparovic), from ETF, Swisserland (D. Pavuna), from University of
Bordeaux and INRA, France (R. Dewar) and others.
In somewhat longer time range, about five years from now, we plan to gather support for
the goal of establishing University Center for interdisciplinary research in life sciences. Such
Centers are quite common in many universities, because it makes sense to concentrate more
expensive equipment in one place, where it is available to all interested researchers. This
initiative emerges quite naturally from the proposed interdisciplinary study programme, and it
follows the developmental pattern of modern universities, which breaks the traditional barriers
among different disciplines. Students and young research workers are then given the
opportunity to be better prepared for novel challenges of life sciences, in biophysics,
functional genomics, proteomics and structural bioinformatics, which usually do not respect
artificial barriers among physics, chemistry, informatics, mathematics, biology and medicine.
• Planning and establishing collaborations relevant to proposed study programme.
The collaboration on construction of this study programme was approved on October 20,
2005 by the Scientific Council of the Ruđer Bošković Institute in Zagreb, and (on the same
date) by the Faculty Council of the Faculty of Natural Sciences, Mathematics and Kinesiology,
University of Split, Split. The collaboration in terms of responsibility for regular or elective
courses of our Ph.D. study has been established with following research workers from the
Ruđer Bošković Institute in Zagreb: V. Svetličić, A. Ambriović-Ristov, B. Lučić, I. Weber, G.
Baranović, B. Rakvin, D. Vikić-Topić, Sanja Tomić, A. Graovac, N. Žarković, K. Pavelić, S.
Kraljević Pavelić, M. Sedić, K. Hock, M. Baus Lončar, and D. Ražem. We expect soon to
have a formal agreement as well between our two institutions, which would ensure high
quality of execution for this study programme. This agreement will be in accord with the letter
of intention (Appendix III) and with existing agreement from November 2005 with respect to
scientific and educational collaboration between University of Split, Ruđer Bošković Institute
in Zagreb, University of Dubrovnik and University of Zadar. We also expect the establishment
of mutually beneficial collaboration with colleagues from the MedILS Institute in Split (B.
Žagrović, M. Radman, I. Đikić) according to agreement we reached with the MedILS
(Appendix III).
Our students will be stimulated to actively participate in high quality interdisciplinary
conferences/workshops, such as those that are regularly organized by colleagues I. Đikić in
Dubrovnik, D. Pavuna in Cavtat, G. Pifat in Rovinj, and A. Graovac in Dubrovnik (Master
Classes of UNESCO). For instance, for the participation in the International Summer School
of Biophysics: Supermolecular Structure and Function our students will earn four ECTS
credits. In addition, we shall be regularly inviting prominent participants of such conferences
to deliver one or more lectures in Split for our students and research workers (the initiative
about regular workshops on modern challenges in interdisciplinary natural sciences, which we
mentioned before). Student’s participation in these workshops will be obligatory.
The collaboration in terms of responsibility for elective courses of our Ph.D. study has
been established with the colleagues from the Faculty of Science, University of Zagreb
(PMF)(V. Paar, S. Supek, M. Vrtar), and with the colleagues from the Institute of Physics in
Zagreb (IFS)(Silvia Tomić). The collaboration also exists with the Medical School, University
of Split (D. Eterović, Z. Đogaš, J. Terzić), with the Institute for Oceanography and Fisheries,
Split (IZOR)(N. Krstulović) and with the MedILS (B. Žagrović, M. Radman, I. Đikić). We
shall establish the collaboration with the PMF-Zagreb such that students of their study
programme in biophysics will be allowed to enroll some of our courses, and that our students
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will be allowed to enroll some of their courses. We shall also aim to establish collaboration
with other research and educational institutions in the country with interest in biophysics, such
as the Medical School University of Zagreb, Faculty of Pharmacy and Biochemistry
University of Zagreb, Institute for Medical Research and Occupational Health, Zagreb,
Institute of Physics, Zagreb, University of Osijek, Osijek …
In neighboring Slovenia we have established the collaboration with colleagues M. Brumen

(elective Ph.D. course) and R. Podgornik (obligatory M.Sc. course, and elective Ph.D. course).
University of Split has permanent agreement with the University of Maribor, Slovenia, which
we used recently to establish scientific and educational collaboration in the field of biophysics
with the research group of Prof. Milan Brumen at Pedagogical and Medical Faculty,
University of Maribor.
The collaboration also exists with researches R. Dewar from France (elective Ph.D. course
and research workshop), H. Lutz from Germany (elective Ph.D. course), B. Žagrović from
Switzerland (elective Ph.D. course, part of obligatory course on physical methods used in
biophysics and summer school research workshop), G. Kilić and V. Parpura from USA
(elective Ph.D. courses), A. Tossi from Italy (student’s research connected with their Ph.D.
thesis work) and with other researchers.
The proposed Ph.D. study in biophysics has already stimulated the collaboration among
different institutions from the University of Split through their researchers who offered
elective Ph.D. courses for the proposed study in biophysics. These are D. Eterović, Z. Đogaš
and J. Terzić from the Medical School in Split, B. Žagrović from the MedILS Institute in Split
and N. Krstulović from the Institute of Oceanography and Fisheries, Split.
In the longer term the proposed study has good potential to stimulate the collaboration with
different research institutes, university institutions/departments, and with biotechnological and
pharmaceutical companies. In 5 to 10 years we expect to have regular productive collaboration
among University of Split, Ruđer Bošković Institute in Zagreb, Medical schools in Split and
Zagreb, MedILS Institute in Split, and Institute of Oceanography and Fisheries, Split, as well
as with some pharmaceutical companies. In particular we expect this study to generate projects
of development and patenting of novel antibiotics, which should be interesting for drug
producing industry and for pharmaceutical companies such as the PLIVA from Zagreb.
• The comparison with similar study programmes offered by well known foreign
universities.
Similar Ph.D. study programmes are easier to find in the USA than in the EU, because
Europe is a bit slower than the USA in introducing interdisciplinary study programmes.
Nevertheless, high quality such programmes exists not only in England, Italy and Germany,
but also in smaller European countries such as Netherland and Denmark.
We shall cite here two examples of Ph.D. programmes in biophysics from USA:
Harvard - http://www.fas.harvard.edu/~biophys/
Johns Hopkins University http://www.jhu.edu/~pmb/program-curriculum.html
and several from Europe:
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Great Britain, University of Oxford: http://biop.ox.ac.uk/www/top.html
Germany, Max-Planck Research School - http://www.mpibp-frankfurt.mpg.de/research-school/
Italy – SISSA, Trieste: http://www.sissa.it/sbp/web/index.php
Netherland, BioCentrum, Amsterdam: http://www.science.uva.nl/biocentrum/
Denmark - http://www.memphys.sdu.dk/graduateschool/ .
The proposed study programme is in accord with the third cycle reform of higher
education according to Bolognia declaration which encourages the creation of interdisciplinary
studies in Europe. It must be pointed out that majority of such programmes have focus on
experimental biophysical research. This is only to be expected, because the biophysics is the
science which is at least 95% devoted to experimental research. It is quite natural then that
students can enter graduate programme in biophysics after earning their B.Sc. or M.Sc. degree
in biochemistry or molecular biology. They can then simply continue to work with system
already well known to them (biomacromolecules or certain organelles or cell types), but
during their study they also learn applications of new biophysical methods, mathematical
modeling and different way of thinking about research problems which is more commonly
used among physicists.
The proposed study offers fundamentals of bio-system modeling. In addition, it offers
training in different experimental methods through work in biophysical laboratories at the
Ruđer Bošković Institute. Anticipated collaboration will medical schools, research institutes
and pharmaceutical companies will also strengthen the experimental part of this study
programme.
Previous experience in the implementation of similar

programmes
In accord with Bologna reform our Faculty (PMFST) has offered the 3+2 study programme in
physics with different two years orientations, one of them being the biophysical orientation. That
programme had positive review and its first school year (2005/2006) has been completed. The
construction of the M.Sc. degree biophysical programme has brought to us valuable experience and
wide contacts with biophysicists inside and outside Croatia, which were very helpful for the present
proposal of the Ph.D. programme in biophysics. The Ruđer Bošković Institute from Zagreb has a long
tradition not only in biophysical and interdisciplinary research, but also in graduate education on
interdisciplinary topics. The MedILS Institute in Split has only started with its work but already has
vibrant young community of researchers working in the field of biophysics and bioinformatics.
During its initial construction phase this study programme will be lead by the ten member
Steering committee consisting of D. Juretić (PMFST)(committee chair), V. Svetličić (IRB-
Zagreb)(committee Co-chair), M. Dželalija (PMFST), D. Eterović (Medical School, University of
Split), A. Graovac (PMFST, and IRB-Zagreb), B. Lučić (IRB-Zagreb), S. Marčelja (PMFST and The
Australian National University, Camberra), M. Radman (MedILS, Split and Necker, University of
Paris, France), Silvia Tomić (IFS, Zagreb), N. Žarković (IRB-Zagreb). We anticipate that other
biophysicists, biomedical experts and structural bioinformaticians from IRB, MedILS, and Universities
from Split and Zagreb will join the committee membership latter or replace retiring members. In the
following text we shall use the same term Study Committee to denote the present ten member
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committee for the construction of a study programme and future Study Committee, which will be
formed in the case if this programme is approved. Prof. Dr. Stjepan Marčelja is the best known
biophysicist of Croatian origin with more than 6000 citations of his research papers and excellent
contacts with biophysicists all over the world. Prof. Dr. Miroslav Radman is the founder of MedILS in
Split and well known member of the French Academy of Sciences. Prof. Dr. Davor Juretić has after his
Ph.D. in biophysics from USA (The Penn. State Univ.) published wide variety of research papers from
physics, biophysics, bioenergetics, microbiology, and structural bioinformatics. Prof. Dr. Ante Graovac
has also shown through his more than 110 published CC papers that he has enviable experience in
creative interdisciplinary research involving physics, chemistry, biology and mathematics. Dr. Vesna
Svetličić is the president of Croatian biophysical society and renewed biophysicist. Dr. Silvia Tomić is
higly cited physicist and biophysicist from the Institute of Physics, Zagreb, who recently performed
excellent studies of DNA solutions. Prof. Dr. Mile Dželalija and Prof. Dr. Neven Žarković are both well
known organizers of international and interdisciplinary study programmes in addition to being top
experts in their fields. For instance, Dr. Neven Žarković is international expert for oxidative stress. Dr.
Bono Lučić is expert modeler of structure-function relationships for biologically active molecules.
Prof. Davor Eterović is well known expert in biophysics, biomedicine and medical physics. The
international recognition of committee members can be judged according to recently introduced h-
number (the maximal number h of papers having h or more citations). It is 48, 36, 18, 16, 15, 15, 14,
13, 11 and 7 respectively for M. R., S. M., S. T., V. S., A. G., M. Dž., B. L., D. J., N. Ž. and D. E.
Student mobility scheme

All of proposed courses will be taught in English language in the case if we succeed in
establishing an international student body. This is of course an important requirement to facilitate
student mobility and participation of foreign students in this study programme. This is the reason our
course leaders as a rule mention in the description of their course that lectures can be held in English
language. We are open to students who graduated and earned their medical degree from medical school,
or have degree in physics, biochemistry, molecular biology,…from all European countries, including,
of course, Croatia neighbors, who wish to enroll into the proposed Ph.D. study programme. Students
mobility will be ensured by consistent application of the ECTS credit system. The most important is
student’s desire to study biophysics, good grades from previous study and clearly shown preference for
scientific research. Our students are expected to spend a part of their studies in biophysical laboratories
from Europe, USA and Australia, according to preliminary agreements we have with research workers
such as Prof. Dr. Milan Brumen, Maribor, Slovenia, Prof. Dr. Alex Tossi, Trieste, Italy, Dr. Roderick
Dewar, Bordeaux, France, Dr. Gordan Kilić, USA, Dr. Vladimir Parpura, USA and other colleagues.
International partners / Joint study

At the present time we have established contacts with several colleagues from foreign
universities who would like to contribute to execution of our study programme (see above). Most are
interested in contributing both to educational and research component of our study programme. Also,
most of them have offered the possibility to receive our students in their laboratories for limited amount
of time (from several months to one year) which will broaden the experience of our students and
decrease the expenses connected with their Ph.D. education. All of our foreign collaborators expressed
their readiness to visit University of Split and to participate in research seminars, workshops,
conferences and educational and scientific activities. In the case of universities (Trieste, Maribor) which
already have formal agreement about collaboration with the University of Split, we plan to activate such
agreements for the specific host laboratories, foreign professors and our students. We shall use such
existing agreements or help to create new agreements between Croatian partner institutions (PMF-Split
10
and IRB-Zagreb) and universities or research institutes from different EU countries in order to find new
research partners for research/education in biophysics and in order to attract graduate students. The lack
of such agreements with other universities will not be an obstacle, because we already have many
examples of students from Split visiting laboratories of foreign professors working there for some time
and returning back to Split with valuable experience and enough interesting and novel results to finish
their Ph.D. thesis work. The Medical School from Split took the lead in such practice, but there is no
reason why our Faculty of Natural Sciences, Mathematics and Kineziology would not follow this lead
in the case of high quality interdisciplinary study programmes that are being offered in 2007.
We plan to use existing or novel collaborations with other EU universities in order to be

able to award European Doctorate to our students. The idea of a European Doctorate (European
PhD or Doctor Europaeus/Europaea) originated from an informal initiative in 1991 of the former
Confederation of European Union Rectors’ Conferences concerning requirements for the awarding
of a “Doctor Europaeus”. The proposed requirements included:
1. The PhD thesis defence will be accorded if at least two professors from two higher
education institutions of two European countries, other than the one where the thesis is
defended, have given their review of the manuscript;
2. At least one member of the jury should come from a higher education institution in another
European country, other than the one where the thesis is defended;
3. A part of the defence must take place in one of the offi cial languages, other than the one(s)
of the country where the thesis is defended;
4. he thesis must partly have been prepared as a result of a research period of at least one
trimester (a minumum of three months) spent in another European country.
In any case, the proposed Ph.D. programme must become in a future an easily recognized joint
study programme, which will be mostly located in attractive Croatian locations such as are Zagreb
(IRB) and Split (PMF and MedILS), and partially at other higher education EU institutions outside
Croatia, which are collaborating with us on this study programme. The study programme is already
constructed in such a way that it would be easy to make necessary arrangements for awarding European
Doctorate. To achieve this goal and to attract high quality graduate students from Croatia and from
aboard we plan to organize mentor’s fair workshops as a part of some already established summer
schools at Adriatic coast. In this way the Ph.D. thesis topics offered specifically for this study
programme (see Section 4.3), prospective mentors offering such topics, and prospective graduate
students, will be brought together in relaxed and informal atmosphere. We shall also encourage the
initiatives of our students to organize annual workshops to present their results, where foreign students
and students from other PhD programmes in Croatia will be invited too. In this way, our students will
gain the opportunity to compare themselves with the corresponding international cohorts.
Other elements and necessary information

One important characteristic of proposed Ph.D. study programme in biophysics is that it allows
the enrolment of students with degree in different fields of natural sciences including medicine.
Supplementary courses are required for students of different background (biochemistry for students
with the M.Sc. in physics, physics for students with the M.Sc. in biochemistry, or with M.D....), and, if
possible, should be completed before enrolment into this study programme, but all students, irrespective
of their background, are granted an equally valid Ph.D. in biophysics after successful Ph.D. study. We
consider this characteristic of the proposed study of key importance for the development of
interdisciplinary study programmes, because the interdisciplinarity is largely lost when, for instance, the
biophysics is forced to be the branch of physics and nothing else (as is the current practice in Croatia).
11
The Ph.D. title after successful thesis defence and study completion should be:
«Interdisciplinary Ph.D. in natural sciences: biophysics». The alternative possibility is that Ph.D. title
takes into account student's M.Sc. background. For instance, students with M.Sc. in physics will after
graduation become: «The Ph.D. in physics with biophysics orientation», students with M.Sc. in biology
will become: «The Ph.D. in biology with biophysics orientation», students with medical degree will
become “The PhD in medicine with biophysics orientation” etc. In either case, the proposed programme
aims to raise biophysics in Croatia to equal position, among other natural sciences, where it rightfully
belongs. In fact, this is already the case for quite some time (several decades) in countries with strong
life sciences. Internationally, biophysics is already an accepted discipline.
Students with M.Sc. in physics, who already had biophysics specialization, will have
considerable advantage if they decide to enrol our Ph.D. programme as well. No additional or
supplementary courses will be required of them. The overlap of present M.Sc. programme in physics
with proposed Ph.D. study programme (both from the PMF-Split with biophysics specialization) may
seem to exist in some elective courses for the Ph.D. programme. Such courses have been chosen due to
their high quality and course leaders have modified the content and planned execution according to
usual expectations for the Ph. D. course standards (D. Ražem, M. Vrtar …). Since we have a great
number of elective courses, students of physics graduating the biophysics orientation (3+2) can easily
choose courses different from ones they already had.
Otherwise, the M. Sc. biophysics orientation and the Ph.D. doctoral programme in biophysics at
the University of Split are independent of one another. The biophysics orientation (two additional years)
of the M.Sc. physics programme in Split, which was constructed in accord with the Bologna Process,
can start no sooner than in the school year 2008/2009. Students earning their M.Sc. degree there can
enter our Ph.D. programme no sooner than in the school year 2010/2011. However, the proposed Ph.D.
study programme can start already in the school year 2007/2008 for students with M.Sc. or equivalent
degree coming from other study programmes, of course assuming the prerequisites have been fulfilled
(the programme passes the review, the closure of the financial construction for this programme).
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2. General description
Programme title The Ph.D. study in biophysics

Research area Interdisciplinary natural sciences: biophysics and biomedicine
Institutions Proposed by University of Split
Participating University of Split, Faculty of Science,
institutions Ruđer Bošković Institute in Zagreb
Mediterranean Institute for Life Sciences in Split
University of Split, Medical School
Duration 3 years (maximum 6 years)

ECTS 180
Development The development of doctoral study programmes with emphasis on
strategy interdisciplinary programmes is the common developmental strategy of the
University of Split (Faculty of Natural Sciences, Mathematics and
Kinesiology) and of Ruđer Bošković Institute in Zagreb. Greater mobility
of doctoral students will be ensured at the national and international level
through broad international collaborations and through obligatory
application of the ECTS credit system. The members of the Steering
Committee for this study programme: S. Marčelja, M. Radman, V.
Svetličić, Silvia Tomić, A. Graovac, M. Dželalija, N. Žarković, B. Lučić,
D. Juretić and D. Eterović are highly cited and productive scientists who
are active in publishing research papers in high quality scientific journals
with research topics ranging from biophysics to biomedicine. All are
project leaders and collaborators on interdisciplinary research topics mainly
from the field of biophysics.
Innovative Interdisciplinarnarity, wide collaboration with other research and academic
character of the institutions in Split, in Croatia and abroad. Entrance in the study
programme programme with background from several different natural sciences and
from biomedicine, instead of only with the physics degree.
Admission B.Sc. or M.Sc. in some of natural sciences or equivalent medical degree.
requirements Demostrated preference for scientific work. Positive outcome of the
selection process by the Study Committee among prospective candidates.
Before enrolling into the first year of the doctoral study the candidate is
expected to submit following documents and to perform following actions:
- The enrollment form prepared by the University of Split must be
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filled out.
- Two recommendations of well known experts are expected to arrive
on candidate behalf.
- A candidate must describe his/her reasons for chosing this doctoral
study (why biophysics, candidate scientific interests, future plans)
in a document not longer than two printed pages.
- The official transcription of candidate grades and the copy of M.Sc.
and/or B.Sc. diploma must be also enclosed (in the case of the B.Sc.
diploma it is expected that it is for the four to six year study period
ending with a degree from biology, physics, chemistry, informatics
or medicine). As a rule, for a grade system from one to five, average
grade must be at least 4.0.
- A candidate is expected to pass the interview session with Study
Committee members.
- A candidate is expected to deliver a short public talk.
- Awards obtained during previous study
- Published scientific works in international journals and/or
conference papers or abstracts (if any) must also be enclosed.
Students are selected through public competition and through Study

Committee analysis of submitted documents and performed actions. The
Study Committee will give special attention to indicators of student affinity
for independent/original research (for instance strong recommendations of
well known experts or high quality of published undergraduate research).
The Book of rules, which will be prepared for this study program, will
associate certain number of credits for each of above mentioned admission
requirements so that candidate lacking credits for one requirement can still
be admitted if total number of collected credits are above certain threshold.
Learning High quality Ph.D. study of interdisciplinary science, such as the proposed
outcomes and study, ensures required flexibility when seeking employment in medical,
competences pharmaceutical or biotehnological insitutions and research institutions as
well, that require broadly educated young experts with research experience.
Acquired competences could be also used for futher specialization anywere
in the world, but in order to aleviate the brain drain of young experts from
Croatia, organisers of this study will give preference to postdoctoral studies
in laboratories which have such agreement with us that includes the expert
return to Croatia after one to three years of specialization.
Qualification Doctor of Philosophy (Ph.D.).
awarded We shall arrange with the University of Split that our students after
successful thesis defense can get additional written statement
accompanying their diploma specifying: attended courses, laboratories
where research was performed, acquired skills during advanced study of
biophysics and the scientific field from which student entered the
programme.
14
3. Degree programme
Type of programme
The full time-study can last at most four years. The part-time study can last at most six years.
The Study Committee can exceptionally allow study period longer than four years if such study period
is still shorter than maximal length regulated by law. For instance, the Study Committee can decide for
students lacking necessary background that the time needed to go through supplementary courses will
be added to the four year limit.
Most courses offered at the Ph.D. level study of biophysics are directly leading to the
specialized Ph.D. thesis work, although some general courses on experimental techniques and
modelling methods are also available such that students can learn standard methods from biophysics,
biomedicine and molecular biology. The selection of courses we offer in this study programme depends
not only on their relevance to biophysics, but also on the international recognition of colleagues that are
offering these courses. Our aim was to select course leaders that have well developed international
collaboration, ambitious and realistic research projects and one or more research topics suitable for
student’s selection as a Ph.D. thesis work. In other words, all of our course leaders can also be mentors
for the Ph.D. thesis work. We have already asked our course leaders to provide at least one research
topic that can lead to high quality student’s thesis work. A list of such topics and corresponding course
leaders (for the preliminary list of thesis topics see Section 4.3) will be made available to our students at
the very beginning of their Ph.D. study with a goal to facilitate their decision whom of our course
leaders to choose as their adviser. The mentor’s fair workshops, mentioned earlier, will bring together
students, project leaders and course leaders to stimulate student research initiation under optimal control
of chosen advisers and Study Committee. The Study Committee will have duty to select the final list of
thesis topics and corresponding advisers for each generation of students.
All of offered courses can be grouped into three study blocks, as can be seen from the Chapter
3.2:
a) Fundamentals of biophysics, physics and biology. These are courses offered by A.

Bilušić and colleagues from the Ruđer Bošković Institute (G. Baranović, B. Rakvin,
V. Svetličić, D. Vikić-Topić, I. Weber), D. Juretić, N. Krstulović, H. Lutz, S.
Marčelja, R. Podgornik, D. Ražem, Silvia Tomić, I. Weber and M. Tolić-Norrelykke
and P. Županović.
b) Modelling and structural bioinformatics. These are courses offered by M. Brumen,

R. Dewar et al., D. Juretić, B. Lučić, A. Graovac, V. Paar, F. Sokolić, Sanja Tomić
and B. Žagrović.
c) Biophysics and Biomedicine. These are courses offered by K. Pavelić and his IRB
collaborators (S. Kraljević Pavelić, M. Sedić, K. Hock, M. Baus Lončar), A.
15
Ambriović-Ristov, D. Eterović, M. Dželalija, Z. Đogaš, G. Kilić, V. Parpura, S.

Supek, J. Terzić, M. Vrtar.
Students have freedom to choose or not to choose from the very beginning of their Ph.D. study
what biophysical orientation they prefer, and accordingly select their courses from block a), block b), or
block c).
The interdisciplinarity of offered courses and of the whole study programme is not only of a
formal nature, but is natural consequence of our intention that the programme should reflect creative
interconections among physics, biology, chemistry, biomedicine, ecology, mathematics and
informatics, with the same goal of better understanding of biological processes and structures at all
levels of organisation – from macromolecules to biosphere.
All colleagues charged with obligatory courses will be asked to put on the Internet (available to
our students) as much material from their lectures as possible, preferably in advance of their lectures.
This will make study easier for all students, but part-time students living and working in Zagreb and
Split and part-time students living and working in places nearby Zagreb and Split are likely to profit
most from such practice. Such students would have to come to our two study locations (Split-PMF,
Zagreb-IRB) at least twice during a year in order to be able to participate in intensive research and
educational workshops. Since personal contact is indispensable for these students too, we expect from
them to take counsel with their advisers when intensive contact periods can be arranged during year in
Split or in Zagreb where most of potential mentors are employed. Such practice would serve as good
preparation in the case that the introduction of distant education practice in deemed desirable for our
Ph.D. study.
From regular students it is expected to study in Split and/or Zagreb most of the year, especially
during first study years, so that they can attend to all lectures and workshops and establish an intensive
communication with advisers (at least as frequent as advised) with respect to their research project.
3.1.1. Arguments for organizing interdisciplinary PhD programme at the University of Split
Is an additional Biophysics PhD programme in Croatia really needed is a legitimate question,

because large University of Zagreb had such programme for more than 30 years and number of enrolled
students was always very small. We argued previously that Faculty of Science at the University of
Zagreb had such concept of biophysics as interdisciplinary scientific discipline that only physicists
could enrol the Biophysics programme, and that our proposal for the Biophysics programme has much
wider spread allowing molecular biologists, chemists, medical doctors and even computer scientists to
enter the Programme. Still, it is important to analyse in some depth what are the reasons for establishing
the Biophysics programme at the small University of Split, which has few laboratories, and no tradition
at all in constructing PhD programmes from the field of natural sciences.
The lack of PhD programmes from natural sciences at the University of Split can not be an
argument to keep such programmes at the University of Zagreb. Split is the second largest town in
Croatia, the main town in the region of Dalmatia with older tradition in scholarship than Zagreb. Present
extreme centralization of all infrastructures for natural sciences in Zagreb is not good for a country as a
whole. The society based on knowledge can not be developed if it is restricted to Zagreb. In particular,
the centralization did not help the development of interdisciplinary fields. In the example of biophysics
the Faculty of Science in Zagreb never established a single biophysical laboratory so that its Biophysics
programme was based on using laboratory facilities from other institutions. One such institution, the
Ruđer Bošković Institute, has recently decided to collaborate with the University of Split in constructing
16
the Biophysics programme and has good reasons for doing it (the letter of intention of the IRB head,
Prof. Dr. Mladen Žinić has been enclosed).
We have collected at the University of Split a respectable number of mentors for PhD students
of biophysics: Stjepan Marčelja (PMFST and Australia), Ante Graovac (PMFST and IRB), Davor
Juretić, Mile Dželalija, Franko Sokolić, Paško Županović (all from PMFST) Davor Eterović, Janoš
Terzić, Zoran Đogaš (all from Medical School in Split). Together with mentors from the MedILS
Institute in Split (Bojan Žagrović at present, but Ivo Sbalzarini, Anita Kriško, Ivan Đikić and Miroslav
Radman are likely to join), from the Institute of Oceanography and Fisheries (Nada Krstulović) and
together with foreign biophysicists who will be giving lectures in Split (Rudi Podgornk, Milan Brumen,
Vladimir Parpura, Roderick Dewar, Gordan Kilić) we have in our programme the same number of
mentors that can work with students at the University of Split (16) as is the number of mentors from
Zagreb that agreed to participate in this programme (Vesna Svetličić, Goran Baranović, Boris Rakvin,
Dražen Vikić-Topić, Igor Weber, Dušan Ražem, Silvia Tomić, Sanja Tomić, Krešimir Pavelić, Neven
Žarković, Vlado Paar, Selma Supek, Andreja Ambriović-Ristov, Mladen Vrtar, Bono Lučić, Ante
Graovac). In addition, Split group of biophysicists offered more research topics for the PhD work in
biophysics (19 topics) than Zagreb group of biophysicists (11 topics). Of course, there are more
biophysicists in Zagreb if we count all of them and not only those that are participating in our PhD
programme. However, the comparison between Zagreb and Split gives advantage to Split if number of
biophysicists as full professors and number of publications from the field of biophysics is compared
between Faculty of Science, Zagreb and PMFST Split. At the University of Split and at MedILS we
have several full professors who are experts in biophysics, bioenergetics, bioinformatics, biomechanics
and medical physics (Stjepan Marčelja, Davor Juretić, Mile Đelalija, Davor Eterović) and several young
biophysicists with high impact publications from these fields (Bojan Žagrović, Anita Kriško, …) so that
our scientific staff in these disciplines is now better than at the Faculty of Science, University of Zagreb.
It is time to start developing interdisciplinary PhD programmes in natural sciences in regional centres
such as Split and it is time to give biophysics new chance in new environment.
Our colleagues Terzić, Đogaš and Eterović from the Medical School in Split (Terzić also
collaborates with Đikić at the MedILS) have well equiped laboratories that can be used for tutoring
medical physics and medical biophysics, but it is true that at the present time our strength is better in
computational biophysics. Importantly, we have clear plans for developing biophysical laboratories at
the University of Split (outlined in the MZOS research programme 1770495 led by Davor Juretić) and
at the MedILS institute where we expect that 15 to 20 doctoral students will be working in the field of
computational and experimental biophysics in a near future and additional mentors will be included in
this study programme (see enclosed letter by the scientific director Bojan Žagrović).
From biophysics syllabus in Split, which is rich in high quality regular and elective courses,
PhD students from related fields and students from the Faculty of Science, University of Zagreb will be
free to choose courses which will be recognized at their study programme. In the same spirit of
Bolognia declaration our PhD students will be free to choose some courses offered by the Faculty of
Science, Zagreb. In this manner two related study programmes from Split and Zagreb will meet in the
spirit of cooperation and collaboration. In fact, such provisions are already mentioned in our
Programme and in the last version of the Biophysics Programme from the Faculty of Science, Zagreb
(the school year 2005/2006). Since professors from the Faculty of Science, Zagreb, are already holding
several elective courses from our Programme in Split (Vladimir Paar, Selma Supek, Mladen Vrtar) this
intention should be easy to establish.
With respect to study organization in Zagreb with the IRB as one collaborating institution and to
study organization in Split with three collaborating institutions (PMFST, Medical School, MedILS) we
expect that the distribution of students will resemble the distribution of mentors i.e. about equal number
of students will have mentors in Zagreb and in Split. Co-mentoring with one mentor in Zagreb and
another in Split will also be encouraged. Such study organization will give similar weight to good
laboratory infrastructure and experts in different biophysical techniques from the IRB, Zagreb, and to
17
experts for computational biophysics, student population with Masters Degree coming from the PMFST
biophysics orientation and development plans for biophysics at PMFST and at MedILS.
Programme structure
1st Semestar: Regular Courses
Course Course Title Course ECTS

Structure *
Code
L+S+E+LE
PMP301 Experimental Methods of Physics in Biophysics (A. 24+4+0+30 10
Bilušić, B. Žagrović, V. Svetličić, B. Rakvin, G.
Baranović, D. Vikić-Topić, I. Weber)
PMP302 Cell biophysics I (I. Weber, I. M. Tolić-Norrelykke, S. 20+5+0+10 8
Marčelja, D. Juretić)
Elective Course I** 6
Elective Course II and/or Student's Research in 6
Biophysics***
TOTAL: 30
*L=Lectures, S=Seminar, E=Exercises, LE=Laboratory Exercises. Exercises (E) are auditory
exercises, while laboratory exercises (LE) are practical work with instruments in a laboratory or
computer modelling/simulations.
**Only students with an excellent background and with adviser's recommendation can apply to
Study Committee to take Student's Research in Biophysics as the Elective Course I.
***Student can take counsel with his advisers and with the Study Committee whether to take
one additional elective instead of starting his/her research work during the first semester. That
elective course can also be from our selection of first semester elective courses. It can be from
course offering of other interdisciplinary doctoral studies and/or it can serve as supplementary
course to help student in acquiring necessary basic knowledge (Appendix I). The Study
Committe can decide to grant these 6 ECTS credits to a student who already acquired education
in some well known laboratory from the field of biophysics, structural bioinformatics, system
biology, functional genomics, proteomics, ..
1st Semester: Elective Courses

Structure *
Code
L+S+E+LE
PMP307 Molecular Structure and Dynamics, Spectroscopy and 20+0+10+5 6
Simulations (F. Sokolić)
PMP308 Nonequilibrium thermodynamics (P. Županović) 30+0+15+0 6
PMP309 The application of irradiation in radiotherapeutical 20+15+0+0 6
oncology (M. Vrtar)
PMP310 Physicochemical Basis of Radiation Biology (D. Ražem) 24+6+6+0 6
PMP311 Multivariate Statistical Methods (D. Eterović) 12+0+0+16 6
PMP312 Physics of DNA, chromatin and viruses (R. Podgornik) 20+0+20+0 6
18
PMP313 Molecular genetics (J. Terzić) 24+10+0+12 6

PMP314 Environmental Microbiology (N. Krstulović) 15+0+0+30 6
PMP315 Models and Methods in Structural Bioinformatics (B. 15+5+15+0 6
Lučić)
PMP316 Methods in Molecular Biology and Medicine (A. 0+0+0+30 6
Ambriović-Ristov)
Student's Research in Biophysics 0+6+0+20 6
* L=Lectures, S=Seminar, E=Exercises, LE=Laboratory Exercises.
2nd Semester: Regular Courses

Structure *
Code
L+S+E+LE
PMP303 Modelling of Biomacromolecules and their Complexes 20+4+8+4 6
(Sanja Tomić, Ante Graovac)
PMP304 Bioinformatics, Biophysics and Bioenergetics of 15+5+10+5 6
Membrane Proteins (D. Juretić, B. Žagrović)
Elective Course III** 6
Elective Course IV and/or Student's Research in 6 to 12
Biophysics***
Participation in a International Summer School ≤4
TOTAL: 30
*L=Lectures, S=Seminar, E=Exercises, LE=Laboratory Exercises.
**Only students with excellent background and with adviser's recommendation can apply to
Study Committee to take Student's Research in Biophysics as the Elective Course III.
***Student can take counsel with his advisers and with the Study Committee whether to take
one additional elective instead of more intensive research work during the second semester.
That elective course can also be from our selection of first semester elective courses. It can
be from course offering of other interdisciplinary doctoral studies and/or it can serve as
supplementary course or courses to help student in acquiring necessary basic knowledge
(Appendix I). Students with greater need for supplementary courses will not participate in a
Summer School during the first year of their study. The Study Committe can decide to grant
certain number of ECTS credits to a student who already acquired education in some well
known laboratory from the field of biophysics, structural bioinformatics, system biology,
functional genomics, proteomics, ..
2nd Semester: Elective Courses

Structure *
Code
L+S+E+LE
PMP306 Higher order repeats in human genome (V. Paar) 20+5+5+5 6
PMP317 Theory and Experiment in the Study of Protein Folding 20+6+0+10 6
(B. Žagrović)
PMP318 Applications of maximum entropy production principle in 5+5+0+10 6
19
physics and biology (R. Dewar, P. Županović, D. Juretić,

S. Marčelja..)
PMP319 Physics of medical diagnostics (D. Eterović) 7+8+0+15 6
PMP320 Cell Biophysics II (G. Kilić) 20+0+10+0 6
PMP321 Mathematical modeling of biological systems; selected 10+5+10+10 6
topics (M. Brumen)
PMP322 Structure and interactions in polyelectrolytes: basic 10+5+0+15 6
theory and experimental verification (Silvia Tomić i T.
Vuletić)
PMP324 Biophysical and Biomedical Aspects of Oxidative Stress 6+4+0+0 2
(N. Žarković)
PMP323 Signal Processing in a Brain (V. Parpura) 10+5+0+0 4
PMP325 Basic Neuroscience (Z. Đogaš) 10+15+0+15 6
PMP326 Neurodynamics (S. Supek) 15+5+0+10 6
PMP327 Nanophysics and Nanotechnology (H. Lutz) 20+10+10+0 6
PMP328 Models and Methods in Structural Bioinformatics (B. 15+5+15+0 6
Lućić)(The course is offered in the first semester as well)
PMP329 Biomechanics (M. Dželalija) 20+0+0+10 6
Student's Research in Biophysics 0+6+0+20 6
3rd Semester: Regular Courses

Structure *
Code
L+S+E+LE
Research in Biophysics (see proposed thesis topics by 23
corresponding mentors in the Chapter 4.3)
PMP325 Basics of systems biomedicine (K. Pavelić, S. Kraljević 10+4+0+0 3
Pavelić, M. Sedić, K. Hock, M. Baus Lončar)
Seminars and Workshops from Interdisciplinary Life 0+20+0+0 4
Sciences (international experts, see course description)
(S. Marčelja and D. Juretić, organizers)
TOTAL: 30
4th Semester: Regular Courses

Structure *
Code
L+S+E+LE
Research in Biophysics and Student's Seminars (see 26
proposed thesis topics by corresponding mentors in the
Chapter 4.3). Student's seminars on chosen research
topics.**
20
Seminars and Workshops from Interdisciplinary Life 0+20+0+0 4

Sciences (international experts, see course description)
(S. Marčelja and D. Juretić, organizers)
TOTAL: 30
*L=Lectures, S=Seminar, E=Exercises, LE=Laboratory Exercises.
** Up to 4 ECTS credits can be earned in this semester too for the active participation (with
poster or lecture) in some International Summer School/Conference. Then there will be
corresponding decrease in the ECTS credits for student's research and seminars.

Structure *
Code
L+S+E+LE
Research related to the chosen Ph.D. thesis research topic 27
Student's research seminars and first seminar about results 3
of student's Ph.D. research.
UKUPNO: 30

Structure *
Code
L+S+E+LE
Research on chosen Ph.D. thesis research topic 27
Two student's seminars about research results pertaining 3
to student's Ph.D. research and thesis defense seminar.
UKUPNO: 30
21
Compulsory and optional activities

The Ph.D. study is concentrated on educating students to perform original independent research
in the chosen field. Each study year is divided into two semesters. All offered courses are one-semester
courses except anticipated seminar sessions and workshops, which can be attended during whole
second study year. The proposed study programme offers 6 compulsory and 2 to 4 elective courses.
Students can choose elective courses among 24 of offered elective courses. The compulsory courses
are restricted to total of 33 ECTS (not counting interdisciplinary seminars and summer schools), which
is 18% of the total number of credits. Students taking 4 elective courses will still have less than 1/3 of
total ECTS load in courses, while more than 2/3 will be devoted to research. In the special case of
advanced students with excellent interdisciplinary background the Study Committee can wave for them
some elective courses, so that their total course load will be decreased, while their research ECTS
credits will increase to 75% or more of the total ECTS load. Students lacking necessary background can
enrol into one to three supplementary courses, but Study Committee recommends for students
interested in biophysics to enrol such supplementary courses during their undergraduate or M.Sc. study
(see Chapter 5.1). The Study Committee can also allow student to enrol into one or two elective or
supplementary courses above student’s normal course load. A student can hold one course of auditory
or laboratory exercises for undergraduate students during first study semesters if student advisors
consider it useful for student.
The experimental methods of physics in biophysics is compulsory first semester course divided
into two modules: the theoretical (4 ECTS) and experimental (6 ECTS). The experimental part will be
led by group of researchers from the Ruđer Bošković Institute in Zagreb. The compulsory third
semester course: Basics of systems biomedicine, is also led by group of researchers from the Ruđer
Bošković Institute in Zagreb. It gives additional strength to biomedical orientation of our study
programme. The remaining compulsory second year is a number of scientific seminars and workshops
led by renewed biophysicists.
The flexibility of choice is very great for elective courses. In the present study proposal we offer
24 elective courses. The Study Committee can allow for advanced students either to take more than two
elective courses or to take the “Student’s Research in Biophysics” course instead of several courses.
Also the Study Committee may allow students to take some elective courses that are not now included
on the list of such courses, either because we do not have yet an appropriate agreement with other
universities, or because new offer of high quality interesting courses may appear in a future for doctoral
students of biophysics.
Active participation in conferences and summer schools is desirable for our students near the
end of second semester and/or near the end of fourth semester and can gain for them up to 4 ECTS per
conference depending on school duration and on degree of student’s participation (through posters,
lectures and round table discussions). When student earns some ECTS credits for the summer school
the same number of credits is decreased in the second and/or fourth semester for student’s research or
for elective course IV. For instance, possible credit combinations in the second semester are: 4 ECTS
for a school and 8 ECTS for research and/or elective course IV, 3 ECTS for a school and 9 ECTS for
research and/or elective course IV, and so on up to 12 ECTS for research and/or elective course IV
when summer school has not been attended by student during that semester. One of possible
combinations in the fourth semester is 4 ECTS for a summer school and 22 ECTS for research and
student’s seminars.
22
Advanced seminars, workshops and short courses in the second study year will be mainly led
by renowned biophysicists from Croatia and from abroad. Seminars will be publicly announced several
months in advance, so that students will get ample time for preparations. We shall expect from our
students to ask questions showing their interest in the subject matter and reflecting their deeper
understanding of relevant research problems. From our lecturers, leaders of seminars and workshops,
we expect to be available to our students during that week in Split or Zagreb, while workshop lasts.
During fourth semester we shall expect from students to prepare and deliver one or more
seminars about chosen research problem, which does not have to be intimately connected with their
chosen topic for the Ph.D. thesis work. During the third study year students will present at least three
additional seminars, which will make clear how well they advance with the research on their thesis
topic. The last of these seminars will be the thesis defence seminar.
During doctoral study students are expected to learn describing their research results in a form
of at least one first-authorship scientific paper intended for high impact international journal with
excellent review process. Student will prepare the first version of a paper and closely collaborate with
his/her mentor through several cycles of criticism, improvements and shortening of a paper without
loosing clarity. As a study goal student should be the first author of at least one paper published or
accepted by high quality journal, before the thesis defence. Accepted or published student’s papers that
are outcome of student’s Ph.D. thesis research will certainly facilitate and accelerate the thesis defence
procedure. Students participation will be encouraged in producing results than can serve for
construction of additional research reports (if research goal is connected to student’s thesis research),
where student does not have to be the first author. However, the decision of the Thesis Committee that
student can proceed with his/her thesis defence procedure will be mainly based on the judgement that
student’s research is of excellent scientific quality.
23
Course information
3.4.1. Obligatory courses:
Course title Experimental methods of physics in biophysics

Course code
Type of course Obligatory course (theoretical and experimental course)
Level of course Basic course, doctoral study
ECTS 10 ECTS (24 lecture hours, 4 seminar hours and 30 hours of laboratory
workshops and exercises): 4 ECTS for theoretical background and 6 ECTS
for the experimental part of the course.
Name of Goran Baranović, Ante Bilušić, Boris Rakvin, Vesna Svetličić, Dražen
lecturer Vikić-Topić, Igor Weber , Bojan Žagrović
Learning Understanding of the theoretical background of experimental methods used

outcomes and in biophysics. The use of the experimental equipment applied in biophysics,
competences the understanding and interpretation of experimental data. Student will be
acquainted with the set of advanced methods and instrumentation used in
biophysical studies within the research institution – Ruđer Bošković
Institute in Zagreb. Targeted biophysical experiments will be performed in
lecturers’ laboratories.
Prerequisites None
Course contents Theoretical introduction to chosen chapters of spectroscopy (nuclear
magnetic resonance, electron paramagnetic resonance, X-ray, visible,
infrared. ultraviolet, fluorescent, Raman, mass and ion-mobility
spectroscopy). Biophysics and nanotechnology.
Experimental: This course includes five modules covering spectroscopic

methods (electron paramagnetic resonance, nuclear magnetic resonance,
infrared spectroscopy), Light microscopy and Atomic force microscopy
(AFM).
Experiments:
EPR topics: Manipulation of spin states in the experiment; Acquisition of
continuous wave and pulsed EPR spectra; EPR methodology in biophysics
– spin probes, spin traps, paramagnetic defects
FT IR spectroscopy of water mixtures
Light microscopy experimental work using a laser scanning confocal
microscope (digital image processing; three-dimensional reconstruction of
spatial fluorescence distributions; selected methods of biophotonics)
AFM imaging of living cells, biomolecules and gel phase
Recommended Theory
reading B. Nölting: Methods in Modern Biophysics, Springer Verlag, 2004
Electron paramagnetic resonance
L.J. Berliner: Spin labeling, The next millenium, Plenum Press 1998.
Infrared and Raman Spectroscopy
24
J. M. Hollas: Modern spectroscopy, John Wiley & Sons, Chicester, 2004.
Light microscopy
Douglas B. Murphy, Fundamentals of light microscopy and electronic
imaging, Wiley-Liss, Inc., 2001.
Atomic Force Microscopy

B. Nölting: Methods in Modern Biophysics, Springer Verlag, 2004 (selected
chapters).
Santos, N.C. & M.A. Castanho (2004). An overview of the biophysical
applications of atomic force microscopy. Biophys Chem 107(2), 133-149.
Supplementary Theory
reading A. Carrington, A. McLachlan: Introduction to magnetic resonance, Harper
and Row, 1978.
C. Slichter, Principles of Magnetic resonance, Springer, 1996.
J. R. Lakowicz, Principles of fluorescence Spectroscopy, Plenum Press,
1986.
Electron paramagnetic resonance
Abragam, B. Bleaney: Electron paramagentic resonance of transition ions,
Clarendon Press, Oxford 1970
Light microscopy
Methods in Enzymology, Vols. 360-361, Biophotonics, G. Marriott and I.
Parker, eds., Academic Press, 2003. (selected chapters)
Methods in Enzymology, Vol. 307, Confocal Microscopy, P. Michael Conn,
ed., Academic Press, 1999. (selected chapters)
Teaching Frontal lessons.
methods Introductory lecture and individually performed targeted biophysical
experiments at appropriate laboratories of the Ruđer Bošković Institute and
Institute of Physics in Zagreb, followed by the written report for each of the
five modules.
Assessment Oral and practical exam. In the final mark the knowledge demonstrated in
methods the written reports will take part.
Language of Croatian/English
instruction
Quality Written questionnaire at the end of the course
assurance
methods
25
Course title Cell biophysics I

Course code
Type of course Obligatory
Level of course Advanced, doctoral study
ECTS 8 ECTS. Topic and concepts seldom taught in undergraduate courses.
Except for the introduction, a literature is available exclusively in English
language. There will be 5 lecture hours of introduction to biophysics, 15
lecture hours devoted to cell biophysics, 5 hours of seminars and 10 hours
of laboratory exercises.
Name of Prof. Dr. Igor Weber; Dr. Iva Marija Tolić-Nørrelykke, Prof. Dr. Stjepan,
lecturer Marčelja, Prof. Dr. Davor Juretić
Learning Introducing multidisciplinary approach to investigation of biological
outcomes and systems based on example of eukaryotic cell. Emphasis is put onto physical
competences principles and research methods as a supplement to prevailing biochemical
approaches to cell biology.
Prerequisites Undergraduate courses in General physics and Cell biology.
Course contents Introduction to biophysics. What is life and why cellular organization is
necessary for life. The importance of insights from connected physical and
biological evolution.
Supramolecular structure of eukaryotic cells. Dimensions and internal
organization of cells and their compartments. Hierarchy of forces in the
world of cells. Structure and function of the cytoskeleton. Viscoelastic
properties of cells. Biological molecular motors, cell motility. Structure and
dynamics of biomembranes. Mechanisms of transport across biomembranes.
Mechanisms of transport inside the cytoplasm. Signaling pathways and
transfer of information in the cell. Experimental methods in cell biophysics.
Cytomics.
Recommended J. Howard, Mechanics of Motor Proteins and the Cytoskeleton,
reading Sinauer Associates, 2001
Supplementary D. Boal, Mechanics of the Cell, Cambridge University Press, 2002
reading D. Juretić: Bioenergetics – work of membrane proteins (Bioenergetika – rad
membranskih proteina, Croatian language), Informator, Zagreb, 1997.
D.G. Nicholls and S.J. Ferguson, “Bioenergetics 3”, Academic Press,
Amsterdam 2002.
Teaching Lectures, colloquia and seminars.
methods
Assessment Oral and written examinations, compulsory seminars.
methods
Language of Croatian / English / German.
instruction
Quality
assurance
methods
26
Course title Modelling of Biomacromolecules and their Complexes

Course code
Type of course Obligatory graduate course
Level of course Fundamental Course, Doctoral Study
ECTS 6 ETCS
Lectures 20 hours, Seminars 4 hours, Auditorial exercises 8 hours,
(Number of
Laboratory excercises on computer about 4 hours ~ 2 ECTS
credits allocated)
About 160 hours of preparations for seminars exercises and exam ~ 6 ECTS
Name of Dr. Sanja Tomić and Prof. Dr. Ante Graovac
lecturer
Learning Perceiving sciences as a model. Understanding algorithms and techniques
outcomes and that are utilized for modelling of biomacromolecules. Fundamentals of
competences stochastical modelling. Understanding that relatively small number od
models unifies very diverse scientific fields. Acquaintance with mostly used
traditional and current models in biology and medicine. Understanding
algorithms and techniques that are utilized for modelling of
biomacromolecules. Practical knowledge in modelling of
biomacromolecules.
Prerequisites Basic Biology, Basic Physics and Basic Informatics.
Course contents The course consists of two modules.
The first module is of more general nature. It describes traditional and
current models of biology and medicine. Basic differential equations of
biology and medicine. Statistical models. Factor analysis. Neural networks.
Computation of energy, properties and reactivity of molecules.
Special attention is given to computational chemistry, molecular mechanics
and molecular dynamics as analytical tools used for modeling protein and
DNA structure with a goal of drug design. Simple models: topological
descriptors in modelling of Quantitative Structure-Property and Quantitative
Structure –Activity Relationships. Shape and similarity of biomolecules.
Geometry, graphs and topology in biology and medicine. Filogenetic trees.
The second module is focused on modeling biomacromolecules.
Modelling of biomacromolecules is a young branch in biosciences that has
rapidly developed during the last decade and has become very popular
among bio scientists. During the course students will learn about the
databases, force fields and techniques that are most commonly used in
modelling of biomacromolecules. They will become familiar with designing
of virtual (in silico) experiment; building complexes and mutants, active site
recognition, substrate docking, parameterisation and optimisation of the
molecules, possible conformational changes of ligands that occur during
binding to the receptor and how to model them (molecular mechanics,
molecular dynamics, stochastic dynamics, Monte Carlo analysis, Normal
modes analysis). They will become aware of importance of solvent and
periodicity in simulation of biomolecules, approximations in approaches for
binding free energy calculation (electrostatic free energy, entropy of
(de)solvatation, conformational/rotational entropy of the substrate and the
amino acid residues in the protein active site). How to calculate amino acid
27
pKa in protein, and how to simulate Brown dynamics of proteins preceding

the complex formation will be also explained. On concrete examples
students will learn about techniques and approaches that are used in 3D-
QSAR (3-dimensional quantitative structure activity relationship) analysis.
Interpretation of models, predicting biological response and suggestions of
the modification that would change this response.
Recommended Andrew R. Leach ‘Molecular Modelling: Principles and Applications’, 2nd
reading edition, Pretince Hall, Harlow, 2001.
Van Gunsteren W. F. , Weiner P. K., and Wilkinson A. J. (Eds) ’Computer
Simulation of Biomolecular Systems’, Spinger, London, 1997.
E.A. Lord and C.B. Wilson, The Mathematical Description of Shape
and Form, Ellis Horwood, Chichester, England, 1984.
G.H. Grant and W.G. Richards, Computational Chemistry, Oxford
University Press, Oxford. 1998.
M. Mintas, S. Raić-Malić, i N. Raos, Načela dizajniranja lijekova,
Hinus, Zagreb, 2000.
Supplementary 1.Van Gunsteren W. F., Klebe G. and Kubinyi H. ’3D QSAR Methods in
reading Drug Design’, ’Molecular Modeling and Prediction of Bioactivity’, Eds.
Gundertofte K. and Jorgensen F. S. Plenum (2000), Kluwer
Academic/Plenum Publishers, New York.
2. ’From Molecular Structure towards Biology’, ed. Quinkert Wiley-, J.
Med. Chem. 43 (2000), 1780-1792.
3. M. Tišler, Sporočilnost molekul, Državna založba Slovenije (DZS),
Ljubljana, 1998.
4. A. Graovac, I. Gutman, and N. Trinajstić, Topological Approach
to the Chemistry of Conjugated Molecules, Springer, Berlin, 1977.
5. I. Pavlić, Statistička teorija i primjena, Tehnička knjiga, Zagreb, 1985.
+ relevant publications in journals
Teaching The course consists of lectures, student seminars, auditory excercises and
methods laboratory exercises on computer. Lecturing by use of different presentation
methods. Discussions during and after lectures. Selection of current and
interesting topics and problems appearing in recent journals and books or on
Internet as subject of auditorial exercises. Problem solving and modelling
in classroom.
Assessment Testing through auditorial exercises and homeworks and through seminars.
methods Final oral exam. Final exam will consist from oral and practical part. In the
practical part of the exam the students must show his/her level of
competence in using bioinformatics tools to solve specific problem.
Language of Croatian or English depending on the composition of a student body

instruction
Quality A questionnaire will be offered to students at the end of the semester with a
assurance goal of finding weak spots in the course conception and delivery.
methods
28
Course title Bioinformatics, Biophysics and Bioenergetics of Membrane Proteins

Course code
Type of course Required graduate course of mostly theoretical nature
Level of course Doctoral study, first year, second semester
ECTS 6 ECTS
Lectures: 15 hours; Seminars: 5 hours; Auditory exercises: 10 hours;

Computer exercises: 10 hours. ~ 2 ECTS
Preparations for lectures, seminars, computer exercises and for exam: 150
hours ~ 6 ECTS
Name of Prof. Dr. Davor Juretić, course holder, Dr. Bojan Žagrović, lecturer
lecturer
Learning After finishing this course students should be able to use principles and
outcomes and some tools developed by bioinformaticians, biophysicists and
competences bioenegeticists to connect structure and function in integral membrane
proteins of key importance for cells and organisms.
Prerequisites General physics - in particular electromagnetism and thermodynamics,
Biochemistry or Molecular Biology, Basic informatics
Course contents Diversity and importance of membrane proteins as about 75% of possible
drug targets. Practical approach to bioinformatics of membrane proteins.
SPLIT and GARLIC as examples for predicting the 2D topology of integral
membrane proteins and of visualisation of a 3D biomacromolecule
structure. How to use evolutionary information to improve 2D and 3D
prediction. Examples of structural motifs important for membrane protein
function. Examples how membrane proteins are creating and using proton-
motive force during photosynthesis, respiration, and cell-cell
communication. Modelling catalytic cycling of membrane channels
transporters and ion pumps by using diagrammatic method. Information
entropy (Shannon’s), entropy production and efficiency associated with
steady state kinetics of membrane proteins acting as molecular motors
(natural nanomachines). Expression in different organs and interaction with
drugs and toxins. Membrane active peptide antibiotics. Membrane proteins
and genetic diseases.
Recommended Juretić, D.: “Bioenergetika – rad membranskih proteina.” Informator.
reading Zagreb, 1997.
D. G. Nicholls and S. J. Ferguson, “Bioenergetics 3”, Academic Press,
Amsterdam 2002.
Cotterill, R. (2006). Biophysics. An Introduction. John Wiley & Sons, New
York.
Glaser, R. (2005) Biophysics. Springer-Verlag, Berlin.
Jackson, M.B.(2006). Molecular and Cellular Biophysics, Cambridge
University Press, New York.
Lesk Arthur, M.: “Introduction to Bioinformatics”, Oxford Univ. Press.
2002.
Jin Xiong: “Essential Bioinformatics” Cambridge Univ. Press, New York,
29
2006.
Supplementary F. M. Ashcroft: Ion Channels and Disease. Channelopathies”. Acad. Press,
reading London, 2000.
Hill, T.L. Free “Energy Transduction in Biology”, Academic Press, New
York 1977.
Jean-Michel Claverie and Cederic Notredame: “Bioinformatics for
Dummies”, Wiley, Indianapolis, 2007.
http://blanco.biomol.uci.edu/reprints/index.html
http://blanco.biomol.uci.edu/Membrane_Proteins_xtal.html
Teaching Lectures, seminars, exercises and computer exercises

methods
Assessment Oral and written exam. Students interest, initiative and activity will be taken
methods into account during this course and will also help in the assignation of the
final grade.
Language of Croatian or English, depending on a student body
instruction
Quality Evaluation by students designed to discover weak spots in course teaching
assurance methods or delivery
methods
30
Subject title Basics of systems biomedicine

Code
Type Obligatory subject, Lectures, Seminars
Level Basic, doctoral study
Year II Semester I
ECTS 3 ECTS - 12 hours (10 lectures, 4 seminars)
(with an
appropriate
explanation)
Lecturer Course holder: Professor Krešimir Pavelić, PhD, MD
Lecturers:
Sandra Kraljević Pavelić, PhD
Mirela Sedić, PhD
Karlo Hock, PhD
Mirela Baus Lončar, PhD
Competencies Upon completion of the course in the basics of systems biomedicine,
that will be students will gain knowledge necessary to understand multi-level and
acquired hierarchic organization of the human body (molecules, organelles, cells,
tissues, organs and whole organism) as well as the knowledge on modern
laboratory approaches based on the so called „-omics“ methods that are
indispensable for understanding and uncovering crucial disease factors.
In addition, students will gain the knowledge on how an integration of the
data obtained in this way might help to define global model of biological
processes leading to a disease, i.e. how can global „-omics“ methods could
be used in an early (pre-symptomatic) disease diagnostics, prognostics and
drug development.
Prerequisites for To be familiar with the basics of molecular biology

taking the course
Course During the course, students will get comprehensive overview of modern
description approaches towards disease study based on simultaneous analysis of
thousands of genes and proteins that constantly interact in the living system.
In this context, an emphasis will be placed on introduction with global,
large-scale „-omics“ methods, such as DNA microarrays, RT-PCR and
proteomics methods and their roles in an early diagnostics, prognostics and
progress of a disease, in discovery of novel drug targets and generally, their
roles in drug discovery and development.
Since global approach to study molecular mechanisms of a disease

generates extremely large quantity of data, students will learn about
bioinformatics and its role in the analysis and interpretation of data obtained
by the „-omics“ methods. Bioinformatics helps to identify crucial disease
factors in the context of the whole system and interactions with other
31
molecules. In addition, students are expected during seminars to

interactively present and creatively discuss with their teacher and colleagues
about one of the offered subjects during the course in systems biomedicine,
which will students independently prepare. Lecturer will partially provide
students with required literature for the preparation of the seminar
presentation. In addition, students will be expected to search the internet
themselves once they select one of the following seminar subjects:
1. „-omics“ methods in modern diagnostics of a disease

2. „-omics“ methods in tumour classification
3. Prognostic bioinformatics test for breast cancer
4. Nanotechnology in the DNA microarrays production
5. Importance of studying proteins changed in the diseased state
6. Importance of studying genes changed in the diseased state
7. Bioinformatics approach towards the analysis of the data obtained
by the „-omics“ methods
8. Ethical aspects and problems related to usage of the „.omics“
methods in medicine
9. Accession and usage of the systems biomedicine databases
available via internet
10. Physical methods in the study of protein structure
11. New visualization methods in biomedicine
Recommended • S. Fontana, G. De Leo, Mirela Sedic, S. Kraljevic Pavelic, R.

literature Alessandro (2006) Proteomics in antitumor research. Drug
Discovery Today: Technologies 3: 441-449
• S. Kraljevic, P.J. Stambrook, K. Pavelic (2004) Accelerating drug
discovery. EMBO reports 5: 837-842
• S. Kraljevic, M. Sedic, M. Scott, P. Gehrig, R. Schlapbach, K.
Pavelic (2006) Casting light on molecular events underlying anti-
cancer drug treatment: what can be seen from the proteomics
point of view?. Cancer Treatment Reviews 32: 619-629
• P. Perco, R. Rapberger, C. Siehs, A. Lukas, R. Oberbauer, G.
Mayer, B. Mayer (2006) Transforming omics data into context:
Bioinformatics on genomics and proteomics raw data.
Electrophoresis 27: 2659-2675.
• Cowell JK, Hawthorn L. The application of microarray
technology to the analysis of the cancer genome. Curr Mol Med.
2007 Feb;7(1):103-20.
• Provenzano M, Mocellin S. (2007) Complementary techniques:
validation of gene expression data by quantitative real time PCR.
Adv Exp Med Biol 593:66-73.
• Nielsen TO (2006) Microarray analysis of sarcomas. Adv Anat
Pathol 13(4):166-73.
Additional S. Kraljevic i M. Mustapic (2004) Functional proteomics in drug discovery,

literature Screening – trends in drug discovery 4:10-12
S. Kraljevic (2004) Mogu li globalne analize genoma i proteoma ubrzati
32
postupak otkrivanja i razvoja lijekova, Medix, 56/57: 55-58
S. Kraljevic i K. Pavelic (2005) Navigare necessere est. EMBO reports

6:1-6
Course modules Lectures, seminars
Means of An exam upon completion of lectures and seminars
knowledge
testing and
examination
Course Croatian, English (due to the literature written mainly in English)
languages
Means of Students questionnaire
monitoring the
quality and
success of every
course and/or
modules
33
Course title Interdisciplinary seminars and courses/workshops from life sciences

Course code
Type of course Obligatory, Doctoral Study
Level of course Advanced, Second year of the Ph.D. study in biophysics
ECTS 8 ECTS
We plan about 20 hours of seminars in each second year semester, with
required reading of review papers and most important research papers and
active participation of students during seminars.
Name of As an example here we list accomplished researchers from Croatia and from
lecturer abroad whom we would like to invite to contribute such seminars: Z. Bačić,
Ž. Bajzer, N. Ban, V. Bonačić-Koutecky, J. Brnjas-Kraljević, M. Brumen,
R. Dewar, I. Đikić, L. Forro, M. Gutman, N. Juranić, G. Kilić, D. Krajinc,
T. Legović, B. Lenhard, B. Martinac, V. Parpura, A. Parsegian, K. Pavelić,
D. Pavuna, G. Pifat, J. Peter-Katalinić, R. Podgornik, A. Parsegian, J. Prost,
M. Radman, M. Randić, I. Štagljar, F. Šeparović, A. Tossi, S. Vuk-
Pavlović, B. Žagrović, N. Žarković, ...In a future there will be also other
appropriate lecturers for this course. Present proposed organisers of this
course are Stjepan Marčelja and Davor Juretić.
Learning During direct communication with accomplished world-class research
outcomes and workers our students will gain important insight for successful approach to
competences scientific work in biophysics.
Prerequisites
Course contents Wide spectrum of research problems where biophysical methods and
application of physical principles to biology can contribute to new insights.
Recommended Lecturers will make available to students required reading list.
reading
Supplementary
reading
Teaching Lectures, Seminars, Excercises
methods
Assessment
methods
Language of English
instruction
Quality At the end of forth semester students will fill out the questionnaire about
assurance course value at will contribute their suggestions for course improvements
methods
34
3.4.2. Elective courses:
Course title Higher order repeats in human genome

Course code
Type of course Elective
Level of course Ph.D. study
ECTS 6 ECTS
Lectures: 20 hours, Seminars: 5 hours, Auditory Exercises: 5 hours,

Laboratory Exercises: 5 hours
Name of Vladimir Paar
lecturer
Learning Understanding and operational skills for identifying and analyzing higher
outcomes and order repeats in given genomic sequences.
competences
Prerequisites Basic knowledge underlying computational genomics.
Course contents Repeats and higher order repeats in centromeric and pericentromeric
regions. Identification of higher order repeats in GenBank sequences.
Chromosome-specific and HOR-specific pattern in human genome. CENP-
B box and pJalpha motif distributions in human genome. Various
computational algorithms for treating HORs. Substitutions, additions and
deletions in HOR structure. Polymorphism in HOR structure.
Recommended 1. Robert H. Tamarin: “Principles of Genetics”, McGraw-Hill, 7th Edition
reading 2001, ISBN: 0072334193
2. K. H. Andy Choo: “The Centromere”, Oxford University Press, Oxford
1997, ISBN: 019857780x
3. selected scientific papers
Supplementary Selected scientific papers
reading
Teaching Lectures, presentation of published articles, test computations.
methods
Assessment Exams, seminars.
methods
Language of Croatian/English
instruction
Quality
assurance
methods
35
Course title Molecular Structure and Dynamics, Spectroscopy and Simulations

Course code
Type of course Lectures, Exercises, Computer work
Level of course Doctoral
ECTS 6 ECTS
Lectures: 20 hours, Auditory Exercises: 10 hours, Laboratory Exercises: 5

hours
Name of Franjo Sokolic
lecturer
Learning Understanding computer simulation techniques and their relationship with
outcomes and spectroscopy.
competences
Prerequisites Quantum mechanics and statistical mechanics.
Course contents Quantum theory of atoms and molecules
Spectroscopical Methods
Computer simulations
Recommended Peter Atkins and Ronald Friedman: Molecular Quantum Mechanics; Fourth
reading Edition, 2004; Oxford University Press.
Supplementary Jeffrey I. Steinfeld: Molecules and Radiation (An Introduction to Modern
reading Molecular Spectroscopy), Second Edition, 2005, Dover Publications.
Teaching Lectures, computer calculations, measurements
methods
Assessment Students will be charged to resolve a simple research problem. Their
methods advancement will be followed.
Language of Croatian, English
instruction
Quality The success of their work will be appreciated through the personal work
assurance they will perform and a final exam.
methods
36
Course title Non-equilibrium thermodynamics
Course code
Type of course Theoretical
Level of course Advanced, PhD level
Year of study I Semester II
ECTS
ACTIVITY Lessons Hours ECTS
(Number of
Lessons 30 22.5 1
credits allocated)
Exercises 15 12 0.5
Uninfluenced work 110 4.0
Tutorial 3 0.475
TOTAL 6.0
Name of Associate Professor, Dr. Paško Županović
lecturer
Learning Understanding of irreversible processes in physics and biology.
outcomes and
competences
Prerequisites Thermodynamics of irreversible processes
Course contents Laws of thermodynamics. Principle of the local equilibrium. Entropy
production. Maximum entropy production principle. Thermodynamic forces
and conjugated fluxes. Onsager's reciprocal relations. Linear irreversible
thermodynamics. Diffusion, heat transfer and viscosity. Thermoelectric
effects. Interference of fluid diffusions. Interference of chemical reactions.
Kirchhoff loop rule and the irreversible thermodynamic. Kinetic design of
the rotary enzyme ATP synthase and maximum entropy production
principle.
Boltzmann’s transport equation. Markov’s processes. Stochastic processes.
Recommended 1.P. Županović: Predavanja iz Opće fizike IV, lecture notes

reading 2.E.T.Jaynes, Phys.Rev. 106 (1957) 620-630.
3.E.T.Jaynes, Phys. Rev. 108 (1957) 171-190.
4.E.T.Jaynes, Information theory and statistical mechanics, in Statistical
mechanics, ed. K.W. Ford, W.A. Benjamin, Inc. NY, (1962), pp 181-218.
5. L.D. Landau and E.M. Lifšic: Statistical physics, Pergamnom press, New
York, 1972.
6.R. Dewar: Information theory explanation of the fluctuation theorem,
maximum entropy production and self-organized critically in non-
equilibrium stationary states, J. Phys. A 36 (2003) 631-641.
7.L.M. Martiyshev: Maximum entropy production principle in physics,
chemistry and bilogy, Physics reports 426 (2006) 1-45.
8. P.Županović, S. Botrić and D. Juretić: Relaxation processes, MaxEnt
formalism andEinstein’s formula for the probability of fluctuations, CCA
2006
37
9. N.G. Van Kampen: Stohastic processes in physics and chemistry, Noth-

Holland, New York, 1981.
10.L. Onsager, Phys. Rev. 37 (1931), 405-426
11.S.R. de Groot and P. Mazur: Non-equilibrium thermodynamics, Dover
publications, New York, 1984
Supplementary 1..I. Prigogine: Uvod u termodinamiku neravnotežnih procesa, Građevinska
reading knjiga, Beograd, 1967.
2.D. Kondepudi and I. Prigogine: Modern thermodynamics, John Wiley &
Sons, NY, 2002
Teaching Lectures. Solving problems instructed by assistant. Uninfluenced solving

methods of problems. Check of the solved problems and discussion on tutorials.
Assessment Preliminary exams. Written exam. Oral exams which include all or partially
methods teaching material.
Language of Croatian
instruction
Quality Student’s opinion poll.
assurance
methods
38
Course title The application of irradiation in radiotherapeutical oncology

Course code
Type of course Lectures (20) +Seminar (15)
Level of course Postgraduate doctor study. Advanced level.
ECTS 6 ECTS:
- 35 hours lectures – 2 ECTS
- about 120 hours student work and learning – 4 ECTS
Name of Prof.dr.sc. Mladen Vrtar
lecturer
Learning Acquaintance with the application of physical methods in radiotherapeutical
outcomes and oncology.
competences
Prerequisites The subjects in general physics from diploma study
Course contents Production and properties of ionizing radiation. Interaction of matter and
radiation: photon beam, kerm, energy fluence, attenuation coefficient,
energy transfer coefficient, energy absorption coefficient, bremsstrahlung,
exposure, and absorbed dose. Units in dosimetry and radiation protection.
Clinical radiation generators in medical radiotherapy: photon and electron
irradiation, linear accelerator, radio nuclide therapy, telecobalt unit,
irradiation of small brain tumors (gamma-knife), application of heavy
particle beams in therapy: neutron generators, proton and heavy ions
generators. Measurement of irradiation and and detectors. Bragg-Grey
cavity theory, ionization chamber theory. Dosimetric protocols in absorbed
dose determination. Dosimetry and calibration of photon and electron
beams. Treatment planning, measurement of radiation in phantoms and
system of dosimetric calculation for patients. Empirical dosimetric
functions, isodose curves and carts, obliquity and tissue inhomogeneity
corrections. Standard and large fields irradiation dosimetry.
Recommended 1. Podgorsak E.B. Review of radiation oncology physics, IAEA, Vienna,
reading Austria 2003. Web address: http://www-
naweb.iaea.org//nahu/dmrp/pdf_files/ToC.pdf
2. Vrtar M. Medicinska fizika. Interna skripta fizičkog odsj. PMF-a, Zagreb
2004.
Supplementary F.M. Khan, The Physics of Radiation Therapy, Williams & Wilkins,
reading Baltimore, Maryland, USA, 1994
Teaching Lectures and seminars from the application of irradiation in radiotherapy
methods
Assessment Oral examination
methods
Language of Croatian, English (dependant on students)
instruction
Quality assu- Preliminary inquiry of knowledge and background before and after lectures
rance methods
39
Course title Physicochemical Basis of Radiation Biology

Course code
Type of course Lectures (26 hours), Seminars (6 hours) and Auditory exercises (6 hours)
Level of course Elective Course. Ph.D programme
Year of study I Semester/trimester I
ECTS 6 ETCS
33 hours of lectures (44 school hours) and six hours of exercises ~ 2 ECTS
(Number of
Around 100 hours of preparations ~ 4 ECTS
credits allocated)
Name of Dušan Ražem
lecturer
Learning Understanding of molecular mechanisms underlying biological radiation
outcomes and effects.
competences
Prerequisites Knowledge of nuclear physics and physical chemistry.
Course contents Introduction: significance, historical overview. Elementary particles and
their interactions, definitions. Defect of mass, binding energy, nuclear
stability. Radioactivity: nuclear disintegrations, law of radioactive decay.
Buildup of periodic system, isotopes, radioactive series, nuclear reactions,
chart of nuclides.
Radiation sources: natural sources, radioecology. Artificial sources:
reactors, artifial isotopes, accelerators.
Interactions between radiation and matter: neutrons, charged particles,
electromagnetic radiations.
Experimental techniques: detection and dosimetry of ionizing radiations.
Time-resolved techniques.
Spatial and temporal distribution of events in irradiated matter. Properties
and fate of reactive species: electrons, positive ions, excited molecules and
free radicals.
Radiation efffects in water: primary yields. The effects of pH and LET.
Radiation effects in biological macromolecules and DNA. Effects of dose,
dose rate, medium, concentration, oxygen, temperature, LET.
Radiation effects in unicellular organisms: direct and indirect effects. Target
theory. Molecular theory.
Radiation effects in complex biological systems: dose – effect relationships.
Somatic and genetic effects. Non-stohactic and stohastic effects. Radiation
epidemiology. Irradiation risk.
Radiation protection: linear hypothesis. Comparison of risks. Cost benefit
analysis. System of dose limitation. ALARA principle.
Recommended MOZUMDER, A. HATANO, Y., Charged Particle and Photon Interactions

reading with Matter. Chemical, Physicochemical, and Biological Consequences
with Applications.
Marcel Dekker, Inc., 2004.
JONAH, C.D. and RAO, B.S.M., (Editors): Radiation Chemistry. Present
40
Status and Future Trends.

Elsevier, 2001.
MOZUMDER, A., Fundamentals of Radiation Chemistry.

Academic Press, 1999.
Supplementary J.W.T. Spinks and R.J. Woods: An Introduction to Radiation Chemistry, 3rd
reading Ed.,Wiley, New York (1990).
Farhataziz and M.A.J. Rodgers (Editors): Radiation Chemistry, VCH,

Weinheim (1987).
Articles in Technical Encyclopaedia of the Croatian Lexicographic Institute

Miroslav Krleža: (in Croatian)
V. Paar: Nuklearna fizika, TE 9,448.

K. Ilakovac: Radioaktivnost, TE 11, 398.
M. Vlatković: Radiokemija i radionuklidi, TE 11, 415.
K. Ilakovac: Nuklearno zračenje, TE 9, 535.
D. Ražem: Radijacijska kemija, TE 11, 374.
J. Galić, A. Milojević: Dozimetrija zračenja, TE 3, 387.
M. Turk: Biološko djelovanje nuklearnog zračenja, TE 9, 555.
Teaching The course consists of lectures, student seminars and auditory exercises.
methods
Assessment Final exam consists of oral examination.
methods
Language of Croatian or English, depending on the composition of a student body.
instruction
Quality Answering a questionnaire will be asked before and after the course.
assurance
methods
41
Course title Multivariate statistical methods

Course code
Type of course lectures (12), laboratory exercises (16)
Level of course postgraduate course
Year of study 1. Semestar/trimestar 1.
ECTS 6 ECTS
(Number of
credits allocated)
Name of Prof. dr. Davor Eterović
lecturer
Learning Student becomes acquinted with research aspects of advanced biostatistical
outcomes and methods, with methods of sampling and allocation according to research
competences design, what is the power of the study and how to assess the optimal sample
size. She or he becomes able to use and interpret the results of most
important multivariate methods in biomedicine.
Prerequisites Acquintance with matehmatical analysis and basics of statistics
Course contents Overview of basic statistics, methods of sampling and allocation to study
groups (randomizacija i minimizacija), the sample size and power of the
study, analysis of variance and GLM models, multiple regression, logistic
regression, survival analyses, factor analysis
Recommended 1. Eterović D, Kardum G: Biostatistika za studente medicine (III. izdanje),
reading Medicinski fakultet Sveučilišta u Splitu, skripta, 2003.
2. Dawson-Saunders B and Trapp RG: Basic and clinical biostatistics.
Appleton & Lange, Connecticut, 1990.
Supplementary 1. Kirkwood BR: Essentials of medical statistics. Blackwell Scientific
reading Publications, Oxford, 1988.
2. Rosner B: Fundamentals of biostatistics. Duxbury Press, Belmont, 1995.
Teaching lectures and laboratory exercises (measurements and other types of data
methods collection, use of statistical computer programs)
Assessment multiple choice test exam, after successful demonstration of use of
methods statistical computer program in solving the assigned tasks
Language of Croatian or English
instruction
Quality questionnarie
assurance
methods
42
Course title Physics of DNA, chromatin and viruses

Course code
Level of course Graduate course
Year of study 1 Semester/trimestar 1
ECTS 6 ECTS
- 20 school hours of lectures ~ 1 ECTS
(Number of
- about 120 hours of student's work ~ 5 ECTS
credits allocated)
-
Name of Rudolf Podgornik
lecturer
Learning A working knowledge of the modern aspects of the physical behavior of
outcomes and DNA in vitro, in chromatin and in viruses.
competences
Prerequisites A course in general biophysics and undergrad physics background
Course contents I will describe a slew of physical problems connected with DNA in various
contexts. I will introduce the osmotic equation of state of DNA, the phase
diagram of DNA and the nature of the condensed mesophases that it makes
at different solution conditions. I will concentrate in detail on the
experimental and theoretical elucidation of the DNA-DNA interactions and
the elasticity of DNA. I will treat the DNA-DNA interactions at various
levels of sophistication and discuss their consequences. For each of the
problems addressed I will explain the physical context and discuss its
possible biological ramifications.
I will discuss the nature of the eucaryotic genome and its structure on
various levels of organization. I will concentrate mostly on the lowest level
defined by nucleosomal core particles (NCP). I will describe the recent
experiments on NCPs in solution at small and large concentrations. For
small concentrations I will address the behaviour of the second virial
coefficient and its relation to the polyelectrolyte bridging interactions
provided by the N-tails of the NCPs. t large NCP concentrations I will
describe their experimental phase diagram and discuss the nature of the
observed mesophases. I will then introduce a simple Landau model that will
allow us to connect and understand the order observed in different NCPO
mesophases.
I will present a few basic notions about the physics of viruses, starting from
the Caspar-Klug (triangulation) number and the icosahedral symmetry of
the capsid of the small viruses. I will give a detailed account of this
symmetry and show that it describes the structure of small viruses. I will
then proceed to discuss larger viruses with big Caspar – Klug numbers. I
will introduce the elastic theory of large viruses and describe the solutions
of the von Karman equation for the shape of larger viruses. I will then
describe the thermodynamics and mechanics of DNA in the viral capsid and
43
the nature of the release of the elastic and osmotic energy in simple
bacteriophages via the “coiled spring” model. I will try to establish a
connection between the physics of DNA “in vitro” and the physics of DNA
“in viro”.
Recommended R. Podgornik, D.Harries, H. H. Strey and V. A. Parsegian, Molecular

reading interactions in lipids, DNA and DNA-lipid complexes, Gene and Cell
Therapy, Second Edition. Ed. Nancy Smyth Templeton. M. Dekker, New
York, 2004. Edward L. Wolf: Nanophysics and Nanotechnology. Wiley
VCH , Weinheim, 2004.
R.Podgornik, Polyelectrolyte-mediated bridging interactions, Journal of
Polymer Science Part B: Polymer Physics Volume 42, Issue 19 , Pages 3539
- 3556.
A. Zlotnick, Viruses and the physics of soft condensed matter, PNAS (101)
no. 44 | 15549-15550
H. Schiessel, The physics of chromatin, 2003 J. Phys.: Condens. Matter 15
R699-R774.
Supplementary Any textbook on bophysics

reading
Teaching Oral presentation
methods
Assessment Written tests
methods
Language of english
instruction
Quality
assurance
methods
44
Course title Molecular genetics

Course code
Type of course Elective. Lectures (24), seminars (10), laboratory exercises (12)
Level of course Fundamental course, Ph.D. study programme

Year of study I Semester/trimestar I
ECTS 6 ECTS
- 46 school hours of lectures ~35 h ~ 2 ECTS
(Number of
- about 115 hours of student work ~ 4 ECTS
credits allocated)
Name of Janoš Terzić, Associate professor
lecturer
Learning Students will be introduced to history of genetics and evolution of DNA.
outcomes and They will be introduced to DNA structure and human genome project.
competences Medical and evolutionary importance of mutations will be emphasized.
Role of DNA molecule in development of genetics disease, cancer will be
elaborated. Use of DNA technology in gene therapy, cloning, GM
organisms will be learned. Students will learn to how to search respective
Internet sites in order to obtain relevant information’s considering certain
genetics problems and how to find scientific articles of interests. Students
will be taught to take critical approach to genetics problems and after this
course students will be able to follow future genetics developments.
Seminars are planed to introduce students to research techniques in genetics
in order to make them understand how genetics discoveries are
accomplished. Also in the seminars student will learn how to read scientific
paper and will be exposed to problem-based learning.
Laboratory exercises are designed in the way that will make students able to
test any genetic mutation they want
Prerequisites Basic biological knowledge
Course contents LECTURES
Cells. History of genetics and evolution of DNA
Structure of DNA molecule. Human genom project.
DNA repair system. PubMed.
Oncogenes and tumor suppressor genes. Transposons.
Identifying human disease genes. Regulation of gene function.
Genetic engineering. GM organisms.
Genetics of dvelopment. Cloning.
Gene therapy. Genetics of immune system.
Medical genetics.
DNA bioinformatics. Ethical dilemmas
Replication and translation of DNA.
Proteom. Prions.
SEMINARS
PCR, RT-PCR. In situ hybridization.
2. DNA and protein electrophoresis. Immuno-hystochemistry.
45
3. DNA sequencing. Cell cultures.

4. Transgenic and knock-our organisms.
5. DNA and cDNA library.
6. DNA chip. 2D electrophoresis. Chromatographic techniques.
Scientific paper 1
8. Scientific paper 2
9. Problem-based learning1
10. Problem-based learning2
PRACTICAL LABORATORY EXCERSISES

DNA extraction.
Amplification of DNA - PCR
Restriction endonucleases and RFLP
DNA electrophoresis
Genotyping
Recommended Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R. Molecular
reading Biology of the Gene. 5. izd.Menlo Park: Benjamin Cummings;2003.
Strachan T, Read A. Human Molecular Genetics. 3. izd. Garland
Science;2003
Supplementary
reading
Teaching Lecturers will hold all the lectures with active involvement (through
methods obligatory questions) of students. Seminars will be prepared and held by
students. The students themselves under supervision of mentor will do
practical exercises
Assessment Main element of the exam is written test consisting of 60 questions.
methods Practical part of the exam will be centered on lab work and Internet
searching. Final part is oral exam.
instruction
Quality Anonymous student questionnaire
assurance
methods
46
Course title Environmental microbiology

Course code
Type of course Lectures, auditory exercises, seminars
Level of course Doctoral - elective
Year of study Semester/trimester
ECTS 6 ECTS
15 hours of lectures
(Number of
30 hours of laboratory excercises
credits allocated)
Name of Prof. Dr. Nada Krstulović
lecturer
Learning Providing the students general understanding about the role of
outcomes and microorganisms in the environments and about the consequences of
competences ecological activities and geochemical transformations carried out by
microorganisms.
Prerequisites Competences in elementary Ecology

Course contents Microorganisms and Ecosystems, Metabolic diversity, Microbial
biodegradation, The role of microorganisms in biogeochemical cycles,
Terrestrial environments, Aquatic and extreme environments,
Microorganisms and organic pollutants, Microorganisms and metal
pollutants, Environmentally transmitted pathogens.
Recommended Mayer, R.M., Pepper, I.L. and Gerba, C.P. 2000. Environmental
reading Microbiology, Academic Press, 585 p.
Perry, J.J. and Staley J.T. 1997. Microbiology: Dynamics & Diversity,
Saunders College Publishing, 1027 p.
Supplementary Scientific papers and web pages
reading
Teaching Combined teaching methods: frontal lectures, work in groups, using modern
methods technologies, practical exercises.
Assessment Regular check-ups of knowledge during the course through exercises and
methods homework assignments.
Final exam.
Language of Croatian.
instruction English (possibility).
Quality At the end of the teaching process: questionnaires about learning outcomes
assurance and competences, and about the course.
methods
47
Course Title Models and methods in structural bioinformatics

Code
Type Elective course
Level Doctoral level
Grade Ist year Semester/trimester 1st or 2end
ECTS 6 ECTS
Lectures (15 hours), Seminars (5 hours), Practice (15 hours)
(including
explanation)
Instructor Dr. Bono Lučić, Scientific Associate
Acquired skills Introduction to general principles of modeling the structure and properties
of proteins, and properties and activities of bioactive molecules. Acquiring
skills needed for critical reading and analysis of scientific results in this
field. Understanding modeling procedure up to the level needed for
performing modeling structure, properties or activities of a selected set of
proteins and bioactive molecules.
Prerequisites Basic knowlecge of biochemistry (molecular biology), basics of physics
statistical analysis, computer science and informatics.
Content The overview of methods for modeling structure and properties of proteins
and bioactive molecules. Algorithms used for model selection. Selection of
representative set of proteins and bioactive molecules for analysis, and
inclusion of similarities between molecules. Description of structural
characteristics of the set of proteins and bioactive molecules by the
molecular descriptors calculated from structure. The use of ensemble of
models in modeling. Model selection, Akaike’s information criterion and
principle of parsimony. Linear and nonlinear models. The use of similarity
between proteins/molecules in improvement of models.
Computation/estimate of 'accuracy' of random models. Estimate of
statistical significance of accuracy parameters of models. Quality
parameters of models related to the learning/training procedure and
assessment of the model quality in prediction. Model stability. Procedures
and statistical parameters in selection of the best model. Accuracy
parameters of models in the fit procedure, cross-validation and external
validation. The overview of accuracy of existing models and methods in
predicting pharmacologically important properties of bioactive molecules,
and properties and structure of proteins. Modeling secondary structure of
proteins, folding and unfolding rate constants, structural (folding) class,
secondary structural content, location of proteins in the cell, and other
global properties of proteins. Modeling 3D structure of proteins based on
similarity. Modeling structure and topology of membrane proteins. The
overview of databases, models and servers and their use in modeling in
structural bioinformatics. Modeling physical and chemical properties
(solubility, lipophilicity, transport, and absorption), biological activity and
toxicity of bioactive molecules.
Suggested 1. K. P. Burnham; D. R. Anderson: “Model Selection and Multi-Model
reading Inference : A Practical Information-Theoretic Approach (2Rev ed)”
Springer Berlin 2004
48
Springer, Berlin, 2004.

2. C. Gibas; P. Jambeck: “Developing Bioinformatics Computer Skills”
O'Reilly and Assoc. Inc., Sebastopol, CA, USA, 2001.
3. EDITORS: E. Parzen; K. Tanabe; G. Kitagawa: “Selected Papers of
Hirotugu Akaike (Springer Series in Statistics / Perspectives in Statistics) “
Springer-Verlag, New York, Berlin Heidelberg, 1998.
4. The most important and the most-cited papers in structural bioinformatics
Additional 1. D. Juretić: “Bioenergetika – rad membranskih proteina” Informator.
reading Zagreb, 1997.
2. D. J. Livingstone: “Data Analysis for Chemists – Application to QSAR
and Chemical Product Design” Oxford Univerity Press, UK, 1995.
Teaching Lectures, seminar work, open discussions, tutorial laboratory work and
participation in publication of final results.
Examination Oral examination, evaluation of seminar work, evaluation of project work
Language of Croatian or english, depending on the students. Student should be able to
instruction read research literature in English.
Monitoring of Questionnaires after 10 hours of the course lectures and seminars, and at the
the quality of end of course. Discussion with students and colleagues. Supervision of each
instruction student. Success of the course will be evaluated yearly by the Joint expert
committee of this doctoral study
49
Course title Methods in molecular biology and medicine

Course code
Type of course Lectures and laboratory work
Level of course
ECTS 6 ECTS
Laboratory exercises: 30 hours + theoretical introduction
Name of Andreja Ambriović-Ristov, PhD
lecturer Collaborators: Dr. sc. Maja Herak Bosnar, Dr. sc. Oliver Vugrek, Dr. sc.
Bojana Vukelić, Dr. sc. Neda Slade, Dr. sc. Brankica Mravinac, Dr. sc.
Anamaria Brozović, PhD
Learning To improve theoretical and practical knowledge about methods used in
outcomes and biology and medicine. For high quality research the choice of right method
competences is a priority. Thus, the good scientific education has to involve theoretical
and practical acquaintance with the methods.
This course is based on two years experience with educational project
"Methodological courses in biology and medicine" organized by A.
Ambriović Ristov in Ruđer Bošković Institute: www.metode.avalon.hr
The practical laboratory work will be performed in lecturers’ laboratories,
but in the future we hope to establish one educational laboratory at Ruđer
Bošković Institute.
Prerequisites B.Sc. in Natural Sciences, Medicine, Veterinary Science or Agriculture
Course contents The course includes following methods: sodium dodecyl sulphate
polyacrilamide gel electrophoresis (SDS-PAGE),Western Blot, expression
of proteins in baculovirus system and their purification, Phastsystem protein
analysis, imunofluorescence, molecular phylogeny, transfection, detection
of apoptosis using a fluorescent microscope.
Recommended -Sambrook J, Fritsch, E., Maniatis, T. (1989) Molecular cloning laboratory
reading manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
-Ausbel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA,
Struhl K. (1992) Short protocols in molecular biology, Harvard Medical
School, Greene Publishing Associates and John Wiley and Sons, USA
-Innis MA, Gelfand DH, Sninsky JJ, White TJ. (1990) PCR Protocols. A
guide to methods and applications. Academic Press, Inc. USA
Supplementary Ambriović Ristov i sur. (2003-2005) Metodološki tečajevi u biologiji i
reading medicini, Institut Ruđer Bošković, Zagreb
Teaching The course is consisted of lectures and laboratory work which includes the
methods most important experimental methods in biology and medicine. Every
lecturer starts with theoretical introduction, followed by the practical
laboratory work.
Assessment The course leader will get feedback information about the program and the
methods leadership success through a survey questionnaire at the end of the course.
instruction
Quality assu- All lecturers are PhD scientists from Ruđer Bošković Institute with at least
rance methods 10 years experience in science.
50
Course Title Theory and experiment in the study of protein folding

Code
Type Elective course
Level Doctoral level
Grade I (graduate level Semester/trimester II
physics-biophysics)
ECTS 6 ECTS
20 hrs lectures, 10 hrs exercises, 10 hrs literature reading
(including
explanation)
Instructor Bojan Žagrović, PhD
Acquired skills Understanding of the basics of the study of protein folding from a combined
theoretical and experimental perspective. Active knowledge and capability
of critical reading of the current research literature on the subject.
Prerequisites Active knowledge of the basics of biochemistry, physics and computer
science
Content The problem and the importance of the process of protein folding. The
basics of the theoretical and analytical understanding of protein folding and
dynamics (analogy with the theory of spin glasses and frustrated systems,
the concept of energy landscape and folding funnel). The importance of
computer simulations in the study of protein folding (molecular and
stochastic dynamics) – the basic results, limitations and challenges. The use
of distributed computing for biomolecular simulations (case study
«Folding@Home project»). The key methods for protein structure
prediction (ab intio, homology modelling, the Rosetta algorithm, CASP
competition).
The foundations of the experimental study of protein folding – key methods

(NMR, CD, T-jump fluorescence), most important results, limitations and
challenges. The transition state of the folding reaction («the -value
analysis»).
The analysis of seconday structure formation. «New view» versus «Old
view» of protein folding (the notion of conformational ensemble, sequential
versus stochastic folding). The unfolded and denatured state of proteins
(the question of residual structure, deviations from the random-walk model).
Protein folding kinetics (the notion of «contact order», structural
determinants of protein folding kinetics).
Interactions between theory and experiment in the field of protein folding –
successes and failures.
Suggested Alan Fersht «Structure and Mechanism in Protein Science: A Guide to
reading Enzyme Catalysis and Protein Folding» W. H. Freeman, 1998
Additional Roger H. Pain(Editor): «Mechanisms of Protein Folding», Frontiers in
reading Molecular Biology, 2000
Jochannes Buchner & Thomas Kiefhaber (Editor): «Protein Folding
Handbook», Wiley, 2005
Scientific research papers from the field
51
Teaching Lectures, discussions, computer exercises
Examination Exam: oral examination of the basics of protein folding; a term paper (5-10
pages) on a selected topic from the protein folding field (literature analysis
and proposal for original research).
Language of Croatian or English, depending on the students; ability to read research
instruction literature in English is a must
Monitoring of Questionaire before the beginning and after the end of the course
the quality of
instruction
52
Course title Applications of the maximum entropy production principle in physics and
biology
Course code
Type of course Elective, Theoretical
Level of course Graduate, Advanced
ECTS 6 ECTS
Lectures: 5 hours, 5 hours of seminars and 10 hours of laboratory excercises
Name of R. Dewar, P. Županović, D. Juretić, S. Marčelja
lecturer
Learning Theoretical understanding of the principle of maximum entropy production
outcomes and (MEP); practical experience in applying MEP to physical and biological
competences systems ; appreciation of the wider implications of MEP for biological and
thermodynamic evolution.
Prerequisites Key concepts of thermodynamics and statistical physics ; basic knowledge
of biology ; basic mathematics up to variational calculus ; elementary
programming skills.
Course contents The course gives balanced coverage to theoretical aspects (1-2), current
applications (3-4) and wider implications (5) of MEP.
Introduction : the prediction problem for equilibrium and non-equilibrium
systems ; statistical physics ; the MaxEnt formalism.
Non-equilibrium predictions of MaxEnt : the Fluctuation Theorem,
maximum entropy production (MEP), maximum transport principles, self-
organized criticality.
Physical applications : planetary climates, turbulence, electrical networks.
Biological applications : biochemical reaction networks, cellular
bioenergetics, biological adaptation, biological evolution.
Wider implications for the relation between biological and thermodynamic
evolution.
Recommended Lecture/seminar notes.
reading Selected bibliography of papers on MaxEnt and MEP.
Kleidon A, Lorenz RD (eds). Non-equilibrium Thermodynamics and the
Production of Entropy : Life, Earth, and Beyond. Springer, 2005.
Supplementary Other background references to MaxEnt will be useful, including :
reading Jaynes ET. Probability Theory : the Logic of Science. Cambridge
University Press, 2003.
Jaynes' papers at http://bayes.wustl.edu/etj/node1.html
Teaching Lectures (5) Seminars (5) Practical exercises (10)
methods
Assessment
methods
Language of English
instruction
Quality
assurance
methods
53
Course title Physics of medical diagnostics

Course code
Type of course lectures (7), seminars (8), laboratory exercises (15)
Level of course fundamental course
Year of study 1. Semestar/trimestar 3
ECTS 6 ECTS
Lectures (7 hours), Seminars (8 hours), laboratory exercises (15 hours)
(Number of
credits allocated)
Name of Prof. dr. Davor Eterović
lecturer
Learning Student realizes that the diagnostic image is determined by interplay of
outcomes and physical characteristics of the imaging machinery and biophysical
competences characteristics and function of the tissues. Student is able to discriminate
the radiogram from nuclear medicine scintigram, echogram or magnetic
resonance tomogram. She or he knows how these images are obtained,
what is displayed and which informations are conveyed by these basic
diagnostic imaging modalities.
Prerequisites basic physics and biology
Course contents elements of nuclear physics, radiation and matter, radiation field, biological
effects of radiation, magnetic resonance imaging, physics of nuclear
medicine, radiology physics, physics of ultrasound, what is common to
methods of diagnostic imaging
Recommended D. Eterović: Fizikalne osnove slikovne dijagnostike, u: S. Janković i D.
reading Eterović: Fizikalne osnove i klinički aspekti slikovne dijagnostike,
Medicinska naklada, Zagreb, 2002.
Supplementary S Webb (editor): The physics of medical imaging, Institute of Physics
reading Publishing, Bristol and Philadelphia, 2000
Teaching lectures (issues that are either very important, complicated or not
methods adequately described in literature), seminars (issues that student are able to
prepare for), laboratory and numerical exercises.
Assessment multiple choice test exam, assuming regular attending of laboratory
methods exercises and taking in account the student activity on seminars
instruction
Quality questionnarie
assurance
methods
54
Course title Cell biophysics II

Course code
Level of course Graduate, Ph.D. level
ECTS 6 ECTS
20 hours lectures. 10 hours of oral presentation. Each student will be
required to select a recent review article and/or topic from the literature, and
present important issues using a Microsoft PowerPoint software. The
presentation can be held in English or Croatian.
Name of Gordan Kilić
lecturer
Learning The importance of membrane protein function as signal transducers through
outcomes and cell membranes and relevance of cell-cell communication for molecular
competences medicine
Prerequisites Undergraduate courses in basic physics, cell biology and biochemistry
Course contents Cell structure. Diversity of cells and of cell functions. Lipids and cellular
membranes. Transmembrane electric potential. Ionic channels and pumps in
cellular membranes. The importance of transmembrane potential in different
cellular functions. Exocytosis and endocytosis. The role of exocytosis and
endocytosis in cellular functions.
Cell communication with outside world. Signal molecules external to cell.
The communication with other cells. Internal signal molecules. Cell
membrane role in signaling. The importance of membrane proteins in cell
communication. Receptors and G proteins. The application of biophysics
and biophysical methods in examining signal transmission by cells.
Defects in signal transmission are one of the most important causes for
different human diseases. Examples from medicine. Cancer and diabetes.
Recommended 1. Molecular Biology of the Cell. 4th edition, Alberts and others. New
reading York: Garland Publishing; 2002.
2. Biochemistry. 5th edition, Berg, Jeremy M., Tymoczko, John L., and
Stryer Lubert, New York: W. H. Freeman and Co.; 2002
Supplementary
reading
Teaching Lectures.
methods
Assessment Oral examination in a form of a presentation as described in ECTS section.
methods
Language of English
instruction
Quality
assurance
methods
55
Course title Mathematical modeling of biological systems; selected topics
Course code
Type of course Elective course
Level of course Graduate, Doctoral study
ECTS 6 ECTS: Lectures 10 hours, Seminars 5 hours, Auditory exercises 10 hours,
Computer exercises 10 hours
Name of Milan Brumen

lecturer
Learning Understanding of biological processes by computer simulation and
outcomes and mathematical modelling.
competences Knowledge of the process studied in such details which may lead to further
research.
Transferable/Key Skills and other attributes:
Ability of mathematical modelling and computer simulation of the model.
Prerequisites General physics and computer science

Course contents Objectives:
A student gets acquainted with a basic knowledge of mathematical
modelling of various biological processes in the living cell as well as in the
human body. However, the major aim is to study selected biological
processes in details by this method so that research could lead to an original
contribution to science, and concomitantly, to a work on doctoral thesis.
Therefore, the syllabus outline contains traditional examples as well as
some actual problems focused on current research.
Content (Syllabus outline):

1. Introduction to methods of mathematical modelling of biological
systems.
2. Selected topics from different levels of complexity and organisation of
biological systems:
- Biochemical reactions (enzyme kinetics, cooperative ligand binding,
glycolysis and glycolitic oscillations)
- Membrane transport (ionic and water transport, passive and active
transport, cell volume regulation)
- Calcium dynamics (diffusion, oscillations, calcium signalling from
agonist effect to muscle contraction)
- Intracellular communication (gap junctions, chemical synapses)
- Circulatory system (blood flow and transport of respiratory gases between
lungs and tissue)
- Cardiac rhythmicity
These are some of examples of selected topics, others can be included
56
according to closer direction of studies of students interested.

Recommended Selected chapters from:
reading J. Keener, J. Sneyd: Mathematical Physiology, Springer 1998
A. Goldbeter: Biochemical Oscillations and Cellular Rhythms, Cambridge
University Press 1996
J.D. Murray: Mathematical Biology, Springer 1993
F.C. Hoppensteadt, C.S. Peskin: Modeling and Simulation in Medicine and
Life Sciences, Springer 2001
Supplementary - S. Bromberg, K.A. Dill: Molecular Driving Forces: Statistical
reading thermodynamics in chemistry and biology, Garland Publishing 2002
- J.A. Tuszynski, M. Kurzynski: Introduction to molecular biophysics, CRC
Press 2003
- relevant publications in journals
- university textbooks on cell and human physiology, and biochemistry
Teaching Lectures, seminars, tutorial, individual work – research project
methods Coursework
Individual study-research project
Assessment Examination, oral, coursework, project:

methods Coursework
Project: the student must prove his/her competence in using mathematical
modeling and computer simulation to solve specific problem.
Language of English
instruction
Quality Student questionnaires and free discussion with students.
assurance
methods
57
Course title Structure and interactions in polyelectrolytes: basic theory and experimental
verification
Course code
Type of course Elective course
Level of course PhD
Year of study
ECTS 6 ECTS
10 hours of lectures, 5 hours of seminars and 15 hours of laboratory
(Number of
exercises
credits allocated)
Name of Dr. Silvia Tomić i Tomislav Vuletić
lecturer
Learning Practical knowledge in dielectric spectroscopy and how it is applied to study
outcomes and the structure and interactions of biopolymers in solution; Basic skills in the
competences field of the experimental biophysics: basic techniques (pH measurements,
dc conductivity, dialysis, electrophoresis and UV spectrophotometry) and
dielectric spectroscopy measurements (frequency range:40 Hz - 100 MHz);
computer programs developed for the data processing and the data analysis;
knowledge of the experimental data presentation, how to contrast them to
the expectations of the standard theoretical models and how to extract
remaining open questions showing the future prospect of the particular
research.
Prerequisites Undergraduate physics background, Basic chemistry, Basic softwares for

data analysis and display
Course contents Charged polymers in the soft matter and in the biological context (DNA as a
paradigm of a stiff, highly charged polymer); link between function,
structure and environment; description of electrostatic interactions in stiff
polyelectrolytes with monovalent counterions and added salt in aqueous
solutions via the Poisson - Boltzmann (PB) theory; Manning-Oosawa (MO)
counterion condensation; screening of electrostatic interactions described by
the Debye-Hueckel equation; polyvalent counterions, correlations and
repulsion-to-attraction inversion; flexibility of polymers described via the
persistence length; Odijk-Skolnick-Fixman (OSF) theory; Fundamental
length scales and scaling laws in dilute and semidilute polyelectrolyte
solutions; de Gennes-Pfeuty-Dobrynin (dGPD) theory; Dielectric
spectroscopy of polyelectrolyte solutions;
Recommended 1.M.Daune, Molecular Biophysics (Oxford University Press, New York,
reading 2003).
2. A.V.Dobrynin and M.Rubinstein, Prog.Polym.Sci. 30, 1049-1118 (2005)
3. F.Bordi, C.Cametti and R.H.Colby, J.Phys.: Condens. Matter 16, R1423-
R1463 (2004)
4. T.Vuletić, T.Ivek and S.Tomić, Dielectric Spectroscopy Center – Manuel
(2006).
5. S.Dolanski Babić, T.Vuletić and S.Tomić, Preparation and
characterization of biosamples in solution – Manuel (2006).
58
Supplementary diverse recent scientific publications

reading
Teaching The course consists of lectures (or tutorials depending on the number of
methods students), student seminars and a sequence of the laboratory exercises which
include: preparation and characterization of samples (dialysis, pH and
conductivity measurements, electrophoresis and UV spectrophotometry)
and dielectric spectroscopy (DS) measurements and data analysis and
presentation
Assessment Final exam will consist from oral presentation and written report on the
methods laboratory experiment (practical part). The students must show her/his level
of competence in using existing programmes for DS experimental data
analysis and presentation, as well as the understanding the link between
theory and experiment

instruction
Quality The students will be followed through the progress of the course. At the end
assurance of the course a questionnaire will be offered to students to express their
opinions and suggestions.
methods
59
Course title Signaling in brain

Course code
Level of course Graduate
ECTS 4 ECTS
Lectures 10 hours, Seminars 5 hours, Intensive independent work of
students in studying original research papers.
Name of Vladimir Parpura
lecturer
Learning Understanding the complexity of signaling between different cell types in
outcomes and brain.
competences
Prerequisites “Temelji neuroznanosti” (Basic Neuroscience) or equivalent
Course contents During this course the students will become familiar with the basic and up
to date knowledge in regard to types of signaling within brain . Classically,
neurons are considered to represent a computational power of the brain.
This is accomplished through the use of synapses which can be chemical
(release of neurotransmitters) or electrical (via gap junctions). According to
the classical view, glial cells were considered to merely serve as “real
cement that binds nervous elements together.” In this course, the students
will be introduced to newer types of signaling that also include glial cells.
Here, glial cells are capable of responding to the neurotransmitters released
from neurons by membrane depolarization or change in intercellular
calcium concentrations. These dynamics occurring in one glia cell can be
transferred to another via, e.g., gap junctions. In addition, glial cells can
also release neurotransmitters to stimulate surrounding neurons. One
consequence of this signaling is the modulation of synaptic transmission.
Thus, all types of communication between neurons and glia cells are
possible, which brings an additional layer of complexity within already
complex central nervous system. A special emphasis will be given to the
use of biophysical methods in investigating bidirectional glia-neuron
interactions.
Recommended Hatton, G.I, Parpura, V. (Eds.) Glial ÙNeuronal Signaling. Kluwer
reading Academic Publishers, Boston, MA. (May 2004, 456 pp)
Supplementary Selected articles
reading
Teaching 10 h lectures + 5h discussion
methods
Assessment Written exam
methods
Language of English/Croatian
instruction
Quality Evaluation by students
assurance
methods
60
Course title Basic Neuroscience

Course code
Level of course Intermediate
ECTS 6 ECTS
10 hours of lectures, 15 hours of seminars and 15 hours of laboratory
exercises
Name of Prof. Zoran Đogaš, MD, PhD
lecturer
Learning Following completion of the course, student will acquire additional
outcomes and knowledge about the normal function of the nervous system in the amount
competences adjusted to the study of biophysics. Besides, student should adopt the
positive attitude of scientific approach to the problems in this area.
Successful completion of the course will enable student to:
understand neurobiological basics of general and specific brain functions,
understand electrophysiological basics of the signalization in the brain,
differentiate neuronal and glial properties,
relate cognitive functions of memory, language, speak, attention, and space
abilities with their neural basics,
understand role of brain plasticity
Prerequisites Elementary physics and biology
Course contents Neuroscience is one of the basic biomedical sciences that studies
morphology and function of healthy nervous system with an emphasis on
the mechanisms by which its role of major control and directing system of
our body is being performed.
Study Content:
Neuron is basic structure-functional unit of the nervous system
Basics of electrophysiology
Biophysical basics of excitability
Cell membrane, ionic channels, passive and active properties of the neuron
Signal mechanisms, signal molecules and its receptors
Neurotransmitters, neuropeptides and their receptors
Synapse and cellular basis of behavior
Organization of the perception, types of senses
Smell and taste – chemical senses
Audio and vestibular system
Physiology of the eye and photo-transduction
Retina, primary visual pathway and primary visual cortex
General organization of motor systems
General brain functions: ascending activating system, EEG, consciousness,
and awareness
Cellular mechanisms of memory and learning
Practical skills:
NeuroSim and Electrophysiology of the neuron
Computer models of membrane and action potentials
Computer models of postsynaptic potentials
61
Computer models of voltage and patch clamp

Computer models of neural networks
Basis of EEG and EMG signals and evoked potentials
In vivo neural recordings on experimental animals
Computer psycho-diagnostic system
Recommended Judaš, M. and Kostović, I.: TEMELJI NEUROZNANOSTI, 1st ed. MD;
reading Zagreb, 2005. (free download)., selected chapters
Đogaš Z. et al.: VODIČ KROZ VJEŽBE IZ TEMELJA
NEUROZNANOSTI, MF Split, Split, 2005.
Supplementary Kandel, E.R., Schwartz, J.H. and Jessel, T.M.: Principles of the neural
reading science, 4.ed., McGraw-Hill; New York, U.S.A., 2000
Shepherd, Gordon M. Neurobiology, 3.ed., Oxford University Press, New
York, U.S.A., 1994
Selected original articles
Teaching Lectures, seminars, problem-based learning, laboratory exercises, computer
methods classroom
Assessment In-course tests; Final written examination
methods
Language of
Croatian or English
instruction
Quality Quality control analysis by the students and peers,
assurance Passing exams proportion analysis,
methods University of Split Committee for the teaching quality control report,
Extramural evaluation (National agency team for quality control, TEEP).
62
Course title Neurodynamics

Course code
Type of course Elective, Lectures (15 hours), Seminars (5 hours) and Laboratory Exercises
on Computer (10 hours)
Level of course PhD level
Year of study I Semester/trimestar II
ECTS 6 ETCS credits
Lectures – 15 hours. Additional 60 hours are required to cover the material.
(Number of
Laboratory exercises – 10 hours require 30 hours for preparation and
credits allocated)
writing three written laboratory reports. Seminar – 5 hours. The literature
review including writing student seminar and preparing the presentation
require total of 50 hours.
Total: 15h + 60 h + 10h + 30 h + 5h + 50h = 1705h ~ 6 ECTS credits
Name of lecturer Assistant Professor Selma Supek
Learning Insight into advanced functional imaging methods, ability of a critical
outcomes and evaluation of their application, ability for designing experiments and
competences selecting toos for data display and analysis
Prerequisites Basic Neuroscience. Cell biophysics.
Course contents Cellular neurodynamics. Bioelectromagnetism. Electro- and
magnetoencephalography (EEG, MEG) – measurements and experimental
design. Transcranial magnetic stimulation (TMS). Cortical connectivity.
Spatio-temporal source localization. Cortical oscillations. Multi-modal
integration. Functional and retinotopic organization of the human visual
cortex. Cognitive neurodynamics.
Recommended Arthur W. Toga, John C. Mazziotta (Eds), Brain Mapping: The Methods,
reading 2nd ed., Elsevier Science, 2002
Malmivuo J. and Plonsey R.: ''Bioelectromagnetism: Principles and
Applications of Bioelectric and Biomagnetic Fields'',
http://butler.cc.tut.fi/~malmivuo/bem/bembook/
Supplementary C.T.W. Moonen and P.A. Bandettini (Eds.), Functional MRI, Springer-
reading Verlag, Berlin, 1999.
W.W. Orrison, J.D. Lewine, J.A. Sanders, and M.F. Hartshorne, Functional
Brain Imaging, Mosby-Year Book, St. Louis, 1995.
Selected recent review and research articles.
Teaching methods Lectures, laboratory exercises (numerical simulations, software tools for
display and analysis of data), student seminar presentations and discussion
of most recent research results.
Assessment During the course: written laboratory reports, written and presented student
methods seminar. Final written exam.
instruction
Quality assu- Discussion and e-mail communication during lectures and laboratory
rance exercises and written questionnaire at the end of the course.
methods
63
Course title Nanophysics and Nanotechnology

Course code
Type of course elective
Level of course doctoral
Year of study I Semester/trimestar II (spring)
ECTS 6 ECTS
Lectures (30 hours), Seminars (10 hours), Exercises (10 hours)
(Number of
credits allocated)
Name of Prof. Dr. Hans O. Lutz
lecturer
Learning Basic understanding of the physics of nanostructures and their application to
outcomes and modern technological developments
competences
Prerequisites Elementary knowledge of quantum mechanics
Course contents Nanostructure physics is a very interdisciplinary subject. We will have to
look into several of the well-known “ladice” of physics, in particular
atomic, molecular, nuclear and solid state physics.
●Introduction: from condensed matter to molecules and atoms; classical
size effects and scaling relations.
●Probing the properties: spectroscopy; microscopy; scanning probe
techniques.
●Geometrical structures and quantum size effects: tiling; electron energies,
localization and confinement.
●Free nanoparticles, properties and production: metal, semiconductor and
rare gas clusters; molecules and carbon structures; gas aggregation; plasma,
chemical and laser methods. Applications.
●Nanostructures in the bulk and on surfaces, properties and production:
electronic structure and magnetism; cluster growth and deposition;
nanopatterning and lithography; atom-by-atom production. Applications.
●Self-organization; nanomachines and molecular assemblers.
●Outlook.
Recommended Lecture notes shall be available. In addition, reference will be made to
reading some recommendable internet addresses.
Supplementary From among the many books on nanophysics and nanotechnology, in
reading particular contents of the following will be used:
Edward L. Wolf: Nanophysics and Nanotechnology. Wiley VCH ,
Weinheim, 2004.
Charles P. Poole and Frank J. Owens: Introduction to
Nanotechnology. Wiley and Sons, NJ, 2003.
Mark Ratner and Daniel Ratner: Nanotechnology. Prentice Hall PTR , NJ,
2003.
R. Schmidt, H.O. Lutz and R. Dreizler: Nuclear Physics Concepts in the
Study of Atomic Cluster Physics. Lecture Notes in Physics Vol. 404,
64
Springer, Berlin, 1992.

S.N. Khanna and A.W. Castleman: Quantum Phenomena in Clusters and
Nanostructures. Springer Series in Cluster Physics, Berlin, 2003.
K.-H. Meiwes-Broer: Metal Clusters at Surfaces. Springer Series in
Cluster Physics, Berlin. 2000.
Teaching Lectures (30 hours)
methods Seminars (10 hours)
Exercises (10 hours)
Assessment Participation and performance in the course; final examination
methods
Language of Understandable English; this will allow the students to practice the «lingua
instruction franca» of physics.
Quality Continuous feedback by the students; course rating by the participants at the
assurance end of the course
methods
65
Course title Biomechanics

Course code
Type of course Theoretical with exercises
Level of course Advanced (PhD) level
ECTS 6 ECTS
(Number of Teaching (lectures 20 lecture hours) ≈ 0,75 ECTS
credits allocated) Laboratory exercises + preparation for exercises (10+20 hours) ~ 1 ECTS
Student studying, about 120 hours ≈ 4,25 ECTS.
Name of Prof. Dr. Mile Dželalija, Professor of Physics
lecturer
Learning Understanding of the main physical laws of classical mechanics and their
outcomes and applications in different locomotion systems. Competences in
competences anthropometric, kinematics and kinetic measurements, and measurement of
electromyography signal and in creation of physical models, simulations,
and visualization of different systems. Originality and creativity in the
discipline. Elementary computing skills.
Prerequisites Competencies in understanding basic laws of classical mechanics.
Course contents Introduction. About Physics and Biomechanics. History of Biomechanics.
Musculoskeletal system. Skeletal system. Muscular system. Joints.
Kinematics. Referent systems. Motion along a straight line and in two and
three dimensions. Circular motion. The Newton’s laws of motion. The
Newton’s law of gravitation. Classifying forces: gravitational force, normal
force, frictional force, tension force, buoyant force, drag force, dynamic
fluid force, Magnus’s force, elastic force. Systems of particles. Circular
motion. Equilibrium. Dynamic equilibrium. Kinetic energy. Work. Potential
energy. Conservation of energy. Power. Biomechanical measurements.
Simple examples in Physics of sport. Application of physical laws in some
sport activities. Physical models of different systems. Introduction in
programming and simulation. Visualization of some simulated systems.
Preparation and some measurements.
Recommended M. Dželalija, Biomechanics, Sveučilište u Splitu, in preparation
reading
Supplementary P.M. McGinnis, Biomechanics of Sport and Exercises, Human Kinetics,
reading ChampaignCollege Physics, Fifth Edition, Saunders College Publishing,
Orlando, 2000.
Biomechanics of the Musculo-skeletal system, Second Edition, ed. B.M.
Nigg, W. Herzog, John Wiley & Sons, Weinheim,1999,
Teaching Combined teaching methods: frontal lectures, work in groups,
methods measurements, using modern technologies.
Assessment Assessments during lectures.
methods Exam: seminar work (definition of problem, creation of physical model,
simulations; presentation).
Language of Croatian and English.
instruction
Quality At the beginning and at the end of the teaching process: questionnaires
assurance about learning outcomes and competences, and about the course.
methods Questionnaire to alumni students and connections their jobs requirements to
competences that are supposed by these activities.
66
Course title Biophysical and Biomedical Aspects of Oxidative Stress

Course code
Type of course Elective course, lectures, seminars
Level of course Fundamental, Ph.D. study
Year I. Semestar II.
ECTS 2 ECTS
(Number of - 10 hours (6 lectures, 4 seminars)
credits allocated) = 10 hours direct teaching ~ 1 ECTS
- 20 hours learning and consulting ~ 1 ECTS
Name of Neven Žarković, MD, PhD, senior scientist
lecturer
Learning Students will gain knowledge on the nature of free radicals and their
outcomes and interactions with bioactive macromolecules. The course is oriented to
competences biophysical sciences stressing in particular processes and consequences of
lipid peroxidation. Students will also learn how to use scientific methods to
study biological and medical problems related to oxidative stress.
Prerequisites Basic knowledge of physics, chemistry and biology
Course contents Oxidative stress is a term used to describe excess in production of oxygen
free radicals and reactive oxygen species. Although oxidative stress is
commonly understood almost as universal mechanisms by which oxygen
damages vital molecules of the living systems (bioactive macromolecules
and cellular structures), oxidative stress is ubiquitary and often necessary
component of the living systems. Therefore, the aim of the course if to teach
students about fundamental features of oxidative stress and its roles in living
systems on the level of molecules, cells and entire organisms.
The content of the course includes following topics:
• Free radicals
• Oxidative stress
• Pro- & anti-oxidants
• Lipid peroxidation
• Reactive aldehydes as second messengers of free radicals
• Interactions of reactive oxygen species and reactive aldehydes with
macromolecules
• Importance of oxidative stress for the living systems (cells, tissues
and mammalian organisms)
• Alterations of macromolecular structures and functions during
oxidative stress
• Biological features of oxidative stress
• Medical relevance of oxidative stress
Recommended 1. Neven Žarković , Suzana Borović , Igor Stipančić, Marija Poljak Blaži,
reading Iva Lončarić, Ana Čipak, Gordana Jurić, Tea Vuković, Willibald Wonisch ,
Georg Waeg i Kamelija Žarković. (2002) Fiziološke i patološke značajke
lipidne peroksidacije U: Oksidativni stres i djelotvornost antioksidansa.
67
(Bradamante V., Lacković Z., ur.), Medicinska naklada, Zagreb, pp. 10-29
2. Neven Žarković (2003) 4-Hydroxynonenal as a bioactive marker of
pathopysiological processes. Mol Asp Med, 24:281-291
3. Zijad Duraković, Neven Žarković: Biologija starenja i gerijatrija, u B.
Vrhovac i sur. Interna medicina, u tisku
Supplementary 1. Oxidative stress and lipid peroxidation: Physiology and pathology of 4-
reading Hydroxynonenal (N. Žarković, R.J. Schaur & G. Poli, Eds.).
http://www.kfunigraz.ac.at/hne-club/, Zagreb, Graz
2. Neven Žarković (2005) Mechanismen der Tumorentstehung. In:
Oxidativer Stress und Pharmaka (Siems Werner, Krämer Klaus, Grune
Tilman, Eds.). Govi-Verlag, Eschborn, 145-158
3. Neven Žarković (2005) Antioxidatien in der Prävention und
Chemotherapie von Tumoren. In: Oxidativer Stress und Pharmaka (Siems
Werner, Krämer Klaus, Grune Tilman, Eds.). Govi-Verlag, Eschborn, 159-
174
4. Ana Cipak, Meinhard Hasslacher, Oksana Tehlivets, Emma J Collinson,
Morana Zivkovic, Tanja Matijevic, Willibald Wonisch, Georg Waeg, Ian
W. Dawes, Neven Zarkovic, and Sepp D Kohlwein (2006) Saccharomyces
cerevisiae strain expressing a plant fatty acid desaturase produces
polyunsaturated fatty acids and is susceptible to oxidative stress induced by
lipid peroxidation. Free Radical Biology and Medicine, 40:897-906
Teaching Lectures, seminars
methods
Assessment Student activity on classes and oral exam at the end of the course
methods
instruction
Quality Questionnaire for students at the end of the course
assurance
methods
68
Programme requirements (degree plan)

Students will be selected after public competition. The preferred type of students for the
proposed Ph.D. study are those who already demonstrated interest both for physics and for life sciences,
in other words for biophysics. We realize, however, that interest for biophysics can arise after the
degree in physics in molecular biology or in medicine. For these students supplementary (preparative)
courses are obligatory. What supplementary courses a student must enrol in, the Study Committee will
decide on case by case basis. Student’s responsibility is to be informed on time what supplementary
courses will Study Committee require in his or her case (at least one year before intended enrolment in
to the biophysics Ph.D. programme). It is also student’s responsibility to reach agreement with the
Study Committee that similar or equivalent supplementary courses are recognized in the case when
such courses are offered by universities other than the University of Split.
Student's responsibility is to learn the rules connected with the Ph.D. study, to have frequent
briefings with mentor with respect to research and to plan research together with mentor and advisers so
that results can be obtained in a required time period. Full-time student in the second and third year of
his study programme and latter until his/her Ph.D. will be expected to spend weekly at least 40 hours at
research (excluding vacations). The study programme will encourage the participation of a student in all
intellectual activities that do not distract the student from his studies. Student's responsibility is to
inform his mentor and Advisory committee about all changes that may have negative influence on his
research or study practice. Student must create written report about his progress at least once per year
for mentor, for advisers and for the Department head.
Efficient three year Ph.D. study programme is very challenging for students. First year students will
have advisers who will help them concerning all decisions and problems connected with the study
programme. To enrol into the second study year students as a rule must have positive grades in all
preparative elective and regular courses taken by them beforehand. In addition, students enrolling into
the second year must have the agreement with their chosen mentor about the topic for their Ph.D. thesis
research. The Advisory Committee (see Chapter 3.6) and Study Committee will closely follow student's
progress in the chosen research field. Advisers and Study Committee must be satisfied with the quality
of student's research seminar and with student’s written research proposal to allow student's enrolment
into the third year study programme. The crucial question to answer is how promising is student's
research with respect to producing novel and important results in the chosen field. Student’s
responsibility is to engage mentor’s help in writing high quality research proposal during the second
study year. This proposal will be submitted to student’s advisers and to Study Committee. Experts for
the proposed research topic may be consulted too. For the Ph.D. thesis topic seminar in the third year
student is expected to enclose for the audience printed research paper as submitted (or accepted) by the
well known (CC) international scientific periodical. The responsibility of student’s advisers is to decide
independently of the journal review process whether student’s research is of so excellent scientific
quality that student can proceed with his/her work on the Ph.D. thesis in accord with detailed
instructions that will be present in the Instructions booklet to be prepared for this study. In order to be
accepted for the thesis defence student must present at least one published or accepted paper in the CC
periodical, with student as the first author. At least one expert for the chosen topic (in addition to thesis
adviser) should be present during the thesis defence. As a rule the Thesis defence committee will have
one member from the University of Split, one from the Ruđer Bošković Institute in Zagreb, and one
internationally recognized expert for the thesis research topic (usually the thesis adviser). Regular
students, who fulfil all study obligations, can have their thesis defence already at the end of the third
study year, but thesis defence during fourth study year will be also in accord with study rules. In other
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words, four years full-time study (up to three years of research work) will be allowed for research topics
requiring longer than two-year research period. Regular students, who fail to fulfil all their obligations
for the enrollment into the third study year after four years of study, will lose the priviledge to continue
with this study programme. They may be helped by the Study Committee to transfer to some related
study specialization.
Thesis supervision and academic advising

The execution of the proposed study is equally shared by the FPMZiK in Split and IRB in
Zagreb. The study programme will be therefore led by the Prof. Dr. Davor Juretić from the University
of Split as Chair and Dr. Vesna Svetličić from the IRB, Zagreb, as Co-Chair. These study leaders will
be responsible for study organization and execution during next several years. Theirs will be the final
responsibility for academic and scientific properties of the programme, for the preparation and
distribution of study information, for students selection, for deposition of study programme documents
and for organisation of seminars, workshops and lectures by guest scientists.
The Study Committee for the proposed Ph.D. study of biophysics will decide about all
important study matters. The official title and membership of the Study Committee will be determined
after the approval of this study programme. Obvious candidates for the membership of the Study
Committee are present members of the Steering Committee: Stjepan Marčelja, Miroslav Radman,
Davor Juretić, Ante Graovac, Davor Eterović, Silvia Tomić, Bono Lučić, Neven Žarković, Vesna
Svetličić and Mile Dželalija. Vesna Svetličić is from the Ruđer Bošković Institute in Zagreb, and she
heads Croatian Biophysical Society. Ante Graovac has joint appointment at that Institute and at the
Faculty of Natural Sciences, Mathematics and Kinesiology, University of Split. Stjepan Marčelja is
leading Croatian biophysicist, previous head of the Ruđer Bošković Institute, presently with joint
appointment at the Faculty of Natural Sciences, Mathematics and Kinesiology, University of Split and
at the Australian National University, Canberra, Australia. Miroslav Radman is member of Academy of
Science in France and founder of the MedILS Institute in Split, Croatia. Davor Eterović is professor of
biophysics at the Medical School, University of Split. Davor Juretić is professor of physics who also
holds lectures on biophysics, bioenergetics and structural bioinformatics at the University of Split and
University of Zagreb. Mile Dželalija is also professor of physics at the University of Split. Silvia Tomić
is leading biophysicist at the Institute of Physics, Zagreb. Bono Lučić and Neven Žarković are well
known biophysicists from the IRB, Zagreb, who entered biophysics from electrical engineering and
medicine, respectively. The Study Committee will decide which students will be allowed to enrol into
proposed Ph.D. study programme and what additional supplementary courses they would be adviced to
take if such need arose (depending on student’s background). Enclosed list of supplementary courses,
available from the University of Split (see the Appendix I), can serve as an orientation to students, so
that they can see in that example the collection of courses among which the Committee can recommend
a couple of supplementary courses. Since similar courses of general nature exist on all universities,
undergraduate students from other universities can enrol into and graduate such courses they obviously
need (biochemistry for physicists, some additional physics for biologists and medical students), if they
decide to study biophysics afterwards.
The Study Committee selects students on the basis of their grades, their demonstrated interest
for biophysics, and on their accomplished research during undergraduate and master’s degree study
(poster or research paper authorship). Recommendation letters of experts will be welcome. Students are
expected to show initiative in talking with all prospective mentors. Since this is an interdisciplinary
study programme, it will not be unusual for a student to have two mentors for his/her Ph.D. research.
Student must achieve agreement with a chosen mentor or mentors concerning student’s Ph.D. thesis
research topic before enrolling into the second study year. The written proposition of a student about his
70
Ph.D. research topic will be considered by the Study Committee at the beginning of the second study
year.
Each student will have three advisers. One of them is student's mentor with main responsibility
to supervise and guide student during his/her Ph.D. research. Second adviser can be student’s co-
mentor. Mentor leads the three member advising committee. Mentor must be one of course leaders of
the proposed study and research worker committed to support the proposed study programme during
the time period of four (full-time) to seven (part-time) years which will student need to finish this
programme. All our course leaders, wishing to be mentors as well, must be able to offer to our students
high quality research topic that can lead to the Ph.D. During first study year we plan to bring together
potential mentors and students at the workshop organized at the University of Split or University of
Dubrovnik.
Mentor's obligation is to explain clearly to student what is expected of him, to discuss student's
progress with other two advisers and after reaching consensus to report yearly in the written form about
student's progress to Study Committee, to Department head and to Faculty committee. An agreement
between mentor and student should be achieved with respect to how often they will meet (at least one
time per month, and much more often is the case of necessity), how student's progress will be followed,
how much of financial resources mentor controls will be devoted to student's research and student's
participation in research meetings and workshops, what new skills student must learn, and how student
can establish contacts with researchers working in the same field. Furthermore, the agreement should
exist between student and mentor from the very beginning of their collaboration, how research results,
coming out of student's work, will be published, how mentor's contribution will be honoured in
authorships of these papers. If research is sponsored by the contract, a student should know all details
and obligations written in the contract.
Mentor will explain to the student all necessary ethical rules connected with chosen research
topic and rules of safety and protection at the work place. The necessity to keep in the safe and orderly
form the primary research data for many years will also be pointed out to a student.
More important decisions with respect to student's work must be put in writing, distributed to
other advisers, given to a student, and enclosed in the yearly report of student's progress. Mentor will
ensure that student can participate in research so that interesting and original results can be produced. If
some difficulties develop mentor will explain to a student in the written form that progress is not
satisfactory and of measures needed to be taken for smooth study continuation. According to previously
agreed plan mentor will ask a student for written material, offer critical comments, give support, or ask
for the modifications in a paper or thesis concept.
Transferable courses and modules

Enclosed list of elective courses (Chapter 3.2) contains courses from other study programmes
that are modified to become suitable for our Ph.D. programme. These are Fundamentals of
Neuroscience, Selected Topics from Medical Physics, Multivariate Statistical Methods (Medical
school), Physics of DNA, chromatin and viruses, Molecular genetics (M.Sc. programme in physics with
biophysics orientation) and others.
The course Methods in Molecular Biology and Medicine is held regularly at the Ruđer
Bošković Institute. As elective course it would be very usefull for our students too. In addition, the
agreement with the Faculty of Science, University of Zagreb, will be sought after such that our students
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can earn certain number of credits by enrolling into their graduate courses with biophysical orientation,
and that their students can similiry earn required credis by enrolling into our courses.
Students can also enroll courses from related interdisciplinary international study programmes
such as: „Molecular biosciences“ and „Biology of Cancer“. Accordingly, students from these
interdisciplinary study programmes can enroll courses offered fior the doctoral programme in
biophysics.
Most of elective courses are offerred specificaly for our Ph.D. programme in biophysics. Since
these courese are as a rule of high quality it would be desirable that students from other Universities in
Croatia and in neighboring countries can also enroll into these courses. The organisers of the Study
programme will undertake necessary steps to ensure the transferability of courses. As example, we
mention here some elective courses that are at present offered only for the Ph.D. programme in
biophysics, but deserve wider distribution: Theory and Experiment in the Study of Protein Folding ,
Mathematical modeling of biological systems; selected topics, Applications of maximum entropy
production principle in physics and biology, Signal Processing in a Brain, Cell biophysics II, Models
and Methods in Structural Bioinformatics, Higher order repeats in human genome, Biophysical and
Biomedical Aspects of Oxidative Stress, Physicochemical Basis of Radiation Biology.
Courses and modules offered in foreign languages

All offered courses from our study programme can be presented either in English or in Croatian
language. English language presentation will be the selection of choice for foreign course leaders (Hans
Lutz, Milan Brumen, Roderick Dewar). All courses will be offered in English in the case of
international student body. Supplementary courses, held at any EU university, will be usually
recognized by the Study Committee, if found appropriate for the advanced study of biophysics and for
student’s undergraduate background. In a future we intend to offer basic courses targeted to fill the
background of graduate students in the PhD biophysics programme who did not have such courses
during previous study (see the Appendix I). Such dedicated supplementary courses will also be offered
either in Croatian or English language. Foreign students will be encouraged to enroll into our Ph.D.
study programme. Those students are expected to have more diverse background, so that supplementary
course requirement can be waived for some of them. Also, with advance information about this study
programme, they should be able to take additional courses (if needed) at the university where they seek
to obtain the undergraduate degree. In the case of study internationalization, when foreign students are
present in the student body, students from Croatia and from neighboring countries such as Bosnia and
Herzegovina, will also have all lectures delivered in the English language.
ECTS recognition
The proposed study programme is flexible and open with respect to possible ECTS credit
transfers. The Study Committee will decide in each specific case how many of ECTS credits student
has already earned prior to enrolment into our study programme. It is expected that recognized courses
and ECTS credits will mainly be from other graduate programmes in biophysics. During our study
programme a student can chose some elective courses that are not in our list of offered electives, if the
Study Committee considers such electives useful for student's intended research topic.
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Admission to Dissertation defense

The conditions for the Ph.D. thesis acceptance and for the positive outcome of the thesis
defence, have been already outlined in the Chapter 3.6. The suitability of chosen research topic is
judged by the Study Committee, student’s mentor and student’s advisers as well as experts for that
topic. At least one high quality research paper accepted or already published in the international journal
with student as the first author is the minimal requirement for a student to be admitted to the PhD thesis
defence, because in their goal to become independent researchers, students must learn not only to
perform research independently, but also to present their main results in a scholarly manner. During the
third or fourth study year (for regular students) sudent has public dissertation defense. The Study
Committee must have good reasons to grant thesis defense date after fourth study year (see Chapter
3.1).
Continuation of studies
The interruption of study programme for regular students is strongly discouraged. On case by
case basis the Study Committee will have to decide if student will be permitted to continue with study
programme after longer interruption or not. Such practice is necessary to ensure the efficiency of
proposed study programme, i.e. that the Ph.D. thesis is defended after no longer than four year time
period.
Certificates requirements for Life-long education

Students unable to finish full Ph.D. study programme in biophysics, or wishing to leave it early,
will get the certificate with detailed specification what requirements of our programme they have
completed. If they wish so, the arrangements will be made to facilitate their transfer to other doctoral
study or to relevant specialization study.
Taught Doctorate course requirements / Non-taught

Doctorate
At least two high quality research papers from the field of biophysics, recently published in the
CC journals as first authorship papers, are necessary minimal requirement if student wishes to apply to
our Ph.D. programme in biophysics with waived requirement to enroll into obligatory courses. These
papers must not be older than four years and must not be used for advancement in some other study
programme. In such a case the Study Committee can decide that first obligation for such a student is to
successfully defend the thesis topic seminar and to write a thesis in English. Such a student is expected
to fulfil requirements for the European Doctorate described in the Chapter 1.4, namely to obtain
positive review of his/her thesis from at least two foreign EU experts and to defend the Ph.D. thesis in
the presence of at least one well known international expert for a chosen topic.
Maximum duration of study

For full-time students four years is as a rule the maximum time period for finishing their studies
and for getting the Ph.D., although the present law in Croatia allows for the maximum period of six
years (see Chapter 3.1). For part-time students maximum time length allowed is six years. The
73
deadlines that full-time students must observe (see Chapter 3.6) are doubled in time duration for part-
time students. The detailed timetables will be available to students in the Study rules brochure.
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4. Institutional information
Location
The study programme takes place at the Faculty of Natural Sciences, Mathematics and
Kinesiology, University of Split, and at the Ruđer Bošković Institute, Zagreb, Croatia, with several
exceptions for shorter time periods outlined here. Some obligatory seminars and week long workshops
may take place at different institutions according to previous agreements (Medical School, University
of Split; Oceanographic Institute, Split; MedILS, Split; University of Zagreb; University of Dubrovnik).
Students will also get opportunity to spend part of their study programme at institutions outside Split
and at foreign academic and research institutions. As the minimum period of three month research work
in some foreign (EU) laboratory is one of European Doctorate requirements, all our students will be
encouraged to fulfil it. They will be also encouraged to participate with posters or lectures at
international conferences and summer schools dealing with biophysical topics.
Premises and equipment
The Faculty of Natural Sciences, Mathematics and Kinesiology, University of Split, and
the Ruđer Bošković Institute, Zagreb, Croatia have necessary laboratory space, lecture halls and
laboratory equipment needed for execution of the doctoral programme in biophysics. The
administrative work connected with the doctoral programme will be performed jointly by the
graduate study office now planned at the University of Split, and at the Education Center, IRB,
Zagreb. The Faculty of Natural Sciences, Mathematics and Kineziology at the University of Split
plans to have several interdisciplinary Ph.D. studies and has already taken steps to ensure
necessary administrative help. Our Faculty and IRB will share relevant additional maintenance
expenses, while administrative expenses will be covered from tuition.
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Research and development projects relative to the

programme
Andrea Ambriović-Ristov
Ruđer Bošković Institute, Zagreb
Projects :
1. Tumor resistance to cytostatics and adenovirus vectors for tumor genoterapy (project leader Andrea
Ambriović-Ristov, Croatian Ministry of Science project No. 098-0982913-2850).
2. Cellular response to genotoxic agents (project leader Dr. Maja Osmak, Croatian Ministry of Science
project No. 0098076 (old) MZOŠ 098-0982913-2748 (new).
Milan Brumen
University of Maribor, Slovenia
Projects:
1. Biophysics of polymers, membranes, gels, colloids and cells ( Prof. dr. Rudolf Podgornik,
University of Ljubljana and Jožef Stefan Institute, Ljubljana; chairperson of the research
programme); founded by the Slovenian Research Agency.
Possible research topics for the Ph.D. thesis work:

1. Mathematical modelling of isometric and isotonic force development in smooth muscle
cells.
2. Different pathways of calcium signaling in smooth muscle cells; a study by mathematical
modelling.
3. Thermodynamic aspects of smooth muscle contraction.
Roderick Dewar
EPHYSE-INRA, Bordeaux, Francuska
Projekti:
1) Evaluating the hypothesis of maximum entropy production for terrestrial ecosystems
Zoran Đogaš
Medical School
University of Split
Projects:
1. Neurotransmitters and the control of breathing (old Croatian Ministry of Science project No.:
0216003.
2. Neural control of breathing in a wakeful state, during sleeping and during anesthesia (new
possible project).
Davor Eterović
Medical School
University of Split
Projects:
1. Regulation of blood flow in stritiated muscle (0216007, old project)
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2. Mechanisms of adverse effects of extracorporeal urinary lithotrypsy (new possible project).
Ante Graovac
Ruđer Bošković Institute and the Faculty of Natural Sciences, Mathematics and Kinesiology,
University of Split
Projects:
1. Modelling of new carbon materials (old project, 0098039).
2. Modelling and spectroscopy of bioactive materials (new programme which gathers project
leaders of six research projects, programme leader: Ante Graovac).
3. Modelling of molecules (new project MZOS, 098-0982929-2940; project leader: Ante
Graovac)
1. Water clustering
2. Graph-theoretical methods for description of DNA and proteins
Davor Juretić
Faculty of Natural Sciences, Mathematics and Kinesiology, University of Split
Projects:
1. Predicting structure and function of membrane polypeptides (old Croatian Ministry of Science
project No.: 0177163).
2. Development and applications of maximum entropy production principle (new project offered
within research programme: Development and applications of new biophysical methods and
models). This new project has been now approved as the Croatian Ministry of Science project
No.: 177-1770495-0476. Collaborators are Stjepan Marčelja, Bojan Žagrović, Paško Županović
and Srećko Botrić.

1. Construction principles for selective antimicrobial peptides
2. Application of the maximum entropy production principle for the selection of optimal
kinetic models for efficient work of natural nanomotors
3. Membrane topology prediction for integral membrane polypeptides.
Bono Lučić
Projects:
1. Development and application of models in chemistry and bioinformatics (0098034, old
research project)
2. Development and application of new biophysical methods and models. The Croatian Ministry
of Science project: 098-1770495-2919 with Nenad Trinajstić as the project leader.
Possible topics of research work which would lead to finishing the doctoral thesis:
1. Development of methods for modeling global properties of proteins based on their primary
structure information: (a) secondary structure content (alpha, beta, undefined); (b)
structural class (alpha, beta, alpha/beta, alpha+beta); (c) classification of proteins (e. g.
77
between soluble and membrane proteins); (d) prediction of protein folding and unfolding
constants
2. Development of novel method for modeling secondary structure of soluble proteins, as
well as for modeling structure of membrane proteins having transmembrane segments in
beta conformation (membrane proteins of beta class)
Stjepan Marčelja
University of Split and the Australian National University Canberra, ACT 0200, Australia)
Projects:
1. Surface forces in aqueous electrolytes
2. Development and application of nonlinear dynamics methods in environmental sciences

1. Multiscale prediction of time series with environmental applications
2. Ion-specific interaction of hydrophobic surfaces in simple electrolytes
Boris Martinac
Professor and Foundation Chair of Biophysics
School of Biomedical Sciences
The University of Queensland
Brisbane, QLD 4072
Phone: 61-7-3365-3113
Fax: 61-7-3365-1766
E-mail: b.martinac@uq.edu.au
Projects:
1. Early evolutionary origins of mechanosensory transduction:structure, function and
phylogenetic studies of the family of mechanosensitive channels in cell-walled organisms.
2. The role of mechanosensitive (MS) ion channels in magnetoreception.
3. Biologically inspired sensory systems: towards an intelligent tactile sensor.
4. Force from lipids: the role of the lipid bilayer in mechanosensory transduction.
1. The role of lipids in function of mechanosensitive ion channels
Rudi Podgornik
Rudi Podgornik
Laboratory of Physical and Structural Biology
National Institute of Child Health and Human Development
National Institutes of Health
9 Memorial Drive, MSC 0924
Bldg. 9, Rm. 1E116
Also employed at:
University of Ljubljana and Jožef Stefan Institute, Ljubljana, Slovenia
Projects:
1. Biophysics of polymers, membranes, gels, colloids and cells ( Prof. dr. Rudolf Podgornik,
University of Ljubljana and Jožef Stefan Institute, Ljubljana; chairperson of the research
programme); founded by the Slovenian Research Agency.
2. Fizika granularne snovi
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3. Interfacial Materials - Computational and Experimental Multi-Scale
Franjo Sokolić
Faculty of Natural Sciences, Mathematics and Kinesiology, University of Split (from spring
2007).
Collaboration in the present project financed by the Croatian Ministry of Science:

177-1770508-0480: Structure, interactions, and transport in water solutions with applications.
Possible topic for the Ph.D. thesis research

1. Microscopic structure and dynamics of aqueous solutions
Selma Supek
Faculty of Science, University of Zagreb
Project: COGNITIVE NEURODYNAMICS (MZOS 119-1081870-1252)
Possible research topics for the Ph.D. thesis work

1. NEURODYNAMICS OF MULTI-MODAL CORTICAL INTEGRATIONS
2. CORTICAL NEURODYNAMICS OF THE VISUAL PERCEPTION
The agreement exists with foreign collaborative institutions/laboratories where students can
perform a part of their Ph.D. research (Helsinki-Finland, Germany, UK, USA)
Vesna Svetličić
Project:
Surface forces on atomic scale applied in marine science and nanotechnology,
MZOS 098-0982934-2744.
The project is aimed to establish a new scientific discipline -marine biophysics, in order to bring
biophysical concepts and approach to the study of the organization and function of the organic
matter continuum in the sea.
Research topic:
1. Biotic and abiotic marine processes at nanoscale: Supramolecular
organization of marine gel phase
Janoš Terzić
Medical school, University of Split
Projects:
1. Studying connections and expression of human genes

1. Molecular basis for diving
79
Sanja Tomić
The Research Project: 'Computational study of bio-macromolecules and development of new

algorithms' The Croatian Ministry of Science, 098-1191344-28601.
Themes for doctoral thesis:
1) Modelling protein-protein interaction (as a part of research on

developing the programme for protein docking)
2) Influence of point mutations on protein structure and function
3) (Computational ) Study of interactions between small molecules and
nucleic acids (collaboration with experimentalist from Ruder Bošković
Institute)
4) (Computational ) Study of protein-ligand interactions (collaboration with
experimentalist from Ruder Bošković Institute)
Silvia Tomić
Institute of Physics, Zagreb
Projects:
1) Systems of reduced dimensionality: from synthetic organic to biomaterials, founded by the
Croatian Ministry of Science, Education and Sport
2) Strongly correlated inorganic, organic and biomaterials, the Croatian Ministry of Science,
Education and Sport, 035-0000000-2836.

1) Fundamental length scales and screening in diverse biomacromolecule systems
Bojan Žagrović
MedILS Institue in Split
Potential projects for a doctoral student:

1) one potential project would deal with the application of Bayesian methods (Jaynes, 2003) from
statistics in structural biology. Bayesian statistics, as a paradigm for making inferences under
uncertain conditions, offers an alternative approach to solving biomolecular structures from
incomplete experimental data. For instance, using the principle of maximum entropy (Jaynes,
2003), it allows one to extract a maximal amount of useful information from a given set of data.
Such an approach is ideally suited for solving molecular structures when the set of experimental
observables (NOE intensities in the case of NMR, or structure factors in the case of X-ray
crystallography) does not uniquely constrain the structure. Michael Nilges' group (Institute
Pasteur, Paris) has in the past several years developed several algorithms for solving NMR
structures based on Bayesian principles (Habeck et al., 2005, Rieping et al., 2005). A potential
doctoral project would include testing and further development of such NMR algorithms, and
development of algorithms for solving X-ray structures. Specifically, the project would include
application of different methods for sampling posterior structural distributions, such as local
elevation or replica exchange, or in other words, take advantage of the already existing methods
80
for sampling highly dimensional spaces in the context of solving biomolecular structures based on
Bayesian principles.
2) the second potential project would deal with development of atomistic force fields with an aid
of Bayesian methods. The empirical force fields in use today (GROMOS, AMBER or
CHARMM) are developed and parameterized based on fitting experimental data and quantum-
mechanical calculations, but in most cases, without a uniform and consistent statistical framework.
Finally, force fields are models based on certain a amount of data, and as such should be treated
with an equal amount of rigor as any other statistical models. The problem is that force fields are
highly dimensional models with a multitude of parameters, while the experimental (or ab initio
theoretical) data is scarce. Bayesian methods are ideally suited for exactly such situations, and a
potential doctoral project would deal with their application. Development of a complete force
field for the simulation of biomolecules is an ambitious project, and in the beginning the student
would work on a simpler problem such as for instance development of a satisfactory atomistic
model of water and other solvents such as methanol or DMSO.
3) the third potential project would deal with dynamic activation of enzymatic function. The
dominant paradigm for explaining the function of proteins is currently the idea of "conformational
change". Analogously to, say, open and closed doors, enzymatic activation is explained by
invoking a conformational change of the protein from inactive to active structure. Dynamic
activation of proteins, on the other hand, postulates that the free energy of activation can be
obtained by changing the dynamics of the protein with no change in the average structure of the
protein. As a 1-dimensional example, a pendulum which oscillates with two different frequencies,
has the same "average structure", but is found in two different energetic states. Recently, several
experimental groups (Joshua Wand, University of Pennsylvania; Dorothee Kern, Brandeis
University and others) have demonstrated the importance of the dynamics activation of enzymes
by using NMR (Eisenmesser et al., 2002, Wand, 2001). The potential doctoral project would deal
with this problem with an aid of atomistic computer simulations of several important enzymes and
most advanced theoretical methods for calculating free energy and entropy.
The common denominator of my research is studying structure and dynamics of proteins with an
aid of atomistic computer simulations. Regarding the computational infrastructure for such
research, in the course of my PhD project I have worked on the development and use of the
Folding@Home distributed computing network that uses volunteer processors from all around the
world coordinated through the world wide web (Zagrovic et al., 2002, Zagrovic et al., 2001). The
network currently includes approximately 200,000 active processors, and based on the sheer
amount of computational power, it is one of the largest computational mega-clusters in the world.
The leader of the Folding@Home project and my doctoral mentor Prof. Dr. Vijay S. Pande
(Stanford University) agrees that a fraction of the Folding@Home network can be used for my
own research. Initially, this would include approximately 5,000 processors, and in connection
with that, in the first phase of the doctoral project, my potential student would work on
establishing and stabilizing this mini network, and adjusting the algorithms and software that we
use to the demands of such network.
Eisenmesser, E. Z., Bosco, D. A., Akke, M. and Kern, D. (2002) Science, 295, 1520-3.
Habeck, M., Rieping, W. and Nilges, M. (2005) J Magn Reson, 177, 160-5.
Jaynes, E. T. (2003) Probability Theory: The Logic of Science, Cambridge University Press.
Rieping, W., Habeck, M. and Nilges, M. (2005) Science, 309, 303-6.
Wand, J. A. (2001) Nat Struct Biol, 8, 926-931.
81
Zagrovic, B., Snow, C. D., Khaliq, S., Shirts, M. R. and Pande, V. S. (2002) J Mol Biol, 323, 153-
64.
Zagrovic, B., Sorin, E. J. and Pande, V. (2001) J Mol Biol, 313, 151-69.
Paško Županović
Project No: 0177165 (old project Croatian Ministry of Science):
Dielectric and photoemission properties of systems with several electronic bands.
The research topics that can lead to the Ph.D. in biophysics.

1. Information entropy and relaxation processes.
2. Information entropy and exactly solvable many body problems.
3. Maximum entropy production principle and phenomenological intermolecular potentials.
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Institutional supervision
At present time three institutions are formally included in execution of proposed doctoral
programme: Faculty of Natural Sciences, Mathematics and Kinesiology (PMFST), University of Split,
Institute Ruđer Bošković, Zagreb and MedILS Institute in Split. We expect that the Medical School,
University of Split will also join in execution of proposed doctoral programme. It would be desirable
that other scientific institutions from Croatia join too (University of Dubrovnik and University of Zadar
already collaborate with University of Split and with the IRB, Zagreb). We shall also seek collaboration
with institutions interested in interdisciplinary research in life sciences such as the Institute of
Oceanography and Fisheries (IZOR) from Split, and with the Institute of Physics (IFS), Zagreb. Until
this happens PMFST , IRB and MedILS will agree on division of privileges and duties.
The supervision of study programme
Programme head. The programme will be supervised by the programme head in Split (Prof. Dr.
Davor Juretić) and with the co-head in Zagreb (Scientific adviser dr. Vesna Svetličić). Dr.
Juretić published 60 scientific papers from biophysics, bioeneregetics, bioinformatics and physics,
which have beed cited 700 times. Dr. Svetličić published 60 scientific papers which dealt with the
ion transport through membranes, self-organisation of organic molecules (monolayers, vesicles,
gels), cell adhesion and see biophysics, which have been cited about 400 times. Study heads are
responsible for all aspect of programme functioning and organization. They have ultimate
responsibility for academic and scientific programme components, for preparation and distribution
of information about programme, for selection of students, for maintaining archive of programme
documents and for organisation of seminars and workshops by guest biophysicists.
Steering Committee members are Prof. Dr. Stjepan Marčelja, Prof. Dr. Miroslav Radman,
Prof. Dr. Ante Graovac, Prof. Dr. Neven Žarković, Dr. Bono Lučić, Dr. Silvia Tomić, Prof.
Dr. Mile Dželalija and Prof. Dr. Davor Eterović in addition to Prof. Dr. Davor Juretić and Dr.
Vesna Svetličić. Dr Marčelja has about 6000 citations of his 73 scientific papers, while Dr.
Graovac has more than 110 CC publications. Prof. Dr. Davor Eterović is full professor of the
Medical School, University of Split, also well known as biophysicist and medical physicist.
Steering Committee members will collaborate closely with programme heads in all aspects of this
study programme.
Study Committee. Will be proposed later on. Study Committee decides about all important
questions connected with this study, and its members are in constant contact either directly or via
e-mail.
Adisory Committee. Will be proposed later on.
The responsibility of Advisory Committee. Advisory comittee will be analysing materials

prepared by Study heads and by Study Committee. Advisory committee responsibilities include:
(1) Advising about public presentation od the Study Programme
(2) Ensuring that enough of high qality mentors have been found, which can ensure
development of the study programme.
(3) Ensuring efficient progress of students through the study programme.
(4) Informing study chairman about progress of thesis research topic for each student.
Advisory Committee will help students who finished this doctoral programme to find
employment. This committe will also supervise yearly all aspects of the study programme.
83
Contractual aspects (student – institution)
During duration of their study students will observe the contract with PMFST concerning their
work. The contract will define rights and obligations both of students and of organisations charged with
this study programme. The policy guidelines and procedures document (Study rules brochure) will also
be prepared, which will regulate the thesis writting process (what the thesis should like, the time frame
of writing it, ..).
84
Lecturers
Lecturer Andreja Ambriović-Ristov, PhD
Institution Ruđer Bošković Institute
E-mail andrea@irb.hr
Personal web- -
page
Biography Born in Zagreb, 1967, Degrees - 1989 - B.Sc. in Medical Biochemistry,
Faculty of Pharmacy and Biochemistry, 1993 - M.Sc. in Molecular and
Cellular Biology, Faculty of Science, University of Zagreb; 1997 - Ph.D. in
Molecular biology, Faculty of Science, University of Zagreb; Major
Research Interests: adenovirus retargeting for tumor gene therapy,
mechanisms of adenoviral infection; resistance mechanisms of tumor cells
against chemotherapeutics, integrins Employments: 1990, research assistant,
Croatian Veterinary Institute, Zagreb; 1991 – 2001, research assistant,
Division of Molecular Biology, RBI, 2001-present, research associate,
Division of Molecular Biology, RBI; Fellowships: Postdoctoral fellowship,
«Institut National de la Recherche Agronomique», March-August, 2001,
Ecole Nationale Veterinaire D’Alfort, Maisons-Alfort, France; FEBS short
term fellowship, June 2000, Ecole Nationale Veterinaire D’Alfort, Maisons-
Alfort, France; French Government Fellowship September/October, 1999,
October/November 1996, November, 1994 – August, 1995, Ecole Nationale
Veterinaire D’Alfort, Maisons-Alfort, France. Educational Activities:
Principal lecturer of postgraduate courses 2002- “Molecular basis of gene
therapy”, Faculty of Science, University of Zagreb; Participation in
postgraduate course at the School of Medicine Dr. sc. Oliver Vugrek «From
disease to gene – from gene to function: the role of recombinant proteins in
functional genomics; Director of educational project «Methodological
courses in biology and medicine».
Publication list Breljak D., Ambriović-Ristov A., Kapitanović S., Čačev T., Gabrilovac J.:
(last 5 years) Comparison of three RT-PCR methods for relative quantification of mRNA,
Food Technology and Biotechnology, in press.
Gabrilovac J., Breljak D., Čupić B., Ambriović-Ristov A.: Regulation of
aminopeptidase N (EC 3.4.11.2.; APN; CD13) by interferon on the HL-60
cell line, Life Sciences, 76: 2681-2697, 2005.
Vuković L., Ambriović-Ristov A., Čimbora-Zovko T., Ćetković H., Brozović
A., Majhen D., Osmak M.: Expression of apoptotic genes in low, clinically
relevant levels of drug resistance, Periodicum Biologorum, 106: 173-177,
2004.
Ambriović-Ristov A., Gabrilovac J., Čimbora-Zovko T., Osmak M.:
Increased adenoviral transduction efficacy in human laryngeal carcinoam
cells resistant to cisplatin isassociated with increased expression of integrin
v 3 and coxsackie adenovirus receptor, International Journal of Cancer,
110: 660-667, 2004.
Ambriović-Ristov A., Mercier S., Eloit M.: Shortening adenovirus type 5
fiber shaft decreases the efficiency of post binding steps in CAR-expressing
85
and non-expressing cells, Virology, 312: 425-433, 2003.

Šprem M., Babić D., Abramić M., Vrhovec I., Škrk J., Miličić D., Ambriović
Ristov A., Kalafatić D., Osmak M.: Glutathione and Glutathione S-
Transferases as Early Markers for Ovarian Carcinomas: Case Series,
Croatian Medical Journal., 42: 624-629, 2001.
Monteil M., Le Pottier M. F., Ambriović Ristov A., Cariolet R., L'Hospitalier
R., Klonjkowski B., Eloit M.: Single inoculation of replication-defective
adenovirus-vectored vaccines at birth in piglets with maternal antibodies
induces high level of antibodies and protection against pseudorabies,
Vaccine, 18: 1738-1742, 2000.
Osmak M., Bordukalo T., Ambriović Ristov A., Jernej B., Košmrlj J., Polanc
S.: Diazenes as modificators of drug-resistance in tumor cells, Neoplasma,
47: 390-395, 2000.
Relevant The initiator and director of educational project «Methodological courses in
references for biology and medicine», 2002- , www.metode.avalon.hr
teaching this
courses
Last election May, 2001
Teaching METHODS IN MOLECULAR BIOLOGY AND MEDICINE
courses
86
Lecturer Dr Goran Baranović

Institution R. Bošković Institute
E-mail baranovi@irb.hr
Personal web- http://www.irb.hr/en/home/baranovi/
page
Biography 2002 – present Project leader "Extended -systems and molecular
spectroscopies"
1999 – present Head of the Laboratory for Molecular Spectroscopy,
Department of Organic Chemistry and Biochemistry, R. Bošković Institute
2004 – present Senior Scientist, R. Bošković Institute, Zagreb, Croatia
1998 – 2004 Senior Research Associate, R. Bošković Institute,
Zagreb, Croatia
1995 – 1998 Research Associate in the Laboratory for Molecular
Spectroscopy
1975 – 1995 Research Associate and Assistant in the Laboratory for
Molecular Physics, R. Bošković Institute, Zagreb,
Croatia
Publication list
(last 5 years) Baranović, Goran. Resonance Raman spectra of deuterated cis-stilbene. J.
Raman Spectrosc. 32 (2001) 293-299.
Ouillon, Robert; Pinan-Lucare, Jean-Paul; Ranson, Piere; Baranović, Goran.

Low-temperature Raman spectra of nitromethane single crystal. Lattice
dynamics and Davydov splittings. J. Chem. Phys. 116 (2002) 4611-4625.
Volovšek, Vesna; Bistričić, Lahorija; Kirin, Davor; Baranović, Goran. Low-

frequency lattice vibrations and dynamics of 4,4‘-dibromobenzophenone. J.
Raman Spectrosc. 33 (2002) 761-768.
Bistričić, Lahorija; Pejov, Ljupčo; Baranović, Goran. A density-functional

theory analysis of Raman and IR spectra of 2-adamantanone. J. Mol. Struct.
Theochem. 594 (2002) 79-88.
Baranović, Goran. Thermochemistry of spin-crossover Fe(II)complexes

calculated with density functional methods. Chem. Phys. Lett. 369 (2003) 668-
672.
W.M. Kwok, C. Ma, D. Phillips, A. Beeby, T.B. Marder, R.Ll. Thomas, C.

Tschuschke, Baranović, Goran, Matousek, Pavel, M. Towrie and A.W.
Parker. Time resolved resonance Raman study of S1 cis-stilbene and its
deuterated isotopomers, J. Raman Spectrosc. 34 (2003) 886-891.
Biliškov, Nikola; Zimmermann, Boris and Baranović, Goran. Vibrational

spectroscopy of macrocyclic oligo(phenyldiacetylenes) – I. A theoretical and
experimental study of octadehydrodibenzo[12]annulene and
dodecadehydrotribenzo[18]annulene, J. Mol. Struct. 661/662 (2003) 65-80.
87
Baranović, Goran and Babić, Darko. Vibrational study of the

Fe(phen)2(NCS)2 spin-crossover complex by density functional calculations,
Spectrochim. Acta Part A 60 (2004) 1013-1025.
Bistričić, Lahorija; Baranović, Goran and Ilijić, Saša. Raman study of

structural relaxation and boson peak in amorphous films of adamantane,
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 61
(2005) 1537-1546.
Zimmermann, Boris and Baranović, Goran. Two-Dimensional Infrared

Correlation Spectroscopic Study on Thermal Polymerization of
Diphenylbutadiyne, Vibrational Spectroscopy 41 (2006) 126-135.
Zimmermann, Boris; Baranović, Goran; Štefanić, Zoran and Rožman,

Marko. Spectroscopic Properties of Macrocyclic Oligo(Phenyldiacetylenes)-
II. Synthesis and Theoretical Study of Diacetylenic Dehydrobenzoannulene
Derivatives with Weak Electron-Donor and -Acceptor Groups, Journal of
Molecular Structure (2006, in press).
Relevant 1998 – present Lecturer at the Postgraduate Study in Physical Chemistry,

references for University of Zagreb, Molecular Spectroscopy
teaching this 1990 – present Ph.D. Thesis (physics and chemistry) and B.Sc. Theses
courses (physics and chemistry), supervisor
Last election 2004

Teaching EXPERIMENTAL METHODS OF PHYSICS IN BIOPHYSICS
courses
88
Lecturer Ante Bilušić

Institution Faculty of Natural Sciences, Education, and Kinesiology, University of Split,
Croatia
E-mail bilusic@pmfst.hr
Personal web- http://www.pmfst.hr/~bilusic/
page
Biography Born: June 9th 1972. in Split, Croatia
Diploma: 1997, University of Zagreb, Faculty of Science, Physics
Department; specialty: solid state physics
MSc.: 1999, University of Zagreb, Faculty of Science; specialty: solid state
physics
PhD: 2003, University of Zagreb, Faculty of Science; specialty: solid state
physics
Employment: 1997-2004: Institute of Physics, Zagreb, Croatia; 2004.-
Faculty of Natural Sciences, Education, and Kineziology, Split
Stays abroad: CNRS-Grenoble, (1 month), ETH-Zürich (9 months), EPF-
Lausanne (2 months)
Publication list Selected publications in last five years:
(last 5 years)
A. Bilušić, …, Journal of Alloys and Compounds, accepted for publication
(2006)
Z. Jagličić, …, A. Bilušić, …, Physical Review B, 73 (2006) 214408/1-9
Ž. Bihar, A. Bilušić,…, Journal of Alloys and Compounds 407 (2006) 65-73
J. Dolinšek, …, A. Bilušić,…, Physical Review B, 72 (2005) 064208/1-11
M. Prester, ..., A. Bilušić, ..., Physical Review B, 69 (2004) 180401(R)/1-4
A.V. Sologubenko, ..., A. Bilušić, ... Physical Review Letters, 91 (2003)
197005/1-4
J. C. Lasajunias, ..., A. Bilušić, ...Physical Review B 66 (2002) 014302/1-11
A. Bilušić, ... Journal of Alloys and Compounds 342 (2002) 413-415
J. Dolinšek, ..., A. Bilušić, ... Journal of Physics: Condensed Matter 14
(2002) 6975-6988
A. Bilušić, D. Pavuna, A. Smontara, Vacuum 61 (2001) 345-348
A. Bilušić, Ž. Budrović, A. Smontara, Fizika A 10 (2001) 121-128
Relevant
references for
All up-mentioned publications.
teaching this
courses
Last election October, 22th 2003 (Natural Sciecnes, Physics)
Teaching Experimental methods of physics in biophysics I
courses
89
Lecturer Srećko Botrić

Institution University of Split,
Faculty of electrical engineering, mechanical engineering and naval
architecture
E-mail botric@fesb.hr
Personal web-
page
Biography 1972
University of Split,
architecture
Electrical engineer
1982
Zagreb
University of Zagreb,
Faculty of Science, Department of Physics
Master of science in physics
1997
Sarajevo
University of Sarajevo, PMF Sarajevo, Department of theoretical physics
Ph D in physics
1972-1999
architecture
R.Boškovića b.b. ,Split
Assistant
1999-2004
architecture
Senior Assistant
2004-2006
architecture
Senior lecturer
Publication list P. Županović, D. Juretić i S. Botrić: "Kirchhoff's loop law and the maximum
(last 5 years) entropy production principle". Phys. Rev. E70, 056108 (2004).
S. Botrić, P. Županović i D. Juretić: “Is the stationary current distribution in a
linear planar electric network determined by the principle of maximum
entropy production”. Croatica Chemica Acta 78, 181-184 (2005).
P. Županović, D. Juretić and S. Botrić: “On the equivalence between
Onsager’s principle of the least dissipation of energy and maximum entropy
production principle”, FIZIKA A (Zagreb) 14, (2005); pp.89-96.
Relevant
90
references for
teaching this
courses
Last election
Teaching
courses
91
Lecturer Prof. Dr. Milan Brumen

Institution University of Maribor, Faculty of Education, Department of Physics and
Medical Faculty, Department of Biophysics, Maribor and Jožef Stefan
Institute, Ljubljana, Slovenia
E-mail milan.brumen@uni-mb.si
Personal web- -
page
Biography 1951 born in Maribor, Slovenia
1976,1980,1985 graduated in physics, master’s in physics ( biophysics),
doctor’s in physics (biophysics), University of Ljubljana, Ljubljana,
Slovenia
university and research career, employment:
1976-1983 research assistant, Jožef Stefan Institute, Ljubljana
1982-1987 teaching and research assistant of biophysics, Medical Faculty,
University of Ljubljana
1982- researcher (part-time position), Jožef Stefan Institute,
Ljubljana
1987- 1992 assistant professor, University of Maribor, Faculty of
Education
1992-1997 associated professor, University of Maribor, Faculty of
Education
1997- professor of physics, University of Maribor, Faculty of
Education and
2004- professor of biophysics, University of Maribor, Medical
Faculty
professional training:
1978-1999 regular 1- to 2-months stay at Institute of Biophysics,
Humboldt University of Berlin Germany
1985, 1986 5-months stay at Department of Biochemistry, University La
Sapienza, Rome
scientific collaboration: see relevant references below
research topics:
biophysics: theoretical research of biological systems: cell, cell membrane,
macromolecular systems; osmotic and metabolic states of the cell, membrane
dynamic structure, intracellular calcium oscillations and signaling;
mathematical modeling
soft matter physics: mechanisms of polymer membrane formation;
distribution of ions in polyelectrolyte hollow shells
Publication list - M. Brumen, A. Fajmut, M. Marhl: Calcium oscillations in the living cell :
(last 5 years) biological relevance of multi-compartment mathematical models. Nonlinear
phenom. complex syst. 2001, Vol. 4, 280-284.
- N. Vogrin, Č. Stropnik, V. Musil, M. Brumen: The wet phase separation:
the effect of cast solution thickness on the appearance of macrovoids in the
membrane forming ternary cellulose acetate/acetone/water system. J. membr.
sci. 2002, Vol. 207, 139-141. - S. Svetina, M. Brumen, M.
Gros, S. Vrhovec, T. Žnidarčič: On the variation of parameters that
characterize the state of a physiological system. Red blood cells as an
92
example. Adv. comput. bioeng. ser. 2003, Vol. 7, 3-14.

- J. Dobnikar, D. Haložan, M. Brumen, H.-H. von Grünberg, R. Rzehak:
Poisson-Boltzmann Brownian dynamics of charged colloids in suspension.
Comput. phys. commun. 2004, Vol. 159, 73-92.
- G. B. Sukhorukov, A. Fery, M. Brumen, H. Möhwald: Physical chemistry
of encapsulation and release. PCCP. Phys. chem. chem. phys. (Print), 2004,
Vol. 6, 4078-4089. - Č. Stropnik, V. Kaser, V. Musil, M.
Brumen: Wet-phase-separation membranes from the polysulfone/N, N-
dimethylacetamide/water ternary system: the formation and elements of their
structure and properties. J. appl. polym. sci. 2005, Vol. 96, 1667-1674.
- R. Šoster, K. Stana-Kleinschek, M. Brumen, V. Ribitsch: Measurements of
zeta potential of poly(tetrafluoroethylene) foils. Mater. sci. forum, 2005, Vol.
480/481, 89-94.
- M. Brumen, A. Fajmut, A. Dobovišek, E. Rou: Mathematical modelling of
Ca[sup]2+ oscillations in airway smooth muscle cells. Journal of biological
physics. 2005, Vol. 31, 515-524.
- D. Haložan, C. Déjugnat, M. Brumen, G. B. Sukhorukov: Entrapment of a
weak polyanion and H+/Na+ exchange in confined polyelectrolyte
microcapsules. Journal of chemical information and modeling (formerly
Journal of chemical information and computer sciences) 2005, Vol. 45,
1589-1592.
- A. Fajmut, M. Jagodič, M. Brumen: Mathematical modeling of the myosin
light chain kinase activation. Journal of chemical information and modeling
(formerly Journal of chemical information and computer sciences) 2005, Vol.
45, 1605-1609. - A. Fajmut, A. Dobovišek, M.
Brumen: Mathematical modeling of the relation between myosin
phosphorylation and stress development in smooth muscles. Journal of
chemical information and modeling (formerly Journal of chemical
information and computer sciences), 2005, Vol. 45, 1610-1615.
- A. Fajmut, M. Brumen, S. Schuster: Mathematical modelling of the
interactions between Ca[sup]2+, calmodulin and myosin light chain kinase.
FEBS lett.. 2005, Vol. 579, 4361-4366.
Relevant Scientific publications from the personal total list.
references for International and domestic scientific colaboration with: Max-Planck Institute
teaching this of coloids and interfaces, Golm; Institute of Physics and Medical Physics,
courses University of Leipzig, Leipzig; Institute of Biology, Humboldt University,
Berlin; Laboratory of Respiratory Physiology, University of Bordeaux II,
Bordeaux; Institute of Chemistry, University of Graz, Graz; Institute of
Biophysics, Medical Faculty, University of Ljubljana, Ljubljana.
Position of full professor at University of Maribor, giving different
lecture/courses in general physics, statistical thermodynamics and biophysics
as well as specialized lectures in graduate and postgraduate study programs at
Faculty of Education and Medical Faculty.
Last election Full professor, from 1997, permanent election
Teaching Mathematical modeling of biological systems
courses
93
Lecturer Roderick Dewar

Institution Unité EPHYSE, INRA Centre de Bordeaux-Aquitaine,
B.P. 81 33883 Villenave d'Ornon, France
E-mail dewar@bordeaux.inra.fr
Personal web- -
page
Biography CV
1997-present : Unité EPHYSE, INRA Bordeaux (Directeur de Recherches
since 2003).
1994-1997 : School of Biological Sciences, University of New South Wales,
Sydney, Australia (Senior Research Fellow)
1989-1994 : Institute of Terrestrial Ecology, Edinburgh, UK (Senior
Scientific Officer)
1986-1988 : Dept. of Theoretical Physics, University of Oxford, UK
(Postdoctoral Research Assistant)
1986 : PhD in Condensed Matter Physics, University of Edinburgh, UK
1982 : BSc Hons. (1st) Mathematical Physics, University of Edinburgh, UK
Current projects and responsibilities
MEREGROWTH (Univ. Helsinki, INRA-EPHYSE) Prediction of the
regional variation of forest productivity using process-based models (2004-
2007). Project co-leader.
MEP (INRA-EPHYSE, Univ. Maryland, CEH Edinburgh) Evaluating the
hypothesis of maximum entropy production for terrestrial ecosystems (2004-
05). Project leader.
Introduction to plant population modelling. Teaching course (20h/yr),
ENITA-Bordeaux (2003-present). Course leader.
Modelling plant populations. Teaching module (20h/yr) for MASTER
“Systèmes Ecologiques”, Univ. Bordeaux I. (2004-present). Module leader.
Publication list Champion I., Dewar R.C., Loustau D., Bert D. & Danjon F. 2000. Coupling
(last 5 years) SAR data with forest growth models. International Journal of Remote
Sensing 21, 1763-1766.
McMurtrie R.E., Dewar R.C., Medlyn B.E. & Jeffreys M.P. 2000. Effects of
elevated [CO2] on forest growth and carbon storage : a modelling analysis of
the consequences of changes in litter quality/quantity and root exudation.
Plant and Soil 224, 135-152.
Medlyn B.E., McMurtrie R.E., Dewar R.C. & Jeffreys M.P. 2000. Soil
processes dominate the long-term response of forest net primary productivity
to increased temperature and atmospheric CO2 concentration. Canadian
Journal of Forest Research 30, 873-888.
Dewar R.C. 2000. A model of the coupling between respiration, active
processes and passive transport. Annals of Botany 86, 279-286.
McMurtrie R.E., Medlyn B.E. & Dewar R.C. 2001. Increased understanding
of nutrient immobilisation in soil organic matter is critical for predicting the
carbon sink strength of forest ecosystems over the next 100 years. Tree
Physiology 21, 831-839.
Quereix A., Dewar R.C., Gaudillere J.-P., Dayau S. & Valancogne C. 2001.
Sink feedback regulation of photosynthesis in vines : measurements and a
94
model. Journal of Experimental Botany 52, 2313-2322.

Dewar R.C. 2001. The sustainable management of temperate plantation
forests : from mechanistic models to decision-support tools. Proceedings of
the IEFC Workshop Models for the sustainable management of temperate
forest plantations, INRA Bordeaux, 7-9 September 2000. European Forest
Institute Proceedings 41 :119-137
McMurtrie R.E., Halliday J.C., Dewar R.C., Tate K.R., Corbeels M. & Scott
N.A. 2001. Modelling long-term changes in forest productivity due to altered
soil nitrogen supply. Proceedings of the IEFC Workshop Models for the
sustainable management of temperate forest plantations, INRA Bordeaux, 7-
9 September 2000. European Forest Institute Proceedings 41 : 59-70.
Dewar R.C. 2002. The Ball-Berry-Leuning and Tardieu-Davies stomatal
models : synthesis and extension within a spatially aggregated picture of
guard cell function. Plant, Cell and Environment 25, 1383-1398.
Dewar R.C. 2003. Information theoretic explanation of maximum entropy
production, the fluctuation theorem and self-organized criticality in non-
equilibrium stationary states. Journal of Physics A 36 :631-641.
Dewar R.C. 2004. Maximum entropy production and non-equilibrium
statistical mechanics. In Non-Equilibrium Thermodynamics and Entropy
Production : Life, Earth and Beyond (eds. Kleidon A, Lorenz R), Springer-
Verlag, pp. 41-55.
Delzon S., Sartore M., Burlett R., Dewar R.C., Loustau D. 2004. Hydraulic
responses to height growth in maritime pine trees. Plant, Cell and
Environment 27, 1077-1087.
Dewar R.C. 2005. Maximum entropy production and the fluctuation
theorem. Journal of Physics A: Mathematical and General 38, L371-L381.
Dewar R.C. , Juretić D., Županović P. 2005. Maximum entropy production
as a selection principle for the evolution of chloroplast ATP synthase. Science
(submitted Sept 2005).
Relevant Refs [10], [11], [13], [14] above.
references for Jaynes ET. Probability Theory : the Logic of Science. Cambridge University
teaching this Press, 2003.
courses Jaynes' papers at http://bayes.wustl.edu/etj/node1.html
Last election
Teaching See biography above
courses
95
Lecturer Prof. Zoran Đogaš, MD, PhD

Institution University of Split School of Medicine
E-mail zdogas@bsb.mefst.hr
Personal web-
page
Biography Date and place of birth: March 29, 1966.; Split, Croatia
Present position held:
Vice Dean; Department of Neuroscience, Chair; Laboratory for Clinical
Neuroscience, Director
Teaching activity:
Course Leader:
-Basic Neuroscience, Medical School in Split, Split, Croatia
-Principals of the Scientific Research in Medicine, Medical School in Split,
Split, Croatia
-Medical informatics, Methods of data acquisition and analysis, Medical
School in Split, Split, Croatia
-Courses: Neuroscience, GABA and glutamate receptors, and Sleep
Medicine, Postgraduate Study Program, Medical School in Split, Split,
Croatia
-Basic Neuroscience, Medical School in Mostar, Mostar, B&H
-Medical informatics, Medical School in Mostar, Mostar, B&H
Participation in teaching:
-Physiology, Medical School in Split, Split, Croatia
-Principals of the Scientific Research in Medicine, Medical School in Mostar,
Mostar, B&H
-Basics of Electrophysiological Methods in Medicine, Postgraduate Study
Program,
Medical School in Zagreb, Zagreb, Croatia
Projects:
Neurotransmitters in the control of breathing, Scientific Research Grant
supported by the Croatian Ministry of Science, #0216003, PI, 2002-
Obstructive sleep apnea - diagnostics and surgical therapy, Technology-
Developmental Grant supported by the Croatian Ministry of Science,
TP/0216-006 investigator, 2000-
Development of the web based application for group psychological testing,
Informatics Technology Application Grant supported by the Croatian
Ministry of Science, PI, 2002-
Education:
Mathematics-Informatics Education Center Split (1984)
M.D., University of Zagreb School of Medicine (1992)
Postdoctoral Fellowship in Neurophysiology, Medical College of Wisconsin,
SAD (1992-1995)
Ph.D., University of Zagreb School of Medicine (1997)
Rewards:
Rector’s reward, University of Zagreb (1988)
Scientific reward “Borislav Nakić” Academy of medical sciences and Pliva -
for best scientific work in 1997/98. (2000)
96
Memberships:
Society for Neuroscience
American Physiological Society
European Sleep Research Society
Croatian Sleep Research Society, president
Croatian Society for Neuroscience
Croatian Society of Physiologists
Croatian Society for Medical Informatics
World Association of Croatian Physicians
Croatian Medical Association
Organizational skills and competencies:
2001 - 2006, Tjedan mozga (Brain Awareness Week) in Split, Croatia
2003, Sleep Medicine; CME Course for Medical Doctors
2004, 4th Croatian Meeting of Pharmacology, Sleep Medicine Symposium
2005 - 2006, Science Festival in Split, Croatia
Publication list Šitum M, Đogaš Z, Vujnović Z, Erceg M, Terzić J, Marušić JM, Mirić D.
(last 5 years) Increased Incidence of Colorectal Cancer in the Split-Dalmatia County:
Epidemiological Study. Croat Med J. 42(2):181-7, 2001.
Terzić J, Meštrović J, Đogaš Z, Furlan D, Biočić M. Children War Casualties
during the 1991-1995 Wars in Croatia and Bosnia and Herzegovina. Croat
Med J. 42(2):156-160, 2001.
Tadin I, Bojić L, Mimica M, Karelović D, Đogaš Z. Hypertensive retinopathy
and pre-eclampsia. Coll Antropol. 25 Suppl:77-81, 2001
Kovačić Z, Marendić M, Šoljić M, Pecotić R, Kardum G, Đogaš Z.
Knowledge and attitude regarding sleep medicine of medical students and
physicians in Split, Croatia. Croat Med J 43(1):71-4, 2002
Đogaš Z, Kardum G, Mirić L, Ševo V, Tolić T, Ursić A, Vasiljević P, Zekić
S. Attitudes towards science and alternative medicine of medical, economics
and business, and electrical engineering students in Split, Croatia. Croat Med
J.44(1):75-9, 2003
Librenjak D, Šitum M, Eterović D, Đogaš Z, Gotovac J. Immunoprophylactic
intravesical application of bacillus calmette-guerin after transurethral
resection of superficial bladder cancer. Croat Med J.44(2):187-92, 2003
Račić G, Kurtović D, Roje Z, Tomić S and Đogaš Z. Primary mucosal
melanoma of the eustachian tube. European Archives of Oto-Rhino-
Laryngology 10.1007/s00405-003-0633-8 (online), 2003.
Maričević A, Đogaš Z. Landmine injury: functional testing outcome. Mil
Med 2004;169(2):147-50.
Račić G, Maslovara S, Roje Z, Đogaš Z, and Tafra R. Hyperbaric oxygen in
the treatment of sudden hearing loss. ORL J Otorhinolaryngol Relat Spec,
2003;65(6):317-20.
Karanovic N, Jukic M, Carev M, Kardum G, Đogaš Z. Rocuronium
attenuates oculocardiac reflex during squint surgery in children anesthetized
with halothane and nitrous oxide. Acta Anaesthesiol Scand. 2004
Nov;48(10):1301-5.
Đogaš Z. Teaching scientific methodology at a medical school: experience
from Split, Croatia. Natl Med J India. 2004 Mar-Apr;17(2):105-7.
Račić G, Matulić J, Roje Z, Đogaš Z, and Vilović K. Abnormally high
bifurcation of the brachiocephalic trunk as a potential operative hazard: case
report. Otolaryngol Head Neck Surg. 2005 Nov;133(5):811-3.
97
Karanovic N, Carev M, Ujevic A, Kardum G, Đogaš Z. Association of

oculocardiac reflex and postoperative nausea and vomiting in strabismus
surgery in children anesthetized with halothane and nitrous oxide. Paediatr
Anaesth. 2006 Sep;16(9):948-54.
Relevant Refs4,9,10,11,13 from above plus refs:
references for 1. ĐOGAŠ, Z., E.A.E. STUTH, F.A. HOPP, D.R. McCRIMMON, AND E.J.
teaching this ZUPERKU. NMDA receptor mediated transmission of carotid body
courses chemoreceptor input to expiratory bulbospinal neurones in dogs. Journal of
Physiology (London) 487.3:639-651, 1995.
2. ĐOGAŠ, Z. In vivo activity of canine expiratory bulbospinal neurones is
differentially affected by two non-NMDA receptor antagonists. Croatian
Medical Journal 37(1):1 5-20, 1996.
3. STUTH E.A.E., Z. ĐOGAŠ, M. KROLO, J.P.KAMPINE, F.A. HOPP,
AND E.J. ZUPERKU. Dose-dependent effects of halothane on the phrenic
nerve responses to acute hypoxia in vagotomized dogs. Anesthesiology,
87:1428-1439, 1997.
4. STUTH E.A.E., Z. ĐOGAŠ, M. KROLO, J.P. KAMPINE, F.A. HOPP,
AND E.J. ZUPERKU. Effects of halothane on the phrenic nerve responses to
carbon dioxide mediated by carotid body chemoreceptors in vagotomized
dogs. Anesthesiology, 87:1440-1449, 1997.
5. McCRIMMON D.R., E.J. ZUPERKU, F. HAYASHI, Z. ĐOGAŠ, C.F.L.
HINRICHSEN, E.A. STUTH, M. TONKOVIĆ-ĆAPIN, M. KROLO, AND
F.A. HOPP. Modulation of the synaptic drive to respiratory premotor and
motor neurons. Respiration Physiology 110,161-176, 1997.
6. ĐOGAŠ, Z., M. KROLO, E.A.E. STUTH, M. TONKOVIC-CAPIN, F.A.
HOPP, D.R. McCRIMMON AND E.J. ZUPERKU. Differential effects of
GABAA receptor antagonists suggest diverse roles for receptor subtypes in
the control of respiratory neurons. Journal of Neurophysiology 80(5):2368-
77, 1998.
7. Krolo, M., E.A.E. STUTH, M. TONKOVIĆ-ĆAPIN, Z. ĐOGAŠ, F.A.
HOPP, D.R. McCRIMMON, AND E.J. ZUPERKU. Differential roles of
ionotropic glutamate receptors in the mediation of excitatory inputs to canine
medullary inspiratory neurons of the ventral respiratory group. Journal of
Neurophysiology 82(1):60-8, 1999.
8. ĐOGAŠ, Z., E.A.E. STUTH, J.TERZIĆ, V. ĐOGAŠ, AND E.J.
ZUPERKU. Uloga NMDA i GABAA receptora u kontroli disanja. Hrvatski
medicinski anali 20:1-12, 1998.
9. TonkoviĆ-Ćapin, M., E. Zuperku, E.A. Stuth, J. Bajic, Z. ĐogaŠ, and F.
Hopp. The effect of central drive on the lung inflation responses of
expiratory bulbospinal (EBS) neurons in dogs. Am J Physiol (Regul Integr
Comp Physiol.) 279(5):R1606-18, 2000.
Ph.D. Thesis: University of Zagreb School of Medicine, 1997. Đogaš, Z.
Uloga NMDA i GABAA receptora u regulaciji respiracijskih bulbospinalnih
neurona, Thesis, 87 pages
Readings:
Guyton and Hall. Medical Physiology 10th ed., Medicinska naklada,
Zagreb (translation of 4 chapters)
Đogaš Z et al. Vodič za vježbe iz Temelja neuroznanosti, University of Split
School of Medicine, 2005.
Išgum V, ed. Elektrofiziološke metode u medicinskim istraživanjima
98
(introductory chapter), Medicinska naklada, Zagreb, 2001.

Marušić M et al. Uvod u znanstveni rad u medicini (Chapter 10), Medicinska
naklada, Zagreb, 2004.
Đogaš Z, Kardum G. Osnove informatike za medicinare, University of Split
School of Medicine, 2004.
New Laboratories started:
Laboratory for Neuroscience (MF Split),
Laboratory for Clinical Neuroscience (w/ Lab for Sleep Disorders, MF
Split/KB Split)
Organizational skills and competencies:
2001 - 2006, Tjedan mozga (Brain Awareness Week) in Split, Croatia
2003, Sleep Medicine; CME Course for Medical Doctors
Last election 03.06.2004., Associate Professor
Teaching Basic Neuroscience, Principals of the Scientific Research in Medicine,
courses Medical informatics, Methods of data acquisition and analysis, Neuroscience,
GABA and glutamate receptors, and Sleep Medicine, Physiology, Basics of
Electrophysiological Methods in Medicine,
99
Lecturer Prof. Dr. Mile Dželalija

Institution University of Split
E-mail mile@pmfst.hr
Personal web-
http://www.pmfst.hr/~mile
page
1964: born, Unešić, Croatia
1987: MSc in Mathematics and Physics, University of Split, Faculty of
Science and Mathematics
1991: MSc in Nuclear and Highenergy Physics, University of Zagreb,
Faculty of Science and Mathematics
1995: PhD in Physics, University of Zagreb, Faculty of Science and
Mathematics
1997: Assistant Professor of Physics, University of Split
2000: Associated Professor of Physics, University of Split
2004: Full Professor of Physics, University of Split
1997-2000: Head of the Department of Physics, University of Split
2001-2005: Vice-Dean for Research, University of Split
Scientific papaers: more than 80, from which more than 40 in Current
Biography Contents.
SCI citions: more than 700 citatations.
Coordinator of research projects: Croatian: 177064, 0177162 MZOŠ;
International: UNESCO-HP, Tempus.
International conferences: more than 15 presentations; in organizational
board: more than 15.
Coordinator of other projects: Croatian: 2 in IT application; International:
Tempus.
Coordinator of graduate study: MSc in Education of Natural Sciences
(2001-2005).
Coordinator of international undergraduate study: BSc in Science and
Technology of the Environment and Territory (2001-2005).
Research activites abroad: CERN-Geneva (20 months); GSI-Darmstadt (25
months); Goethe Institut-Freiburg (4 months); ICTP Trieste (2 months)
M. Dželalija, Z. Basrak, R. Čaplar, “Cell-size and generalized entropy
determination in heavy-ion reactions”, Nuclear Physics A 738 (2004) 483-
486.
W. Reisdorf,..., M. Dželalija,..., “Nuclear Stopping from 0.09 to 1.93 GeV
and Its Correlation to Flow”, Physical Review Letters 92 (2004) 232301:1-4.
W. Reisdorf,…, M. Dželalija,..., “Droplet formation in expanding nuclear
matter: a system size dependent study”, PhysicsLetters B 595 (2004) 118-
Publication list
126.
(last 5 years)
G. Stoicea ,..., M. Dželalija,..., “Azimuthal Dependence of Collective
Expansion for Symmetric Heavy-Ion Collisions”, Physical Review Letters 92
(2004) 071303:1-5.
M. Dželalija, N. Rausavljević, B. Jošt, “Relationship between jump length
and the position angle in ski jumping”, Kinesiologia Slovenica 9 (2003) 81-
90.
M. Dželalija, N. Rausavljević, M. Žvan, “Influence of body mass on
100
performance in downhill skiing”, Kinesiologia Slovenica 9 (2003) 74-80.

A. Andronic,..., M. Dželalija,..., “Directed flow Au+Au, Xe+CsI, and Ni+Ni
collisions and the nuclear equation of state”, Physical Review C 67 (2003)
034907:1-19.
M. Dželalija, Z. Basrak, R. Čaplar, “Determination of Generalized Entropy in
Heavy-ion Collisions”, Fizika B 12 (2003) 73-80.
S. Abdullin,..., M. Dželalija,..., “Discovery potential for supersymmetry in
CMS”, Journal of Physics G 28 (2002) 469-594.
B. Hong, …, M. Dželalija,…, “Proton and deuteron rapidity distributions and
nuclear stopping in 96Ru(96Zr)+96Ru(96Zr) collisions at 400A MeV”, Physical
Review C 66 (2002) 034901:1-9.
A. Andronic,..., M. Dželalija,..., “Differential directed flow in Au+Au
collisions”, Physical Review C 64 (2001) 041604:1-5.
P. Crochet,..., M. Dželalija,..., “Results from FOPI on strangeness in nuclear
matter at SIS energies”, Journal of Physics G 27 (2001) 267-273.
A. Andronic,..., M. Dželalija,..., “Transition from in-plane to out-of-plane
azimuthal enhancement in Au + Au collisions”, Nuclear Physics A 679,
(2001) 765-792.
M. Dželalija, Ž. Antunović, S. Abdullin, F. Charles, “Low luminosity SUSY
searches at large tanβ in CMS”, Modern Physics Letters A 15, (2000) 465-
473.
P. Crochet,…, M. Dželalija,…, “Sideward flow of K- mesons in Ru + Ru and
Ni + Ni reactions near threshold”, Physics Letters B 486 (2000) 6-12.
M. Dželalija, “Observability of HSUSY → ττ decays in CMS at the LHC”,
CMS CR 2000/009 (2000) 1-5.
Relevant M. Dželalija, Ionization Radiation in the Environment, University of Split,
references for 2006.
this program - and the above references.
Last election September 30th, 2004: Full professor of Physics, University of Split
Taught
courses/
Ionization Radiation in the Environment
Research
activity
101
Lecturer Davor Eterović

Institution Split University Medical School
E-mail eterovic@bsb.mefst.hr
Personal web-
page
Biography -Born in Vinkovci, Croatia at December 21, 1953.
-Graduated theoretical physics at Zagreb University Faculty of Natural
Sciences. Since 1983 affiliated as the physicist at the Department of Nuclear
Medicine, University Hospital, Split.
- Ph. D. thesis: Indicator kinetics in pulsating vascular compartments (1993).
- Since 1997- head of the Department of Biophysics and Scientific
Methodology at the Split University Faculty of Medicine; since 1999-
assistant coordinator of the Postgraduate studies in basic and clinical medical
sciences at the Split University Faculty of Medicine; since 2005-professor of
biophysics.
- In total 51 papers published in CC/SCI journals in various fields, i.e.
nuclear medicine cardiology, medical physics, respiration and applied
physiology, clinical medicine (the selected list is in the following)
- Currently the project leader: The regulation of the blood flow in skeletal
muscles, sponsored by the Croatian Ministry of science
- Ranked No. 11 scientist in Croatia, No. 2 in the field of Biomedicine,
according to scintimetric study
- In 2003 awarded the National since award for significant discoveries in
respiration physiology and birth control
- Since 2003-the statistical referee in Lancet and Lancet Oncology
Publication list CC publications (full papers)
(last 5 years) 1. Pintarić I, Eterović D, Tocilj J, Reiner Ž. Effect of Simvastatin on
Micropulmonary Red Cell Mass in Patients with Hyperlipoproteinemia.
Atherosclerosis 2001; 154: 493-496.
2. Čulić V, Mirić D, Eterović D. Correlation between symptomatology and
site of acute myocardial infarction. Int J Cardiol 2001; 77: 163-168.
3. Čulić V, Mirić D, Eterović D. Different circumstances, timing, and
symptom presentation at onset of Q-wave non-Q-wave acute myocardial
infarction. Am J Cardiol 2002; 89: 456-490.
4. Čulić V, Eterović D, Mirić D, Silić N. Symptom presentation of acute
myocardial infarction: influence of sex, age and risk factors. Am Heart J
2002; 144: 1-6.
5. Strinic T, Bukovic D, Eterovic D, Stipic I, Silovski H, Stanceric T, Videc
L. Pulmonary ventilatory function in premenopausal women with and
without genital descensus. Coll Antropol 2002; 26: 139-142.
6. Librenjak D, Šitum M, Eterović D, Đogaš Z, Gotovac J. Post-transurethral-
resection immunoprophylaxis in patients with superficial bladder cancer
using six week + six month course of intravesical application of Bacillus
Calmette-Guerin. Croat Med J 2003; 44: 187-192.
7. Strinić T and Eterović D. Oral contraceptives improve lung mechanics.
Fertil Steril 2003; 79: 1070-1073.
8. Baković D, Valić Z, Eterović D, Vuković I, Obad A, Marinović-Terzić I,
102
Dujić Ž. Spleen volume and blood flow response to repeated breath-hold

apneas. J Appl Physiol 2003; 95: 1460-1466.
9. Dujić Ž, Duplančić D, Marinović-Terzić I, Baković D, Ivančev V, Valić Z,
Eterović D, Normal + Times New Roman, 12 pt, Justified, Before: 6 pt,
After: 6 ptPetri NM, Wisloff U, Brubakk AO. Aerobic exercise before
diving reduces venous gas bubble formation in humans. J Physiol 2004;
555.3: 637-642.
10. Čulić V, Eterović D. Triggering of ventricular tachycardia by
meterological and emotional stress. Protective effect of beta-blockers and
anxiolitics in elderly. Am J Epidemiol, 2004, 160: 1047-1058.
11. Dujić Ž, Baković D, Marinović-Terzić I, Eterović D. Acute effects of
single open-sea air dive and post-dive body posture on cardiac output and
pulmonary gas exchange in recreational divers. British Journal of Sports
Medicine, 2005; 39: e-34.
12. Valic, Z, Duplančić D, Baković D, Ivančev V, Eterović D, Wisløff U,
Brubakk AO, Dujić. Diving-induced venous gas emboli do not increase
pulmonary artery pressure. International Journal of Sports Medicine, 2005;
26: 626-631.
13. Čulić V, Eterović D, Mirić D. Meta analysis of possible external triggers
of acute myocardial infarction. Int J Cardiol, 2005; 99: 1-8.
14. Eterović D, Šitum M, Juretić-Kuščić Lj, Dujić Ž. A decrease in blood
pressure following pyelolithotomy, but not extracorporeal lithotripsy. Urol
Res, 2005; 33: 93-98.
15. Baković D, Eterović D, Saratlija-Novaković Ž, Palada I, Valic Z,
Bilopavlovic N, Dujić Ž. Effect of human spleen contraction on variation in
circulating blood cell counts. Clin Exp Pharm Physiol, 2005; 32: 944-951.
16. Bakovic D, Eterovic D, Valic Z, Saratlija-Novakovic Z, Palada I, Obad
A, Dujic Z. Increased pulmonary vascular resistance and reduced stroke
volume, in association with CO2 retention and inferior vena cava dilatation. J
Appl Physiol. 2006 May 25; epub
17. Dujic Z, Ivancev V, Valic Z, Bakovic D, Marinovic-Terzic I, Eterovic D,
Wisloff U. Postexercise hypotension in moderately trained athletes after
maximal exercise. Med Sci Sports Exerc. 2006;38:318-22.
18. Eterović D, Titlić M, Čulić V, Zadro R, Primorac D. Lower Contribution
of Factor V Leiden or G200210A mutations to ischemic stroke in patients
with clinical risk factors: pair-matched case-control study. Clin Appl Thromb
Hemo, 2006, in print.
Relevant 1. Eterović D, Tukić A, Tocilj J, Čapkun V. Perfect-mixer retention function
references for by analytical deconvolution of tracer histograms: application to evaluation of
teaching this left-ventricular contractility and competence. Phys Med Biol 1991; 36:1585-
courses 1597.
2. Eterović D, Dujić Ž. First-pass versus gated equilibrium radioangiography.
J Nucl Med 1992; 33:2056-2058.
3. Dujić Ž, Eterović D, Denoble P, Krstačić G, Tocilj J. Lung diffusing
capacity in a hyperbaric environment: assessment by a rebreathing technique.
Brit J Ind Med 1992; 49:254-259.
4. Dujić Ž, Eterović D, Denoble P, Krstačić G, Tocilj J, Gošović S. The
effect of a single air-dive on pulmonary diffusing capacity in professional
divers. J Appl Physiol 1993; 74:55-62.
5. Eterović D, Dujić Ž, Tocilj J, Čapkun V. High resolution pulmonary
103
computed tomography scans quantified by analyisis of density distributions:

application to asbestosis. Brit J Ind Med 1993; 50:514-519.
6. Dujić Ž, Eterović D, Tocilj J, Kusić Z, Čapkun V. About mechanisms of
prostaglandin E1 induced deterioration of pulmonary gas exchange in COPD
patients. Clin Physiol 1993; 13:497-506.
7. Eterović D, Popović S, Dujić Ž. Non-stationary theory of blood-borne
tracers. Nucl Med Comm 1994; 15:786-794.
8. Eterović D, Dujić Ž. Theoretical considerations on the validity of the
Stewart-Hamilton principle in measuring cycle-averaged flows via histogram
of indicator in the pulsating compartment. Med Phys 1994; 21:293-298.
9. Eterović D, Dujić Ž, Tocilj J, Popović S. Model for radionuclide
quantification of left-to-right ductal shunts. Clin Physiol 1994; 14:87-101.
10. Eterović D, Dujić Ž, Popović S. Deconvolving out indicator smearing in
the right ventricle facilitates left-to-right shunt quantification. Eur J Nucl
Med 1994; 21:525-530.
12. Eterović D, Dujić Ž, Popović S. Gated versus first-pass radioangiography
in the evaluation of left-to-right shunts. Clin Nucl Med 1995; 20:534-537.
13. Pintarić I, Eterović D, Tocilj J, Reiner Ž, Lipovac V. An increase in
micropulmonary red cell mass in hyperlipidemic patients. Clin Physiol 1995;
15:365-376.
14. Eterović D, Pintarić I, Tocilj J, Reiner Ž. Determinants of plasma
viscosity in primary hyperlipoproteinemias. Clin Hemorheol 1995; 15:841-
850.
15. Strinić T, Eterović D, Dujić Ž, Marković V, Tocilj J. Spirometric
disorders in women with genital descensus. Acta Obstet Gynecol Scand
1997; 76:879-883.
16. Eterović D, Juretić-Kuščić Lj, Čapkun V, Dujić Ž. Pyelolithotomy
improves while extracorporeal lithotripsy impairs kidney function. J Urol
1999; 161: 39-44.
17. Eterović D, Strinić T, Dujić Ž, Boban M. Blood gases and sex hormones
in women with and without genital descensus. Respiration 1999; 66: 400-
406.
18. Pintarić I, Eterović D, Tocilj J, Reiner Ž. Effect of Simvastatin on
Micropulmonary Red Cell Mass in Patients with Hyperlipoproteinemia.
Atherosclerosis 2001; 154:493-496.
19. Strinić T and Eterović D. Oral contraceptives improve lung mechanics.
Fertil Steril 2003; 79: 1070-1073.
21. Čulić V, Eterović D. Triggering of ventricular tachycardia by
meterological and emotional stress. Protective effect of beta-blockers and
anxiolitics in elderly. Am J Epidemiol, 2004; 160:1047-1058
21. Čulić V, Eterović D, Mirić D. Meta analysis of possible external triggers
of acute myocardial infarction. Int J Cardiol 2005; 99:1-8.
22. Eterović D, Šitum M, Juretić-Kuščić Lj, Dujić Ž. A decrease in blood
pressure following pyelolithotomy, but not extracorporeal lithotripsy. Urol
Res, 24. 12. 2004. e-pub.
Editor and author of six chaters in the edition: S. Janković i D. Eterović:
Physical bases and clinical aspects of diagnostic imaging, Medicinska
naklada, Zagreb, 2002.
From 2004- the statistical reviewer for The Lancet and Lancet Oncology.
104
Last election June 2005: full professorship

Teaching 1. Modelling and measurements in medicine; 2. Multivariate statistical
courses methods
105
Lecturer Ante Graovac

Institution Present status: Scientific Adviser at The "R. Boskovic" Institute in Zagreb;
Professor
of Chemistry at the Faculty of Science, University of Split; Professor at
Postgraduate
Studies in Chemistry, Faculty of Science, University of Zagreb; Professor at
Postgraduate
Studies in Physics, Faculty of Science, University of Split; and Co-worker at
Institute of
Physics, Physics and Mechanics, Ljubljana, R. Slovenia.
E-mail graovac@irb.hr
Personal web- http://www.irb.hr/hr/str/zfk/labs/GTK/clanovi/
page
Biography Place & date of birth: Split, Croatia, July 15, 1945.
Children: Son Ivan (born 1971) & daughter Lidija (born 1976). Grandsons:
Grandson Marin (born 2000).
Education: B.Sc. in Physics, Faculty of Science, 1970, M.Sc. in (Theoretical)
Chemistry,
Postgraduate Studies in Chemistry, 1972, Ph.D. in (Theoretical) Chemistry,
Faculty of
Science, 1974, all at University of Zagreb.
Visits: Research Assistant at University of Utah, Salt Lake City, Utah, USA,
1973; Visiting
Professor at the Max-Planck-Institut fuer Strahlenchemie, Muelheim/Ruhr,
FR Germany,
1981-83, summer of 1986, autumn of 1993; R.A. Welch Fellow at Texas
A&M University,
Galveston, Texas, USA, winters of 1987, 1990, and 1995; Visiting Professor
at the Technical
University, Ilmenau, FR Germany, 2001.
Employment: 1970-76, Research Assistant; 1977-79, Research Associate;
1980-88, Higher
Research Associate; 1989-, Scientific Adviser; all at the The "R. Boskovic"
Institute in Zagreb;
1999- (part-time) Professor of Chemistry at the Faculty of Science,
University of Split, Split.
Research: Molecular properties. Molecular integrals. Applications of discrete
mathematics in
chemistry. Pure carbon cages. Author of 100 scientific papers, 15
professional and popular
papers, one monograph (Springer Verlag, Berlin, 1977), and Editor of 22
proceedings.
Projects: Co-worker on NSF projects (1975-88); coordinator of Fedearal
project "Graph theory
and combinatorics with applications in natural and computer sciences"
(1989-91); coordinator
of Croatian-Slovenian projects "Discrete mathematics in chemistry" (1989-
106
2001) & “Novel

Carbon Compounds” (2002.-); and director/co-director of annual
international Inter-University
Center (Dubrovnik, Croatia) MATH/CHEM/COMP meetings (1986-).
Coordinator of the MZT
RH project No. 0098039 (2002-).
Memberships: Croatian Chemical Society (through years Chairman of
Division of Theoretical
Chemistry & organizer of the Colloquia of the Society); Federal UNESCO
Divison for Natural
& Exact Sciences (1987-90); International Society of Mathematical
Chemistry; International
Society of Theoretical Chemical Physics (national representative); COST,
Action D3 (national
representative, 1995-98); COST, Action D19 (national representative, 2000-
); New York
Academy of Sciences; American Chemical Society; American Physical
Society.
Awards: The City of Zagreb Award for Achievements in Science, 1996.
Publication list 86. Patrick W. Fowler, Tomaz Pisanski, Ante Graovac, and Janez Zerovnik,
(last 5 years) A Generalized Ring Spiral Algorithm for Coding Fullerenes and Other Cubic
Polyhedra, DIMACS Series in Discrete Mathematics and Theoretical
Computer Science 51 (2000) 175-187.
87. Ante Graovac, Dejan Plavsic, Matjaz Kaufman, Tomaz Pisanski, and
Edward C. Kirby,
Application of the Adjacency Matrix Eigenvectors Method to Geometry
Determination of Toroidal Carbon Molecules, J. Chem. Phys. 113 (2000)
1925-1931.
88. Dejan Plavsic and Ante Graovac, On Calculation of Molecular
Descriptors Based on Various Graphical Bond Orders, in: Mircea V. Diudea,
Ed., QSAR/QSPR Studies by Molecular Descriptors, Nova Science
Publishers, Inc., Huntington, New York, 2001, pp. 39-61.
89. Ivan Gutman, Tanja Soldatovic, Ante Graovac, and Slavko Vukovic,
Approximating the Total pi-Electron Energy by Means of Spectral
Moments, Chem. Phys. Lett. 334 (2001) 168-172.
90. Ante Graovac, Ivan Gutman, Peter E. John, Dusica Vidovic, and Ivana
Vlah, On Statistics of Graph Energy, Z. Naturforsch. 56a (2001) 307-311.
91. Istvan Laszlo, Andre Rassat, P.W. Fowler, and Ante Graovac,
Topological Coordinates for Toroidal Structures, Chem. Phys. Lett.342
(2001) 369-374.
92. Mircea V.Diudea and Ante Graovac, Generation and Graph-Theoretical
Properties of C4-Tori, MATCH Commun. Math. Comput. Chem. 44 (2001)
93-102.
93. Ante Graovac, Alen Orbanic, and Tomaz Pisanski, Geometry versus
Topology: Overlapping Spheres Model Corrected for Angles, MATCH
Commun. Math. Comput. Chem. 44 (2001) 305-317.
94. Istvan Laszlo, Andre Rassat, Patrick W. Fowler, and Ante Graovac,
Topological Coordinates for Carbon Nanostructures, in: H. Kuzmany et al.,
Eds., Electronic Properties of Molecular Nanostructures, American Institute
of Physics Conference Proceedings (AIP CP) 591 (2001) 438-441.
107
95. Istvan Lukovits, Ante Graovac, Erika Kalman, Gyorgy Kaptay, Peter
Nagy, Sonja Nikolic,
Jaroslav Sytchev, and Nenad Trinajstic, Nanotubes: Number of Kekule
Structures and Aromaticity, J. Chem. Inf. Comp. Sci. 43 (2003) 609-614.
96. Mircea V. Diudea, Peter E. John, Ante Graovac, Miljenko Primorac, and
Tomaz Pisanski,
Leapfrog and Related Operations on Toroidal Fullerenes, Croat. Chem. Acta
76 (2003) 153-159.
97. M.V. Diudea, B. Parv, P.E. John, O. Ursu, and A. Graovac, Distance
Counting in Tori,
MATCH Commun. Math. Comput. Chem. 49 (2003) 23-36.
98. Ante Graovac, Martin Juvan, Marko Petkovsek, Aleksandar Vesel, and
Janez Zerovnik,
The Szeged Index of Fasciagraphs, MATCH Commun. Math. Comput.
Chem. 49 (2003) 47-66.
99. Mircea V. Diudea, Teodor Silviu Balaban, Edward C. Kirby, and Ante
Graovac, Energetics and pi-Electronic Structure of Polyhex Nanotubes,
Phys. Chem. Chem.Phys. 5 (2003) 4210-4214.
100. Damir Vukicevic and Ante Graovac, On Modified Wiener Indices of
Thorn Graphs,
MATCH Commun. Math. Comput. Chem. 50 (2004) 93-108.
101. Tomaz Pisanski, Marko Boben, Dragan Marusic, Alen Orbanic, and
Ante Graovac,
The 10-Cages and Derived Configurations, Discr. Math. 275 (2004) 265-
276.
102. Ivan Gutman, Damir Vukicevic, Ante Graovac, and Milan Randic, On
Algebraic Kekule Structures of Benzenoid Hydrocarbons, J. Chem. Inf.
Comp. Sci. 44 (2004) 296-299.
103. Damir Vukicevic and Ante Graovac, On Molecular Graphs with
Valencies 1, 2 and 4 with Prescribed Number of Bonds, Croat. Chem. Acta
77 (2004)b 313-319.
104. Damir Vukicevic and Ante Graovac, Which Valence Connectivities Are
Realizing Monocyclic Graphs: Generating Algorithm and Its Application to
Test Discriminative Properties of Zagreb and Modified Zagreb Index, Croat.
Chem. Acta 77 (2004) 481-490.
105. Damir Vukicevic and Ante Graovac, Valence Connectivity Versus
Randic, Zagreb and Modified Zagreb Index: A Linear Algorithm to Check
Discriminative Properties of Indices in Acyclic Molecular Graphs, Croat.
Chem. Acta 77 (2004) 501-508.
106. Mircea V. Diudea, Dusanka Janezic, and Ante Graovac, Topology
Counting in Nanostructures, Carpath. J. Math. 20 (2004) 223-234.
107. Mircea V. Diudea, Csaba L. Nagy, Ioan Silaghi-Dumitrescu, Ante
Graovac, Dusanka Janezic, and Drazen Vikic-Topic, Periodic Cages, J.
Chem. Inf. Model. 45 (2005) 293-299.
108. Damir Vukicevic and Ante Graovac, Compact Valence Sequences for
Molecules with Single, Double and Triple Covalent Bonds, to be submitted.
Relevant 63. D. Babic, A. Graovac, and N. Trinajstic, On the HOMO-LUMO
references for Separation in Fullerenes, Croat. Chem. Acta 66 (1993) 35-47.
teaching this 65. D. Babic, A. Graovac, and I. Gutman, Comment on "Characteristic
courses Polynomials of Fullerene Cages", Chem. Phys. Lett. 206 (1993) 584-585.
108
courses 69. N. Trinajstic, Z. Mihalic, and A. Graovac, The Interplay Between Graph
Theory and Molecular Orbital Theory, in: D. Bonchev and O. Mekenyan,
Eds., Graph Theoretical Approaches to hemical Reactivity, Kluwer
Academic Publishers, 1994, pp. 37-72.
71. D. Babic, S. Bassoli, M. Casartelli, F. Cataldo, A. Graovac, O. Ori, and
B. York, Generalized Stone-Wales Transformations, Mol. Sim. 14 (1995)
395-401.
72. D.J. Klein, A. Graovac, N. Trinajstic, and Z. Mihalic, Excitation Spectra
for Degenerate Rearrangements, J. Mol. Struct. (THEOCHEM) 341 (1995)
157-164.
74. D. Vikic-Topic, Edwin D. Becker, M. Hodoscek, and A.Graovac,
Lowdin Atomic Charges for Modeling Long Range Deuterium Isotope Shifts
in C-13 NMR Spectra of BinuclearAromatic Compounds, Croat. Chem. Acta
68 (1995) 193-203.
75. Tomaz Pisanski, Bor Plestenjak, and Ante Graovac, NiceGraph Program
and Its Applications in Chemistry, Croat. Chem. Acta 68 (1995) 283-292.
76. Bor Plestenjak, Tomaz Pisanski, and Ante Graovac, Generating
Fullerenes at Random, J. Chem. Inf. Comp. Sci. 36 (1996) 825-828.
77. Bor Plestenjak, Tomaz Pisanski and Ante Graovac, The Minimal Non-
Fullerene Voronoi Polyhedra, MATCH Commun. Math. Chem. 33 (1996)
157-168.
78. Tomaz Pisanski, Marko Razinger and Ante Graovac, Geometry versus
Topology: Testing Self-Consistency of the NiceGraph Program, Croat.
Chem. Acta 69 (1996) 827-836.
79. Matjaz Kaufman, Tomaz Pisanski, Dragan Lukman, Branko Borstnik,
and Ante Graovac, Graph Drawing Algorithms versus Molecular
Mechanics Geometries in Fullerenes, Chem. Phys. Lett. 259 (1996) 420-424.
83. Tomaz Pisanski, Matjaz Kaufman, Drago Bokal, Edward C. Kirby, and
Ante Graovac, Isoperimetric Quotient for Fullerenes and Other Polyhedral
Cages, J. Chem. Inf. Comp. Sci. 37 (1997) 1028-1032.
Last election 1999. god.
Teaching Modelling of Biomacromolecules and their Complexes
courses Modelling in Chemistry
Research in Biophysics
109
Lecturer Davor Juretić

Institution Faculty of natural sciences, mathematics and kineziology
E-mail juretic@pmfst.hr
Personal web- www.pmfst.hr/~juretic
page
Biography I was born October 23, 1944 in Split, Croatia. My B. Sc. from theoretical
physics in 1968 is from the University of Zagreb, Croatia, Faculty of natural
sciences and mathematics (PMF). My M. Sc. in theoretical solid state physics
is also from PMF, Zagreb in 1971. My Ph. D. in biophysics is from the
Pennsylvania State University, PA, USA in 1976. From 1977 to 1985 I
worked as assistant professor of physics at the University of Rijeka, Croatia.
There, I continued with research in biophysics and membrane bioenergetics
both experimentally and theoretically. My second period in the USA from
1985 to 1989 I spent working as guest associate scientist mostly at the
National Institutes of Health, Bethesda, Washington DC. Research topics were
secondary structure prediction for membrane proteins and bioenergetics of
cytochrom c oxidase liposomes and rat liver mitochondria. After returning to
Croatia I became associate professor of physics at the Faculty of natural
sciences, mathematics and education, University of Split. In addition to high
teaching load in general physics courses I had developed research topics in
structural bioinformatics, bioenergetics, biophysics and thermodynamics of
irreversible processes. In the year 1994 I received the „Ruđer Bošković“
national award. Next year I become full professor of physics. In 1996 I
received national medal „Danica Hrvatska“ for scientific accomplishments. In
1997 my first book on bioenergetics (in Croatian) was published in Zagreb by
Informator. In 1998 that book received national award from „Matica
Hrvatska“. In the same year, together with Dr. Damir Zucić from the
University of Osijek, I created the first Croatian scientific server for the
calculations in the field of structural bioinformatics. By the name of my native
town of SPLIT this server serves about 310 universities from 52 countries and
many more laboratories and scientists interested in secondary structure
predictions for membrane proteins. In addition to general physics I maintain
courses in biophysics, bioenergetics and bioinformatics at the University of
Split and University of Zagreb both at undergraduate and graduate study
programmes. From 2002 I am tenured full professor of physics. In 2004 and
2005 two of my graduate students wrote their masters thesis in biophysics and
molecular biology under my supervision. During last several years I made
available to students the complete typed text of my general physics lectures
and introduced M. Sc. degree study of biophysics, which was not available
previously at the University of Split. Currently (2006), I am working on
constructing Ph. D. study programme in biophysics as joint undertaking of the
University of Split and „Ruđer Bošković“ institute in Zagreb. Together with
scientists from Split and from abroad I organized (2006) two international
conferences in Split, one at the Mediterranean Institute for Life Sciences and
another at our Faculty of natural sciences, mathematics and kinesiology. For
more than 10 years, until year 2005, I was the member of the National
Committee for Physics in Zagreb. In addition to structural bioinformatics the
110
focus of my research lately is application of maximum entropy and maximum

entropy production principle in bioenergetics of membrane proteins. Another
research topic from biomedicine and membrane bioenergetics is the analysis
of construction principles for selective peptide antibiotics. I shall collaborate
on this project with several EU experts.
Publication list
(last 5 years) D. Juretić, L. Zoranić and D. Zucić: “Basic charge clusters and predictions
of membrane protein topology”. J. Chem. Inf. Coput. Sci. 42, 620-632
(2002).
D.Juretić i P. Županović: “Photosynthetic Models with Maximum Entropy
Production in Irreversible Charge Transfer Steps”, Computational Biology
and Chemistry 27, 541-553 (2003).
P. Županović and D. Juretić: "The chemical cycle kinetics close to the
equilibrium state and electrical circuit analogy". Croatica Chemica Acta
77, 561-571 (2004).
P. Županović, D. Juretić and S. Botrić: "Kirchhoff's loop law and the
Maximum entropy production principle". Phys. Rev. E70, 056108 (2004).
D. Zucić and D. Juretić: “Precise annotation of transmembrane segments
with Garlic – a free molecular visualization program”, Croatica Chemica
Acta 77, (2004).
S. Botrić, P. Županović i D. Juretić: “Is the stationary current distribution in
a linear planar electric network determined by the principle of maximum
D. Juretić, B. Lučić i N. Trinajstić: “Why focusing on bioinformatics?”
Periodicum Biologorum 107, 379-383 (2005).
D. Juretić i P. Županović: “The free-energy transduction and entropy
production in initial photosynthetic reactions” in Non-equilibrium
Thermodynamics and the Production of Entropy, Eds. A. Kleidon i
R.D. Lorenz, pp. 161-171, Springer,-Verlag, Berlin 2005.
Onsager’s principle of the least dissipation of energy and maximum
entropy production principle”, FIZIKA A (Zagreb) 14, (2005); pp.89-96.
P. Županović. S. Botrić, D Juretić: Relaxation processes, MaxEnt
formalism and Einstein’s formula for the probability of
fluctuations. Croatica Chemica Acta. 79(2006), 335-338.
R.C. Dewar, D. Juretić and P. Županović: “The functional design of
the rotary enzyme ETP synthase is consistant with the maximum
entropy production principle”. Chem. Phys. Lett. 430, 177-182 (2006) (2006).
Relevant 60 scientific publications in the CC periodicals that have been cited
references for 700 times.
teaching this
courses 1. Published book on bioenergetics (in Croatian):
D. Juretić: Bioenergetics – the work of membrane proteins, Informator,
Zagreb, 1997.
Last election 2002
Teaching Bioinformatics, Biophysics and Bioenergetics of Membrane Proteins
courses
111
Lecturer Gordan Kilic, Ph.D.

Institution University of Texas Southwestern Medical Center
E-mail gordan.kilic@utsouthwestern.edu
Personal web- None
page
Biography Education/Trainning: University of Zagreb, Croatia, B.S. 1983-1988,
Physics; International School for Advanced Studies, Trieste, Italy, Ph.D.
1988-1992.
Employment:
1992-1996 Research Fellow, Biophysics: Max-Planck Institute,
Heidelberg, Germany,
1996-1999 Research Fellow, University of Colorado, Denver,
2000-2001 Research Fellow at Department of Medicine, University of
Colorado, Denver
Instructor at Department of Medicine, University of
Colorado, Denver
Assistant Professor at Department of Medicine, University of Colorado,
Denver
2004-present Assistant Professor at Department of Internal Medicine,
University of Texas Southwestern Medical Center, Dallas
Publication list 11. Roman R, Feranchak AP, Troetsch M, Dunkelberg JC, Kilic G, Schlenker
(last 5 years) T, Schaack J, Fitz JG (2002) Molecular characterization of volume-sensitive
SK(Ca) channels in human liver cell lines. American Journal Physiology
(Gastrointest. Liver Physiol.) Jan;282(1):G116-22.
12. Kilic G and Fitz JG (2002) Heterotrimeric G-proteins activate Cl-
channels through stimulation of a cyclooxygenase-dependent pathway in a
model liver cell line. Journal of Biological Chemistry 277(14):11721-7.
13. Doctor RB, Dahl R, Fouassier L, Kilic G and Fitz G (2002)
Cholangiocytes exhibit dynamic, actin-dependent apical membrane turnover.
American Journal Physiology (Cell Physiol.) May;282(5):C1042-52.
14. Kilic G (2002) Exocytosis in bovine chromaffin cells. studies with patch-
clamp capacitance and FM1-43 fluorescence. Biophysical Journal 83:849-
57.
15. Fernachak AP, Kilic G, Wojtaszek PA, Qadri I and Fitz JG (2003)
Volume-sensitive tyrosine kinases regulate liver cell volume through effects
on vesicular trafficking and membrane Na+ permeability. Journal of
Biological Chemistry 278(45):44632-8.
16. Gatof D, Kilic G and Fitz JG (2004) Regulation of volume-sensitive ATP
release in biliary cells through vesicular exocytosis. American Journal
Physiology (Gastrointest. Liver Physiol.) April;286(4):G538-46.
17. Puljak L, Pagliassotti MJ, Wei Y, Qadri I, Parameswara V, Esser V, Fitz
JG and Kilic G (2005) Inhibition of cellular responses to insulin in a rat liver
cell line. A role for PKC in insulin resistance. Journal of Physiology
(Lond.) 563(2):471-82.
18. Puljak L and Kilic G (2006) Emerging roles of chloride channels in
human diseases. Biochimca Biophysica Acta. 1762(4):404-13.
Relevant
112
references for
teaching this
courses
Last election 6/1/04
Teaching N.A.
courses
113
Lecturer Nada Krstulović

Institution Institute of Oceanography and Fisheries, Split, Croatia
E-mail krstulovic@izor.hr
Personal web-
page
Biography 1989 Ph.D. in Biology, PMF, University of Belgrade
1975 M.Sc. in Oceanology, PMF, University of Zagreb
1973 B.Sc. in Biology, PMF, University of Zagreb
Work experience and important duties:
Institute of Oceanography and Fisheries (IOF), Split since 1973.
Head of Laboratory for Microbiology since 1984.
Senior scientific officer, permanent appointment, since 2003.
University of Split, Center for Marine Studies, Professor, permanent
appointment (courses: General microbiology and Marine microbiology).
Professor at postgraduate studies at Faculty for chemical technology at
University of Split (course: Sanitary microbiology) and at Oceanology,
Faculty of Science, University of Zagreb (course: Marine microbiology).
Publication list Krstulović, N., M. Šolić, 2001. Distribution of phototrophic sulfur bacteria
(last 5 years) throughout the time scale of the anoxic water renewal in the Rogoznica Lake.
Fresenius Env. Bulletin, vol. 10: 586-589.
Bojanić, N., M. Šolić, N. Krstulović, I. Marasović, Ž. Ninčević and O. Viđak.
2001. Seasonal and vertical distribution of the ciliated protozoa and
micrometazoa in Kaštela Bay (central Adriatic). Helgol. Mar. Res. 55: 150-
159.
Šolić, M., N. Krstulović and S. Šestanović. 2001. The roles of predation,
substrate supply and temperature in controlling bacterial abundance:
interaction between spatial and seasonal scale. Acta Adriatica, 42: 35-48.
Krstulović, N. & M. Šolić. 2001. Total and sulfur bacteria during holomictic
period and period of stratification in the saline Rogoznica Lake (Central
Adriatic). Rapp. Comm. int. Mer Medit., 36: 194-195.
Šestanović, S., M. Šolić and N. Krstulović, 2004. Seasonal and vertical
distribution of planktonic bacteria and heterotrophic nanoflagellates in the
middle Adriatic Sea. Helgol. Mar. Res. 58: 83-92.
Šestanović, S., M. Šolić and N. Krstulović. 2004. Bacterial biomass in
sediments of coastal Adriatic Sea. Rapp. Comm. int. Mer Medit., 37: 289-
290.
Bojanić, N., M. Šolić, N. Krstulović, S. Šestanović, I. Marasović & Ž.
Ninčević. 2005. Temporal variability in abundance and biomass of ciliates
and copepods in the eutrophicated part of Kaštela Bay (Middle Adriatic Sea).
Helgolander Marine Research, 59: 107-120.
Šestanović, S., M. Šolić, N. Krstulović, D. Šegvić, I. Ciglenečki. 2005.
Vertical structure of microbial community in an eutrophic meromictic saline
lake. Fresenius Environmental Bulletin, 14: 668-675.
Šestanović, S., M. Šolić, N. Krstulović and D. Bogner. 2005. Volume,
abundance, and biomass of sediment bacteria in the eastern mid Adriatic Sea.
Acta Adriat., 46: 177-193.
Relevant Published 2 books, over 70 scientific papers in the field of microbiology,
114
references for numerous popular expert papers, teaching experience at undergraduate,

teaching this graduate and postgraduate level, advisor on doctoral, master and
courses undergraduate thesis.
Last election May 2003 Senior scientific officer, permanent appointment
October 2005 Professor, permanent appointment
Teaching Environmental Microbiology
courses
115
Lecturer Bono Lučić

E-mail lucic@irb.hr
Personal web- http://www.irb.hr/korisnici/lucic
page
Biography Education:
1984-1989 B. Sc. University of Zagreb, Faculty of Electrical Engineering and
Computing, Microelectronics
1994 M. Sc. Degree – University of Zagreb, Faculty of Science and
Mathematics, Physics - Molecular biophysics
1997 Ph. D. Degree - University of Zagreb, Faculty of Science and
Mathematics, Chemistry - Theoretical chemistry
Work experience:
1991 - 1992 Faculty of natural sciences, mathematics, and education, Split
1992 - Ruđer Bošković Institute (RBI), Zagreb
Languages: Croatian, English, German (only listening and reading)
Publications: 33 scientific papers (29 published in CC journals), 2 papers as
chapter in books, 3 mini-review papers
Organisational skills and competencies:
- Secretary of the Croatian Biophysical Society (2002-);
- Member of Editorial Board of Croatica Chemica Acta (2000-);
- Member of Editorial Board of Internet Electronic Journal of Moalecular
Design (2004-).
Publication list 1. D. Juretić; B. Lučić; N. Trinajstić, Why focusing on bioinformatics?.
(last 5 years) Period. Biologorum 107 (2005) , 4; 379-383.
2. F. Supek; T. Šmuc; B. Lučić, A prototype structure-activity relationship
model based on National Cancer Institute cell line screening data, Period.
Biologorum 107 (2005) 451-455
3. T. Piližota; B. Lučić; N. Trinajstić, Use of variable selection in modeling
the secondary structural content of proteins from their composition of amino
acid residue, J. Chem. Inf. Comput. Sci. 44 (2004) 113-121.
4. B. Lučić; D. Nadramija; I. Bašic; N. Trinajstić, Toward generating simpler
QSAR models: Nonlinear multivariate regression versus several neural
network ensembles and some related methods, J. Chem. Inf. Comput. Sci. 43
(2003) 1094-1102.
5. B. Lučić; I. Bašic; D. Nadramija; A. Miličević; N. Trinajstić; T. Suzuki; R.
Petrukhin; M. Karelson; A. R. Katritzky, Correlation of liquid viscosity with
molecular structure for organic compounds using different variable selection
methods, ARKIVOC IV (2002) 45-59.
6. B. Lučić; I. Lukovits; S. Nikolić; N. Trinajstić, Distance-related indexes in
the quantitative structure-property relationship modeling, J. Chem. Inf.
Comput. Sci., 41 (2001) 527-535.
7. B. Lučić; D. Amić; N. Trinajstić, Nonlinear multivariate regression
outperforms several concisely designed neural networks on three QSPR data
sets, J. Chem. Inf. Comput. Sci., 40 (2000) 403-413.
8. A. R. Katritzky; K. Chen; Z. L. Wang; M. Karelson; B. Lučić; N.
Trinajstić; T. Suzuki; G. Schüürmann, Prediction of liquid viscosity for
116
organic compounds by a quantitative structure-property relationship, J. Phys.

Org. Chem. 13 (2000) 80-86.
9. S. C. Basak; B. D. Gute; B. Lučić; S. Nikolić; N. Trinajstić, A comparative
QSAR study of benzamidines complement-inhibitory activity and benzene
derivatives acute toxicity, Comput. Chem. 24 (2000) 181-191.
Relevant 1) 30 scientific papers published in Current Contents (CC) related to the
references for modeling structure and properties of proteins, and properties and activities of
teaching this biactive molecules.
courses 2) Citations:
a) more than 500 citations in Web of Science database
b) 14 papers having 14 and more than 14 citations
3) Reviewer of papers submitted to several
international scientific CC journals:
- Chemical Reviews
- Croatica Chemica Acta
- Journal of Chemical Information and Computer Science/Journal of
Chemical Information and Modeling
- Bioorganic Medicinal Chemistry
- Bioorganic Medicinal Chemistry Letters
- Acta Chimica Slovenica
- ARKIVOC
- Computers and Chemistry
- Journal of Chromatography A
and other journals (SCI):
- Internet Electronic Journal of Molecular Design
- Periodicum Biologorum
- Acta Pharmaceutica
- Kemija u industriji
Last election November 2002 - Scientific associate, Theoretical chemistry group (RBI)
Teaching Models and methods in structural bioinformatics
courses
117
Lecturer Prof. Dr. Hans O. Lutz

Institution Bielefeld University, Germany
E-mail lutz@physik.uni-bielefeld.de
Personal web- http://www.physik.uni-bielefeld.de/experi/d0/Holutz.html
page
Biography 1956 -High-school graduation (Abitur)
1958-First university degree (Vordiplom) Technical University München
1961-Second university degree (Hauptdiplom) Technical University München
1964-Dr. rer. nat., Technical University München
1970-Habilitation, Technical University Aachen
1964 – 1965-Research Associate, Technical University München
1965 – 1967-Research Associate, Oak Ridge National Laboratory, U. S. A.
1968 – 1973-Research Associate, Nuclear Physics Institute,Nuclear Research
Center (KFA) Jülich
1974 – 1977-Associate Professor, University Bielefeld
1977 – 2002-Full Professor, University Bielefeld
Since 1.10.2002-Professor emeritus University Bielefeld
Publication list 190. M. Ye. Zhuravlev, H. O. Lutz, A. V. Vedyayev, ''Size effects in the giant
(last 5 years) magnetoresistance of segmented nanowires'' Phys. Rev. 63,174409 (2001)
191. U. Werner, B. Siegmann, R. Mann, N. M. Kabachnik, H. O. Lutz,
''Kinetic energy release distributions in the fragmentation of O2 molecules
induced by fast highly charged ions'' Physica Scripta T92, 244 (2001)
192. B. Siegmann, U. Werner, H. O. Lutz, R. Mann, ''Multiple ionization and
fragmentation of H2O in collisions with fast highly charged Xe-ions'' J. Phys.
B 34, L587 (2001)
193. A. Reinköster, U. Werner, N. M. Kabachnik, H. O. Lutz, ''Experimental
and theoretical study of ionization and fragmentation of C60 by fast-proton
impact'' Phys. Rev. A 64, 023201 (2001)
194. M. Ye. Zhuravlev, H. O. Lutz, A. V. Vedyayev, ''The construction of the
Green Function for GMR structures of complex geometry'' J. Phys. A 34, 8383
(2001)
195. Z. Kaliman, N. Orlic, N. M. Kabachnik, H. O. Lutz, ''Theoretical study of
orientation effects in multiple ionization of molecules by fast ion impact''
Phys. Rev. A 65, 012708 (2001)
196. B. Siegmann, U. Werner, R. Mann, Z. Kaliman, N. M. Kabachnik, H. O.
Lutz, ''Orientation dependence of multiple ionization of diatomic molecules in
collisions with fast highly-charged ions'' Phys.Rev. A 65, 010704 (R) (2001)
197. M. Ehrich, U.Werner, H. O. Lutz, T. Kaneyasu, K. Ishii, K. Okuno, U.
Saalmann, ''Simultaneous polarization and fragmentation of N2 molecules in
slow keVcollisions with Kr8+ ions'' Phys. Rev. A 65, 030702 (R) (2002)
198. M. Ye. Zhuravlev, W. Schepper, S. Heitmann, H. Vinzelberg, P. Zahn, I.
Mertig, H.O. Lutz, A. V. Vedyayev, G. Reiss, A. Hütten, ''Reliable prediction
of Giant Magnetoresistance (GMR) characteristics'' Phys. Rev. B65, 144428
(2002)
199. M. Ye. Zhuravlev, W. Schepper, S. Heitmann, H. O. Lutz, A. V.
Vedyayev, G. Reiss, A. Hütten, ''Model Calculation of the Giant
Magnetoresistance in Multilayers with an Arbitrary Number of Layers.''
118
Lecture Notes in Physics 593 43 (2002)

200. B. Siegmann, U. Werner, H.O. Lutz, R. Mann, ''Complete Coulomb
fragmentation of CO2 in collisions with 5.9 MeV u-1 Xe18+ and Xe43+'' J.
Phys. B 35, 3755 (2002)
201. B. Siegmann, U. Werner, Z. Kaliman, Z. Roller-Lutz, N.M. Kabachnik,
H.O. Lutz, ''Multiple ionization of diatomic molecules in collisions with 50 -
300 keV hydrogen and helium ions'' Phys. Rev. A 66, 052701 (2002)
202. A. Reinköster, B. Siegmann, U. Werner, B.A. Huber, H.O. Lutz,
''Multifragmentation of C60 after collisions with Arz+ ions'' J. Phys. B 35,
4989 (2002)
Relevant 190. M. Ye. Zhuravlev, H. O. Lutz, A. V. Vedyayev, ''Size effects in the giant
references for magnetoresistance of segmented nanowires'' Phys. Rev. 63,174409 (2001)
teaching this 191. U. Werner, B. Siegmann, R. Mann, N. M. Kabachnik, H. O. Lutz,
courses ''Kinetic energy release distributions in the fragmentation of O2 molecules
induced by fast highly charged ions'' Physica Scripta T92, 244 (2001)
192. B. Siegmann, U. Werner, H. O. Lutz, R. Mann, ''Multiple ionization and
fragmentation of H2O in collisions with fast highly charged Xe-ions'' J. Phys.
B 34, L587 (2001)
193. A. Reinköster, U. Werner, N. M. Kabachnik, H. O. Lutz, ''Experimental
and theoretical study of ionization and fragmentation of C60 by fast-proton
impact'' Phys. Rev. A 64, 023201 (2001)
194. M. Ye. Zhuravlev, H. O. Lutz, A. V. Vedyayev, ''The construction of the
Green Function for GMR structures of complex geometry'' J. Phys. A 34, 8383
(2001)
195. Z. Kaliman, N. Orlic, N. M. Kabachnik, H. O. Lutz, ''Theoretical study of
orientation effects in multiple ionization of molecules by fast ion impact''
Phys. Rev. A 65, 012708 (2001)
196. B. Siegmann, U. Werner, R. Mann, Z. Kaliman, N. M. Kabachnik, H. O.
Lutz, ''Orientation dependence of multiple ionization of diatomic molecules in
collisions with fast highly-charged ions'' Phys.Rev. A 65, 010704 (R) (2001)
197. M. Ehrich, U.Werner, H. O. Lutz, T. Kaneyasu, K. Ishii, K. Okuno, U.
Saalmann, ''Simultaneous polarization and fragmentation of N2 molecules in
slow keVcollisions with Kr8+ ions'' Phys. Rev. A 65, 030702 (R) (2002)
198. M. Ye. Zhuravlev, W. Schepper, S. Heitmann, H. Vinzelberg, P. Zahn, I.
Mertig, H.O. Lutz, A. V. Vedyayev, G. Reiss, A. Hütten, ''Reliable prediction
of Giant Magnetoresistance (GMR) characteristics'' Phys. Rev. B65, 144428
(2002)
199. M. Ye. Zhuravlev, W. Schepper, S. Heitmann, H. O. Lutz, A. V.
Vedyayev, G. Reiss, A. Hütten, ''Model Calculation of the Giant
Magnetoresistance in Multilayers with an Arbitrary Number of Layers.''
Lecture Notes in Physics 593 43 (2002)
Last election Permanent professor
Teaching Regular lectures on numerous topics, in particular
courses Basic physics course
Solid state physics
Nanostructure and cluster physics
Atomic physics
Molecular physics
Atomic collision physics
119
Lecturer Stjepan Marčelja

Institution Department of Applied Mathematics
The Australian National University
E-mail marcelja@irb.hr
Personal web-
page
Biography Born 22. 9. 1941.
1965-1967: Teaching Assistant, Department of Physics,University of Zagreb
1967-1970: Graduate Student and Teaching Assistant, Department of
Physics and Astronomy, University of Rochester,Rochester, New
York
1970-1971: Research Associate/Associate Instructor,Department of Physics
University of Utah,Salt Lake City, Utah
1971-1975 Lecturer at Department of Physics
1977-1978: University of Zagreb, Zagreb, Croatia
1973-1974: Guest Scientist, Institut für Theoretische Physik, Freie
Universitat Berlin, Germany
1975-1977: and 1978 - 1982 Senior Research Fellow
1983 - 1994 Senior Fellow
1994 - 2002 Professor, Department of Applied Mathematics, Research
School of Physical Sciences, Institute of Advanced Studies,
Australian National University, Canberra, Australia
2002 - 2004 Director General, Ruđer Bošković Institute,Zagreb, Croatia
2005 - Visiting Fellow, Australian National University
Visiting Professorships
Université de Paris-Sud Orsay, May-July 1981
Collège de France, October-November 1993
Göteborg University, April 1998-March 1999
Tel Aviv University (‘Sackler Scholar’) October 1999-January 2000
Honours and Awards
Eastman Kodak Award, University of Rochester, Rochester, New York, 1969.
Ruđer Bošković Award, Science Research Council, Croatia, Croatia, 1974.
Fellow, Australian Academy of Science, 1991
Corresponding Fellow, Croatian Academy of Sciences and Arts, 1997
Publication list 71. Lyubartsev, A. P. and Marčelja, S. “Evaluation of effective ion-ion
(last 5 years) potentials in aqueous electrolytes” Physical Review E 65 (2002) 041202-1
72. Marčelja, S.“Short-range forces in surface and bubble interaction”
Current Opinion in Colloid and Interface Science 9 (2004) 165-167.
73. Marčelja, S., Selective coalescence of bubbles in simple electrolytes
Journal of Physical Chemistry B 110 (2006) 13062-13067 .
Relevant All of the above mentioned papers and activities. Approximately 6000
references for citations of scientific papers from the field of physics and biophysics.
teaching this
courses
Last election 1994.
Teaching courses
120
Lecturer Prof. Dr. Vladimir Paar

Institution University of Zagreb, Faculty of Science, Department of Physics and
Croatian academy of sciences and arts, Zagreb, Croatia
E-mail paar@hazu.hr
Personal web- http://mahazu.hazu.hr/~paar/
page
Biography 1942 born in Zagreb, Croatia
1965,1969,1971 B.Sc. in physics, M.Sc. in physics, Ph.D. in physics,
University of Zagreb, Zagreb, Croatia
university and research career, employment:
1965-1975 research assistant, Inst. R. Boskovic, Zagreb
1975-1979 associated professor in physics, Faculty of Science, Physics
Dept., University of Zagreb
1980- professor of physics, Faculty of Science, Physics Dept.,
University of Zagreb
1992- fellow of Croatian academy of sciences and arts
Professional training:
1969-1971 Niels Bohr Institute, University of Copenhagen, Denmark
Guest scientist or professor (shorter or longer visits, total duration five years)
Niels Bohr Institute, Copenhagen
FA Juelich, Germany
Free University, Natuurkundig Laboratorium, Amsterdam
Centre de Spectrometrie Nucleaire, Orsay
Lawrence Livermore National Laboratory, University of California Berkeley
Technical University Muenchen
Federal University of Rio de Janeiro
University of Sussex, Brighton
University of Maryland, College Park
Scientific collaboration: see relevant references on personal web page
Research topics:
theoretical nuclear physics, nuclear field theory, nuclear level density,
quantum chaos, nonlinear dynamics and classical chaos, transient chaos,
biological oscillators, encryption methods, robotics, gastroenterology,
computational genomics, higher order repeats
Publication list V. Paar, N. Pavin, A. Rubčić, J. Rubčić, N. Trinajstić, Scale invariant power
(last 5 years) law and fractality for molecular weights, Chemical Physics Letters 336
(2001) 129-134.
A. Gizon, J. Timar, J. Gizon, B. Weiss, D. Barneoud, C. Foin, J. Genevey, F.
Hannachi, C.F. Liang, A. Lopez-Martens, P. Paris, B.M. Nyako, L. Zolnai,
J.C. Merdinger, S. Brant, V. Paar, Low-lying levels and collective bands in
doubly-odd Cs-124, Nuclear Physics A694 (2001) 63-102.
H. Buljan, V. Paar, Many-hole interactions and the average lifetimes of
chaotic transients that precede controlled periodic motion, Physical Review E
6306 (2001) 6205-6211.
V. Paar, N. Pavin, M. Rosandić, Link between truncated fractals and coupled
oscillators in biological systems, Journal of Theoretical Biology 212 (2001)
47-56.
121
J. Timar, J. Gizon, A. Gizon, D. Sohler, B. M. Nyako, L. Zolnai, Gh. Cata-

Danil, D. Bucurescu, A. J. Boston, D. T. Joss, E. S. Paul, A. T. Semple, C. M.
Parry, S. Brant, V. Paar, Three-quasiparticle rotational bands in 101Rh:
IBFBPM description and signature inversion of the pi g9/2 orbital, Nuclear
Physics A696 (2001) 241-271.
Patent: V. Paar, N. Paar, N. Pavin, Encryption method using nonrepetitive
assignment of symbols to chaotic solutions of nonlinear robotic equation,
Državni zavod za intelektualno vlasništvo, Patent HR P980607A A2
(30.04.2001).
V. Paar, N. Paar, N. Pavin: "Encryption method using nonrepetitive binary
ASCII code depending on odd-even signature of number of digits in chaotic
solutions of nonlinear robotic equation " (Državni zavod za intelektualno
vlasništvo, P990240A, 381-03/99-01/1156, 559-03-99-01).
V. Paar, N. Paar, N. Pavin: "Encryption method of arrays of symbols with
selective transformation of binary ASCII code using chaotic solutions of
nonlinear Duffing equation" (Državni zavod za intelektualno vlasništvo,
P990248A, 381-03/99-01/1195, 559-03-99-01).
H. Buljan, V. Paar, Parry measure and the topological entropy of chaotic
repellers embedded within chaotic attractors, Physica (Amsterdam) D 2994
(2002) 1-13.
V. Paar, N. Pavin, A. Rubčić, J. Rubčić, Fractality of abundance-weighted
N,Z-chart of isotopes and systematics of atomic weights of chemical
elements, Croatica Chemica Acta 75 (2002) 121-129.
V. Paar, N. Pavin, A. Rubčić, J. Rubčić, Power laws and fractal behavior in
nuclear stability, atomic weights and molecular weights, Chaos, Solitons and
Fractals (Cambridge) 14 (2002) 901-916.
H. Buljan, V. Paar, Naturally invariant measure of chaotic attractors and the
conditionally invariant measure of embedded chaotic repellers, Physical
Review E 6503(2002) 036218
M. Rosandić, V. Paar, I. Basar, Key-string segmentation algorithm and
higher-order repeat 16mer (54 copies) in human alpha satellite DNA in
chromosome 7, Journal of theoretical Biology (Cambridge) 221 (2003) 29-
37.
M. Rosandić, V. Paar, M. Glunčić, I. Basar, N. Pavin, Key-string algorithm –
Novel approach to computational analysis of repewtitive sequences in human
centromeric DNA, Croatian Medical Journal 44 (2003) 386-406.
V. Paar, N. Pavin, Regularity-partial chaos – regularity transition and
overlapped KAM scenarios in a conservative system of two linearly coupled
double-well oscillators, Modern Physics Letters B 17 (2003) 941-948.
V. Paar, N. Pavin, I. Basar, M. Rosandić, I. Luketin, S. Durajlija Žinić,
Spectral densities and frequencies in the power spectrum of higher order
repeat alpha satellite in human DNA molecule, Croatica Chemica Acta 77
(2004) 73-81.
V. Paar, N. Pavin, Overlapping of two truncated crisis scenarios: Generator
of peaks in mean lifetimes of chaotic transients, Physical Review E 68 (2003)
036222 1-6.
V. Paar, N. Pavin, M. Rosandić, M. Glunčić, I.Basar, R. Pezer, S. Durajlija
Žinić, ColorHOR – novel graphical algorithm for fast scan of alpha satellite
higher-order repeats and HOR annotation for GenBank sequence of human
genome, Bioinformatics 21 (7) (2005) 846-852.
122
M. Rosandić, V. Paar, I. Basar, M. Glunčić, N. Pavin, KSA for CENP-B box

and pJalpha motif distributions in human chromosomes, Chromosome Res.
2006 (accepted for publication).
Relevant Scientific publications from the personal total list.

references for M. Rosandić, V. Paar, I. Basar, Key-string segmentation algorithm and
teaching this higher-order repeat 16mer (54 copies) in human alpha satellite DNA in
courses chromosome 7, Journal of theoretical Biology (Cambridge) 221 (2003) 29-
37.
M. Rosandić, V. Paar, M. Glunčić, I. Basar, N. Pavin, Key-string algorithm –
Novel approach to computational analysis of repewtitive sequences in human
centromeric DNA, Croatian Medical Journal 44 (2003) 386-406.
V. Paar, N. Pavin, Regularity-partial chaos – regularity transition and
overlapped KAM scenarios in a conservative system of two linearly coupled
double-well oscillators, Modern Physics Letters B 17 (2003) 941-948.
V. Paar, N. Pavin, I. Basar, M. Rosandić, I. Luketin, S. Durajlija Žinić,
Spectral densities and frequencies in the power spectrum of higher order
repeat alpha satellite in human DNA molecule, Croatica Chemica Acta 77
(2004) 73-81.
V. Paar, N. Pavin, Overlapping of two truncated crisis scenarios: Generator
of peaks in mean lifetimes of chaotic transients, Physical Review E 68 (2003)
036222 1-6.
V. Paar, N. Pavin, M. Rosandić, M. Glunčić, I.Basar, R. Pezer, S. Durajlija
Žinić, ColorHOR – novel graphical algorithm for fast scan of alpha satellite
higher-order repeats and HOR annotation for GenBank sequence of human
genome, Bioinformatics 21 (7) (2005) 846-852.
M. Rosandić, V. Paar, I. Basar, M. Glunčić, N. Pavin, KSA for CENP-B box
and pJalpha motif distributions in human chromosomes, Chromosome Res.
2006 (accepted for publication).
Position of full professor at University of Zagreb, giving different

lecture/courses in general physics, nonlinear dynamics, use of computational
methods as well as specialized lectures in graduate and postgraduate study
programs
Last election Full professor, from 1987, permanent election
Teaching Higher order repeats in human genome
courses
123
Lecturer Vladimir Parpura

Institution University of California Riverside
E-mail vlad@ucr.edu
Personal web- http://www.cbns.ucr.edu/index.php?content=people/faculty/parpura/parpura.h
page tml
Biography 09/84-07/89 School of Medicine in Split, University of Zagreb, Croatia;
received M.D. degree in July 1989; Major Professors: Drs. I. Kracun and C.
Cosovic
01/90-12/93 Dept. of Zoology & Genetics and Program for Neuroscience,
Iowa State University, Ames, IA; received Ph.D. degree in December 1993;
Major Professor Dr. Philip G. Haydon
01/94-11/94 Postdoctoral research associate. Glia-neuron signaling. Dept.
of Zoology & Genetics, Iowa State University, Ames, IA (Dr. P.G. Haydon)
09-10/94 Visiting postdoctoral research associate. Dept. of
Pharmacology and Cell Biology, Yale University Medical School, New
Haven, CT (Dr. R Jahn).
12/94-11/96 Postdoctoral research fellow. Dept. of Physiology &
Biophysics, Mayo Clinic, Rochester, MN (Mentor: Dr. J.M. Fernandez)
01/96- 07/02 Visiting scientist, Cornell Nanofabrication Facility, Knight
Laboratory, Cornell University, Ithaca, NY
12/96-7/00 Affiliate Assistant Professor. Dept. of Zoology & Genetics,
Iowa State University, Ames,IA
05/98-7/00 A Graduate Faculty in Dept. of Zoology & Genetics, Iowa
State University, Ames, IA
10/98-7/00 A Graduate Faculty in Program for Neuroscience, Iowa State
University, Ames, IA
7/00-6/05 Assistant Professor, Dept. of Cell Biology and Neuroscience,
Univ. of California, Riverside, CA
9/00- Member, Graduate Program in Neuroscience, Univ. of California,
Riverside, CA
9/00- Member, Graduate Program in Cell, Molecular and Developmental
Biology, Univ. of California, Riverside, CA
7/05-present Associate Professor (with tenure), Dept. of Cell Biology and
Neuroscience, Univ. of California, Riverside, CA
12/05- Member, Biomedical Sciences Graduate Program, Univ. of
California, Riverside, CA
Publication list ARTICLES (PEER-REVIEWED JOURNALS):
(last 5 years)
Parvizi, J., Parpura, V., Greenleaf, J.F., Bolander, M.E. (2002). Calcium
signaling is required for ultrasound-stimulated aggrecan synthesis by rat
chondrocytes J. Orthopaedic Res. 20:51-57.
Grima G., Benz B., Parpura V., Cuenod M., Do K.Q. (2003).Dopamine-
induced oxidative stress in neurons with glutathione deficit: implication for
schizophrenia. Schizophr Res. 62:213-24.
Liu, W., Montana, V., Chapman, E.R., Mohideen U., Parpura, V. (2003).
Botulinum Toxin type B
124
Micromechanosensor, Proc. Natl. Acad. Sci. USA. 100: 13621-13625.

Li, Q.-J., Yao, M., Wong, L., Parpura, V., Martins-Green, M. (2004). N- and
C- terminal peptides of hIL-8/CXCL8 are ligands for hCXCR1 and hCXCR2.
FASEB J. 18:776-778. (full version of this article available at
http://www.fasebj.org, The FASEB Journal Express Article
doi:10.1096/fj.02-1175fje)
Parpura, V., Scemes, E., Spray, D.C. (2004). Mechanisms of glutamate
release from astrocytes: gap junction "hemichannels", purinergic receptors
and exocytotic release. Neurochem Int. 45:259-264.
Hua, X., Malarkey E.B., Sunjara, V., Rosenwald, S.R., Li, W-H., Parpura, V.
(2004). Ca2+-dependent glutamate release involves two classes of
endoplasmic reticulum Ca2+ stores in astrocytes. J. Neurosci. Res. 76: 86-97.
Prasad, S., Zhang. X., Yang, M., Ni, Y., Parpura, V., Ozkan, C.S., Ozkan, M.
(2004). Separation of
individual neurons using dielectrophoretic alternative current fields. J.
Neurosci. Meth. 135:79-88.
Montana, V., Ni, Y., Sunjara, V., Hua, X., Parpura. V. (2004). Vesicular
glutamate transporter-dependent glutamate release from astrocytes, J.
Neurosci. 24:2633-2642.
Hu, H., Ni. Y., Montana, V., Haddon, R.C., Parpura, V. (2004). Chemically
functionalized carbon nanotubes as substrates for neuronal growth. Nano
Lett. 4: 507-511.
Parpura, V. (2005). Nanofabricated carbon-based detector. Anal. Chem.
77:681-686.
Bekyarova, E., Ni, Y., Malarkey, E.B., Montana, V., McWilliams, J.L.,
Haddon, R.C., Parpura, V. (2005). Applications of carbon nanotubes in
biotechnology and biomedicine. J. Biomed. Nanotech. 1:3-17.
Li, Q.-J., Yao, M., Dueck, M., Fuegate, J.E., Parpura V., Martins-Green, M.
(2005). cCXCR1 is a receptor for cIL8 (9E3/cCAF) and its N- and C-
terminal peptides, and is also activated by hIL8 (CXCL8). J. Leukoc. Biol.
77: 421-431.
Hu, H., Ni. Y., Mandal, S.K., Montana, V., Zhao, B., Haddon, R.C., Parpura,
V. (2005). Polyethyleneimine functionalized single-walled carbon nanotubes
as a substrate for neuronal growth. J. Phys. Chem. B 109:4285-4289.
Ni, Y., Hu, H., Malarkey E.B., Zhao, B., Montana, V., Haddon, R.C.,
Parpura, V. (2005). Chemically functionalized water soluble single-walled
carbon nanotubes modulate neurite outgrowth. J Nanosci. Nanotechnol. 5:
1707-1712.
Parpura, V., Chapman, E.R. (2005) Detection of botulinum toxins:
micromechanical and fluorescence- based sensors. Croat. Med. J. 46:491-
497.
Ponzio. T.A., Ni, Y., Montana, V., Parpura, V., Hatton, G.I. (2006). Vesicular
glutamate transporter expression in supraoptic neurons suggests a
glutamatergic phenotype. J. Neuroendocrinol. 18:253-265.
Liu, W., Montana, V., Bai, J., Chapman, E.R., Mohideen U., Parpura, V.
(2006). Single molecule mechanical probing of the SNARE protein
interactions. Biophys J In Press
Montana, V., Malarkey E.B., Verderio, C., Matteoli, M. Parpura, V. (2006)
Vesicular transmitter release from astrocytes. Glia In Press
125
OTHER PUBLICATIONS (PEER-REVIEWED

Prasad, S., Yang, M., Zhang, X., Ni, Y., Parpura, V., Ozkan, C.S., Ozkan, M.
(2003) Electric Field Assisted Localization of Neurons on Pt Microelectrode
Arrays, Mat. Res. Soc. Symp. Proc. 773: N4.6.1-9.
Cardullo, R.A., Parpura, V. (2003). Fluorescence Resonance Energy
Transfer: Theory and Instrumentation, Methods Cell Biol. 72:415-430.
Parpura, V. (2004). Glutamate-mediated bi-directional signaling between
neurons and astrocytes. In: Glial ÙNeuronal Signaling (Hatton, G.I,
Parpura, V., eds). Kluwer Academic Publishers, Boston, MA, pp. 365-395.
Bekyarova, E., Haddon, R.C., Parpura, V. (2005). Biofunctionalization of
Carbon Nanotubes. In: Nanotechnologies for the Lifesciences. Vol. 1
Biofunctionalization of Nanomaterials (Kumar, C.S.S.R., ed.) Wiley-VCH,
Wienhein-Berlin, Germany, pp 41-71.
Malarkey, E.B., Parpura, V. (2006) Glutamate release from astrocytes:
impact on neuronal function. In: Hepatic Encephalopathy and Nitrogen
Metabolism. (Häussinger, D., Kircheis, G., Schliess, F., eds.) Springer,
London-Heidelberg, pp 59-86.
Lee, W., Parpura, V. (2006) Exocytotic release of glutamate from astrocytes:
comparison to neurons. In: Protein trafficking in neurons (Bean, A., ed.)
Elsevier, Amsterdam, The Nederlands, In Press.
EDITED VOLUMES:
Hatton, G.I, Parpura, V. (Eds.) Glial ÙNeuronal Signaling. Kluwer
Academic Publishers, Boston, MA. (May 2004, 456 pp)
DISCLOSURES AND PATENTS:

Mohideen, U., Parpura, V. Micromechanical Sensor for Rapid Botulinum
Toxin Detection. UC Case No.: 2003-440-1; Disclosure, Date Disclosed:
May 2, 2003
Parpura, V. Nanofabricated carbon-based detector. UC Case No.: 2005-015-
1; Disclosure, Date Disclosed: July 20, 2004
Parpura, V. Water soluble carbon nanotubes as modulators of calcium influx
and neuronal growth. UC Case No. 2005-669-1; Disclosure, Date Disclosed:
May 10, 2005
Parpura, V., Mohideen, Umar. Botulinum toxin type B sensor based on
nanomanipulation. UC Case No. 2006-531-1; Disclosure, Date Disclosed:
March 23, 2006
Parpura, V., Mohideen, Umar. Biological nanozippers and nanocuffs. UC
Case No. 2006-532-1; Disclosure, Date Disclosed: March 23, 2006
Relevant Hatton, G.I, Parpura, V. (Eds.) Glial ÙNeuronal Signaling. Kluwer
references for Academic Publishers, Boston, MA. (May 2004, 456 pp)
teaching this Malarkey, E.B., Parpura, V. (2006) Glutamate release from astrocytes:
courses impact on neuronal function. In: Hepatic Encephalopathy and Nitrogen
Metabolism. (Häussinger, D., Kircheis, G., Schliess, F., eds.) Springer,
London-Heidelberg, pp 59-86.
Lee, W., Parpura, V. (2006) Exocytotic release of glutamate from astrocytes:
comparison to neurons. In: Protein trafficking in neurons (Bean, A., ed.)
Elsevier, Amsterdam, The Nederlands, In Press.
Parpura, V., Basarsky, T.A., Liu, F., Jeftinija, K., Jeftinija, S., Haydon, P. G.
(1994). Glutamate-mediated astrocyte-neuron signalling. Nature 369: 744-
126
747.
Basarsky, T.A., Parpura, V., Haydon, P. G. (1994). Hippocampal
synaptogenesis in cell culture: Developmental time course of synapse
formation, calcium influx and synaptic protein distribution. J. Neurosci. 14:
6402-6411.
Parpura, V., Doyle, R.T., Basarsky, T.A., Henderson, E., Haydon, P.G.
(1995). Dynamic imaging of individual purified synaptic vesicles.
Neuroimage, 2: 3-7.
Parpura, V., Liu, F., Brethorst, S., Jeftinija, K., Jeftinija, S., Haydon, P.G.
(1995). - latrotoxin stimulates glutamate release from cortical astrocytes.
FEBS Lett., 360: 266-270.
Parpura, V., Liu, F., Jeftinija, K., Haydon, P.G., Jeftinija, S. (1995).
Neuroligand-evoked calcium-dependent release of excitatory amino acids
from Schwann cells. J. Neurosci. 15: 5831-5839.
Tan, W., Parpura, V., Haydon, P.G., Yeung, E.S. (1995). Neurotransmitter
imaging in living cells based on native fluorescence detection. Anal. Chem.
67: 2575-2579.
Parpura, V., Fang, Y., Basarsky, T. A., Jahn, R., Haydon, P.G. (1995).
Expression of synaptobrevin II, cellubrevin and syntaxin in cultured
astrocytes. FEBS Lett. 377:489-492.
Araque, A., Parpura, V., Sanzgiri, R.P., Haydon, P.G. (1998). Glutamate-
dependent astrocyte modulation of synaptic transmission between cultured
hippocampal neurons. Eur. J. Neurosci. 10: 2129-2142.
Araque, A., Sanzgiri, R.P., Parpura, V., Haydon, P.G. (1998). Calcium
elevation in astrocytes causes an NMDA receptor-dependent increase in the
frequency of miniature synaptic currents in cultured hippocampal neurons. J.
Neurosci. 18: 6822-6829.
Parpura, V., Haydon, P.G. (1999). UV photolysis using a micromanipulated
optical fiber to deliver UV energy directly to the sample. J. Neurosci. Meth.
87: 25-34.
Araque, A., Parpura, V., Sanzgiri, R.P., Haydon, P.G. (1999). Tripartite
synapses: Glia, the unacknowledged partner. Trends Neurosci. 22: 208-215.
Trudeau, L-E., Parpura, V., Haydon, P.G. (1999). Activation of
neurotransmitter release in hippocampal nerve terminals during recovery
from intracellular acidification. J. Neurophysiol. 81: 2627-2635.
Parpura, V., Haydon, P.G. (1999). “Uncaging” using optical fibers to
deliver UV-light directly to the sample. Croat. Med. J. 40: 340-345.
Araque, A., Sanzgiri, R.P., Parpura, V., Haydon, P.G. (1999). Astrocyte-
induced modulation of synaptic transmission. Can. J. Physiol. Pharmacol.
77: 699-706.
Innocenti, B., Parpura, V., Haydon, P.G. (2000). Imaging extracellular waves
of glutamate during calcium signaling in cultured astrocytes. J. Neurosci. 20:
1800-1808.
Parpura, V., Haydon, P.G. (2000). Physiological astrocytic calcium levels
stimulate glutamate release to modulate adjacent neurons. Proc. Natl. Acad.
Sci. USA. 97: 8629-8634.
Parpura, V., Scemes, E., Spray, D.C. (2004). Mechanisms of glutamate
release from astrocytes: gap junction "hemichannels", purinergic receptors
and exocytotic release. Neurochem Int. 45:259-264.
Hua, X., Malarkey E.B., Sunjara, V., Rosenwald, S.R., Li, W-H., Parpura, V.
127
(2004). Ca2+-dependent glutamate release involves two classes of

endoplasmic reticulum Ca2+ stores in astrocytes. J. Neurosci. Res. 76: 86-97.
Montana, V., Ni, Y., Sunjara, V., Hua, X., Parpura. V. (2004). Vesicular
glutamate transporter-dependent glutamate release from astrocytes, J.
Neurosci. 24:2633-2642.
Ponzio. T.A., Ni, Y., Montana, V., Parpura, V., Hatton, G.I. (2006). Vesicular
glutamate transporter expression in supraoptic neurons suggests a
glutamatergic phenotype. J. Neuroendocrinol. 18:253-265.
Montana, V., Malarkey E.B., Verderio, C., Matteoli, M. Parpura, V. (2006)
Vesicular transmitter release from astrocytes. Glia In Press
Last election July 1, 2006 promoted to Associate Professor with tenure
Teaching 01/96-06/96 Taught in 8300 Nrsci. Concepts in Neurophysiology. Mayo
courses Graduate School, Mayo Foundation
02/97 Taught in Neuro557. Techniques in Neuroscience. Program for
Neuroscience. Iowa State Univ.
08/98-12/98 In charge of combined Neuro 690 (Journal Club in
Neuroscience) and ZOOL 690/696C (Seminars and Research Seminars in
Neurobiology). Program for Neuroscience and Dept. of Zoology & Genetics,
Iowa State University. 12 graduate students enrolled.
02/99 Taught in Neuro557. Techniques in Neuroscience. Program for
Neuroscience. Iowa State Univ.
08/99-12/99 In charge of combined ZOOL 690C (Seminars in
Neurobiology) and ZOOL 690D (Seminars in Physiology). Dept. of Zoology
& Genetics, Iowa State University. 7 graduate students enrolled.
1/00-5/00 In charge of combined ZOOL 690/696D (Seminars and
Research Seminars in Physiology). Dept. of Zoology & Genetics, Iowa State
University. 5 graduate students enrolled.
10/00-12/00 In charge of NRSC 289 (Special Topics in Neuroscience,
“Synaptic plasticity”). Dept of Cell Biology and Neuroscience, University of
California Riverside. 1 undergraduate and 17 graduate students.
4/01-6/01 Co-charge (with R.A. Cardullo) of CMDB 281E (Seminars in
Cell Biology: “Regulated exocytosis: From sectretagogue to secretion”), Dept
of Cell Biology and Neuroscience, University of California Riverside. 5
undergraduate and 6 graduate students.
10/01-12/01 In charge of NRSC 289 (Special Topics in Neuroscience,
“Glia-more than just a glue”). Dept of Cell Biology and Neuroscience,
University of California Riverside. 16 graduate students.
3/27-6/14/02 In charge of NRSC 106 (Introduction to Neuroscience). Dept
9/24-12/15/02 In charge of NRSC 289 (Special Topics in Neuroscience),
“Trilogy: Stem Cells, Apoptosis and Classical Paper in Neuroscience”. Dept
3/26/-6/13/03 In charge of NRSC 106 (Introduction to Neuroscience). Dept
9/22-12/13/03 -In charge of NRSC 289 (Special Topics in Neuroscience),
“Toxins as tools in neuroscience”. Dept of Cell Biology and Neuroscience,
128

-Taught in NRSC 201 (Advanced Techniques in Neuroscience).
Dept. of Cell Biology and Neuroscience. 4 graduate students.
undergraduate students.
9/20/-12/11/04 In charge of NRSC 289 (Special Topics in Neuroscience),
“Glial Neuronal Interactions”. Dept of Cell Biology and Neuroscience,
9/26/-12/17/05 -In charge of NRSC 289 (Special Topics in Neuroscience),
“Neuroscience in the news”. Dept of Cell Biology and Neuroscience,
-Taught in NRSC 201 (Advanced Techniques in Neuroscience).
Dept. of Cell Biology and Neuroscience. 3 graduate students.
129
Lecturer Lecture holder: Professor Krešimir Pavelić, PhD

Lecturers:
Sandra Kraljević Pavelić, PhD
Mirela Sedić, PhD
Karlo Hock, PhD
Mirela Baus Lončar, PhD
Employer University of Split, Faculty of Science, Mathematics and Education
E-mail pavelic@irb.hr
skraljevic@irb.hr
msedic@irb.hr
khock@irb.hr
mbausloncar@yahoo.com
Personal web http://www.irb.hr/hr/str/zmm/KPavelic/
page
Short resume Name and surname: Krešimir Pavelić
Address: Šestinski vijenac 62A, Zagreb, Croatia
Phone: +385 1 46 80 094, +385 1 45 61 114
Fax: +385 1 45 61 010
E-mail:pavelic@irb.hr
Citizenship: Croatian
Date of birth: 19th July 1952
Register of researchers entry number: 35262
Work experience:
Date of employment: 1st October 1975
Institution: «Ruđer Bošković» Institute
Professional position: university professor, senior researcher
Professional appointments:
Head of Division of Molecular Medicine at the "Ruđer Bošković" Institute,
from 1993 until recent
Chair of the Expert Committee for the State Awards in Natural Sciences, from
2004 until recent
Member of the Committee for the State Awards of the Croatian Parliament,
Member of the National Council for Science, from 2004 until recent
Croatian delegate in the EMBC (European Molecular Biology Conference),
Vice-chair of the European Molecular Biology Conference (EMBC), from 2004
until recent
Director of the “Cancer research“ National Programme, Croatian Ministry of
Science and Technology, from 1996 until 2002
Chair of the Scientific Council of the “Ruđer Bošković“ Institute, from 1987
until 1992
Member of the University of Zagreb Scientific Council (Council of deans),
from 1987 until 1992
Member of the Republic Committee for Scientific Awards in the Republic of
Croatia, from 1988 until recent
Head of Laboratory for Molecular Oncology at the Division of Molecular
130
Medicine, "Ruđer Bošković" Institute, from 1991 until 1997

Field of expertise: biomedicine and health
List of papers PAVELIĆ K., KATIĆ M., ŠVERKO V., MAROTTI T., BOŠNJAK B.,
published in BALOG T., STOJKOVIĆ R., RADAČIĆ M., ČOLIĆ M., POLJAK-BLAŽI M..
the past five Immunostimulatory effect of natural clinoptilolite as a possible mechanism of
years its antimetastatic ability. J. Canc. Res. Clin. Oncol., 128:37-44, 2002.
HEĆIMOVIĆ S., BAGO R., MUŽINIĆ D., BEGOVIĆ D., PAVELIĆ K.: The
first case of the FRAXE form of inherited mental retardation in Croatia. Eur. J.
Pediatr. 161:112-113 (2002).
HEĆIMOVIĆ S., PETEK TARNIK I., BARIĆ I., ČAKARUN Ž., PAVELIĆ
K.: Screening for fragile X syndrome: results from a school for mentally
retarded children. Acta Paediatr. 91:535-539, 2002.
HEĆIMOVIĆ S., KLEPAC N., VLAŠIĆ J., VOJTA A., JANKO D., ŠKARPA-
PRPIĆ I., CANKI-KLAIN N., MARKOVIĆ D., BOŽIKOV J., RELJA M.,
PAVELIĆ K.: Genetic background of Huntington disease in Croatis: Molecular
analysis of CAG, CCG, and d2642 (E2642del) polymorphysms. Human
Mutation #526 2002.
PAVELIĆ J., PAVELIĆ LJ., KARADŽA J., KRIŽANAC Š., UNEŠIĆ J.,
SPAVENTI Š., PAVELIĆ K.: Insulin-like growth factor family and combined
antisense approach in therapy of lung carcinoma. Molecular Medicine 8:149-
157, 2002.
PEĆINA-ŠLAUS N., GALL-TROŠELJ K., KAPITANOVIĆ S., PAVELIĆ J.,
PAVELIĆ K.: Novel alleles of the D16S752 polymorphic genetic marker linked
to E-Cadherin Gene – A potential population marker. Coll. Antropol. 26:85-88,
2002.
PAVELIĆ K., BUKOVIĆ D., PAVELIĆ J.: The role of insulin-like growth
factor 2 and its receptors in human tumors. Review. Molecular Medicine,
8:771-780, 2002.
DOGAN-KORUŽNJAK J., SLADE N., ZAMOLA B., PAVELIĆ K.,
KARMINSKI-ZAMOLA G.: Synthesis, photochemical synthesis and antitumor
evaluation of novel derivatives of thieno(3‘,2‘:4,5)thieno(2,3-c)quinolones.
Chem. Pharm. Bull., 50:656-660, 2002.
COLIC M., PAVELIC K.: Molecular, cellular and medical aspects of the action
of nutraceuticals and small molecules therapeutics: from chemoprevention to
new drug development. Drugs Exptl. Clin. Res. 26:169-175, 2002.
COLIC M., PAVELIC K.: Cellular mechanisms of immunomodulatory
activities of silicate materials. J. Tumour Marker Oncol., 18:63-68, 2002.
DZOLIC Z., KRISTOFOR V., CETINA M., NAGL A., HERGOLD-
BRUNDIC D., MRVOS-SERMEK T., BURGEMEISTER M., GRDISA N.,
SLADE K., PAVELIC K., BALZARINI J., DECLERCQ E., MINTAS M.:
Synthesis, structural studies and biological evaluation of some purine
substituted 1.aminocyclopropane-1-carboxylic acids and 1-amino-1-
hydroxymethylcyclopropanes. Nucleosides Nucleotide & Nucleic Acid
22:373-389, 2003.
. ZARKOVIC N., ZARKOVIC K., KRALJ M., BOROVIC S., SABOLOVIC
S., POLJAK BLAZI M., CIPAK A., PAVELIC K.: Anticancer and
antioxidative effects of micronized zeolite clinoptilolite. Anticancer Res.
23:1589-1596, 2003.
DZOLIC Z., CETINA M., KOVACEK D., HERGOLD-BRUNDIC A.,
MRVOS-SERMEK D., NAGL A., SLADE N., PAVELIC K., BALZARINI J.,
131
DE CLERCQ E., ZERBE O., FOLKERS G., SCAPOZZA L., MINTAS M.:
Molecular structures and ab initio molecular orbital calculations of the optically
active derivatives of 1-aminocyclopropane-1-carboxylic acid. J. Mol. Struct.
655:229-241, 2003.
SARIC T., MULLER D., SEITZ H.J., PAVELIC K.: Non-covalent interaction
of ubiquitin with insulin-degrading enzyme. Mol. Cell. Endocrinol. 204:11-20,
2003.
DOGAN KORUZNJAK J., GRDISA M., SLADE N., ZAMOLA B.,
PAVELIC K., KARMINSKI-ZAMOLA G.: Novel derivatives of
benzo(b)thienol(2,3-c)quinolones: synthesis, photochemical synthesis and
antitumor evaluation. J. Med. Chem. 46:4516-4524, 2003.
KRALJ M., PAVELIĆ K.: Medicine on a small scale. How molecular
medicine can benefit from self-assembled and nanostructured materials?
EMBO Rep. 4: 1008-1002, 2003.
HRANJEC M., GRDIŠA M., PAVELIĆ K., BOYKIN D.W., KARMINSKI-
ZAMOLA G.: Synthesis and antitumor evaluation of some new substituted
amidino-benzimidazolyl-furyl-phenyl-acrylates and naphthol/2,1,-b/furan-
carboxylates. Il Farmaco 58:1319-1324, 2003.
PAVELIC K., KOLAK T., KAPITANOVIC S., RADOSEVIC S., SPAVENTI
S., KRUSLIN B., PAVELIC J.: Gastric cancer: the role of insulin-like growth
factor 2 (IGF 2) and its receptors (IGF 1R and M6-P/IGF 2R). J. Pathol.
201:430-438, 2003.
PREKUPEC S.,SVEDRUŽIĆ D., GAZIVODA T., MRVOŠ-SERMEK D,
NAGL A., GRDIŠA M., PAVELIĆ K., BALZARINI J., DECLERCQ E.,
FOLKERS G., SCAPOZZA L., MINTAS M., RAIĆ-MALIĆ S.: Synthesis and
biological evaluation of iodinated and fluorinated 9-(2-hydroxypropyl) and 9-
(2-hydroxyethoxy)methyl purine nucleoside analogues. J. Med. Chem.,
46:5763-5772, 2003.
GRCE M., HUSNJAK K:, MATOVINA M., MILUTIN N., MAGDIĆ L.,
HUSNJAK K., PAVELIC, K.: Human papillomavirus, cytomegalovirus, and
adeno-associated virus infections in pregnant and nonpregnant women with
cervical intraepithelial neoplasia. J. Clin. Microbiol. 42:1341-1344, 2004.
POPOVIĆ-HADŽIJA M., RADOŠEVIĆ S., KOVAČEVIĆ D., LUKAČ J.,
HADŽIJA M., SPAVENTI R., PAVELIĆ K., KAPITANOVIĆ S.: Status of the
DPC4 tumor suppressor gene in sporadic colon adenocarcinoma of Croatian
patients: identification of a novel somatic mutation. Mutation Res. 548:61-73,
2004.
RAIC-MALIC.S., TOMASKOVIC L., MRVOS-SERMEK D., PRUGOVECKI
B., CETINA M., GRDISA M., PAVELIC K., MANNSCHRECK A.,
BALZARINI J., DE CLERCQ E., MINTAS M.: Spirobipyridopyrans,
spirobinaphtopyrans, indolinospiropyridopyrans, indolinospironaphthopyrans
and indoliunospironaphtho-1,4,-oxazines: synthesis, study of X-ray crystal
structure, antitumoral and antiviral evaluation. Bioorganic Medicinal
Chemistry 12: 1037-1045, 2004.
KOWANETZ K., HUSNJAK K., HOLLER D., KOWANETZ M.,
SOUBEZRAN P., HIRSCH D., SCHMIDT M.H.H., PAVELIC K., DE
CAMILLI P., RANDAZZO P.A., DIKIC I.: CIN85 associates with multiple
effectors controlling intracellular trafficking of EGF receptors. Mol. Biol. Cell.,
15:3155-3166, 2004.
ĆALETA I., GRDIŠA M., MRVOŠ-SERMEK D., CETINA M., TRALIĆ-
132
KULENOVIĆ V., PAVELIĆ K., KARMINSKI-ZAMOLA G.: Synthesis,

crystal structure and antiproliferative evaluation of some new substituted
benzothiazoles and styrylbenzothiazoles. Il Farmaco. 59:297-305, 2004.
PEĆINA-ŠLAUS N., GALL-TROŠELJ K., ŠLAUS M., RADIĆ K.,
NIKUŠEVA-MARTIĆ T., PAVELIĆ K.: Genetic changes of the E-cadherin
and APC tumor tuppressor genes in clear cell renal cell carcinoma. Pathology
36: 1-7, 2004.
KRALJEVIC S., STAMBROOK P.J., PAVELIC K.: Accelerating drug
discovery. EMBO Rep. 5: 837-842, 2004.
BATINAC S., MRVOŠ SERMEK D., CETINA M., PAVELIĆ K., MINTAS
M., RAIĆ-MALIĆ S.: Sinthesis of the novel bicyclic oxepinopyrimidine and
fluorinated pyrrolidinopyrimidines. Heterocycles, 63:2523-2536, 2004.
KAPITANOVIĆ S., ČAČEV T., RADOŠEVIĆ S., SPAVENTI Š., SPAVENTI
R., PAVELIĆ K.,: APC gene loss of heterozygosity, mutations, E1317Q, and
I1317K germ-line variants in sporadic colon cancer in Croatia. Exp. Mol.
Pathol. 77:193-200, 2004.
POPOVIĆ-HADŽIJA M., HRAŠČAN R., HERAK-BOSNAR M., ZELJKO Ž.,
HADŽIJA M., ČADEŽ J., PAVELIĆ K., KAPITANOVIĆ S.: Alterations of
the DPC4 tumor-suppressor gene in renal cell carcinoma. Urolog. Res. 32:229-
235, 2004.
KAPITANOVIĆ S., ČAČEV T., BERKOVIĆ M., POPOVIĆ-HADŽIJA M.,
RADOŠEVIĆ S., SEIWERTH S., SPAVENTI Š., PAVELIĆ K., SPAVENTI
R.: nm23-H1 expression and loss of heterozygosity in colon adenocarcinoma. J.
Clin. Pathol. 57: 1312-1318, 2004.
JARAK I., KRALJ M., ŠUMAN L., PAVLOVIĆ G., DOGAN J., PAVELIĆ
K., KARMINSKI-ZAMOLA G.: 2-carboxanilides and benzo(b) thieno(2, 3-
c)quinolones: synthesis, photochemical synthesis, crystal structure
determination and antitumor evaluation. Part 2. J. Med. Chem. 48:2346-2360,
2005.
PREKUPEC S., KALOKIRA B., GRDIŠA M., PAVELIĆ K., DECLERCQ E.,
MINTAS M., RAIĆ-MALIĆ S. Synthesis and comparative cytostatic activity of
the new N-7 acyclic purine nucleoside analogues with natural N-9 regioisomers.
Heterocycles 65:787-797, 2005.
OPAČIĆ N., BARBARIĆ M., ZORC B., CETINA M., NAGL A., FRKOVIĆ
D., KRALJ M., PAVELIĆ K., BALZARINI J., ANDREI G., SNOECK R., DE
CLERCQ E., RAIĆ-MALIĆ S., MINTAS M.: The novel L- and D-amino acid
derivatives of hydroxyurea and hydantoins: synthesis, X-ray crystal struczure
study, cytostatic and antiviral evaluations. J. Med. Chem., 48:475-482, 2005.
PAVELIĆ J., KRIŽANAC Š., KAPITANOVIĆ S., PAVELIĆ LJ.,
SAMARŽIJA M., PAVIČIĆ F., SPAVENTI Š., JAKOPOVIĆ M., HERCEG-
IVANOVI Z., PAVELIĆ K.: The consequences of insulin-like growth
factors/receptors dysfunction in lung cancer. Am. J. Respir. Cell Mol. Biol.,
32: 65-71, 2005.
KRALJ M., KRALJEVIĆ S., SEDIĆ M., KURJAK A., PAVELIĆ K.: Global
approach to perinatal medicine: functional genomics and proteomics. J. Perin.
Med., 33 : 5-16, 2005.
GRCE M., PAVELIĆ K.: Antiviral properties of clinoptilolite . Micropor.
Mesopor. Mater., 79:165-169, 2005.
GAZIVODA T., PLEVNIK M., PLAVEC J., KRALJEVIĆ S., KRALJ M.,
PAVELIĆ K., BALZARINI J., DE CLERCQ E., MINTAS M., RAIĆ-MALIĆ
133
S.: The novel pyrimidine and purine derivatives of L-ascorbic acid: synthesis,
one- and two-dimensional 1H and 13C NMR study, cytostatic and antiviral
evaluation. Biorg. Med. Chem. 13: 131-139, 2005.
BARBARIĆ M., URŠIĆ S., PILEPIĆ V., ZORC B., HERGOLD-BRUNDIĆ
A., NAGL A., GRDIŠA M., PAVELIĆ K., SNOECK R., ANDREI G.,
BALZARINI J., DECLERCQ E., MINTAS M.: Synthesis, X-ray cristal
structure study, cytostatic and antiviral evaluation of the novel cycloalkyl-N-
aryl-hydroxamic acids. J. Med Chem , 48:884-887, 2005.
PREKUPEC S.,MAKUC D., PLAVEC J.., KRALJEVIĆ S., KRALJ M..,
PAVELIĆ K., ANDREI G., SNOECK R., BALZARINI J., DECLERCQ E.,
RAIĆ-MALIĆ S., MINTAS M..: The novel 5-methyl 6-acyclic chain
substituted pyrimidine derivatives: synthesis, 1H and 13C NMR conformational
analysis, antiviral and cytostatic evaluation. Antiviral Chemistry.
Chemotherapy.., 16:327-338, 2005.
SIROTKOVIĆ-SKERLEV M., KRIŽANAC S., KAPITANOVIĆ S.,
HUSNJAK K., UNUŠIĆ J., PAVELIĆ K..: Expression of c-myc, erbB-2, p53
and nm23-H1 gene product in benign and malignant breast lesion: Coexpression
and correlation with clinicopathologic parameters. Exp. Mol. Pathol. 79 : 42-
50, 2005.
ČAČEV T., RADOŠEVIĆ S., SPAVENTI R., PAVELIĆ K., KAPITANOVIĆ
S.: NF1 gene loss of heterozygosity and expression analysis in sporadic colon
cancer. Gut, 54:1129-1135, 2005.
KRALJEVIĆ S. PAVELIĆ K.: Navigare necessere est. EMBO Rep 6 : 695-
700, 2005.
PAVELIĆ K., ETRA A., GALL-TROSELJ K.: Insights from the front lines of
nutraceutical research: The Third International Conference on Mechanisms of
Action of Nutraceuticals (ICMAN 3). J. Altern. Complem. Med. 11: 735-738,
2005.
MALOJČIĆ G., PIANTANIDA I., MARINIĆ, M., ŽINIĆ M., MARJANOVIĆ
M., KRALJ M., PAVELIĆ K., SCHNEIDER-H.-J. : A novel bis-
phenanthridine triamine with pH controlled binding to nucleotides and nucleic
acid. Organ. Biomol. Chem. 2005 (in press).
KAPITANOVIĆ S., ČAČEV T., ANTICA M., KRALJ M., CAVRIĆ G.,
PAVELIĆ K., SPAVENTI R.: Effect of indometacin on E-cahherin and -
catenin expression in HT-29 colon cancer cells. Exp. Mol. Path.. 80:91-96,
2006.
ČAČEV T., JOKIĆ M., SPAVENTI R., PAVELIĆ K., KAPITANOVIĆ S.:
Loss of heterozygosity testing using real-time PCR analysis of single nucleotide
polymorphism. J. Canc. Res. Clin. Oncol. In press (2005).
KATIC M., BOŠNJAK B., GALL-TROŠELJ K., DIKIC I., PAVELIC K.: A
clinoptilolite effect on cell media and the consequent effects on tumor cells in
vitro. Front. Biosciu. 11:1722-1732, 2006.
S. Kraljevic, M. Sedic, M. Scott, P. Gehrig, R. Schlapbach, K. Pavelic (2006)
Casting light on molecular events underlying anti-cancer drug treatment: what
can be seen from the proteomics point of view?. Cancer Treatment Reviews
32, 619-629
Publications; The lecture holder gives course in Molecular Biology at the University of
Qualifications Zagreb Faculty of Pharmacy and Biochemistry, from 1990 until recent.
required for In addition, he undertakes the following postgraduate teaching:
holding the
134
course • Postgraduate study in Oncology, Faculty of Medicine, University of

Zagreb, from 1977 until recent: Hormones and cancer, growth factors,
oncogenes, novel aspects of cancer treatment, novel diagnostic
procedures.
• Postgraduate study in Preclinical and Experimental Pharmacology,
Faculty of Medicine, University of Zagreb, from 1987 until 1989:
Molecular pharmacology
• Postgraduate study in Endocrinology, Faculty of Medicine, University
of Zagreb, from 1988 until 1989: Growth factors
• International postgraduate study in Diabetology, Faculty of Medicine,
University of Zagreb, from 1988 until 1989: Growth factors, hormones
and cancer
• Postgraduate study in Neurology, Faculty of Medicine, University of
Zagreb, from 1993 until 1994: Cancer genetics
• Postgraduate study in Cytology, Faculty of Medicine, University of
Zagreb, from 1994 until recent: Molecular genetics of cancer
• Postgraduate study in Medical Genetics, Faculty of Medicine,
University of Zagreb, from 1994 until recent: Molecular genetics of
cancer
• Postgraduate study in Medical Microbiology, Faculty of Medicine,
University of Zagreb, from 1994 until 1995: Principles and application
of recombinant DNA technology to medical microbiology
• Postgraduate study in Biomedicine, University of Rijeka, from 1996
until recent: Molecular oncology
Associates that will also give lectures are expert and educated scientists in the
field of Biomedicine. Their scientific activity resulted in the following
publications:
• S. Fontana, G. De Leo, M. Sedic, S. Kraljevic Pavelic, R. Alessandro
(2006) Proteomics in antitumor research. Drug Discovery Today:
Technologies 3: 441-449
• S. Kraljevic, M. Sedic, M. Scott, P. Gehrig, R. Schlapbach, K.
Pavelic (2006) Casting light on molecular events underlying anti-
cancer drug treatment: what can be seen from the proteomics point of
view?. Cancer Treatment Reviews 32: 619-629
• M. Cindrić, T. Kajfež Novak, S. Kraljević, M. Kralj, B. Kamenar.
(2006) Structural and antitumor activity study of γ-octamolybdates
containing aminoacids and peptides. Inorganica chimica acta
359:1673-1680
• S. Kraljevic i K. Pavelic (2005) Navigare necessere est. EMBO
reports 6:1-6
• M. Kralj, S. Kraljević, M. Sedić, A. Kurjak, K. Pavelić (2005)
Global approach to perinatal medicine: functional genomics and
proteomics. J Perinat Med 33:5-16
• T. Gazivoda, M. Plevnik, J. Plavec, S. Kraljević, M. Kralj, K.
Pavelić, J. Balzarini, E. De Clercq, M. Mintas, S. Raić-Malić (2005)
The Novel Pyrimidine and Purine Derivatives of 3-O-Benzyl-2-
hydroxy- and 2,3-Dihydroxy-4,5-didehydro-5,6-dideoxy-L-ascorbic
Acid: Synthesis, One- and Two-Dimensional 1H and 13C NMR
Study, Cytostatic and Antiviral Evaluation. Bioorganic and Medicinal
135
Chemistry 13:131-9
• S. Kraljevic, P.J. Stambrook, K. Pavelic (2004) Accelerating drug
discovery. EMBO reports 5: 837-842
• S. Prekupec, D. Makuc, J. Plavec, S. Kraljević, M. Kralj, K. Pavelić,
G. Andrei, R. Snoeck, J. Balzarini, E. De Clercq, S. Raić-Malić, M.
Mintas (2005) Antiviral and cytostatic evaluation of the novel 6-
acyclic chain substituted thymine derivatives. Antiviral Chemistry and
Chemotherapy 16; 327-338
• Hock, K. and R. Huber (2007). Effects of fighting decisions on
formation and structure of dominance hierarchies. Marine and
freshwater behaviour and physiology 40, p.45-61.
• Hranilovic, D., Bujas-Petkovic, Z., Vragovic, R., Vuk, T., Hock, K.
and B. Jernej (2006). Hyperserotonemia in adults with autistic
disorder. Journal of autism and developmental disorders, Epub ahead
of print.
• Hock, K. and R. Huber (2006). Modeling the acquisition of social
rank in crayfish: winner and loser effects and self-structuring
properties. Behaviour 143, p.325-346.
• Baus M, Medjugorac-Popovski M, Brown D, Sabolic I. (2000) In
colchicine treated rats, cellular distribution of AQP-1 in convoluted
and straight proximal tubule segments is differently affected.
Pflugers Arch. Jan;439(3):321-30
• Loncar Baus M , Al-azzeh E, Sommer PSM, Marinovic M, Schmel
K, Kruschewski M, Blin N, Stohwasser R, Gött P, Kayademir T.
(2003) Tumour necrosis factor alpha and nuclear factor kappaB
inhibit transcription of human TFF3 encoding a gastrointestinal
healing peptide. Gut. 2003 Sep;52(9):1297-303.
• Azarschab P, Stembalska A, Baus Loncar M, Pfister M, Sasiadek
MM, Blin N. (2003) Epigenetic control of E-cadherin (CDH1) by
CpG methylation in metastasising laryngeal cancer. Oncol Rep. 2003
Mar-Apr; 10(2): 501-3.
• Baus-Loncar M, Al-azzeh E, Romanska H, Lalani EN, Stamp GWH,
Blin N, Kayademir T (2004) Transcriptional control of TFF3
(intestinal trefoil factor) via promoter binding sites for the nuclear
factor kappaB and C/EBPbeta. Peptides. May;25(5):849-54.
• Broghammer M, Leistenschneider P, Baus Loncar M, Blin N,
Sasiadek MM, Pusch C (2004) Reduced expression of connexin
31.1 in larynx cancer is not caused by GJB5 mutations. Cancer
Letters 214:225-229.
• Broghammer M, Leistenschneider P, Baus Loncar M, Blin N,
Sasiadek MM, Pusch C (2004) Reduced expression of connexin 31.1
in larynx cancer is not caused by GJB5 mutations. Cancer Letters
214:225-229.
• Baus-Loncar M, Schmid J, Lalani EN, Rosewell I, Goodlad RA,
Stamp GWH, Blin N, Kayademir T (2005) Trefoil Factor 2 deficiency
in murine digestive tract influences the immune system. Cell Physiol
Biochem. 16(1-3):31-42.
• Baus-Loncar M and Giraud AS (2005) Multiple regulatory pathways
for trefoil factor (TFF) genes (2005) Cellular and Molecular Life
136
Sciences. 62 (24):2921- 2931.

• Baus-Loncar M, Kayademir T, Takaishi S, Wang T. (2005) Trefoil
factor family 2 deficiency and immune response. Cellular and
Molecular Life Sciences. 62 (24): 2947- 2955.
Date of the
last
promotion
Subject title Basics of systems biomedicine
137
Lecturer Rudolf Podgornik

Institution Univerza v Ljubljani, Fakulteta za matematiko in fiziko, Jadrnska 19,
Ljubljana
E-mail rudolf.podgornik@fmf.uni-lj.si
Personal web- http://www-f1.ijs.si/~rudi/
page
Biography
1977-1982 Research Assistant, Institute of Biophysics, Medical Faculty,
Ljubljana, Slovenia.
1983-1986 Research Assistant, Institute Jozef Stefan, Ljubljana, Slovenia.
1986-1987 Staff Member, J. Stefan Institute, Ljubljana, Slovenia.
1987-1989 Visiting Fellow, Laboratory of Molecular Forces and Assembly,
National Institutes of Health, Bethesda, Maryland 20892, USA
1990-1992 Senior Staff Member, J. Stefan Institute, Ljubljana, Slovenia.
1992-1993 Visiting scientist, Division of Physical Chemistry II, University
of Lund, Lund S - 22100, Sweden.
1993-1995 Visiting Scientist, Laboratory of Structural Biology, DCRT,
National Institutes of Health, Bethesda, Maryland 20892, USA.
1995- 1998 Assistant Professor, Dept. of Physics, University of Ljubljana,
Slovenia.
1995-1997 Visiting Scientist, Laboratory of Structural Biology, DCRT,
National Institutes of Health, Bethesda, Maryland 20892, USA.
1997- Senior Fellow, Laboratory of Physical and Structural Biology, National
Institute of Child Health and Human Developement, National Institutes of
Health, Bethesda, Maryland 20892-5626, USA.
1997 A three month sabbatical at Aspen Institute for Physics, Colorado
1998 A four month sabbatical at Institute of Theoretical Physics, University
of California at Santa Barbara
1998- 2001 Associate Professor of Physics, Dept. of Physics, University of
Ljubljana, Slovenia
2001- Full Professor, Dept. of Physics, University of Ljubljana, Slovenia
2002 A three month sabbatical at Laboratoire de Physique des Solides,
Universite Paris Sud, Orsay.
2004 Starting Jan 1st member of the Editorial Board of Physical Review E in
the areas of polyme physics and biological physics.
Publication list 51. PODGORNIK, Rudolf, HANSEN, Per Lyngs, PARSEGIAN, V. Adrian.
(last 5 years) Elastic moduli renormalization in self-interacting stretchable polyelectrolytes.
J. chem. phys., 2000, 113, str. 9343-9350. [COBISS.SI-ID 1231460]
52. ZIHERL, Primož, PODGORNIK, Rudolf, ŽUMER, Slobodan. Pseudo-
Casimir structural force drives spinodal dewetting in nematic liquid crystals.
Phys. rev. lett., 2000, 84, str. 1228-1231. [COBISS.SI-ID 1109604]
53. STREY, H. H., WANG, J., PODGORNIK, Rudolf, RUPPRECHT, A.,
YU, L., PARSEGIAN, V. A., SIROTA, E. B. Refusing to twist :
demonstration of a line hexatic phase in DNA liquid crystals. Phys. rev. lett.,
2000, 84, str. 3105-3198. [COBISS.SI-ID 1146468]
54. ZIHERL, Primož, KARIMI HADDADAN POUR, F., PODGORNIK,
Rudolf, ŽUMER, Slobodan. Pseudo-Casimir effect in nematic liquid crystals
in frustrating geometries. Phys. rev., E Stat. phys. plasmas fluids relat., 2000,
138
61, str. 5361-5371. [COBISS.SI-ID 1165412]

55. DOBNIKAR, Jure, PODGORNIK, Rudolf. Pseudo-Casimir force in
confined nematic polymers. Europhys. lett., 2001, 53, str. 735-741.
[COBISS.SI-ID 1288804]
56. HANSEN, Per Lyngs, PODGORNIK, Rudolf. Wormlike chains in the
large-d limit. J. chem. phys., 2001, 114, str. 8637-8648. [COBISS.SI-ID
1302884]
57. PODGORNIK, Rudolf, DOBNIKAR, Jure. Casimir and pseudo-Casimir
interactions in confined polyelectrolytes. J. chem. phys., 2001, 115, str. 1951-
1959. [COBISS.SI-ID 1352804]
58. LORMAN, V., PODGORNIK, Rudolf, ŽEKŠ, Boštjan. Positional,
reorientational, and bond orientational order in DNA mesophases. Phys. rev.
lett., 2001, letn. 87, str. 218101-1-4. [COBISS.SI-ID 1387620]
59. HANSEN, Per Lyngs, PODGORNIK, Rudolf, PARSEGIAN, V. Adrian.
Osmotic properties of DNA : critical evaluation of counterion condensation
theory. Phys. rev., E Stat. phys. plasmas fluids relat., 2001, 64, str. 021907-1-
4. [COBISS.SI-ID 1358180]
60. HANSEN, Per Lyngs, COHEN, Joel A., PODGORNIK, Rudolf,
PARSEGIAN, V. Adrian. Osmotic properties of poly(ethylene glycols) :
quantitative of brush and bulk scalling laws. Biophys. j., 84, str. 350-355.
61. PODGORNIK, Rudolf, HANSEN, P. L. Membrane pinning on a
disordered substrate. Europhys. lett., 2003, 62, str. 124-130. [COBISS.SI-ID
1625188]
62. PODGORNIK, Rudolf. Two-body polyelectrolyte-mediated bridging
interactions. J. chem. phys., 2003, 118, str. 11286-11296. [COBISS.SI-ID
1674852]
63. PODGORNIK, Rudolf, HANSEN, Per Lyngs, PARSEGIAN, V. Adrian.
On a reformulation of the theory of Lifshitz-van der Waals interactions in
multilayered systems. J. chem. phys., 2003, 119, str. 1070-1077.
64. KUTNJAK, Zdravko, FILIPIČ, Cene, PODGORNIK, Rudolf,
NORDENSKIÖLD, Lars, KOROLEV, Nikolay. Electrical conduction in
native deoxyribonucleic acid : hole hopping transfer mechanism?. Phys. rev.
lett., 2003, 90, str. 098101-1-4. [COBISS.SI-ID 1608804]
65. MKRTCHIAN, Vanik, PARSEGIAN, V. Adrian, PODGORNIK,
Rudolf, SASLOW, Wayne M. Universal thermal radiation drag on neutral
objects. Phys. rev. lett., 2003, 91, str. 220801-1-4. [COBISS.SI-ID 1707364]
66. PODGORNIK, Rudolf, PARSEGIAN, V. Adrian. van der Waals
interactions across stratified media. J. chem. phys., 2004, 120, str. 3401-3405.
67. PODGORNIK, Rudolf, PARSEGIAN, V. Adrian. Van der Waals
interactions in a dielectric with continously varying dielectric function. J.
chem. phys., 2004, 121, str. 7467-7473. [COBISS.SI-ID 1776228]
68. PODGORNIK, Rudolf. Polyelectrolite-mediated bridging interactions.
J. polym. sci., B, Polym. phys., 2004, 42, str. 3539-3556. [COBISS.SI-ID
1775204]
69. PODGORNIK, Rudolf. Electrostatic contibution to the persistence
length of a semilexible dipolar chain. Phys. rev., E Stat. nonlinear soft matter
phys. (Print), 2004, 70, str. 031801-1-11. [COBISS.SI-ID 1774948]
139
70. LORMAN, V., PODGORNIK, Rudolf, ŽEKŠ, Boštjan. Correlated and

decorrelated positional and orientational order in the nucleosomal core
particle mesophases. Europhys. lett., 2005, 69, str. 1017-1023. [COBISS.SI-
ID 1811300]
Relevant BORŠTNIK, Anamarija, PODGORNIK, Rudolf, VENCELJ, Matjaž. Rešene
references for naloge iz mehanike kontinuov, (Zbirka izbranih poglavij iz fizike, 35).
teaching this Ljubljana: DMFA - založništvo, 2001. 155 str., ilustr. ISBN 961-212-118-4.
courses [COBISS.SI-ID 112974592]
Last election 1.1.2001
Teaching Mehanika kontinuov, Elektromagnetno polje, Biofizika, Fizika mehke snovi
courses
140
Lecturer Boris Rakvin

Institution ''Ruđer Bošković'' Institute
E-mail rakvin@irb.hr
Personal web- http://www.irb.hr/hr/str/zfk/labs/LMR/03/001/
page
Biography Born in Zagreb, 1948. where he finished his education. He graduated in
Experimental Physics at the Faculty of Natural Sciences and Mathematics of
the University of Zagreb (PMF) in 1972. In 1974 he obtained the Master
degree and in the 1980 Ph. D. degree at the same Faculty. From 1972 up to
now he is employed at the "Ruder Boskovic" Institute, Zagreb. He is senior
scientist and head of the Laboratory for magnetic resonance in the Division of
Physical Chemistry, IRB, Zagreb. Since 1997 he has given lectures and
became full professor of physics at the Faculty of Veterinary Medicine,
University of Zagreb, Zagreb. He spent postdoctoral fellowship on the
University of Alabama, USA and he was visiting professor on the West
Virginia University, SAD and Florida State University, USA. His main
scientific interest is in the molecular physics, physics of the solid state and
EPR spectroscopy. Up to now he published 100 scientific papers with more
than 900 citations in the scientific literature in the field of the EPR
spectroscopy and applications in the molecular physics and the physics of the
solid state.
Publication list (100) Boris Rakvin, Dijana Žilić, Naresh S. Dalal, Andrew Harter, Yiannis
(last 5 years) Sanakis; Low-field EPR Studies of Levels Near the Top of the Barrier in
Mn12-Acetate Reveal a New Magnetization Relaxation Pathway; Solid State
Communications. xx (2006), xxx-xxx.
(99) Marina Kveder, Mladen Andreis, Janja Makarević, Milan Jokić, Boris
Rakvin; EPR study of low molecular weight organogels by means of
nitroxide spin probe. Chemical Physics Letters. 420 (2006); 443-447.
(98) N. Maltar-Strmečki, B. Rakvin; Evidence for disorder in L-alanine
lattice detected by Pulsed-EPR spectroscopy at cryogenic temperatures.
Spectrochimica Acta Part A. 63 (2006); 784-787.
(97) E. Tkalčec, B. Gržeta, J. Popović, H. Ivanković, B. Rakvin ; Structural
studies of Cr-doped mullite derived from single-phase precursors, Journal of
Physics and Chemistry of Solids. 67 (2006); 828-835.
(96) Kveder, Marina; Merunka, Dalibor; Ilakovac, Amon; Makarević, Janja;
Jokić, Milan; Rakvin, Boris.
Direct evidence for the glass-crystalline transformation in solid ethanol by
means of a nitroxide spin probe. Chemical Physics Letters. 419 (2005); 91-
95.
(95) Rakvin, Boris; Žilić, Dijana; Dalal Naresh S.; Spin-echo EPR spin-probe
measurement of the microsecond-range magnetic field fluctuations near the
surface of crystals of the nanomagnet Mn12-Ac: Solid State Communications.
136 (2005), 518-522.
(94) Rakvin B., Maltar-Strmecki N., Study of the first stable L-alanine
paramagnetic center by 2D-HYSCORE spectroscopy: Detection of 14N
hyperfine and quadrupole splitting; Chemical Physics Letters. 415 (2005); 3;
375-380.
(93) Maltar-Strmecki N., Rakvin B., Thermal stability of radiation-induced
141
free radicals in gamma-irradiated L-alanine single crystals; Appl. Radiat.

Isotopes. 63 (2005), 3; 375-380.
(92) Bermanec V. Wegner R. Kniewald G. Rakvin B. Palinkas LA. Rajic M.
Tomasic N. Furic K. The role of uranium(V) ion in the chemical composition
of meta-autunite from pegmatites of Quintos de Baixo, Brazil. [Article]
Neues Jahrbuch fur Mineralogie-Abhandlungen. 181 (2005), 1; 27-38.
(91) 5. Merunka, Dalibor; Rakvin, Boris.
Displacive and order-disorder behavior of KDP-type ferroelectrics on the
local scale. Solid State Communications. 129 (2004), 6; 375-377.
(90) Merunka, Dalibor; Rakvin, Boris.
Correlation between hydrogen bond geometry and phase transition
temperature in KDP-type ferroelectrics. 393 (2004), 4-6; 558-562.
(89) 7. Merunka, Dalibor; Rakvin, Boris.
Modified strong dipole-proton coupling model and local properties of EPR
probe in the KDP-type ferroelectrics. Applied Magnetic Resonance. 27
(2004); 215-224.
(88) Merunka, Dalibor; Rakvin, Boris.
Development and application of the modified strong dipole-proton coupling
model for KDP-type crystals. Ferroelectrics. 313 (2004); 99-103.
(87) Rakvin, Boris; Maltar-Strmečki, Nadica; Ramsey, Chris M.; Dalal,
Naresh S.
Heat capacity and electron spin echo evidence for low frequency vibrational
modes and lattice disorder in L-alanine at cryogenic temperatures. Journal of
Chemical Physics. 120 (2004), 14; 6665-6673.
(86) Rakvin, Boris; Žilić, Dijana; Dalal Naresh S.; North, J.Micah; Cevc,
Pavle; Arčon, Denis; Zadro, Krešo.
An EPR method for probing surface magnetic fields, dipolar distances, and
magnetization fluctuations in single molecule magnets. Spectrochimica Acta
Part A. 60 (2004); 1241-1245.
(85) Rakvin B, Žilić D, North JM, Dalal NS, Probing magnetic fields on
crystals of the nanomagnet Mn12-acetate bz electron paramagnetic
resonance. J. Mag. Res. 165 (2003); 260-264 .
(84) Cage B. Cotton FA. Dalal NS. Hillard EA. Rakvin B, Ramsey CM. EPR
probing of bonding and spin localization of the doublet-quartet states in a
spin frustrated equilateral triangular lattice: Cu-3(O2C16H23)(6) center dot
1.2C(6)H(12). Comptes Rendus Chimie. 6 (2003); 1; 39-46.
(83) Cage B, Cotton FA, Dalal NS, Hillard EA, Rakvin B, Ramsey CM.
Observation of symmetry lowering and electron localization in the doublet-
states of a spin-frustrated equilateral triangular lattice: Cu-
3(O2C16H23)center dot 1.2C(6)H(12). Journal of the American Chemical
Society. 125 (2003); 18; 5270-5271.
(82) Merunka D, Rakvin B. Molecular dynamics simulation of the soft
mode for hydrogen-bonded Ferroelectrics. Phys. Rev. B 66 (2002); 17; art
no.174101.
(81) Maltar-Strmecki N., Rakvin B., Cevc P. et al. Relaxation mechanism
in gamma–ray-irradiated L-alanine studied by transfer Saturation EPR and
pulse EPR. Appl. Magn. Reson. 22 (2002); 4; 551-560.
(80) Gil A.M., Alberti E., Perreira C., Rakvin B. et al A fast MAS H-1 NMR
study of amino acids and proteins J. Mol. Struct. 602 (2002); 357-266
142
(79) Pivac B., Rakvin B., Tonini R. Et al. Reply to comments on ′EPR study
of He-implanted Si′ by Pivac, B. Rakvin, R.Tonini, F. Corni, G. Ottaizani,
Published in Mater. Sci. Eng. B73 (200) 60-63. Written by M. Kakazey, M.
Vlasova, and J. G. Gonzales-Reply to discussion Mat. Sci. Eng.B-Solid 90
(2002); 1-2; 211-212.
(78) Mikšić V. Pivac B., Rakvin B., et al. DLTS and EPR study of defects in
H implanted silicon. Nucl. Instrum. Meth. B 186 (2002); 36-40.
Relevant Rakvin B., Maltar-Strmecki N., Study of the first stable L-alanine
references for paramagnetic center by 2D-HYSCORE spectroscopy: Detection of 14N
teaching this hyperfine and quadrupole splitting; Chemical Physics Letters. 415 (2005); 3;
courses 375-380.
Rakvin, Boris; Maltar-Strmečki, Nadica; Ramsey, Chris M.;Dalal, Naresh S.
Heat capacity and electron spin echo evidence for low frequency vibrational
modes and lattice disorder in L-alanine at cryogenic temperatures. Journal of
Chemical Physics. 120 (2004), 14; 6665-6673.
Experience in teaching Physics and Biophysics courses on Veterinarian
faculty University of Zagreb (since 1997)
Last election 18. 03. 2004 senior scientist
Teaching Experimental methods of physics in biophysics
courses
143
Lecturer Dusan Ražem

E-mail razem@irb.hr
Personal web-
page
Biography 1975
Zagreb, Croatia
Faculty of Science and Mathematics, Department of Chemistry,
Ph.D. in chemistry
1971
Zagreb, Croatia
Faculty of Science and Mathematics, Department of Chemistry, University of Zagreb
M. Sc. in chemistry
1968
Split, Croatia
Faculty of Chemical Technology Split, University of Zagreb
B.Sc. (Dipl. ing.) in chemistry
1971
Jülich, Germany
Institut für physikalische Chemie, Kernforschungsanlage Jülich
Radiation chemistry
From 22 September, 1975 to 21 September, 1977
South Bend, Indiana, SAD
Radiation Laboratory, University of Notre Dame
Radiation chemistry
Publication list Ražem, Dušan; Kovacs, Andras.
(last 5 years) Standard practice for use of the ethanol - chlorobenzene dosimetry
system // Annual Book of ASTM Standards.
West Conshohocken, PA 19428 : American Society for Testing and
Materials, 2006.
1. Katušin-Ražem, Branka; Hamitouche, Katia; Maltar-Strmečki, Nadica;

Kos, Karmen; Pucić, Irina; Britvić-Budicin, Smiljana; Ražem, Dušan.
Radiation sterilization of ketoprofen. // Radiation physics and chemistry.
73 (2005) , 2; 111-116.
2. Ilijaš, Boris; Ražem, Dušan; Miljanić, Saveta; Cerovac, Zdravko;
Orehovec, Zvonimir.
Optoelectronic reader for CET dosimeter, a radiation accident
chemical dosimetry system. // Radiation Physics and Chemistry. 68 (2003)
; 1005-1010.
3. Katušin-Ražem, Branka; Mihaljević, Branka; Ražem, Dušan.
Microbial decontamination of cosmetic raw materials and personal
care products by irradiation. // Radiation Physics and Chemistry. 66
144
(2003) ; 309-316.
4. Katušin-Ražem, Branka; Ražem, Dušan.
Availability of oxygen in radiation-induced peroxidation of unsaturated
fatty acids. // Radiation Physics and Chemistry. 67 (2003) ; 475-478.
5. Mihaljević, Branka; Ražem, Dušan.
Oxidation kinetics of iron(II) ion with t-butoxyl radical.. // Radiation
Physics and Chemistry. 67 (2003) ; 269-274.
6. Mihaljević, Branka; Ražem, Dušan.
Monothiocyanatoiron(III) complex in dichloromethane: methanol
solvent mixture.. // Croatica Chemica Acta. 76 (2003) ; 249-255.
7. Garaj-Vrhovac, Vera; Kopjar, Nevenka; Ražem, Dušan; Vekić, Branko;
Miljanić, Saveta; Ranogajec-Komor, Maria.
Application of the alkaline comet assay in biodosimetry:Assessment of
in vivo DNA damage in human peripheral leukocytes after a gamma
radiation incident. // Radiation Protection Dosimetry. 98 (2002) , 4; 407-
416.
8. Ražem, Dušan; Katušin-Ražem, Branka.
Dose requirements for microbial decontamination of botanical
materials by irradiation. // Radiation Physics and Chemistry. 63 (2002) ;
697-701.
9. Katušin-Ražem, Branka; Novak, Boris; Ražem, Dušan.
Microbiological decontamination of botanical raw materials and
corresponding pharmaceutical products by irradiation. // Radiation
Physics and Chemistry. 62 (2001) ; 261-275.
Relevant About 100 scientific, professional and popular papers published on the
references for subject of the course
teaching this
courses
Last election Senior scientist, 1998
Teaching Physico-chemical Basis of Radiation Biology
courses
145
Lecturer Franjo Sokolić

Institution Actually: LASIR, USTL, 59655 Villeneuve d'Asq, France.
Next year: PMF, Nikole Tesle 12, 21000 Split, Croatia.
E-mail sokolic@univ-lille1.fr
Personal web- http://lasir.univ-
page lille1.fr/pages/Page_Perso.php?NomVar=Sokolic&PrenomVar=Franjo
Biography Franjo Sokolić was born on Feb. 21st 1954 in Mali Losinj, Croatia. He got
his BSc at the University of Zagreb in Theoretical Physics in 1977; MSc at
the University of Zagreb in Molecular Physics in 1981; PhD at Rugjer
Boscovic Institute in Zagreb in Theory of Liquids in 1985.
From 1979 to 1989 he was working at Rugjer Boscovic Institute in Zagreb,
from 1989 to 1992 at the University Paris VI, and since 1992 the University
of Lille. He is working on computer simulations of liquid mixtures.
Publication list A. Perera, F. Sokolic, L. Almasy, Y. Koga: Kirkwood-Buff integrals of
(last 5 years) aqueous alcohol binary mixtures, J. Chem. Phys. 124, (2006) 124515.
A. Perera, F. Sokolic, L. Almasy, P. Westh, Y. Koga: On the evaluation of
Kirkwood-Buff integrals of aqueous acetone mixtures, J. Chem. Phys. 122,
(2005) 024503.
A. Perera, F. Sokolic: Modeling nonionic aqueous solutions: The acetone-
water mixture, J. Chem. Phys. 121, (2004) 11272.
F. Sokolic, A. Idrissi, A. Perera: Concentrated aqueous urea solutions: A
molecular dynamics study of different models, J. Chem. Phys. 116, (2002)
1636.
F. Sokolic, A. Idrissi, A. Perera: A molecular dynamics study of structural
properties of aqueous urea solutions, J. Mol. Liquids, 101, (2002) 81.
A. Idrissi, S. Longelin, F. Sokolic: Study of aqueous acetone solutions at
vaious concentrations: Low-frequency Raman and molecular dynamics
simulations, J. Phys. Chem. B105, (2001) 6004.
A. Idrissi, F. Sokolic, A. Perera: A molecular dynamics study of urea/water
mixture, J. Chem. Phys. 112, (2000), 9479.
Relevant Peter Atkins and Ronald Friedman: Molecular Quantum Mechanics, Oxford
references for University Press, Fourth Edition 2004.
teaching this Jeffrey I. Steinfeld: Molecules and Radiation: An Introduction to Modern
courses Molecular Spectroscopy, Dover Publications, Second Edition 2005.
Last election 2006
Teaching Molecular Structure and Dynamics, Spectroscopy and Simulations
courses
146
Lecturer Doc.dr. sc. Selma Supek

Institution Department of Physics, Faculty of Science, University of Zagreb
E-mail selma@phy.hr
Personal web-
page www.phy.hr, www.brain.hr
Biography Selma Supek received her undergraduate Diploma and M.Sc. degree in
physics at the Department of Physics. In 1993 she defended at the same
department her doctoral thesis on the functional organization of the human
visual cortex and spatio-temporal resolution of the magnetoencephalography.
Thesis research has been done at the Biophysics Group at Los Alamos
National Laboratory where she worked for 6 years (NIH/NEI EY08610).
After returning back to Zagreb she collaborates with laboratories for
functional brain imaging at Los Alamos, Heidelberg, and Helsinki. She is
principal investigator of the MZOS project number 0119265. She published
26 scientific papers in journal and proceedings that were cited more than 160
times,55 abstracts at international and national scientific meetings, she is
editor of the NFSI-99 Proceedings and the Book of Abstracts, invited speaker
at 13 international conferences and courses, she gave 18 seminars and public
lectures, chaired 2nd Internatiional Symposium on Noninvasive Functional
Source Imaging (NFSI-99) (www.brain.hr) that was held in Zagreba
September 3-7, 1999, she is director of a series of Internationa course on
Mind and Brain (www.brain.hr) at the InterUniversity Centre in Dubrovnik,
reviewer of 8 international journals and book series IMIA Yearbook of
Medical Informatics, member of the scientific committees at several
international meetings, and a member of 9 scientific societies (SFN, IBRO,
OHBM, ISBET, HFD, HBD, HDN, HDMBT, ISACM). She coordinated
and/or participated at several round tables on biophysics and functional brain
imaging. She was a mentor and co-mentor of 20 diploma thesis. Currently she
is mentor of two students (MSc and PhD) in the postgraduate program in
physics – biophysics. She co-organized and, from 2003 till the end of 2004,
co-directed the first University interdisciplinary postgraduate study
''Language Communication and Cognitive Neuroscience'' at the University of
Zagreb and was a member of its Coordination committee. She is member of
the Managment Board of the MedILS in Split.
Publication list 1. Supek, S.: Dynamic imaging of the working human brain, In: R.
(last 5 years) Magjarevic (ed.) IFMBE Proceedings - MEDICON 2001, IX Mediterranean
Conference on Medical and Biological Engineering and Computing, Volume
I, pp. 27-30, 2001.
2. Supek, S.: Dynamic MSI: Temporally constrained vs. temporally
unconstrained models, Biomedizinische Technik, 46-S2, 233-236, 2001.
3. Supek, S.: Are temporally restricted models advantageous in MSI?,
7th Annual Meeting of the Organization for Human Brain Mapping, June 10-
14, 2001, Brighton, UK, NeuroImage, 13, S262, 2001.
4. Supek, S.: Timecourse estimation in magnetoencephalography,
Society for Neuroscience 32nd Annual Meeting, Orlando, Florida, November
2-7, 2002
5. Kult, A., Rupp, A., Pressnitzer, D., Scherg, M., and Supek, S.: MEG
147
study on temporal asymmetry processing in the human auditory cortex.

NeuroImage, 19(2),2003.
6. Sušac, A., Ilmoniemi, R., and Supek, S.: Faces in the visual oddball
paradigm: A possible mismatch negativity. NeuroImage, 19(2), 2003.
7. Sušac A, Ilmoniemi RJ, Pihko E, Supek S. Neurodynamic Studies on
Emotional and Inverted Faces in an Oddball Paradigm. Brain Topogr.,
16(4):265-68, 2004.
8. Sušac A, Ilmoniemi RJ, Supek S. Early visual responses to upright
and inverted faces. Proceedings of the 14th International Conference on
Biomagnetism Biomag 2004, Halgren E, Ahlfors S, Hamalainen M, Cohen
D. (Eds), Boston, 2004, pp 445-46
9. Susac, A., Ilmoniemi, J. R., Pihko E., Nurminen, J.., Supek, S.: Early
dissociation of face and object processing: a magnetoencephalographic study
(NeuroReport., submitted).
Relevant 1. Aine, C.J., George, J.S., Medvick, P.A., Supek, S., Flynn, E.R.,
references for Bodis-Wallner, I.: Identification of multiple sources in transient evoked
teaching this neuromagnetic responses. In: Advances in Biomagnetism, Plenum Press,
courses New York, 1989, pp. 193-196.
2. Supek, S., Aine, C.J.: Simulation studies of multiple dipole
neuromagnetic source localization: Model order and limits of source
resolution. IEEE Transactions on Biomedical Engineering, 40:529-540,
1993.
3. Aine, C.J., Supek, S., George, J.S.: Temporal dynamics of visual-
evoked neuromagnetic sources: Effects of stimulus parameters and selective
attention. Intern. J Neuroscience, 80:79-104, 1995.
4. Aine, C.J., Supek, S., George, J.S., Ranken, D., Lewine, J., Sanders,
J., Best, E., Tiee, W., Flynn, E.R., and Wood, C.C.: Retinotopic organization
of human visual cortex: Departures from the classical model. Cerebral
Cortex, 6:354-361, 1996.
5. Supek, S., Aine, C.: Spatio-temporal modeling of neuromagnetic
data: I. Multi-source location vs timecourse estimation accuracy, Human
Brain Mapping, 5: 139-153, 1997.
6. Supek, S., Aine, C.: Spatio-temporal modeling of neuromagnetic
data: II. Multi-source resolvability of a MUSIC-based location estimator,
Human Brain Mapping, 5: 154-167, 1997.
7. Supek, S., Aine, C.J.: Temporal dynamics of multiple neuromagnetic
sources: Simulation and empirical studies. Biomedizinische Technik, 42-S1:
64-67, 1997.
8. Huang, M., Aine, C.J., Supek, S., Best, E., Ranken, D., Flynn, E.R.:
Multi-start Downhill Simplex Method for Spatio-temporal Source
Localization in Magnetoencephalography, Electroencephalography and
Clinical Neurophysiology - Evoked Potentials, 108/1, 32-44, 1998.
9. Supek, S. (Ed.) The NFSI-99 Proceedings: 2nd International
Symposium on Noninvasive Functional Source Imaging within the Human
Brain and Heart, September 3-7, 1999, Zagreb, Croatia, Biomedizinische
Technik, Vol. 44. Supplement 2, 1999
Last election January 1-st, 2005.
Teaching Functional Brain Imaging Methods
courses
148
Lecturer Vesna Svetličić

E-mail svetlicic@irb.hr
Personal web- http://nereus.irb.hr/lem/vesna.htm www.biofizika.hr
page
Biography education
1984, Ph.D., Ruđer Bošković Institute, Zagreb
1976, M. Sc. Degree, Faculty of Natural Sciences,University of Zagreb
1973, B.Sc. Degree, Faculty of Chemical Engineering, University of Zagreb
additional education
1974, Biomembranes – Lipids, Proteins and Receptors, Advanced Study
Institute, Portugal and 1973, Summer Graduate School “Structural
Biophysics”, University of Zagreb and University of Ljubljana
research at Ruđer Bošković Institute, since 1973
research abroad
Scripps Institution of Oceanography, Marine Biology Research Division,
UCSD, USA, guest scientist, 2004-
University of Minnesota, Department of Chemistry, Minneapolis, USA,
research associate 1985-19893(3years), visiting professor 1991-1999(3years),
affiliated academic staff 1991-2003
Laboratoire d'Electrochimie Interfaciale, Meudon, CNRS, regular scientific
missions within collaboration projects, since 1979
Universite P. et M.Curie, Paris, Laboratoire d'Electrochimie, CNRS,
scientific missions within collaboration projects, since 1979
teaching
1998- Oceanography Graduate School, University of Zagreb; Marine Oxido-
Reduction Processes
1991-1999 (3 years) University of Minnesota, Department of Chemistry,
Minneapolis, USA, Graduate Program, specialized courses in
electrochemistry
mentor: 3 Ph.D. thesis in progress
main activities: Surface imaging at nanoscale using Scanning Probe
Microscopy (AFM), Supramolecular organization of organic molecules et
electrodes and at natural interfaces; fundamental research, application in
ocean science and marine biophysics
Author of over 50 scientific papers in internationally reviewed journals in the
field of surface and colloid chemistry, biophysics and material sciences
Publication list Svetličić V, Ivošević N, Kovač S, Žutić V. Charge displacement by adhesion
(last 5 years) and spreading of a cell. Bioelectrochem. 2001; 53: 79-86.
Svetličić V, Hozić A. Probing cell surface charge by scanning electrode
potential. Electrophoresis. 2002; 23: 2080-2086.
Smodlaka N., Degobbis D., Svetličić V.(urednici), Effect of phosphorus on
particle dynamics during phytoplankton blooms. Northern Adriatic
mesocosmos experiment Rovinj 2003. Special issue Period Biolog. 2004;
106, 79 str.
149
Svetličić V, Žutić V, Hozić Zimmermann A. Biophysical Scenario of Giant Gel

Formation in the Northern Adriatic Sea. Ann NY Acad Sci. 2005; 1048: 524–
527.
Svetličić V, Žutić V. Formation and function of giant gel network in marine
ecosystem. Eur Biophys J with Biophys Lett. 2005; 34:729.
Svetličić V, Balnois E, Žutić V, Chevalet J, Hozić Zimmermann A, Kovač S,
Vdović N. Electrochemical Detection of Gel Microparticles in Seawater.
Croat Chem Acta. 2006;79,107-113.
Relevant Publication list , last 5 years
references for Leader of AFM facility
teaching this
courses
Last election 2003. senior scientist
courses
150
Lecturer Janoš Terzić. prof. dr.

Institution University of Split, Faculty of medicine
E-mail jterzic@bsb.mefst.hr
Personal web-
page
Biography EDUCATION
1985-1991 Medical Doctor – University of Zagreb, Medical School
1991-1993 Postdoctoral fellowsip, Health Center-University of Connecticut,
USA
1994-1997 Master of Science – University of Zagreb, School of Natural
Sciences
1995 – Short therm fellowship, Max Planck Institute Göttingen, Germany
1997-1998 Ph.. D. – University of Zagreb, Medical School
1997 – One month fellowship, Imperial College of Science, Medicine and
Technology, London, UK
1999 – Short term fellowship, Max Planck Institute Tübingen, Germany
2002 – Two months fellowship, Ludwig Institute, Uppsala, Sweden
POSITION
2001-present -Associated professor at the department for Physiology and
Immunology at Split University School of Medicine, Croatia
TEACHING EXPERIENCE
1993 – 2001 Teaching assistant, Courses in Immunology, Molecular Genetics
and Physiology
2001 – Assistant professor, Courses in Immunology, Molecular Genetics and
Physiology
Presently Associate professor
Publication list 1. Vedrana Čikeš, Irina Abaza, Vjekoslav Krželj, Ivana Marinović Terzić,
(last 5 years) Robert Tafra, Silvija Trlaja, Eugenija Marušić, Janoš Terzić. The prevalence
of factor V-Leiden and G6PD 1311-silent mutation in Dalamatian population.
Arch Med Res 2004;35:546-548.
2. Kowanetz K, Terzic J, Dikic I. Dab2 links CIN85 with clathrin-mediated
receptor internalization. FEBS Lett 2003;554:81-87.
3. Marinovic Curin J, Terzić J, Bujas Petković Z, Zekan Lj, Marinović
Terzić I, Marasović Šušnjara I. Lower cortisol and higher ACTH levels in
individuals with autism. J Autism Dev Disord 2003;33:443-448.
4. Skrabic V, Zemunik T, Situm M, Terzic J. Vitamin D receptor
polymorphism and susceptibility to type 1 diabetes in the Dalmatian
population. Diabetes Res Clin Pract 2003;59:31-5.
5. Kalajzic I+, Terzic J+, Rumboldt Z, Mack K, Naprta A, Ledgard F,
Gronowicz G, Clark SH, Rowe DW. Osteoblastic response to the defective
matrix in the osteogenesis imperfecta murine (oim) mouse. Endocrinology
2002;143(5):1594-601. +equal contribution.
6. Mayer WE, O’Huigin C, Tichy H, Terzic J, Saraga-Babic M.
Identification of two Ikaros-like transription factors in lamprey. Scand J
Immunol 2002;55:162-71.
7. Krzelj V, Zlodre S, Terzic J, Mestrovic M, Jaksic J, Pavlov N. Prevalence
of G-6-PD deficiency in the Croatian Adriatic Coast population. Arch Med
151
Res. 2001;32:454-7.
8. Terzic J, Mestrovic J, Dogas Z, Furlan D, Biocic M. Children war
casualties during the 1991-1995 wars in Croatia and Bosnia and Herzegovina.
Croat Med J. 2001;42:156-60.
9. Šitum M, Đogaš Z, Vujinović Z, Erceg M, Terzić J, Marušić J, Mirić D.
Increased incidence of colorectal cancer in the Split-Dalmatia county:
Epidemiological study. Craot Med J 2001;42:181-187.
10. Shintani S, Terzic J, Sato A, Saraga Babic M, O’hUigin C, Tichy H,
Klein J. Do lampreys have lymphocytes? The Spi evidence. Proc Natl Acad
Sci U S A. 2000;97:7417-22.
11. Terzić J, Saraga-Babić M. Expression pattern of PAX3 and PAX6 genes
during human embryogenesis. Int J Dev Biol 1999;43:501-8.
Relevant
references for
teaching this
courses
Last election 11. december 2001. godine
Teaching Molecular genetics
courses
152
Lecturer Iva Tolic-Norrelykke

Institution Max Planck Institute of Molecular Cell Biology and Genetics, D-01307
Dresden, Pfotenhauerstr. 108, Germany
E-mail tolic@mpi-cbg.de
Personal web- http://www.mpi-cbg.de/research/groups/tolic-norrelykke/tolic-
page norrelykke.html
Biography 1992-1996: University of Zagreb, Croatia. Diploma in molecular biology
1996-1999: Institute Rugjer Boskovic and University of Zagreb, Croatia.
Graduate studies in biomathematics. Research assistant in the group of Prof.
Nenad Trinajstic (theoretical chemistry)
1999-2001: Harvard School of Public Health, Boston, MA, USA. PhD work
in the laboratory of Prof. Ning Wang (cellular traction forces and tensegrity
models)
2001-2002: Niels Bohr Institute, Copenhagen, Denmark. Post-doctoral
research in the laboratory of Assoc. Prof. Lene Oddershede (microrheology
of living cells)
2003-2004. LENS - European Laboratory for Non-Linear Spectroscopy,
Firenze, Italy. Post-doctoral research in the laboratory of Prof. Francesco
Pavone (laser microsurgery on the mitotic spindle; lymphocyte locomotion)
2004-present: Group Leader, Max Planck Institute of Molecular Cell Biology
and Genetics, Dresden
Publication list Sacconi, L., I.M. Tolic-Nørrelykke, M. D’Amico, F. Vanzi, M. Olivotto, R.
(last 5 years) Antolini, and F.S. Pavone. (2006) Cell imaging and manipulation by
nonlinear optical microscopy. Cell Biochem. Biophys. 45, in press.
Hansen, P.M., I.M. Tolic-Nørrelykke, H. Flyvbjerg, and K. Berg-Sørensen.
(2006) tweezercalib 2.0: Faster version of MatLab package for precise
calibration of optical tweezers. Comput. Phys. Commun. 174: 518–520.
Galimberti, M., I.M. Tolic-Nørrelykke, R. Favillini, R. Mercatelli, F.
Annunziato, L. Cosmi, F. Liotta, V. Santarlasci, E. Maggi, and F.S. Pavone.
(2006) Hypergravity speeds up the development of T-lymphocyte motility.
Eur. Biophys. J. 35: 393-400.
Tolic-Nørrelykke, I.M., L. Sacconi, C. Stringari, I. Raabe, and F.S. Pavone.
(2005) Nuclear and division-plane positioning revealed by optical
micromanipulation. Curr. Biol. 15: 1212-1216.
Sacconi, L., I.M. Tolic-Nørrelykke, C. Stringari, R. Antolini, and F.S.
Pavone. (2005) Optical micromanipulations inside yeast cells. Appl. Opt. 44:
2001-2007.
Sacconi, L., I.M. Tolic-Nørrelykke, R. Antolini, and F.S. Pavone. (2005)
Combined intracellular three-dimensional imaging and selective nanosurgery
by a nonlinear microscope. J. Biomed. Opt. 10: 014002.
Tolic-Nørrelykke, I.M. and N. Wang. (2005) Traction in smooth muscle cells
varies with cell spreading. J. Biomech. 38: 1405-1412.
Tolic-Nørrelykke, I.M., L. Sacconi, G. Thon, and F.S. Pavone. (2004)
Positioning and elongation of the fission yeast spindle by microtubule-based
pushing. Curr. Biol. 14: 1181–1186.
Tolic-Nørrelykke, I.M., E.-L. Munteanu, G. Thon, L. Oddershede, and K.
Berg-Sørensen. (2004) Anomalous diffusion in living yeast cells. Phys. Rev.
153
Lett. 93: 078102.

Tolic-Nørrelykke, I.M., K. Berg-Sørensen, and H. Flyvbjerg. (2004) MatLab
program for precision calibration of optical tweezers. Comput. Phys.
Commun. 159: 225-240.
Tolic–Nørrelykke, I.M. and N. Wang. (2003) Traction, trypsin, and
tensegrity. Internet Electron. J. Mol. Des. 2: 642–652.
Stamenovic, D., S.M. Mijailovich, I.M. Tolic-Nørrelykke, and N. Wang.
(2003) Experimental tests of the cellular tensegrity hypothesis. Biorheology
40: 221-225.
Butler, J.P., I.M. Tolic-Nørrelykke, B. Fabry, and J.J. Fredberg. (2002)
Traction fields, moments, and strain energy that cells exert on their
surroundings. Am. J. Physiol.-Cell Ph. 282(3): C595-605.
Wang, N., I.M. Tolic-Nørrelykke, J. Chen, S.M. Mijailovich, J.P. Butler, J.J.
Fredberg, and D. Stamenovic. (2002) Cell prestress. I. Stiffness and prestress
are closely associated in adherent contractile cells. Am. J. Physiol.-Cell Ph.
282(3): C606-616.
Stamenovic, D., S.M. Mijailovich, I.M. Tolic-Nørrelykke, J. Chen, and N.
Wang. (2002) Cell prestress. II. Contribution of microtubules. Am. J.
Physiol.-Cell Ph. 282(3): C617-624.
Tolic-Nørrelykke, I.M., J.P. Butler, J. Chen, and N. Wang. (2002) Spatial and
temporal traction response in human airway smooth muscle cells. Am. J.
Physiol- Cell Ph. 283(4): C1254-1266.
Wang, N., K. Naruse, D. Stamenovic, J.J. Fredberg, S.M. Mijailovich, I.M.
Tolic-Nørrelykke, T. Polte, R. Mannix, and D.E. Ingber. (2001) Mechanical
behavior in living cells consistent with the tensegrity model. Proc. Natl.
Acad. Sci. U.S.A. 98(14): 7765-7770.
Relevant Published 24 scientific publications, 20 among them referred in Current
references for Contents, which are cited more than 200 times according to Science Citation
teaching this Index. Participated at more than 25 international conferences with scientific
courses contributions. Held more than 15 invited lectures at international scientific
conferences and institutions. Member of the Croatian Biophysical Society.
Head of the Research group at the Max Planck Institute of Molecular Cell
Biology and Genetics, Dresden. Principal investigator in the research project
"Mechanics of cell division" at the Max Planck Institute of Molecular Cell
Biology and Genetics, Dresden. Supervisor of one master and one doctoral
thesis in preparation at the Technical University Dresden. Past lecturing
activities: Numerical tutorials in Molecular biophysics, Faculty of natural
sciences and mathematics, Zagreb University, lecturer. Active knowledge of
English, Italian, and Danish; passive knowledge of German.
Last election November 2004: Group leader.
Teaching Cell biophysics I
courses
154
Lecturer Sanja Tomić

Institution Institut “Ruđer Bošković”
E-mail sanja.tomic@irb.hr
Personal web- http://www.irb.hr/hr/str/zfk/labs/LKBK/zaposlenici/sanja/
page
Biography Employed at Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, since
01.09.1982.
15.06.1987-15.05.1988. Maternal break
01.03.1992-01.09.1992. Maternal break
Education
1996-1998 - Alexander von Humboldt fellowship - EMBL, Heidelberg,
Germany
Ph.D. in natural sciences - 1993.
M.Sc. in natural sciences – 1986
Diploma thesis (Engineer in physics) – 1982
Qualification publications:
"Conformational Analysis of Glycosidic Conjugates of Indol-3-yl Acetic Acid
and Tryptophol by X-ray Diffraction and Computational Chemistry Methods",
Ph. D thesis, 1993, "Ruđer Bošković" Institute, University of Zagreb
"Determination of Concentration of Elements in Biological Samples Using X-
ray Spectroscopy, and Interpretation of Results", M. Sc. thesis, Faculty of
Natural Sciences and Mathematics (Department of Physics), University of
Zagreb
"Convergence Problem in the Method of Complex Molecular Orbitals”,
Diploma thesis, Faculty of Natural Sciences and Mathematics (Department of
Physics), University of Zagreb
Publication list Tomić S.¸ Dobovičnik V., Šunjić V., Kojić-Prodić B., Enantioselectivity of the
(last 5 years) Pseudomonas cepacia lipase towards 2-methyl-3-(or 4)-arylalkanols: an
approach based on stereoelectronic theory and the molecular modeling,
Croatica Chemica Acta, 74 (2001), 343-357.
Tomić S. and Wade C. R., COMBINE analysis of nuclear receptor-DNA
binding specificity: Comparison of two datasets, Croatica Chemica Acta, 74
(2001), 295-314.
Ramek M. and Tomić S., Ab initio Hatree-Fock investigation of 1-H-
pyrrolo[3,2 b]pyridine-3-yl acetic acid, Spectrochimica Acta A, 57 (2001),
1951-1957.
Luić M , Tomić S., Leščić I., Ljubović E., Šepac D., Šunjić V., Vitale Lj.,
Saenger W., and Kojić-Prodić B., Complex of Burkholderia cepacia lipase
with transition state analogue of 1-phenoxy-2-acetoxybutane, Eur. J.
Biochem. 268 (2001), 3964-3973.
Tomić S., and Kojić-Prodić B., A Quantitative Model for Predicting Enzyme
Enantioselectivity: Application to Burkholderia cepacia lipase and 3-
(Aryloxy)-1,2-propanediol Derivatives, Journal of Molecular Graphics and
Modelling, 21 (2002), 3; 241-252.
Antoloć S., Dolušić E, Kožić E., Kojić-Prodić B. Magnus V., Ramek M.,
Tomić S. Auxin activity and molecular structure of 2-alkylindole-3-acetic
acids, Plant Growth regulation, 39 (2003), 3; 235-252.
155
Bertoša B., Kojić-Prodić B., Ramek M., Piperaki S., Tsantili-Kakoulidou A.,
Wade R., and Tomić S. A new approach to predict the biological activity of
molecules based on similarity of their interaction fields and the logP and logD
values: application to auxins, The Journal of Chemical Information Computer
Sciences 43 (2003), 1532-1541.
Tomić S., Bertoša B., Kojić-Prodić B. and Kolosvary I., Stereoselectivity of
Burkholderia cepacia lipase towards secondary alcohols: molecular modelling
and 3D QSAR approach, Tetrahedron: Asymmetry 15 (2004), 1163-1172.
Ramek M., and Tomić S., Ab initio Hartree-Fock investigation of 2-methyl-3-
indole acetic acid, Croatica Chemica Acta 77 (2004), 371-376.
Wang T., Tomić S., Gabdouline R. R., Wade C. R., How optimal are the
binding energetics of barnase and barstar?, Biophysical J. 87 (2004), 1618-
1630.
Tumir L-M., Piantanida I., Juranović I., Meić Z., Tomić S., Žinić M.,
Recognition of homo-polynucleotides containing adenine by
phenanthridinium bis-uracil conjugate in aqueous media, Chem. Comm. 20
(2005), 2561 – 2563.
Tomić S. and Ramek M., Quantum mechanical study of Burholderia cepacia
lipase enantioselectivity, Journal of Molecular Catalysis B: Enzymatic, 38
(2006), 139-147.
Relevant Tomić S., Gabdouline R. R., Kojić-Prodić B., Wade R. Classification of auxin
references for plant hormones by interaction property similarity indices, J. Comp. Aided Mol.
teaching this Design, 12
courses Tomić S., Nilsson L. and Wade R. C., Nuclear receptor-DNA binding
Specificity: A Combine and Free-Wilson QSAR Ananlysis, J. Med. Chem. 43
(2000), 1780-1792. .
Tomić S.¸ Dobovičnik V., Šunjić V., Kojić-Prodić B., Enantioselectivity of the
Pseudomonas cepacia lipase towards 2-methyl-3-(or 4)-arylalkanols: an
approach based on stereoelectronic theory and the molecular modeling,
Croatica Chemica Acta, 74 (2001), 343-357.
Tomić S., and Kojić-Prodić B., A Quantitative Model for Predicting Enzyme
Enantioselectivity: Application to Burkholderia cepacia lipase and 3-
(Aryloxy)-1,2-propanediol Derivatives, Journal of Molecular Graphics and
Modelling, 21 (2002), 3; 241-252.
Tomić S., Bertoša B., Kojić-Prodić B. and Kolosvary I., Stereoselectivity of
Burkholderia cepacia lipase towards secondary alcohols: molecular modelling
and 3D QSAR approach, Tetrahedron: Asymmetry 15 (2004), 1163-1172.
Wang T., Tomić S., Gabdouline R. R., Wade C. R., How optimal are the
binding energetics of barnase and barstar?, Biophysical J. 87 (2004), 1618-
1630.
Tomić S. and Ramek M., Quantum mechanical study of Burholderia cepacia
lipase enantioselectivity, Journal of Molecular Catalysis B: Enzymatic, 38
(2006), 139-147.
Last election Higher research associate, since 2003.
Teaching ‘Modelling of Biomacromolecules - Structure & Function’, PMF, Zagreb,
courses postgraduate study in Biophysics
‘Molecular modelling', PMF, Split, graduate study,
' Modelling of Biomacromolecules & their complexees’ (sharing with Prof. A.
Graovac), PMF, Split, postgraduate study in Biophysics
156
Lecturer Silvia Tomic

Institution Institut za fiziku
E-mail stomic@ifs.hr
Personal web- http://real-science.ifs.hr
page http://real-science.ifs.hr/pages/silvia.html
Biography 1981 -1986
Orsay, France
Laboratoire de Physique des Solides, Université Paris-Sud, associated to
CNRS
Docteur en Sciences Physiques, these d’etat
1977 - 1981
Zagreb, Croatia
Postgraduate study of Solid State Physics at the Faculty of Science,
Master of Science
1971 - 1977
Zagreb, Croatia
Faculty of Science, University of Zagreb
Graduated Engineer in Physics (Bachelor in Physics)
2002-2006
Institute of Physics
Scientific research
Scientific adviser, permanent
Project leader of 0035015 “Systems of reduced dimensionality: from
synthetic organic to biomaterials”; students (PhD, diploma, internship)
superviser
1999-2002
Scientific research
Scientific adviser
Project leader of 00350103 “Novel electronic states in molecular
conductors” and of 0035015
“Systems of reduced dimensionality: from synthetic organic to
biomaterials”; students (PhD,
master of science, diploma, internship) superviser
1991-1999
Scientific research
Senior scientific associate
Project leader of "Novel anisotropic conductors and superconductors"
and of 00350103
“Novel electronic states in molecular conductors”, students (phD,
master of science, diploma,
internship) superviser
1986-1991
Institute of Physics of the University
Scientific research
157
Scientific associate
Collaborator (until 1989) and leader (since 1989) of the project
"Synthetic conductors and
superconductors"
1981-1986
Scientific research
Research assistent
Research in organic conductors and superconductors leading to doctoral
thesis at
Laboratoire de Physique des Solides, Université Paris-Sud
1977-1981
Scientific research
Research assistent
Research in calorimetric properties of the phase transitions in inorganic quasi-one-dimens
conductors leading to Master of Science thesis at University of Zagreb
Publication list 82. “Low-frequency dielectric spectroscopy of commensurate density waves”
(last 5 years) S.Tomić, M.Pinterić, T.Vuletić, J.U.von Schütz and D.Schweitzer, Synthetic
Metals 120, 695-698 (2001).
83.”Non-ohmic electrical transport in the Peierls-Mott state of deuterated
copper-DCNQI systems”
T.Vuletić, M.Pinterić, M.Lončarić, S.Tomić and J.U.von Schütz, Synthetic
Metals 120, 1001-1002 (2001).
84.”Influence of quantum Hall effect on linear and nonlinear conductivity in
the FISDW states of the organic conductor (TMTSF)2PF6”
T.Vuletić, C.Pasquier, P.Auban-Senzier, S.Tomić, D. Jérome, K.Maki and
K.Bechgaard, Eur. Phys. J B21, 53-60 (2001).
85.”Complex low-frequency dielectric relaxation of the charge-density wave
state in the (2,5(OCH3)2DCNQI)2Li”
M.Pinterić, T.Vuletić, S.Tomić and J.U.von Schütz, Eur. Phys. J B 22, 335-
341 (2001).
86.”Superconductivity and magnetism in organic layered superconductors”
S.Tomić, M.Pinterić, M.Prester, D.Drobac and K.Maki, Physica C 364-365,
247-250 (2001).
87.”Coexistence of superconductivity and spin density wave orderings in the
organic superconductor (TMTSF)2PF6”
T.Vuletić, P.Auban-Senzier, C.Pasquier, S.Tomić, D. Jérome, M.Heritier and
K.Bechgaard, Eur. Phys. J B 25, 319-331 (2002).
88. “Charge-density wave formation in Sr14Cu24O41”
B.Gorshunov, P.Haas, T.Rôôm, M.Dressel, T.Vuletić, B.Korin-Hamzić,
S.Tomić, J.Akimitsu and T.Nagata, Phys.Rev.B 66 060508(R) (2002).
89. “Genuine superconducting ground state in -(BEDT-
TTF)2Cu[N(CN)2]Br: an understanding after decade of controversy”
S.Tomić, M.Pinterić, M.Prester, Đ.Drobac and K.Maki, Synthetic Metals
137/1-3, 1327-1329 (2003).
90. “Influence of internal disorder on the superconducting state in the organic
layered superconductor -(BEDT-TTF)2Cu[N(CN)2]Br”
M.Pinterić, S.Tomić, M.Prester, Đ.Drobac and K.Maki, Phys.Rev.B66 ,
174521 (2002).
158
91.”Modalities od self-oganized charge response in low dimensional

systems”
S.Tomić, T.Vuletić, M.Pinterić and B.Korin-Hamzić, J.de Physique IV
France 12, PR9-211 – PR9-214 (2002).
92. “Coexistence of superconductivity and spin density wave orderings in
Bechgaard and Fabre salts”
C.Pasquier, P.Auban-senzier, T.Vuletić, S.Tomić, M.Héritier and D.Jérome,
J.de Physique 12, PR9-197 – PR9-200 (2002).
93. “Suppression of the charge-density wave state in Sr14Cu24O41 by calcium
doping”
T.Vuletić, B.Korin-Hamzić, S.Tomić, B.Gorshunov, P.Haas, T.Rôôm,
M.Dressel, J.Akimitsu and T.Nagata, Phys.Rev.Lett.90, 257002 (1-4)
(2003).
94. “Variable-range hopping conductivity in the copper-oxygen chains of
La3Sr3Ca8Cu24O41”
T.Vuletić, B.Korin-Hamzić, S.Tomić, B.Gorshunov, P.Haas, M.Dressel,
J.Akimitsu, T.Sasaki and T.Nagata, Phys.Rev.B67, 184521 (1-4) (2003).
95. “Mott-Peierls phase in deuterated copper-DCNQI systems: a
comprehensive study of longitudinal and transverse conductivity and aging
effects”
M.Pinterić, T.Vuletić, M.Lončarić, K.Petukhov, B.Gorshunov, J.U.von
Schütz, S.Tomić and M.Dressel, J.of Physics, Condensed Matter, 15, 7351-
7364 (2003).
96. “Properties of Mott-Peierls insulating phase in deuterated copper-DCNQI
systems”
M.Pinterić, T.Vuletić and S.Tomić, Proceedings of 39th International
Conference on Microelectronics, Devices and Materials MIDEM’03, Ptuj,
Slovenia, 231-236 (2003).
97. «The superconducting order parameter in the organic layered
superconductor -(BEDT-TTF)2Cu[N(CN)2]Br”
M.Pinterić, S.Tomić and K.Maki, J.de Physique IV France 114, 245-249
(2004).
98. «Gossamer superconductivity in -(BEDT-TTF)2X?”
M.Pinterić, S.Tomić and K.Maki, Physica C 408-410, 75-76 (2004).
Special issue: Proceedings of the International Conference on Materials and
Mechanisms of Superconductivity. High Temperature Supercondictors VII,
M2SRIO - Edited by W.Ortiz, E. Mello, E. Granato and Elisa Baggio
Saitovitch
99. “Anisotropic Charge Modulation in the Ladder Planes of Sr14-
xCaxCu24O41”
T.Vuletić, T. Ivek, B.Korin-Hamzić, S.Tomić, B.Gorshunov, P.Haas,
M.Dressel, J.Akimitsu, T. Sasaki and T.Nagata, Phys.Rev.B 71, 012508
(2005).
100.“Anisotropy and field-dependence of the spin-density wave dynamics in
the quasi one-dimensional conductor TMTSF2PF6”
P.Zornoza, K.Petukhov, M.Dressel, T.Vuletić, N.Biškup and S.Tomić, Eur.
Phys. J. B 46, 223–230 (2005).
101. “Phase diagrams of (La,Y,Sr,Ca)12Cu24O41: switching between the
ladders and the chains”,
T.Vuletić, T. Ivek, B.Korin-Hamzić, S.Tomić, B.Gorshunov, P.Haas,
159
M.Dressel, C.Hess, B.Büchner, and J.Akimitsu, J.de Physique IV, 131, 299-
304 (2005).
102. “The spin-ladder and spin-chain system (La,Y,Sr,Ca)12Cu24O41:
electronic phases, charge and spin dynamics”
T.Vuletić, B.Korin-Hamzić, T. Ivek, S.Tomić, B.Gorshunov, M.Dressel, and
J.Akimitsu, Physics Reports 428, 169-258 (2006).
Relevant Conferences/workshops
references for 1. “Komora za mjerenje kompleksne vodljivosti uzoraka biomaterijala u
teaching this tekućoj fazi”
courses T.Vuletić, M.Vukelić, K.Radmanović, S.Tomić,
3. znanstveni sastanak hrvatskih biofizičara, Zagreb, 13 lipnja 2003
(predavanje).
2. “Dielektrična spektroskopija biomaterijala”
S.Tomić, T.Vuletić, S.Dolanski Babić, S.Krča, D.Ivanković, L.Griparić,
D.Zanchi, A.Vernhet, C.Poncet-Legrand,
Četvrti znanstveni sastanak Hrvatskog fizikalnog društva, Zagreb, 13 – 15
studeni 2003 (predavanje)
3. “Dielectric spectroscopy of genomic DNA solutions”
.S. Tomić, T.Vuletić, S.Dolanski Babić, D.Vurnek, S.Krča, D.Ivanković,
L.Griparić
International Conference “From Solid State to Biophysics”, Cavtat, Croatia
(2004), http://dubrovnik2004.epfl.ch/ (predavanje).
4. «Dielectric response of genomic DNA solutions: preparation,
spectrophotometry and dielectric spectroscopy measurements»
S.Dolanski Babić, T.Vuletić, D.Vurnek, S.Tomić, S.Krča, D.Ivanković,
L.Griparić
(2004), http://dubrovnik2004.epfl.ch/ (poster).
T.Vuletić, S.Tomić, S.Dolanski Babić, S.Krča, D.Ivanković, L.Griparić
International Conference on Biological Physics, Gothenburg, Sweden (2004),
http://fy.chalmers.se/icbp2004/. (poster)
6. ”Low-frequency dielectric spectroscopy of aqueous solutions”
T.Vuletić, R.Žaja, M.Vukelić, S.Tomić, I.Sondi
Workshop on Biopolymers: Thermodinamics, Kinetics and Mechanics of
DNA, RNA and Proteins, ICTP, Trieste, Italy (2005). (predavanje i poster).
T.Vuletić, S.Dolanski Babić, S.Tomić, S.Krča, D.Ivanković, L.Griparić
15th IUPAB and 5th EBSA Intrenational Biophysics Congress, August 27th –
September 1st, Montpellier, France (2005) (poster)
8.” Dielektrična relaksacija genomske deoksiribonukleinske kiseline”
S.Tomić, S.Dolanski Babić, T.Vuletić, S.Krča, D.Ivanković, R.Žaja,
R.Podgornik, L.Griparić,
4.znanstveni sastanak hrvatskih biofizičara, Institut R.Bošković, Zagreb (9
rujna 2005) (plenarno predavanje).
9.”Niskofrekventna dielektrična spektroskopija polistirenskog latexa”
T.Vuletić, B. Frka-Petešić, M.Ujević, S.Tomić, I. Sondi,
rujna 2005) (predavanje).
160
10. “Dielectric relaxation of genomic deoxyribonucleic acid”

S.Tomić, S.Dolanski Babić, T. Vuletić, D.Vurnek, S. Krča, D. Ivanković, R.
Žaja, R. Podgornik and L. Griparić
4th Symposium of Science and Technology of Nanomaterials, Ljubljana,
Slovenia (2005) (predavanje).
11. “Dielectric relaxation of nanosized particles dispersed in water”
T. Vuletić, B. Frka-Petešić, S.Tomić, I.Sondi
4th Symposium of Science and Technology of Nanomaterials, Ljubljana,
Slovenia (2005) (predavanje).
12. “Dielectric spectroscopy of DNA aqueous solutions”
S.Tomić, S.Dolanski Babić, T. Vuletić, S. Krča, D. Ivanković, L. Griparić
and R. Podgornik
International conference on synthetic metals ICSM 2006, Dublin, Ireland
(2006) (predavanje).
13. „Screening and fundamental length scales in semidilute Na-DNA
solutions“
S.Tomić, T.Vuletić, S.Dolanski Babić, S.Krča, D.Ivanković, L.Griparić and
R.Podgornik
(2006), http://dubrovnik2006.epfl.ch/ (predavanje).
Lectures/seminars
1. “Dielectric relaxation of DNA aqueous solutions”
S.Tomić, Internal seminar for the group of Prof.F.Livolant and of
Dr.H.Bouchiat: Laboratoire de Physique des Solides, Université Paris-Sud,
Paris (December 2005).
Diploma and internship reports

1.K.Radmanović: «Komora za mjerenje dielektrične konstante uzoraka u
tekućoj fazi», diplomski rad, Prirodoslovno-matematički fakultet Sveučilišta
u Zagrebu (2006); voditelj: S.Tomić.
2.B.Frka-Petešić, „Utilisation de la spectroscopie dielectrique basse
frequence dans l'etude de systems colloidaux“, Rapport de stage u okviru
studija Master M1 de Physique (Magistere de physique) pri Université Denis
Diderot Paris VII; rad izrađen u Laboratoriju za biofiziku, Institut za fiziku,
Zagreb; voditelji: S.Tomić i T.Vuletić.
Publications
1.”Screening and fundamental length scales in semidilute Na-DNA
solutions”
S.Tomić, S.Dolanski Babić, T. Vuletić, S. Krča, D. Ivanković, R. Podgornik
and L. Griparić, Phys. Rev. Lett. 97, 098303 (2006).
2.”Dielectric relaxation of DNA aqueous solutions”
S.Tomić, S.Dolanski Babić, T. Vuletić, S. Krča, D. Ivanković, R. Podgornik
and L. Griparić, cond-mat/0602255
Last election 2004
Teaching
courses
161
Lecturer Dražen Vikić-Topić

Institution Ruđer Bošković Institute (RBI), NMR Center
E-mail dvtopic@mzos.hr
Personal web- www.irb.hr nmr.center
page
Biography Birthdate: May 4, 1954 in Zagreb, Croatia; married, three children
1979 - Ruđer Bošković Institute (RBI) - NMR facility; Lab for molecular
spectroscopy, Zagreb
1996 - Head of NMR Center, RBI
1998.-2002. Senior Research Associate (Assoc. Prof. at RBI)
2000 - Assoc. Professor of Chemistry at University of Zagreb
2002 - Senior Scientist (Full Prof. at RBI)
2002.-2004. Adviser of Director for Organizational Issues
2004.-2005. Chairman of Scientific Council of RBI
2005.- Adviser of Director for Science and Education
Education:
1978, B. Sc. in Inorganic Chemistry, Faculty of Science, Zagreb
1986, M. Sc. in Theoretical and Physical-organic Chemistry, Faculty of
Science, Zagreb
1988, Ph. D. in NMR spectroscopy, Faculty of Science, Zagreb
Research Experience:
1989, postdoc, Institute "B. Kidrič", prof. Jurka Kidrič, Ljubljana;
1990, 3 months Indian Institute of Science, prof. C. L. Khetrapal, Bangalore,
India;
1990, 2 months NIH (National Institutes of Health), prof. E. D. Becker,
Bethesda, MD, USA
1991 - 1993, Visiting Associate with prof. E. D. Becker, NIH, Bethesda,
MD, USA
1993 - 1994, Senior Research Assoc. with prof. S. I. Macura, Mayo Clinic,
Rochester, Minnesota, USA
1999, 3 months, Visiting Professor, with prof. J. Plavec, National Institute of
Chemistry, NMR Centre Ljubljana, Slovenia
Scientific activities:
86 CC/SCI papers, 3 booklets on NMR, 5 professional papers and 4 popular
scientifical papers
Collaborations: Austria, Slovenia, USA, Hungary, Macedonia, Czech Republic.
Twenty three lectures abroad and more than thirty domestic lectures
Teaching activities:
1985 - 1987, Depart. of General and Inorganic Chem., Faculty of Science,
Univ. Zagreb
1996 - Graduate Studies in Analytical Chem., Faculty of Science, University of
Zagreb
1996 - Graduate Studies in Organic Chem., Faculty of Science, University of
Zagreb
1999 - Faculty of Food Science & Biotechnology
2000 - School of Health Studies, University of Zagreb
2002 - Graduate Studies in Environmental Chem., Faculty of Technology,
University of Osijek
162
2004 - Graduate Studies in Medicinal Chem., Medical School, University of

Zagreb
Organizational activities:
1991 Member of Org. Committee of European Congress on Molecular
Spectroscopy, Zagreb
1993 - Member of Org. Committee of Math/Chem/Comp Conferences, IUC,
Dubrovnik
1997 – 2005 Co-director of Math/Chem/Comp Conferences, IUC, Dubrovnik
2000, 2003, 2005 Co-director of Central Europe Chemical Meeting,
Varaždin
1996, 1998 - 2005 Guest-editor of Croatica Chemica Acta; 1999 - Member
of Editorial Board
2003 - Assistant Editor of Croatica Chemica Acta
1997 - 1998 Moderator of Seminars of Croatian Chemical Society (CCS);
2000 - Head of Section for Pure and Applied Spectroscopy of CCS; 2000 -
Member of Advisory Board of Croatian Chemical Soc.
1999, 2000, 2003 Organizer of Dubrovnik International NMR Courses and
Conferences, Dubrovnik
2000 Guest-editor of Journal of Chemical Information & Computer Science-
American Chem. Soc.
2003 International Advisory Board of Summer School on Biomolecular
Structure and Dynamics, Otočec, Slovenia
Research Interests:
Isotope effects in NMR spectroscopy; Long-range deuterium isotope effects
(LRDIE); Experimental and theoretical aspects and calculations of NMR
spectral parameters and their relations to molecular structure and conformation;
NMR of bioorganic and pharmaceutical molecules; NMR of organometallic
molecules (Hg, Pt, Pd); Spectroscopic investigations (NMR, EPR, MS, IR,
UV,VIS) of small peptides, their bioactivity and pharmaceutical utility,
modeling and theoretical calculations.
Publication list 1. Z. Popović, D. Matković-Čalogović, G. Pavlović, Ž. Soldin, G. Giester,
(last 5 years) M. Rajić and D. Vikić-Topić: Mercury(II) Complexes of Heterocyclic
Thiones. Preparation, Thermal Analysis and Spectral Characterisation of the
1:1 Complexes of Mercury(II) Halides and Pseudohalides with 3,4,5,6-
Tetrahydropyrimidine-2-Thione. Crystal Structures of Bis(3,4,5,6-
Tetrahydro pyrimidinium-2-Thiolato-S)Mercury(II) Tetrachloro and
Tetrabromomercurate (II).
Croat. Chem. Acta 74, 359-380 (2001)
2. D. Vikić-Topić and Lj. Pejov: Computational Studies of Chemical Shifts
Using Density Functional Optimized Geometries. II. Isotropic 1H and 13C
Chemical Shifts and Substitutent Effects on 13C Shieldings in 2-
Adamantanone.
Croat. Chem. Acta 74, 277-293 (2001)
3. B. Žinić, I. Krizmanić, D. Vikić-Topić, D. Srzić and M. Žinić:
Synthesis, NMR and MS Study of Novel N-Sulfonylated Purine Derivatives.
Croat. Chem. Acta 74, 399-414 (2001)
4. D. Vikić-Topić and Lj. Pejov: On the Choice of Optimal Methodology for
Calculating of 13C and 1H NMR Isotropic Chemical Shifts in Cage-like
Systems. Case Studies of Adamantane, 2-Adamantanone and 2,4-Methano-
2,4-Dehydroadamantane.
163
J. Chem. Inf. Comput. Sci. 41, 1478-1487 (2001)

5. V. Pilepić, M. Lovrek, D. Vikić-Topić and S. Uršić:
An Unusual Case of Carbon-Nitrogen Bond Formation. Reactivity of C-
Nitroso Group toward Acyl Chlorides.
Tetrahedron Lett. 42, 8519-8522 (2001)
6. V. Smrečki, P. Novak, D. Vikić-Topić, T. Hrenar, and Z. Meić:
Deuterium Isotope Effects in 13C NMR Spectra of trans-N-
Salicylideneaniline Isotopomers.
Croat. Chem. Acta 75, 41-49 (2002)
7. G. Pavlović, J. Matijević Sosa, D. Vikić-Topić and I. Leban:N-(3-
Chlorophenyl)-2-Hydroxy-1-Naphthaldimine at 200 K.
Acta Cryst. E58, 317-320 (2002)
8. B. Nigović, N. Kujundžić, D. Vikić-Topić and K. Sanković:
Complex Formation between Transition Metals and 2-Pyrrolidone-5-
Hydroxamic Acid.
Acta Chim. Slovenica 49, 525-535 (2002)
9. D. Fleš, R. Vuković, A. Erceg Kuzmić, G. Bogdanić, V. Piližota, D.
Karlović, K. Markuš, K. Wolsperger, and D. Vikić-Topić:
Synthesis and Spectroscopic Evidences of N-Arylmaleimides and N-Aryl-
2,3-Dimethylmaleimides.
Croat. Chem. Acta 76, 69-74 (2003)
10. Ž. Marinić, M. Ćurić, D. Vikić-Topić and Lj. Tušek-Božić:Assignment
of 1H and 13C NMR Data for Diethyl 2- and 8-Quinolylmethylphosphonates
and their Palladium(II) Dihalide Complexes.
Magn. Reson. Chem. 41, 969-973 (2003)
11. M. Jadrijević-Mladar Takač, D. Vikić-Topić and T. Govorčinović:
FT-IR and NMR Spectroscopic Studies of Salicylic Acid Derivatives. I.
Gentisamide – a Metabolite of Salicylamide.
Acta Pharm. 54, 163-176 (2004)
12. J. Mastelić, I. Jerković, M.Vinković, Z .Džolić and D.Vikić-Topić:
Synthesis of Selected Naturally Occurring Glucosides of Volatile
Compounds.Their Chromatographic and Spectroscopic Properties.
Croat. Chem. Acta 77, 491-500 (2004)
13. M Jadrijević-Mladar Takač and D. Vikić-Topić:
FT-IR and NMR Spectroscopic Studies of Salicylic Acid Derivates. II.
Comparison of 2-Hydoxy- and 2, 4- and 2, 5-Dihydroxy Derivatives.
Acta Pharm. 54, 177-191 (2004)
14. I. Nemet, D. Vikić-Topić and L. Varga-Defterdarović:
Spectroscopic Studies on Methylglyxal in Water and Dimethylsulfoxide.
Bioorg. Chem. 32, 560-570 (2004)
15. P. Konjevoda, N. Štambuk, D. Tješić-Drinković, D. Tješić-Drinković,
N. Gotovac, D. Ježek, D. Vikić-Topić, A. Votava-Raić: Effects of α-MSH on
Experimentally Induced Mucosal Injury of Rat Gastrointestinal System.
Period. Biol. 106, 355-359 (2004)
16. I. Jerković, J. Mastelić, I. Blažević, M. Šindler-Kulyk and D. Vikić-
Topić: GC-MS Characterization of Acetylated O-Glucofuranosides: Direct
Glucosylation of Volatile Alcohols from Unprotected Glucose.
Croat. Chem. Acta 78, 313-318 (2005)
17. M. V. Diudea, C. L. Nagy, I. Silaghi-Dumitrescu, A. Graovac, D.
Janežić and D. Vikić-Topić: Periodic Cages.
164
J. Chem. Inf. Model. 45, 293-299 (2005)

18. V. Šimunić-Mežnarić, E. Meštrović, V. Tomišić, M. Žgela, D. Vikić-
Topić, H. Čičak, P. Novak, and H. Vančik: Nitrosobenzene Library: A
Model for Studying Selectivity in the Solid State Nitroso-Azoxide
Dimerization.
Croat. Chem. Acta 78, 511-518 (2005)
19. D. Tješić-Drinković, D. Tješić-Drinković, N. Štambuk, P. Konjevoda, A.
Votava-Raić, M. Vinković, and D. Vikić-Topić: Alfa-Melanocyte
Stimulating Hormone Reduces Colonic Damage in Rat Model of
Inflammatory Bowel Disease.
Croat. Chem. Acta 78, 535-539 (2005)
20. M. Randić, D. Vikić-Topić, A. Graovac, N. Lerš, D. Plavšić: Novel
Graphical and Numerical Representations of DNA.
Period. Biol. 107, 437-444 (2005)
21. G. Pavlović, V. Tralić-Kulenović, M. Vinković, D. Vikić-Topić, I.
Matanović and Z. Popović:
Supramolecular Amide and Thioamide Synthons in Hydrogen Bonding
Patterns of N-Aryl-Furamides and N-Aryl-Thiofuramides.
Struct. Chem. (2005) in press
22. V. Pilepić, C. Jakobušić, D. Vikić-Topić and S. Uršić: Evidence for
Proton Transfer from Carbon to Chloride Ion in Solution.
Tetrahedron. Lett. 47, 371-375 (2006)
23. Z. Popović, D. Matković-Čalogović, Ž. Soldin, D. Vikić-Topić, G.
Giester: On the Interaction Between Mercury(II) Salts and 3-
Methylpyrazoline-5-one. The First Crystal Structure of a Cyclic
Organomercuric Compound with a Dimercurated Methylenic Carbon Atom.
Struct. Chem. (2006) in press
24. M. Kveder, Ž. Marinić, A. Krišto, D. Vikić-Topić, G. Pifat: Lipid-Protein
Interactions in Human Plasma LDL Evidenced by Magnetic Resonance.
Chem. Phys. Lipids (2006) in press.
25. Popović, G. Pavlović, M. Vinković, D. Vikić-Topić and M. Rajić
Linarić: Coordination modes of 3-hydroxypicolinic acid (OH-picH):
synthesis and characterization of cadmium(II) complexes. Crystal and
molecular structures of [CdX(OH-pic)(OH-picH)(H2O)]2 X = Cl−, Br−.
Polyhedron (2006) in press
Relevant Horst Friebolin; Basic One- and Two-Dimensional NMR Spectroscopy;
references for Wiley-VCH, Weinheim, 1998
teaching this U. Holzgrabe, I. Wawer, B. Diehl; NMR Spectroscopy in Drug Development
courses and Analysis; Wiley-VCH, Weinheim, 1999
L. Pavić, M. Radoš; Mali medicinski leksikon magnetske
rezonancije;Školska knjiga, Zagreb, 2005.
Last election 2000. associate professor of chem., Faculty of Natural Science; 2002. Senior
Scientist at RBI
courses
165
Lecturer Prof.dr.sc. Mladen Vrtar

Institution Permanent: Clinic of Oncology, University Hospital Center Zagreb
Honorary: Department of Physics, Faculty of Science, Zagreb
E-mail mladen.Vrtar@kbc-zagreb.hr
Personal web-
page
Biography 1963. Finished gymnasium in Zagreb
Finished study of physics, Faculty of science - Diploma engineer of physics
(Dipl.Eng.)
1968. - 1972. Assistant, theoretical physics department “Ruđer Bošković
Institute”.
Master of science, Faculty of science (Mr.sc.)
- till today, radiophysicist, Clinic of oncology and radiotherapy, University
Hospital Centre Zagreb
- 1983. specialisation in radiotherapy physics: Manchester (1974), London
(1982), Paris (1982) Uppsala (1983).
1987. - till today, head of radiophysics unit, Clinic of Oncology and
Radiotherapy UHC Zagreb
1989. - Doctor of physical science (Dr.sc.), Faculty of science Zagreb
1994. - till today, president of medical physics division of CROMBES
(Croatian Medical and Biological Engineering Society) and long term
Croatian delegate at EFOMP
1995. - till today, lecturer at Faculty of science, subjects: “Medical physics"
(diploma study), “Radiological and radiotherapeutical physics" and
“Dosimetry and radiation protection" (postgraduate study)
1999. - Docent at Physics department of Faculty of science
2000. - till today, head of the scientific direction of postgraduated doctor
study of Medical physics
2003. - till today, founder and head of interdisciplinary postgraduated
specialist study of Medical physics
Publication list Only in journals:
(last 5 years) 1.Vrtar M. Total body irradiation dosimetry of a low dose rate 60Co gamma
field. Fizika B Vol 10, No 4, 255-268, 2001.
2. Vrtar M. A dosimetric method of total body irradiation. Cellular &
Molecular Biology Letters 7: No.2, 337-340, 2002
3. Labar B., Bogdanić V., Nemet D., Mrsić M., Serventi-Seiwerth R., Sertić
D., Golubić-Čepulić B., Vrtar M., Šantek F., Batinić D., Mikulić M., Pulanić
D. Allogeneic Stem Cell Transplantation in Treatment of Aggressive
Lymphomas: Case Series. Cro Med J. 43 (5): 565-568, 2002.
4. Faj D., Vrtar M. , Krajina Z. Jurković S., Margaretić D. Model of Total
Skin Electron Treatment Using the "Six-Dual-Field" Technique. Coll.
Antropol. 27: 713-721, 2003.
5. Kovačević N., Vrtar M., Vekić B. A simple calculation method for
106Ru-106Rh eye applicators. Radiotherapy and Oncology 74 : 293-299,
2005.
Relevant More than100 scientific and specialistic publications, conference summaries
references for and other activities: 29 scientific papers (including 14 CC), 27 edited
teaching this presentations on international conferences, 34 on domestic conferences, 8
166
courses scientific and specialistic editions in books, and student papers, 8 specialistic
presentations on domestic and international meetings, 2 heads of scientific
projects (including 1 IAEA project), 3 collaborations in realisation of
scientific projects, 2 times reviewer in scientific project, 5 invited lectures on
international meetings and 9 on domestic. Citation number: 85 SCI
Last election 2005. - Professor of physics at Physics department of the Faculty of science,
Teaching Lecturer at Faculty of science, subjects: “Medical physics" (diploma study),
courses “Radiological and radiotherapeutical physics" and “Dosimetry and radiation
protection" (postgraduate study), head of the scientific direction of
postgraduate doctor study of Medical physics, founder and head of
interdisciplinary postgraduate specialist study of Medical physics
167
Lecturer Tomislav Vuletić

Institution Institut za fiziku, Zagreb
E-mail tvuletic@ifs.hr
Personal web- www.ifs.hr/~tvuletic
page
Biography Education:
2004. Ph.D. in Solid State Physics, Faculty of Science, University of

Zagreb, Croatia
Thesis: ‘Collective Electronic States of the New Quasi-one-
dimensional Materials ’
1998. B.Sc. in Physics, Faculty of Science, University of Zagreb, Croatia
title: ‘Nonlinear conductivity in quasi-one dimensional organic
conductors (TMTSF)2PF6 and (TMTSF)2AsF6 ’
Employment, positions:
2004. - … Assistant researcher (post-doc level) in the group of S. Tomic

at the Institute of Physics, Zagreb
1998.-2004. Ph.D. student in the group of S. Tomic at the Institute of
Physics, Zagreb
1999.-2000. visitor for 10 months in the group of D. Jérome at Laboratoire
de Physique des Solides, Université Paris-Sud, Orsay, France
Publication list 1. T.Vuletić, T. Ivek, B.Korin-Hamzić, S.Tomić, B.Gorshunov, M.Dressel
(last 5 years) and J.Akimitsu, The Spin-Ladder and Spin-Chain System
(La,Y,Sr,Ca)14Cu24O41: Electronic Phases, Charge and Spin Dynamics,
Phys. Rep. 428, 169-258 (2006).
2. P. Zornoza, K. Petukhov, M. Dressel, N. Biskup, T. Vuletić, and S.
Tomić, Anisotropy and field-dependence of the spin-density-wave
dynamics in the quasi one-dimensional conductor (TMTSF)2PF6, Eur.
Phys. J. B 46, 223-230 (2005).
3. T.Vuletić, T. Ivek, B.Korin-Hamzić, S.Tomić, B.Gorshunov, P.Haas,
M.Dressel, J.Akimitsu, T. Sasaki and T.Nagata, Anisotropic Charge
Modulation in the Ladder Planes of Sr14-xCaxCu24O41 by calcium doping,
Phys. Rev. B 71, 012508(4) (2005).
4. M. Pinterić, T. Vuletić, M. Lončarić, K. Petukhov, B. Gorshunov, J. U.
von Schütz, S. Tomić and M. Dressel, Mott–Peierls phase in deuterated
copper-DCNQI systems: a comprehensive study of longitudinal and
transverse conductivity and ageing effects, J. Phys.: Condens. Matter 15,
7351-7364 (2003).
5. T.Vuletić, B.Korin-Hamzić, S.Tomić, B.Gorshunov, P.Haas, T.Rôôm,
M.Dressel, J.Akimitsu and T.Nagata, Suppression of the charge-density
wave state in Sr14Cu24O41 by calcium doping, Phys. Rev. Lett 90,
257002(4) (2003).
6. T. Vuletić, B. Korin-Hamzić, S. Tomić, B. Gorshunov, P. Haas, M.
Dressel, J. Akimitsu, T. Sasaki, T. Nagata, Variable-range hopping
168
conductivity in the copper-oxygen chains of La3Sr3Ca8Cu24O41, Phys.

Rev. B 67, 184521(4) (2003).
7. B. Gorshunov, P. Haas, T. Room, M. Dressel, T. Vuletić, B. Korin-
Hamzić, S. Tomić, J. Akimitsu, T. Nagata, Charge Density Wave
formation in Sr14Cu24O41, Phys. Rev. B 66, 060508R(4) (2002).
8. T. Vuletić, P. Auban-Senzier, C. Pasquier, S. Tomić, D. Jérome, M.
Héritier and K. Bechgaard, Coexistence of Superconductivity and Spin
Density Wave orderings in the organic superconductor (TMTSF)2PF6,
Eur. Phys. J. B 25, 319-331 (2002).
9. M. Pinterić, T. Vuletić, S. Tomić and J.U. von Schütz, Complex low-
frequency dielectric relaxation of the charge-density wave state in the
(2,5(OCH3)2DCNQI)2Li, Eur. Phys. J. B 22, 335 - 341 (2001).
10. T. Vuletić, C. Pasquier, P. Auban-Senzier, S. Tomić, D. Jérome, K. Maki
and K. Bechgaard, Influence of quantum Hall effect on linear and
nonlinear conductivity in the FISDW states of the organic conductor
(TMTSF)2PF6, Eur. Phys. J. B 21, 53 - 60 (2001).
11. T.Vuletić, T. Ivek, B.Korin-Hamzić, S.Tomić, B.Gorshunov, M.Dressel,
C. Hess, B. Büchner and J.Akimitsu, Phase diagrams of
(La,Y,Sr,Ca)14Cu24O41: switching between the ladders and the chains, J.
Phys. IV France 131, 299-305 (2005).
12. C. Pasquier, P. Auban-Senzier, T. Vuletić, S. Tomić, M. Héritier, D.
Jérome, Coexistence of superconductivity and spin density wave
orderings in Bechgaard and Fabre salts, J. Phys. IV France 12, Pr9-197-
200 (2002).
13. S. Tomić, T. Vuletić, M. Pinterić, B.Korin-Hamzić, Modalities of Self-
Organized Charge Response in Low Dimensional Systems, J. Phys. IV
France 12, Pr9-211-214 (2002).
14. T. Vuletić, M. Pinterić, M. Lončarić, S. Tomić and J.U. von Schütz, Non-
ohmic electrical transport in the Peierls-Mott state of deuterated copper-
DCNQI systems, Synth. Metals 120, 1001-1002 (2001).
15. S. Tomić, M. Pinterić, T. Vuletić, J.U. von Schütz and D. Schweitzer,
Low-frequency dielectric spectroscopy of commenurate density waves,
Synth. Metals 120, 695-698 (2001).
Relevant CONFERENCES/WORKSHOPS
references for 1. “Komora za mjerenje kompleksne vodljivosti uzoraka biomaterijala u
teaching this tekućoj fazi” T.Vuletić, M.Vukelić, K.Radmanović, S.Tomić,
courses 3. znanstveni sastanak hrvatskih biofizičara, Zagreb, 13 lipnja 2003 (ORAL).
2. «Dielectric response of genomic DNA solutions: preparation,
spectrophotometry and dielectric spectroscopy measurements» S.Dolanski
Babić, T.Vuletić, D.Vurnek, S.Tomić, S.Krča, D.Ivanković, L.Griparić
(2004), http://dubrovnik2004.epfl.ch/ (POSTER).
3. “Dielectric spectroscopy of genomic DNA solutions” T.Vuletić, S.Tomić,
S.Dolanski Babić, S.Krča, D.Ivanković, L.Griparić
International Conference on Biological Physics, Gothenburg, Sweden (2004),
http://fy.chalmers.se/icbp2004/. (POSTER)
4. ”Low-frequency dielectric spectroscopy of aqueous solutions” T.Vuletić,

R.Žaja, M.Vukelić, S.Tomić, I.Sondi
Workshop on Biopolymers: Thermodinamics, Kinetics and Mechanics of
169
DNA, RNA and Proteins, ICTP, Trieste, Italy (2005). (ORAL & POSTER).
5. “Dielectric spectroscopy of genomic DNA solutions” T.Vuletić,
S.Dolanski Babić, S.Tomić, S.Krča, D.Ivanković, L.Griparić
15th IUPAB and 5th EBSA Intrenational Biophysics Congress, August 27th –
September 1st, Montpellier, France (2005) (POSTER)
6.”Niskofrekventna dielektrična spektroskopija polistirenskog latexa”
T.Vuletić, B. Frka-Petešić, M.Ujević, S.Tomić, I. Sondi,
rujna 2005) (ORAL).
7. “Dielectric relaxation of nanosized particles dispersed in water” ; T.
Vuletić, B. Frka-Petešić, S.Tomić, I.Sondi; 4th Symposium of Science and
Technology of Nanomaterials, Ljubljana, Slovenia (2005) (ORAL).
SEMINARS
T. Vuletić: Fundamental length scales in aqueous Na-DNA, Kyoto University
and Tokyo University, Japan (2006)
B.Frka-Petešić, „Utilisation de la spectroscopie dielectrique basse frequence
dans l'etude de systems colloidaux“, Rapport de stage for Master M1 de
Physique (Magistere de physique) at Université Denis Diderot Paris VII;
work made at Biophysics lab, Institut za fiziku, Zagreb; SUPERVISORS:
S.Tomić and T.Vuletić.
Last election October 21st 2005.

Teaching
courses
170
Lecturer Igor Weber

Institution Ruđer Bošković Institute, Department of molecular biology
E-mail iweber@irb.hr
Personal web- http://www.irb.hr/hr/str/zmg/
page
Biography Diploma in physics, PMF Zagreb, 1988.
MSc in physics, molecular biophysics, PMF Zagreb, 1991.
PhD in physics, Technische Universität München, 1995.
Postdoctoral fellow, Department of cell biology, Max-Planck-Institut für
Biochemie, Martinsried, Germany, 1995.- 1999.
Research assistant, Cell dynamics research group, Max-Planck-Institut für
Biochemie, Martinsried, Germany, 1999.- 2002.
Currenty employed as senior research associate in the Laboratory for electron
microscopy, Department of molecular biology, Ruđer Bošković Institute in
Zagreb, 2002.-
Publication list Weber, I. (2005). Receptor occupancy on ellipsoidal cell in the presence of a
(last 5 years) point source of chemoattractant. J. Chem. Inf. Model. 45, 1647-1651.
Weber, I. (2005). Cryoelectron tomography: implications for actin
cytoskeleton research. Croat. Chem. Acta 78, 325-331.
Htun van der Horst, E., Weber, I. and Ulrich, A. (2005). Tyrosine
phosphorylation of PYK2 mediates Heregulin-induced glioma invasion:
Novel Heregulin/HER3-stimulated signaling pathway in glioma. Int. J.
Cancer 113, 689-698.
Herak Bosnar, M., De Gunzburg, J., Bago, R., Brečević, L., Weber, I. and
Pavelić, J. (2004). Subcellular localization of A an B Nm23/NDPK subunits.
Exp. Cell Res. 298, 275-284.
Barišić, K. and Weber, I. (2004). Dictyostelium discoideum: a model
organism on the eve of the genome sequencing completion. Period. Biol. 106,
103-114.
Gerisch, G., Benjak, A., Köhler, J., Weber, I. and Schneider, N. (2004). GFP-
golvesin constructs to study Golgi tubulation and post-Golgi vesicle
dynamics in phagocytosis. Eur. J. Cell Biol. 83, 297-303.
Weber, I. (2003). Reflection interference contrast microscopy. In:
Biophotonics (G. Marriott and I. Parker, eds.), Methods in Enzymology, Vol.
361, pp. 34-47. Elsevier Science (USA), ISBN 0-12-182264-8.
Schneider, N., Weber, I., Faix, J., Prassler, J., Müller-Taubenberger, A.,
Köhler, J., Burghardt, E., Gerisch, G. and Marriott, G. (2003). A Lim protein
involved in the progression of cytokinesis and regulation of the mitotic
spindle. Cell Motil. Cytoskeleton 56, 130-139.
Weber, I. (2003). Confocal microscopy of the plant cytoskeleton. Period.
Biol. 105, 237-249.
Weber, I. (2003). Dynamic organization of the actin cytoskeleton in
Dictyostelium. Recent Res. Devel. Mol. Cell. Biol. 4, 273-295.
Weber, I., Niewöhner, J., Du, A., Röhrig, U. and Gerisch, G. (2002). A talin
fragment as an actin trap visualizing actin flow in chemotaxis, endocytosis,
and cytokinesis. Cell Motil. Cytoskeleton 53, 136-149.
Medalia, O., Weber, I., Frangakis, A.S., Nicastro, D., Gerisch, G. and
171
Baumeister, W. (2002). Macromolecular architecture in eukaryotic cells

visualized by cryoelectron tomography. Science 298, 1209-1213.
Bretschneider, T., Jonkman, J., Köhler, J., Medalia, O., Barišić, K., Weber, I.,
Stelzer, E.H.K., Baumeister, W. and Gerisch, G. (2002). Dynamic
organization of the actin system in the motile cells of Dictyostelium. J.
Muscle Res. Cell Motil. 23, 639-649.
Müller-Taubenberger, A., Bretschneider, T., Faix, J., Konzok, A., Simmeth,
E. and Weber, I. (2002). Differential localization of the Dictyostelium PAKa
kinase during cytokinesis and cell migration. J. Muscle Res. Cell Motil. 23,
751-763.
Albrecht, R. and Weber, I. (2002). Interference reflection microscopy. In:
Encyclopedia of Life Sciences, Vol. 10, pp. 369-371 (www.els.net). Nature
Publishing Group, London, ISBN 0-333-72621-9.
Weber, I. and Gerisch, G. (2002). Cortexillins. In: Wiley Encyclopedia of
Molecular Medicine, Vol. 1, pp. 914-916. John Wiley & Sons, Inc., New
York, ISBN 0-471-37494-6.
Tuxworth, R. I., Weber, I., Wessels, D., Addicks, G. C., Soll, D. R., Gerisch,
G. and Titus, M. A. (2001). A role for myosin VII in dynamic cell adhesion.
Curr. Biol. 11, 318-329.
Faix, J., Weber, I., Köhler, J., Mintert, U., Lottspeich, F. and Marriott, G.
(2001). The recruitment of cortexillins to the cleavage furrow is controlled by
IQGAP-related proteins DGAP1/GAPA and links Rac1-signaling to
cytokinesis. EMBO J. 20, 3705-3715.
Insall, R., Müller-Taubenberger, A., Machesky, L., Köhler, J., Simmeth, E.,
Atkinson, S. J., Weber, I. and Gerisch, G. (2001). Dynamics of the
Dictyostelium Arp2/3 complex in endocytosis, cytokinesis and chemotaxis.
Cell Motil. Cytoskeleton 50, 115-128.
Weber, I. (2001). On the mechanism of cleavage furrow ingression in
Dictyostelium. Cell Struct. Funct. 26, 595-602.
Relevant Published 35 scientific papers in internationally peer-reviewed publications,
references for among them 28 papers referred to in the Current Contents database. More
teaching this than 660 citations in international scientific literature. Principal investigator
courses in three research projects, including one bilateral project with Germany.
Supervised three diploma theses, currently supervising one diploma thesis
and one PhD thesis. Lecturing undergraduate and postgraduate courses in
physics and biology at Universities in Zagreb and Osijek. Over 20
contributions to international scientific conferences. Over 15 invited lectures
at international and national scientific meetings, societies and institutions.
Active knowledge of English and German languages.
Last election March 20th 2005, senior research associate
Teaching Cell biophysics I
courses Experimental methods of physics in biophysics II
172
Lecturer Bojan Zagrovic

Institution Swiss Federal Institute of Technology Zurich
E-mail zagrovic@igc.phys.chem.ethz.ch
Biography 01 April 2004
Stanford, CA, USA
Stanford University
PhD in Biophysics
Publication list 1. Zagrovic B, Sorin EJ, Pande, VS (2001) “ -hairpin folding simulations in
(last 5 years) atomistic detail using an implicit solvent model”, Journal of Molecular
Biology, 313(1): 151-169.
2. Zagrovic B, Snow CD, Khaliq S, Shirts MR, Pande VS (2002)“Simulation
of folding of a small alpha-helical protein using worldwide distributed
computation”, Journal of Molecular Biology, 323(5): 927-937.
3. Zagrovic B, Snow CD, Khaliq S, Shirts MR, Pande VS (2002) “Native-
like mean structure in the unfolded ensemble of small proteins”,
Journal of Molecular Biology, 323(1): 153-164.
4. Snow CD, Zagrovic B, Pande VS (2002) “Trp Cage: Folding kinetics and
unfolded state topology”, Journal of the American Chemical Society,
24(49): 14548-14549.
5. Pande VS, Baker I, Chapman J, Elmer S, Khaliq S, Larson SM, Rhee YM,
Shirts MR, Snow CD, Sorin EJ, Zagrovic B. (2002) "Atomistic protein
folding simulations on the hundreds of microsecond timescale using
worldwide distributed computing." Biopolymers 68 (1), 91-109.
6. Zagrovic B & Pande VS (2003) “Solvent Viscosity Dependence of the
Folding Rate of a Small Protein: Distributed Computing Study”, Journal of
Computational Chemistry 24, 1432-1436.
7. Zagrovic B & Pande VS (2003) “How Can Proteins be Unfolded and yet
Have Native-like Properties: Structural Correspondence between the Alpha
Helix and the Random-flight Chain”, Nature Structural Biology 10 (11), 955-
961.
8. Lenz P, Zagrovic B, Shapiro J & Pande VS (2004) “Folding Probabilities:
A Novel Approach to Folding Transitions and the Two-dimensional Ising
Model”, Journal of Chemical Physics 120 (14) 6769-6778.
9. Kohn J, Millett IS, Jacob J, Zagrovic B, Dillon TM, Cingel N, Dothager
RS, Seifert S, Thiyagarajan P, Sosnick TR, Hasan ZM, Pande VS, Ruczinski
I, Doniach S & Plaxco KW (2004) “Do the dimensions of chemically
unfolded proteins differ significantly from the expectations of a random-coil
model?”, PNAS 101 (34), 12491-6.
10. Zagrovic B & Pande VS (2004) “How does averaging affect protein
structure comparison on the ensemble level?”, Biophysical Journal 87,
2240-6.
11. Zagrovic B, Lipfert J, Sorin EJ, Millet IS, van Gunsteren WF, Doniach S
& Pande, VS (2005) “Unusual compactness of a polyproline type II
structure”, Proceedings of the National Academy of Sciences USA,
102 (33), 11698-11703.
12. Zagrovic B, Jayachandran G, Millet IS, Doniach S & Pande, VS (2005)
“How large is an -helix? Studies of the radii of gyration of helical
173
peptides by small-angle X-ray scattering and molecular dynamics”,

Journal of Molecular Biology, 353 (2), 232-241.
13. Zagrovic B & van Gunsteren WF (2006) “Comparing atomistic
simulation data with the NMR experiment: how much can NOEs actually tell
us?”, Proteins, 63 (1), 210-218.
14. Zagrovic B & Pande VS (2006) “Simulated unfolded-state ensemble and
the experimental NMR structures of villin headpiece yield similar wide-angle
solution X-ray scattering profiles”, Journal of the American Chemical
Society, 128 (36), 11742-11743.
15. Zagrovic B & van Gunsteren WF (2007) “Computational analysis of the
mechanism and thermodynamics of inhibition of phosphodiesterase 5A by
synthetic ligands”, Journal of Chemical Theory and Computation, 3, 301-311.
Relevant More than 20 CC papers with about 600 citations. Experience in theoretical
references for and experimental research about protein folding.
teaching this
courses
Last election 01. june 2004 status of postdoctoral fellow in the group of Wilfred F. van
Gunsteren.
Teaching
courses
174
Lecturer Neven Žarković, MD, PhD, senior scientist

Institution «Ruđer Bošković» Institute
E-mail zarkovic@irb.hr
Personal web- http://www.irb.hr/en/str/zmm/LABS/LabOS/Neven
page
Biography Born in Zagreb on August 25th 1960. Graduated (MD) at the Medical Faculty
in Zagreb in 1984, followed by M.Sc. in biology at the Faculty of Science in
Zagreb in 1986, and PhD at the University in Zagreb in 1989.
Since 1985 employed at the «Ruđer Bošković» Institute. Between 1992 and
2004 postdoctoral fellowship at the Institute of Biochemistry in Graz,
afterwards permanent guest scientist at the same Institute. During 2003 and
2004 acted as Associated Director for Science at «Ruđer Bošković» Institute,
afterwards, until summer 2005 as counselor for international collaborations.
Head of Laboratory for Oxidative Stress.
Publication 1. Fiorella Biasi, Luciana Tessitore, Danialla Zanetti, J.C. Citrin, B. Zingaro,
list (last 5 Ellena Chiarpotto, Neven Žarković, G. Serviddio and Giuseppe Poli (2002)
years) Associated changes of lipid peroxidation and TGF 1 levels in human
cancer during tumor progression. Gut, 50: 361-367
2. Thomas Semlitsch, Hilmar M. Tillian, Neven Žarković, Suzana Borović,
Martin Purtscher, Otmar Hohenwarter and Rudolf J. Schaur (2002)
Differential Influence of the Lipid Peroxidation Product 4-Hydroxynonenal
on the Growth of Human Lymphatic Leukaemia Cells and Human
Peripheral Blood Lymphocytes. Anticancer Res, 22:1689-1697
3. Neven Žarković , Suzana Borović , Igor Stipančić, Marija Poljak Blaži, Iva
Lončarić, Ana Čipak, Gordana Jurić, Tea Vuković, Willibald Wonisch ,
Georg Waeg i Kamelija Žarković. (2002) Fiziološke i patološke značajke
lipidne peroksidacije U: Oksidativni stres i djelotvornost antioksidansa.
(Bradamante V., Lacković Z., ur.), Medicinska naklada, Zagreb, pp. 10-29
4. Neven Žarković, Kamelija Žarković, Marijeta Kralj, Suzana Borović, Senka
Sabolović, Marija Poljak Blaži, Ana Čipak and Krešimir Pavelić (2003)
Anticancer and antioxidative effects of micronized zeolite clinoptilolite,
Anticancer Res, 23:1589-1596
5. Mircea Cazacu, Traian Oniu, Cornel Lungoci, Anca Mihailov, Ana Cipak,
Rainer Klinger, Thomas Weiss and Neven Zarkovic (2003) The influence of
Isorel on the advanced colorectal cancer. Cancer Bioth & Radipharm,
18:27-34
6. P. Sikiric, S. Seiwerth, S. Mise, M. Staresinic, D. Mikus, G. Aralica, D.
Perovic, M. Gjurasin, A. Boban-Blagaic, T. Ziger, L. Batelja, N. Zarkovic,
S. Borovic, S. Zutekovic, D. Rabic, S. Babic, S. Suknaic, N. Kolombo, D.
Blagojevic, N. Kokic, I. Fattorini, M. Kopljar, A. Marovic, A. Tonkic, G.
Buljat, T. Anic, M. Petek, R. Rucman (2003) Corticosteroids-impairment
healing and gastric pentadecapeptide BPC 157 creams in burned mice.
Burns, 29: 323-334
7. Neven Žarković (2003) 4-Hydroxynonenal as a bioactive marker of
pathopysiological processes. Mol Asp Med, 24:281-291
8. Staresinic M, Sebecic B, Patrlj L, Jadrijevic S, Suknaic S, Perovic D,
175
Aralica G, Zarkovic N, Borovic S, Srdjak M, Hajdarevic K, Kopljar M,

Batelja L, Boban-Blagaic A, Turcic I, Anic T, Seiwerth S, Sikiric P (2003)
Gastric pentadecapeptide BPC 157 accelerates healing of transected rat
Achilles tendon and in vitro stimulates tendocytes growth. J Orthop Res 21:
976-983
9. Renate Wildburger, Neven Zarkovic, Suzana Borovic, Kamelija Zarkovic,
Walter Petek, Andreas Meinitzer (2003) Die hypertrophe Kallusbildung bei
Patienten mit schwerem Schädel-Hirn-Trauma. In: Höhepunkte, Fehler und
Komplikationen in der Unfallchirurgie. (Rudolf Szyszkowitz, ed.), Leykam
Nfg. & Co. KG, Graz, 529-553
10. Greta Pifat Mrzljak, Neven Žarković (Eds.) (2003): Towards the European
University Networks: Trends and Challenges in Higher Education.
Hrvatsko-austrijsko Društvo, Zagreb
11. Branka Mazul-Sunko, Neven Žarković, Nada Vrkić, Nataša Antoljak,
Miroslav Bekavac Bešin, Vjeran Nikolić Heitzler, Mladen Širanović,
Ankica Krizmanić-Dekanić, Rainer Klinger (2004) Proatrial natriuretic
peptide (1-98), but not cystatin C, is predictive for occurrence of acute renal
insufficiency in critically ill septic patients. Nephron Clinical Practice.
97(3):103-107
12. Neven Žarković, Darija Mahović , Marija Poljak-Blaži, Iva Lončarić, Franz
Tatzber, Kamelija Žarković, Damir Petravić, Willibald Wonisch, Niko
Zurak (2004) Changes of plasma peroxides in patients with stroke: Indices
of differential systemic response to oxidative stress in patients with
ischemic stroke or with intracerebral hemorrhage. Neurologia Croatica,
53:79-86
13. Živković Morana, Žarković Kamelija, Škrinjar Ljubomir, Georg Waeg,
Poljak-Blaži Marija, Borović Suzana, Schaur Rudolf Jörg, Žarković Neven
(2005) A new method for detection of HNE-histidine conjugates in rat
inflammatory cells. Croatica Chemica Acta, 78: 91-98
14. Igor Stipančić, Neven Zarković, Dražen Servis, Senka Sabolović, Franz
Tatzber, Željko Busić (2005) Oxidative stress markers after laparoscopic
and open cholecystectomy, Journal of Laparoendoscopic & Advanced
Surgical Techniques,Part A, 15: 347-352
15. Neven Žarković (2005) Mechanismen der Tumorentstehung. In: Oxidativer
Stress und Pharmaka (Siems Werner, Krämer Klaus, Grune Tilman, Eds.).
Govi-Verlag, Eschborn, 145-158
16. Neven Žarković (2005) Antioxidatien in der Prävention und Chemotherapie
von Tumoren. In: Oxidativer Stress und Pharmaka (Siems Werner, Krämer
Klaus, Grune Tilman, Eds.). Govi-Verlag, Eschborn, 159-174
17. Mircea Bogdan Enesel, Iurie Acalovschi, Vasile Grosu, Adriana Sbarcea,
Catrinel Rusu, Adrian Dobre, Thomas Weiss and Neven Zarkovic (2005)
Perioperative Application of the Viscum Album Extract Isorel in Digestive
Cancer Patients. Anticancer Research, 25: 4583-4590
18. Kamelija Zarkovic, Gordana Juric, Georg Waeg, Danijela Kolenc and
Neven Zarkovic (2005) Immunohistochemical appearance of HNE-protein
conjugates in human astrocytomas. Biofactors, 24: 33-40
19. Suzana Borovic Sunjic, Ana Cipak, Filip Rabuzin, Renate Wildburger and
Neven Zarkovic (2005) The Influence of 4-Hydroxy-2-nonenal on
Proliferation, Differentiation and Apoptosis of Human Osteosarcoma Cells.
Biofactors, 24: 141-148
176
20. Ana Cipak, Suzana Borovic, Mira Scukanec-Spoljar, Iva Kirac, Neven
Zarkovic (2005) Possible Involvement of 4-Hydroxynonenal in Splenocyte
Regulated Liver Regeneration. Biofactors, 24: 217-226
21. Morana Zivkovic, Marija Poljak-Blazi, Gerd Egger, Suzana Borovic Sunjic,
Rudolf Jörg Schaur, Neven Zarkovic (2005) Oxidative Burst and Anticancer
Activities of Rat Neutrophils. Biofactors,24: 305-312
22. Ana Cipak, Meinhard Hasslacher, Oksana Tehlivets, Emma J Collinson,
Morana Zivkovic, Tanja Matijevic, Willibald Wonisch, Georg Waeg, Ian
W. Dawes, Neven Zarkovic, and Sepp D Kohlwein (2006) Saccharomyces
cerevisiae strain expressing a plant fatty acid desaturase produces
polyunsaturated fatty acids and is susceptible to oxidative stress induced by
lipid peroxidation. Free Radical Biology and Medicine, 40:897-906
23. Suzana Borovic, Gunars Tirzitis, Dace Tirzite, Ana Cipak, Gholam A.
Khoschsorur, Georg Waeg, Franz Tatzber, Mira Scukanec-Spoljar, Neven
Zarkovic (2006) Bioactive 1,4-dihydroisonicotinic acid derivatives prevent
oxidative damage of liver cells. European Journal of Pharmacology, 537:
12-19
24. Maja Prutki, Marija Poljak-Blazi, Marko Jakopovic, Davor Tomas, Igor
Stipancic and Neven Zarkovic (2006) Altered Iron Metabolism, Transferrin
Receptor 1 and Ferritin in Patients with Colon Cancer. Cancer Letters,238:
188-196
25. Kamelija Zarkovic, Koji Uchida, Danijela Kolenc, Ljiljana Hlupic, Neven
Zarkovic (2006) Tissue distribution of lipid peroxidation product acrolein in
human colon carcinogenesis. Free Radical Resarch., 40: 543-552
26. Fiorella Biasi, Barbara Vizio, Cinzia Mascia, Ezio Gaia, Neven Zarkovic,
Elena Chiarpotto, Gabriella Leonarduzzi, Giuseppe Poli (2006) JNK up-
regulation as a key event in the pro-apoptotic interaction between TGF-ß1
and 4-hydroxynonenal in colon mucosa. Free Radical Biology and
Medicine, 40: 443-454
27. Suzana Borovic, Filip Rabuzin, Georg Waeg, Neven Zarkovic (2006)
Enzyme-linked immunosorbent assay for 4-hydroxynonenal-histidine
conjugates. Free Radical Research,40:809-820
28. Vjeran Nikolic-Heitzler, Filip Rabuzin, Franz Tatzber, Nada Vrkic, Nikola
Bulj, Suzana Borovic, Willibald Wonisch, Branka Mazul Sunko, Neven
Zarkovic (2006) Persistent oxidative stress after myocardial infarction
treated by percutaneous coronary intervention. Tohoku Journal of
Experimental Medicine, 210: 247-255
29. Maja Prutki, Marija Poljak-Blazi, Branka Mihaljevic, Visnja Orescanin,
Neven Zarkovic (2006) Uptake of anti-anemic substance ferric-sorbitol-
citrate by normal and malignant cells and its effects on expression of
transferrin receptor 1 and ferritin. Cancer Bioth & Radipharm,21:636-644
30. Morana Zivkovic, Marija Poljak-Blazi, Kamelija Zarkovic, Danijela
Mihaljevic, Rudolf Joerg Schaur and Neven Zarkovic (2007) Oxidative
burst of neutrophils against melanoma B16-F10. Cancer Letters, 246:100-
108
31. Suzana Borovic, Ana Cipak, Andreas Meinitzer, Zvonko Kejla, Darko
Perovic, Georg Waeg, Neven Zarkovic (2007) Differential effect of 4-
hydroxynonenal on normal and malignant mesenchimal cells. Redox Report,
207:50-54
32. Aleksandar Gopcevic, Branka Mazul-Sunko, Jasminka Marout, Ante
177
Sekulic, Natasa Antoljak, Mladen Siranovic, Zeljko Ivanec, Marko

Margaritoni, Miroslav Bekavac-Beslin, Neven Zarkovic (2007) Plasma
interleukin-8 as a potential predictor of mortality in
adult patients with severe traumatic brain injury. Tohoku Journal of
Experimental Medicine, 211: 387-393
Relevant Publications are listed among references and the course literature.
references for The course convener also acts as study director for the interdisciplinary PhD
teaching this studies “Molecular Biosciences” and convener of five biomedical courses on
courses oxidative stress and lipid peroxidation on PhD studies “Biomedicine and Public
Health”, “Molecular Biosciences” and “Biology of Neoplasm”.
He is also member of the board of the International 4-Hxydroxynonenal Club
(SFRR), and the Chairman of the COST B35 Action «Lipid Peroxidation
Associated Disorders».
He acts as person in charge for collaboration of the «Ruđer Bošković» Institute
and Universities in Split, Zadar, Dubrovnik and Osijek.
Last election December 15th 2002
Teaching Biophysical and Biomedical Aspects of Oxidative Stress
courses
178
Lecturer Doc. dr. sc. Paško Županović

Institution University of Split, Faculty of natural sciences, mathematics and kinesiology
E-mail pasko@pmfst.hr
Personal web-
page
Biography 1977
Split
University of Split, Faculty of Faculty of Electrical Engineering,
Mechanical Engineering and Naval Architecture
Electrical engineer
1985
Zagreb
PMF Zagreb
Master of science in physics
1998
Zagreb
PMF Zagreb
Ph D in physics
1977-1980
University of Split, Faculty of technology
Assistant
1981-2005
University of Split, Faculty of natural sciences and kinesiology
Assistant professor
Head of department
Publication list R.C. Dewar, D. Juretić and P. Županović: “The functional design of the
(last 5 years) rotary enzyme ETP synthase is consistant with the maximum entropy
production principle”. Chem. Phys. Lett., 430 (2006), 177-182.
P. Županović. S. Botrić, D Juretić: Relaxation processes, MaxEnt formalism
and Einstein’s formula for the probability of fluctuations. Croatica Chemica
Acta. 79 (2006), 335-338.
Ž. Bonačić-Lošić, P. Županović and A. Bjeliš: "Photoemission properties of
quasi one-dimensional conductors", J. Phys. Condens. Matter 18 (2006); pp.
3655-3670.
S. Botrić, P. Županović i D. Juretić: “Is the stationary current distribution in a
linear planar electric network determined by the principle of maximum
D. Juretić i P. Županović: “The free-energy transduction and entropy
production in initial photosynthetic reactions” in Non-equilibrium
Thermodynamics and the Production of Entropy, Eds. A. Kleidon i R.D.
Lorenz, pp. 161-171, Springer,-Verlag, Berlin 2005.
Onsager’s principle of the least dissipation of energy and maximum entropy
production principle”, FIZIKA A (Zagreb) 14, (2005); pp.89-96.
P. Županović and D. Juretić: The Chemical Cycle kinetics Close to the
179
Equiliobrium State and Electrical Circuit Analogy, CCA, 77, 561 (2004)
P. Županović D. Juretić and S. Botrić: Kirchhoff's loop law and the
maximum entropy production principle, Phys. Rev. E, 70, 056108 (2004)
Ž. Agić, P. Županović, and A. Bjeliš: Effects of transverse electro dispersion
on photo-emission spectra of quasi-one-dimensional systems, J. Phys. IV,
114, 95 (2004)
D. Juretić and P. Županović: Photisynthetic models with maximum entropy
production in irreversible charge transfer steps, Comp. Biol. And Chem., 27,
541, (2003)
Ž. Agić, P. Županović, and A. Bjeliš: Photo-emission propeerties of
quasi.one-imensional conductors, J. Phys. IV,12,Pr9-53 (2002)
P. Županović, A. Bjeliš and Ž. Agić: Discrete approach to incoherent
excitations in conductors, Fizika A (Zagreb), 10, 203 (2001)
Relevant 1. D. Juretić and P. Županović: The Freee-energy Transduction and Entropy
references for production in Initial Photosynthetic Reactions, poglavlje u knjizi
teaching this Non.equilibrium Thermodynamics and the Production of Entropy, eds. Axel
courses Kleidon and Ralph D. Lorenz, 2004, Springer, Berlin.
2. M. Grbac,T. Dadić i P. Županović Demonstracija prijelaza potencijalne
gravitacijske energije u kinetičku pomoću mjerača deformacije, VII simpozij
o nastavi fizike, Šibenik 2005.
3. M. Grbac,T. Dadić i P. Županović Princip rada elektroničke vage, VII
simpozij o nastavi fizike, Šibenik 2005.
4. M. Grbac,T. Dadić i P. Županović Mjerači deformacije (tenzometri,
rastezne trakice) VII simpozij o nastavi fizike, Šibenik 2005.
Last election 23. january 2003.
Teaching
courses
180
Field work and professional practice (research bases and

practice sites)
The proposed study will take place mostly at the Faculty of Natural Sciences, Mathematics and
Kinesiology, University of Split, and at the Ruđer Bošković Institute, Zagreb, but some courses will be
held at the MedILS Institute in Split and at the Medical School, University of Split. Research base will
be partially located in domestic and foreign laboratories where agreement has been reached about
collaboration with our study programmee. As a rule, student selects adviser who is already the lecturer
in our study programme. The CV of all lecturers has been enclosed above.
During the first three year period, before moving to University Campus, theoretical modelling
will be more important part of proposed study programme in Split, although some experimental
research topics are also possible (mainly by collaboration with foreign laboratories). Therefore, already
existing computer equipment and replacements with more up-to-date hardware should be sufficient for
this initial study period. However, students will have obligation (three required courses) and possibility
(several elective courses) to get familiar with basic biophysical and biomedical techniques at the Ruđer
Bošković Institute in Zagreb. Well equipped biophysical laboratories have been established there some
time ago. Learning experimental methods used by biophysicists will be excellent preparation for our
students for anticipated shorter visits to foreign biophysical laboratories, which are as a rule much more
oriented toward experimental than theoretical research. Our students should learn to combine
experimental and theoretical work effortlessly.
Optimal number of students

Optimal number of students is around 10 to 15 students in the first study year.
Cost assessment (per student)

This study programme will be supported by the Croatian Ministry of Science, Technology and
Sport, which supports other interdisciplinary and collaborative PhD programmes. We expect tuition
cost per student around 12000 kunas yearly (1650 euros). The tuition will be waved for scientific
assistants accepted by the study programme, who are employed by our two institutions. In the case of
students exibiting scientific excellence, but unable to cover the tuition cost, it is anticipated that Study
Committee can use several stipendies collected for this study to cover their tuition.
Financial aspects
The study will not start before we are sure that necessary financial resources have been ensured
for smooth study process and for planned mobility of students and lecturers.
Students already employed as young researchers or assistants will retain that source of financing
from Croatian Ministry of Science. We also aim to ensure at least five stipends each year for our
students. The research administrators and commercial firms will be encouraged to offer stipends for
our students irrespective of their nationality or citizenship. We plan to enter into competition for
relevant funds inside Croatia supported by our Ministry of Science and National Foundation for
Science, Higher Education and Technological Development, and for relevant Europeans funds from
181
European Science Foundation and EMBO. We shall point out in all these applications that supporting
the development of high quality doctoral programmes in life sciences in the regional university center
such as Split is in complete agreement with often expressed desire of Croatian authorities to strengthen
science in regional centers, to stimulate interdisciplinarity and to promote broad collaboration among
different scientific institutions inside Croatia and the collaboration of scientists from Croatia and from
abroad. We also plan to participate in European projects supporting scientific developments and higher
education developments in biophysics, structural bioinformatics and biomedicine. The resources gained
from such projects can be partially used to strengthen the Ph.D. programme in biophysics.
Study Chair will once per year prepare the financial report for the Study Committee. Students
are expected to apply on time for financial support needed to ensure their mobility. This is necessary
because anticipated tuition will not be enough to support students visiting and doing research for shorter
time periods in other institutions and outside Croatia.
It will be also necessary to reach agreement with respect to division of expenses and obligations
among all institutions interested in supporting this doctoral programme. Since most of lecturers are
from Split and Zagreb it will be possible for them to execute their courses at the institution were they
are employed. Students will be helped to move between Split and Zagreb as their study programme
requires. Most of guest lecturers, foreign students and students from other universities will be
accommodated at the new student hostel in Spinut, only the 10 minutes walk from our Faculty of
Natural Sciences in Split. The University of Split has 10 apartments in that student hostel that can be
used for guest scientists or guest graduate students. Since MedILS in Split has also decided to
participate in the execution of this doctoral study, we expect that agreement will be reached with
MedILS, as well, to accommodate our guest scientists and graduate students for shorter time periods.
All these agreements and actions should lower the expenses of the proposed study programme. In
addition, we shall certainly apply for sponsorship from commercial firms and pharmaceutical,
biomedical and biotechnological companies. We expect regional interest for this study programme not
only from Croatian universities, but also from the nearby universities of Mostar and Sarajevo in the
Bosnia and Herzegovina. University of Split has long and successful collaboration with University of
Mostar. Other regional universities from neighboring countries will also have interest in this Ph.D.
programme which is unique in the central and Eastern Europe.
After Ph.D. thesis defense and successful study completion, the Study Committee, lecturers and
advisers, will take care to help find one or two year postdoctoral specialization for these students,
mainly in foreign laboratories interested in collaboration with our study programme. At the same time,
the return to Croatia would be planned for these students, at places of employment where they can use
their broad interdisciplinary and research competence.
182
Quality assessment methods

• As for any other doctoral programme the quality of our programme will be judged by national
committee of experts. We shall suggest some well known foreign biophysicists as possible
referees too. All our lecturers and mentors have anticipated quality assessment methods for their
courses (see above). The whole study programme will be assessed by students when close to
finishing it.
• One important goal of this programme is to achieve as great scientific and educational
flexibility as possible in our students and lecturers with respect to transfer among different
natural sciences bordering with physics and biology. That is why we expect that our students
would easily fulfill new needs of employers in the field of medical physics, bio-
nanotechnology, biomedicine, system biology, bioinformatics and ecology, and not only
biophysics. We shall ask for regular reports about performance of our past and present students
and postdoctorands from laboratory heads and employers. At the same time we shall help our
postdoctorands to find jobs in which their interdisciplinary competence can flower. Reports of
mentors, laboratory heads and employers will be used to remove deficiencies in our study
programme.
• We shall use different institutional mechanisms for improving the quality of the doctoral
programme (self-evaluation, questionnaires, performance parameters, research into quality of
programme execution).
• The quality of Ph.D. programme depends on the number and quality of research projects and
programmes offered by organizers, course leaders and institutions collaborating in the
programme. Our goal will be more ambitious than just producing published papers by our
students and lecturers (as obligatory part of the thesis theme research). Our additional goal will
be that other researchers or private companies can easily use our research results, either for
additional research, or for commercial development. Therefore, we shall stimulate our lecturers
and students to publish their research results in the best cited journals, to create web servers for
free on-line scientific calculations and other activities, and to patent discoveries with potential
application of commercial development. As good longer time indicators of quality of our
students and of the proposed doctoral programme we consider accomplishment of significant
academic and/or industrial carrier for some of our students, the number of earned Ph.D., the
number of useful scientific servers for modeling biomacromolecules, the number of original
software packages, the number of patents, and the number of spin-off commercial
developments initiated by us. Broadening the circle of research institutions collaborating in our
doctoral programme will also be good indicator of its quality increase.
183
5.Additional remarks
Appendix I: Supplementary Courses
Supplementary Courses
Efficient research in an interdisciplinary field such as biophysics requires basic knowledge from
physics, chemistry and biology. Therefore, it is advisable for students planning to enter this
interdisciplinary field to plan as well an early aquisition of necessary basic knowledge. For instance,
physics students ned to enroll as early as possible into biochemistry or molecular biology course, while
biology students and pre-medical or medical students must broaden their knowledge of physics (which
includes acquiring necessary mathematical skills).
These additional courses are most easily enrolled during undergraduate study at the university
where student expects to earn the B.Sc. or M.Sc. degree. Organisers of the proposed Ph.D. study
programme will gladly talk with potential students to facilitate their choice of needed supplementary
courses, because the Study Committee recomands such practice. Such course of action is preffered for
aquisition of necessary basic knowledge. However, for those students who have not done this before
enrollement into the Ph.D. programme, we anticipate the possibility of acquiring needed basic
knowledge through taking these basic courses during the first year of doctoral study.
As an example we present the list of available supplementary courses at the University of Split.
Several of these courses are specialized and will be interesting only to students planning research
requiring such knowledge. Similar basic courses can be taken at the University of Zagreb or at some
other university.
The Study Committee can advise student to take one, two or even three supplementary courses
instead of elective courses II and/or IV during the first study year and to postpone taking one or two
elective courses until the second study year.
Student can also take initiative to suggest taking some courses from other interdisciplinary
doctoral studies as supplementary or elective courses during the first study year.
Example: Supplementary courses that can be enrolled at the Univerity of Split
184
Supplementary Courses in the Odd (Winter) Semester*

Structure **
Code
L+S+V+LE
PMP114 Statistical Physics (S. Kilić) 30+15+15+0 5
PMC115 Biochemistry I (M. Pavela-Vrančić) 30+0+15+0 6
PMP149 Physical Chemistry I (I. Tominić) 30+0+15+0 6
PMB010 Cell Biology (N. Bezić) 30+0+0+15 4
PMP274 Molecular modelling (S. Tomić) 15+0+15+0 6
*These undergraduate courses are enrolled at some Faculty of natural sciences and mathematics
according to student's need as determined by the Study Committee. This Table enlists course
offering at the University of Split. The Study Committe can advise student to enroll one of
offered basic courses in the first study semester of doctoral programme as the elective course II
(see Chapter 3.2).
** L=Lectures, S=Seminar, E=Exercises, LE=Laboratory Exercises.
Supplementary Courses in the Even (Spring) Semester*

Structure **
Code
L+S+V+LE
PMP072 Programming Applications 30+0+30+0 5
PMM113 Mathematics IV (T. Vučićić) 30+0+30+0 6
PMP116 Quantum Physics I (S. Kilić) 30+15+15+0 6
PMC116 Biochemistry II (M. Pavela-Vrančić) 30+0+15+0 6
PMB068 Molecular Biology (J. Puizina) 30+0+0+15 6
PMP167 Life and Physical Environment (M. Šolić) 15+0+0+0 2
*These undergraduate courses are enrolled at some Faculty of natural sciences and mathematics
according to student's need as determined by the Study Committee. This Table enlists course
offering at the University of Split. The Study Committe can advise student to enroll one or even
two of offered basic courses in the second study semester of doctoral programme as the elective
course IV (see Chapter 3.2).
** L=Lectures, S=Seminar, E=Exercises, LE=Laboratory Exercises.
These supplementary courses are at present time identical to regular courses offered at the
University of Split for the B.Sc or M.Sc. study level. In a future we intend to offer basic courses
targeted to fill the background of graduate students in the PhD biophysics programme who did not
have such courses during previous study. For instance, in the case of molecular biologists,
biochemists and medical doctors, weak in physics background, such courses can be „Selected
chapters of classical physics for biologists“ in the first study semester, and „selected chapters of
statistical and quantum physics for biologists“ in the second study semester. In the case of
physicists with weaknesses in biology/biochemistry background, such courses can be „Selected
chapters of biochemistry for physicists“ in the first semester and „Selected chapters of molecular
185
biology for physicists“ in the second study semester. Since students and lecturers at the PhD study
level can have individual approach for each student and for each lecture topic, the majority of
teaching activities would not consist of classical lectures, but would consist instead of intensive
tutorials and frequent assessments how student progresses in acquiring necessary skills and
knowledge.
ECTS credits obtained for supplementary courses are not counted as credits required for the PhD (180
credits). Corresponding ECTS research credits will be collected by student in the fourth study year.
186
Appendix II: List of Abbreviations

AMBER Assisted Model Building with Energy Refinement
B.Sc. Bachelor of Science
CC Current Contents
CHARMM Chemistry at HARvard Molecular Mechanics (also a programme
for macromolecular simulations)
DMSO Dimethylsulfoxide solvent
ECTS European Credit Transfer System
EMBO European Molecular Biology Organisation
ETF Swiss Federal Institute of Technology, Zurich
EU European Union
EUA European University Association
GROMOS Force field for molecular dynamics developed at the University of
Groningen and ETH Zurich
IFS Institute of Physics, University of Zagreb
INRA Institut National de la Recherche Agronomique, Bordeaux
IRB Ruđer Bošković Institute, Zagreb
IZOR Institute of Oceanography and Fisheries, Split
MedILS Mediterranean Institute For Life Sciences, Split
M.Sc. Master of Science
MZOS Ministry of Science, Education and Sport, Croatia
NIH National Institutes of Health, SAD
NOE Nuclear Overhauser Effect
Ph.D. Doctor of Philosophy
PKHZ The First Congress of Croatian Scientists
PMFST Faculty of Natural Sciences, Mathematics and Kinesiology,
University of Split
SISSA Scuola Internazionale Superiore di Studi Avanzati, Trst
187
Appendix III: Official letters of intention to participate in the

execution of this programme from the Ruđer Bošković
Institute in Zagreb, from the Mediterranean Institute for Life
Sciences in Split and from the University of Split Medical
School
Ruđer Bošković Institute – letter of intention
Mediterranean Institute for Life Sciences – short supporting letter
Mediterranean Institute for Life Sciences – longer supporting letter after referee reports
Medical School, University of Split – letter of intention
188

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University of Split

Faculty of Natural Sciences, Mathematics and Kinesiology

PROPOSAL FOR THE POSTGRADUATE DEGREE PROGRAMME

Ph.D. programme in biophysics

Split, May, 2007

Postgraduate Degree Programme: Ph. D. Programme in

Faculty of Natural Sciences, Mathematics and Kineziology

Reasons for establishing this study programme

• Interdisciplinary sciences such as the biophysics have increasingly important role in

An important conceptual role of science in human society is to provide rational answers to

Courses offered by our Ph.D. programme are a combination of focused interdisciplinary

• Interdisciplinary study programme in biophysics as the part of state initiative to

uniform development of scientific research by strengthening the study of life sciences

• Present plans of constructing new buildings at the University Campus, where

Planned interdisciplinary graduate study of biophysics has anticipated this need by

• Planning and establishing collaborations relevant to proposed study programme.

In neighboring Slovenia we have established the collaboration with colleagues M. Brumen

Johns Hopkins University http://www.jhu.edu/~pmb/program-curriculum.html

and several from Europe:

Great Britain, University of Oxford: http://biop.ox.ac.uk/www/top.html

Germany, Max-Planck Research School - http://www.mpibp-frankfurt.mpg.de/research-school/

Italy – SISSA, Trieste: http://www.sissa.it/sbp/web/index.php

Netherland, BioCentrum, Amsterdam: http://www.science.uva.nl/biocentrum/

Previous experience in the implementation of similar

Student mobility scheme

International partners / Joint study

We plan to use existing or novel collaborations with other EU universities in order to be

Other elements and necessary information

Programme title The Ph.D. study in biophysics

Duration 3 years (maximum 6 years)

Students are selected through public competition and through Study

a) Fundamentals of biophysics, physics and biology. These are courses offered by A.

b) Modelling and structural bioinformatics. These are courses offered by M. Brumen,

Ambriović-Ristov, D. Eterović, M. Dželalija, Z. Đogaš, G. Kilić, V. Parpura, S.

Is an additional Biophysics PhD programme in Croatia really needed is a legitimate question,

1st Semestar: Regular Courses

Course Course Title Course ECTS

1st Semester: Elective Courses

Course Course Title Course ECTS

PMP313 Molecular genetics (J. Terzić) 24+10+0+12 6

2nd Semester: Regular Courses

Course Course Title Course ECTS

2nd Semester: Elective Courses

Course Course Title Course ECTS

physics and biology (R. Dewar, P. Županović, D. Juretić,

3rd Semester: Regular Courses

Course Course Title Course ECTS

4th Semester: Regular Courses

Course Course Title Course ECTS

Seminars and Workshops from Interdisciplinary Life 0+20+0+0 4

5th Semester: Regular Courses

Course Course Title Course ECTS

6th Semester: Regular Courses

Course Course Title Course ECTS

Compulsory and optional activities

Course title Experimental methods of physics in biophysics

Learning Understanding of the theoretical background of experimental methods used

Experimental: This course includes five modules covering spectroscopic

J. M. Hollas: Modern spectroscopy, John Wiley & Sons, Chicester, 2004.

Atomic Force Microscopy

Course title Cell biophysics I

Course title Modelling of Biomacromolecules and their Complexes

pKa in protein, and how to simulate Brown dynamics of proteins preceding