Bioengineering 1

Faculty of Engineering, Department of

—Bioengineering

This publication refers to the session 2009–10. The information given, including that relating to the
availability of courses, is current at the time of publication; 5 October 2009; and is subject to alteration.

© Imperial College London 2009

For details of postgraduate opportunities go to www.imperial.ac.uk/pgprospectus.

2 Undergraduate syllabuses

Bioengineering
The field of biomedical engineering is developing rapidly both nationally and internationally, and its
progress is reflected in changes occurring at Imperial College London. Our courses are updated continually
to keep abreast of current developments in the subject and enhance the career prospects of our
graduates. They offer entry into the broad field of biomedical engineering, providing students with sound
foundations in engineering and physical principles. The Department also provides MPhil/PhD training for
which there are currently about 85 students, and a recently restructured streamed MSc course targeting
advanced principles in medical physics, biomechanics and neurotechnology.
The Department is active in many areas of research including biomedical sensors, mathematical
modelling of biological and physiological processes, theoretical and experimental neuroscience, medical
imaging, exercise biomechanics, microbionics and bio-inspired circuit design, surgical planning,
engineering approaches to the aetiology, diagnosis and management of cardiovascular, respiratory and
musculoskeletal diseases, software for healthcare, and the analysis and interpretation of biomedical data.
Staff are drawn from fields ranging from mathematics, the physical sciences and engineering to chemistry,
the biological sciences and medicine. Much of the research is undertaken in collaboration with other
departments at Imperial, with medical colleagues from hospitals associated with the College, and
externally with colleagues from around the world. In the 2008 Research Assessment Exercise (RAE)
conducted by the Higher Education Funding Council for England, 75% of the Department of
Bioengineering's returned research was judged to be either world-leading or internationally excellent.
The taught undergraduate courses are accredited by two major engineering institutions, the IET and
the IMechE.

Undergraduate courses
BH81 BEng in Biomedical Engineering (three years)
BH9C MEng in Biomedical Engineering (four years)
Both the BEng and MEng have a common first two years, and MEng students spend the additional year
taking more specialist courses which are usually concentrated in one of the traditional engineering
disciplines, usually Electrical Engineering, Mechanical Engineering or Computing. Final decisions about
whether to take the three or four-year course can be delayed until the end of the second year.
The first two years include fundamental training in mathematics, engineering and medical science
including material on bioengineering techniques and design. The final year includes courses on applied
biomedical engineering topics and a research project. There is also an expanding year abroad programme
with exchanges already in place with Institutions in the Netherlands and the USA.
Students must normally have A2 level passes in mathematics and physics, plus an additional A2 level
subject or two AS level subjects with high grades (AAB or above). Knowledge of chemistry and/or biology
is useful but not essential. Competence in English must be proven.
The course consists of lectures supported by study groups and tutorials with additional practical
classes. Design projects are included in many of the modules.

FIRST YEAR
BE1-HMCP Molecules, cells and processes
BE1-HMATH1 Mathematics I
BE1-HVAW Mathematical tools, vibrations and waves
BE1-HEE1 Electrical engineering I
BE1-HEMO1 Electromagnetics and optics I
BE1-HLDS Logic and digital systems
BE1-HMS1 Medical science I
BE1-HPROG1 Programming I
Bioengineering 3

BE1-HITM Introduction to mechanics

BE1-HHMT1 Heat and mass transport I
BE1-HEEL Electrical engineering labs
BE1-HEIM Engineering in medicine labs
BE1-HWLS Wet lab skills
BE1-HTIB Topics in biomedical engineering
BE1-HEBP Electronics build project

SECOND YEAR
BE2-HMS2 Medical science II
BE2-HMATH2 Mathematics II
BE2-HEM02 Electromagnetics and optics II
BE2-HPROG2 Programming II
BE2-HEE2 Electrical engineering II
BE2-HFLM Fluid mechanics
BE2-HHMT2 Heat and mass transport II
BE2-HSAS Signals and systems
BE2-HSDM Solid mechanics
BE2-HCTRL Control systems
BE2-HMDP Mechanics design project
BE2-HMEW Mechanics workshop
BE2-HAMSS Atomic and molecular and semiconductor structure
BS-0821 Project management

THIRD OR FOURTH YEAR

BE3-HIPR Image processing
BE3-HBIMG Biomedical imaging
BE3-HPMDA Physiological monitoring and data analysis
BE3-HMIB Modelling in biology
BE3-HHEDM Health economics and decision making
BE3-HBIP Final year BEng project
BE3-MBMX Biomechanics
BE4-MAMI Advanced medical imaging
BE3-MABM Advanced biological modelling
BE3-MCNS Computational neuroscience
BE3-MSYNB Synthetic biology
BE4-MMGP MEng third year group project
BE4-MMIP MEng fourth year individual project
BE4-MBMI Brain-machine interfaces
BE4-MNMC Neuromuscular control
BE4-MCBMX Cellular biomechanics
BE4-MOBMX Orthopaedic biomechanics
BE4-MMLNC Machine learning and neural computation
Modules external to the department of bioengineering. Please note that availability of these modules is
subject to change.
4 Undergraduate syllabuses

Department of Mechanical Engineering options

ME3-HFFM Fundamentals of fracture mechanics
ME3-HMSD Machine system dynamics
ME3-HSAN Stress analysis
ME3-HSPAP Structure properties and applications of polymers
ME3-HFMX Fluid mechanics
ME3-HTRB Tribology
ME3-HCCM Computational continuum mechanics
Department of Electrical and Electronic Engineering options
E.3.01 Analogue integrated circuits and systems
E.3.02 Instrumentation
E.3.05 Digital system design
E.3.07 Digital signal processing
E.3.09 Control engineering
E.3.11 Advanced electronic devices
E.3.12 Optoelectronics
E.3.16 Artificial intelligence
Department of Computing options
Comp.493 Intelligent data analysis and probabilistic inference
Comp.341 Introduction to bioinformatics
Department of Materials options
MSE.315 Biomaterials and artificial organs
Bioengineering 5

Syllabuses

FIRST YEAR

BE1-HMCP Molecules, cells and processes1

PROFESSOR R. KRAMS, DR M. BOUTELLE
Metabolism: Protein structure: protein formation from amino acids, primary, secondary, tertiary
protein structures, and intermolecular forces that stabilise them. Energetics and enzymes: induced fit
model of enzymatic action, description of enzyme kinetics using Michaelis-Menten equation, Lineweaver
Burke plots.
Metabollic pathways: ATP and pyruvate production by glycolysis in cytosol, sources of actyl-CoA,
production of NADH in TCA cycle, oxidative phosphorylation, production of proton gradient in
mitochondria, generation of ATP.
Cells: Identification of cellular components, structure and function of cell membranes, function of
membrane transporters and proteins. Genetics: nucleic acids and chromosomes, DNA
replication and mitosis, gene organisation and transcription, protein translation and post
translational modification.

BE1-HMATH1 Mathematics I1
DR A. WALTON, DR D. BUCK
The course will begin with the nine lecture Basic Mathematics Course which is a revision of the A-level
Mathematics syllabus. The topics covered are: 1 Numbers and Arithmetic, 2 Algebra,
3 Combinatorics – Binomial Theorem, 4 Functions and Graphs, 5 Cartesian Geometry, 6 Trigonometry, 7
Differential Calculus, 8 Integral Calculus, 9 Vectors and Mechanics. The regular syllabus is as follows:
Analysis: Functions of one variable: exponential, logarithmic, and trigonometric functions: odd, even,
inverse functions. Limits: continuous and discontinuous functions.
Differentiation: implicit and logarithmic differentiation; Leibnitz’s formula; stationary points and points of
inflection; curve sketching; polar coordinates. Taylor's and Maclaurin’s series; l’Hopital’s rule.
Convergence of power series; ratio test; radius of convergence.
Complex numbers: the complex plane; polar representation; de Moivre’s theorem; ln z and exp z.
Hyperbolic functions: inverse functions; series expansions; relations between hyperbolic and
trigonometric functions
Integration: definite and indefinite integrals; the fundamental theorem; improper integrals; integration by
substitution and by parts; partial fractions; applications
Linear algebra: vector algebra: basic rules; cartesian coordinates; scalar and vector products; application
to geometry; equations of lines and planes; triple products; linear dependence.
Matrix algebra: double suffix notation; basic rules; transpose, symmetric, diagonal, unit, triangular,
inverse and orthogonal matrices.
Determinants: basic properties; Cramer’s rule.
Linear algebraic equations: consistency; elementary row operations; linear dependence; Gauss-Jordan
method; Gaussian elimination; LU factorisation. Eigenvalues, and Eigenvectors; diagonalisation.
Ordinary differential equations: first order equations: separable, homogeneous, exact and linear. Second
order linear equations with constant coefficients. Fourier series: Standard formulae; even and odd
functions; half range series,; complex form. Parseval’s theorem. Differentiation and integration of series.

1
The syllabus is subject to changes in 2009/10
6 Undergraduate syllabuses

BE1-HVAW Mathematical tools, vibrations and waves

MR M. HOLLOWAY
Mathematical Introduction: basic functions and their plotting; differentials and derivatives; first order
ODE’s; basic vector algebra; complex number basics; dimensional analysis; PART 2 Vibrations & Waves:
simple and damped harmonic motion: SHM of mechanical and electrical oscillators; damped oscillation,
light, critical and heavy damping, Q value; superposition of two SHMs- Lissajou’s figures.Forced
oscillations: steady-state, variation of displacement and velocity with the frequency of the driving force;
resonance, bandwidth, transients. Transverse wave motion: waves on a string, wave equation, travelling
waves; characteristic
impedance and phase velocity; reflection and transmission at boundaries; group velocity; dispersion;
waves in periodic structures. Waves on transmission lines:circuit model, phase velocity, impedance, group
velocity; lossy lines, dispersion,impedance matching, reflection at mismatches.

BE1-HEE1 Electrical engineering I

PROFESSOR R.A. SPENCE, DR S. SCHULTZ
The design process: circuits are interconnections of components.
Components: resistors and sources: Ohm’s law.
Interconnections: Kirchhoff’s Laws.
Equivalence.
Circuit analysis: systematic, leading to nodal equations. Superposition. Thevenin Equivalent Circuits.
Voltage-controlled current sources. Nonlinear components: load-line analysis. Operational amplifiers:
large-signal and linear operation. Common circuits employing op-amps: A-D converters, Schmitt Triggers,
D-A converters, integrators. Alternating current behaviour: Phasor diagrams. Complex currents and
voltages. AC properties of capacitors and inductors: AC circuit analysis. Similarity between DC and AC
circuit analysis: examples. Frequency domain behaviour: asymptotes. The analysis of change: example
using Zener diode circuit. Small-change circuit analysis, and its similarity to DC analysis. The exponential
diode and its small-signal characterisation. The application of small-signal analysis.

BE1-HEMO1 Electromagnetics and optics I

DR E.M. DRAKAKIS, PROFESSOR R. KRAMS
Electromagnetics: electrostatics: force between point charges, electric field, flux,flux density, gauss’ law,
electrostatic potential, capacitance, energy of an electrostatic system; magnetostatics: magnetic field,
force on current carrying conductor, magnetic flux density, biot-savart law, magnetic field intensity,
permeability, ampere’s circuital law, inductance, energy in a static magnetic field, mutual inductance,
coupling coefficient; motion of charged particles within electric and magnetic fields, mass-spectrometer
basics.
Geometric optics: rays, fermat’s principle, the laws of geometrical optics;reflection and refraction of
paraxial rays by spherical surfaces; image formation properties of thin lenses; optical instruments: the
microscope.

BE1-HLDS Logic and digital systems

DR M. TANG
Term 1: Logic gates, truth tables, Boolean algebra, Karnaugh maps, binary number representations,
combinational arithmetic circuits. Flip-flops, counters and registers; binary multiplication. Monostables,
multiplexers and memories; ROM, EPROM, RAM. Example medical applications. Data representations.
Computer architecture: simple 8-bit CPU registers, bus, I/O and memory; machine code. Assembly
language essentials, ALU instructions, stack operations, subroutines, input/output programming.
Analogue-to-digital conversion. DMA, disk drives, serial port and USB.

BE1-HPROG1 Programming I
MR M. HOLLOWAY
The C language: variables, types and expressions; assignment statements; input and output; control
statements; variables and identifiers; loops; constants; input/output streams; interaction of C with UNIX
Bioengineering 7

and Windows shells; terse syntax in assignments; functions and variable scope; function arguments and
the stack; recursive functions. Arrays; null
terminated character strings; passing arrays to functions;
multidimensional arrays, array initialisation. Pointers; string library functions; type conversion and
casting; data structures. Program design: bottom-up and top-down strategies, defensive design, pseudo-
code, testing, debugging and documentation.

BE1-HMS1 Medical science I

PROFESSOR P.D. WEINBERG
The respiratory system: structure and function of the airways, ventilation and lung mechanics, alveolar
structure, gas transport, control of breathing. The Cardiovascular System: overview of the system, heart
anatomy, mechanics of the cardiac cycle, cardiac electrophysiology, the ECG, control of cardiac output, the
large arteries, introduction to haemodynamics, roles of arterioles, control of arterioles, water and solute
exchange in the microcirculation, return of substances to the heart in lymph and veins, integrated control
of the cardiovascular system. The nature of physiological control systems will be emphasised throughout.
Aviation physiology will be used to demonstrate physiological and technological solutions to challenges
presented by unusual environments.

BE1-HITM Introduction to mechanics

DR S. SHEFELBINE
Basic concepts and Newton’s laws. Statics: Particles and bodies, centre of mass, symmetry, levers, free
body concept. Kinematics/trajectories. Work/energy/momentum: Potential energy, kinetic energy,
conservative force fields, conservation of energy, rotational kinetic energy, linear momentum, angular
momentum, impulse, power. Solving differential equations, Oscillations: Homogeneous linear first order,
inhomogeneous linear first order, homogeneous linear second order, inhomogeneous linear second order.
Systems of particles: Centre of mass, linear momentum, angular momentum, inertia. Rigid body motion:
Centre of mass, moment of interia, dynamics of a solid body.

BE1-HHMT1 Heat and mass transport I

DR D. O’HARE
The scope of thermodynamics: energy, heat, and work. Units and sign conventions. Examples of the role of
thermodynamics in biomedical engineering. The laws of thermodynamics: types of systems (open, closed,
isolated, adiabatic, diathermic). Types of thermal processes. The unique scale of temperature: the zeroth
law. Internal energy and the conservation of energy: Quantifying changes in heat and work. PV work, the
work of expansion. Reversible and irreversible work. State functions versus path functions. Exact
differentials. Heat capacity: constant pressure and constant volume and their relationship. The
temperature dependence of heat capacity. Enthalpy. Enthalpy changes in chemical systems, standard
states,
enthalpy of formation, Hess’s Law. Temperature dependence of enthalpy–Kirchoff’s Law. The
measurement of enthalpy. The second law of thermodynamics: spontaneous or natural processes and
reactions. Entropy, classical and statistical definitions of the second law. The Clausius inequality. Absolute
entropy, standard entropy and the third law. The temperature dependence of entropy. Gibbs free energy
and Helmholtz free energy: Pressure and temperature dependence of free energy, the Gibbs-Helmholtz
equation. The van’t Hoff isochore. Chemical potential and chemical equilibrium: The variation of free
energy with concentration. Free energy, equilibrium and the equilibrium constant. Le Chatelier’s principle.
Chemical potential. Ionic activity. Free energy changes in biochemical systems- the biochemist’s standard
state. ATP/ADP as an example of using coupled reactions. Solutions: Intermolecular forces. Ideal
solutions, Raoult’s Law. Non-ideal solutions. Colligative properties, electroplyte solutions. Solubility: Ionic
solubility. The unique properties of water. Why do ionic solids dissolve? The ionic solubility product and its
application in biology. Complexation, the common ion effect. pH and buffer solutions. Henry’s Law,
expressions of gas solubility. Temperature dependence of gas solubility. Introduction to heat: transfer.
Modes of heat transfer: radiation, convection, conduction. 13. Heat conduction. Fourier’s Law. Thermal
conductivity. Thermal diffusivity. One dimensional heat conduction: Heat transfer through composite
walls. The general equation for heat conduction.
8 Undergraduate syllabuses

Transient heat transfer, three dimensional problems.

Forced convection: boundary layers, laminar flow, turbulent flow, the Reynolds number. Heat transfer in
laminar flow. Newton's law of cooling and the heat transfer coefficient. Introduction to
dimensionless groups. Further Heat Transfer: transfer correlations for external laminar flow. Turbulent flow
in ducts. Temperature transients and lumped parameters–the Biot number. Heat exchangers.
Radiation: revision of the electromagentic spectrum. Absorptivity, reflectivity and transmissivity. Black
body radiation and the Stefan-Boltzmann Law. The relative significance convective and radiative heat
transfer and the effect of temperature. Wien’s displacement law. Planck’s Law and the spectral distribution
of black body radiation. Black body temperature. Definition and properties of view factors, cosine law,
heat exchange between black bodies. Real surfaces–grey bodies.

BE1-HEEL Electrical engineering labs

DR R. DICKINSON
Bipolar transistor operation, OFF, linear and ON regions, Saturation, hFE, VCESAT, diode threshold switching.
Signal inversion, cascaded circuits, NPN and PNP, parallel switching, logic gate, bistable switch, level
detector. Circuit emulation using SPICE, op-amp circuits, low and high pass filter, band-pass filter.

BE1-HEIM Engineering in medicine labs

DR A. BULL, MR. S.D. MASOUROS, PROFESSOR P. WEINBERG, DR M RAMPLING
Four lectures Experimental methods: measurement, error analysis, descriptive statistics, experimental
methods, report writing, maintaining log books. Properties of engineering materials (stress/strain,
stiffness, Young’s modulus, tangent modulus, Poisson’s ratio, fatigue, viscoelasticity).
Four lab sessions two in mechanical engineering (beam bending, stress concentration, properties of
materials) and two in medical science (cardiac electrophysiology and measurement of lung volumes).

BE1-HEBP Electronics build project

MR. M. HOLLOWAY
Small IET-sponsored build project to gain electronics construction experience, including PCB mounting,
soldering and circuit connection.

BE1-HWLS Wet lab skills

DR M. BOUTELLE, DR D. OVERBY, DR M. RAMPLING
Laboratory Safety and Basic Techniques: The laboratory environment; Dispensing methods commonly
used in a research laboratory; Safety. Dye Binding to Serum Albumin: principles of ligand binding and
relation to Beer-Lambert’s Law. Presentation, sources of error. Introduction to Microscopy and
Microbiology: Use and care of a light microscope. Limits of microscopic resolution of a light microscope,
use of staining techniques to characterise bacteria. pH and Buffer Action: Principles and importance of
measuring pH and buffering capacity in experimental biochemistry. Graphical and tabular presentation
using a spreadsheet. Substrate Sensitivity and pH of Protease Enzymes: Chromogenic reactions and the
use of a spectrophotometer. pH dependence and substrate specificities of digestive enzymes.
Determination of Red Blood Cell Parameters: estimating the number and concentration of red cells, the
concentration of haemoglobin in a blood sample. Calculation of mean cell volume, cellular haemoglobin
and the mean cell haemoglobin concentration.

BE1-HTIB Topics in biomedical engineering

DR A. BULL AND OTHERS
A series of lectures, and a group project designed to explore some principles and applications in
biomedical engineering with specific reference/connections to core taught material.
Bioengineering 9

SECOND YEAR

BE2-HMS2 Medical science II

DR H. KRAPP, DR MARTINA WICKLEIN, DRLINDSEY CLARKE
Nervous System: Gross anatomy and functional organization, foundations of bioelectrical signals; signal
transmission, propagation and integration; sensory systems; postural reflexes; oculomotor system;
premotor/motor cortex; conceptual models of motor control; overview on autonomic nervous system.
Musculoskeletal System: Functional design and physiological properties of bones and joints; micro/macro
structure and physiological mechanisms underlying the function of skeletal muscles; functional
comparison between skeletal, smooth and cardiac muscles. Endocrine System: Functional features of the
endocrine system; homeostasis and feedback control; hormonal vs. neuronal control; major control loops
of hormone secretion; blood glucose regulation; clinical aspects of hormonal dysfunction; hormonal
control of female reproduction. Reproductive System: Anatomical and physiological organization of male
and female reproductive systems; fertilization and early foetal development. Renal System: Gross
anatomy and functional design of urinary system and kidneys; physiological mechanisms underlying
filtration, secretion and reabsorption of solutes; regulation of plasma osmolality and fluid volume;
hormonal and neuronal control of renal function. Gastrointestinal System: Anatomical compartments and
functional properties of the gastrointestinal system; physiological mechanisms of nutrient and water
absorption.

BE2-HMATH2 Mathematics II
PROFESSOR J. ELGIN, TBA
Mathematics for signal processing: Review of linear dependence/independence, basis, inner products -
vectors, complex numbers, functions. The Dirac delta function. Review of Fourier series. Brief introduction
to Fourier transforms (to be revisited towards end of course).
Partial differentiation: Differentiation as linearization. Functions of more than one variable: partial
differentiation, Jacobian; total differentials, chain rule, changes of variable. Taylor’s theorem for a function
of two variables; stationary values; contours.
Vector calculus: parameterised curves; scalar and vector fields; grad, div and curl; arc length; line
integrals; conservative fields; double and triple integrals; Jacobians; Green’s theorem in the plane; surface
integration; Gauss’ and Stokes’ theorems.
Partial differential equations: application to the description of biological and engineering problems;
classification; wave equation; characteristics. Diffusion equation; similarity solutions. Laplace’s equation.
Separation of variables.
Complex variables: analyticity, differentiability in a region, Cauchy-Riemann equations, Laplace’s
equation. Simple mappings, multivaried functions. Conformal mappings. Cauchy's theorem and the
residue theorem. Evaluation of complex and improper integrals including poles on the real axis.
Transforms: Fourier transforms; definition, inverse and properties. Fourier convolution theorem.
Application to the solutions of PDE’s. Laplace transforms: definition, inverse and properties. Laplace
convolution theorem. Use in solving ODE’s.

BE2-HEM02 Electromagnetics and optics II

MR. M. HOLLOWAY, DR R.J. DICKINSON
Electromagnetic Waves: Differential forms; for electrostatics, the divergence of an electrostatic field;
Laplace’s and Poisson’s equations; for magnetostatics; the curl of a vector field. Vector magnetic
potential. Continuity of charge and concept of displacement current. Maxwell’s equations in differential
form. The Helmholtz equation; plane waves, phase velocity, polarisation, impedance, power flow,
Poynting’s theorem. Boundary conditions; reflection and refraction of plane waves from conductors and
dielectrics at plane and oblique incidence,
total reflection, Brewster angle. Waveguides, conducting boundaries, dielectric waveguides, optical fibres.
Masers and Lasers; Stimulated emission, Einstein Coefficients, population inversion, gain.
Physical Optics: Spherical waves, Huygens principle, diffraction, diffraction from an rectangular and
circular aperture, Fourier optics, propagation through a dielectrics slab and a lens, imaging using lens,
10 Undergraduate syllabuses

resolution (airy disc), coherence, holography, synthetic aperture (radar and sonar), elastic wave equation,
longitudinal waves, acoustic wave parameters, intensity parameters, safety, generation and detection,
Schieleren detection, reflection, acoustic impedance.

BE2-HPROG2 Programming II
DR P.M.M. CASHMAN, MR. M HOLLOWAY
Review of ANSI C structs and pointers. Application example: complex numbers. Dynamic memory
allocation; linked lists; self ordering lists; binary trees; recursion; sorting algorithms; hash tables.
Command line processing; file handling; introduction to object-oriented problems in C. Data abstraction
and encapsulation. The C++ class and data member access permissions; function and operator
overloading, polymorphism and inheritance. Message passing; cin and cout streams. Re-implementation
in C++ of complex numbers example. Class constructors and destructors. Simple Windows applications:
the Document/View architecture. Professional software engineering: 5 reasons why software projects may
fail; properties of good software. The waterfall and evolutionary development models; data
representations; requirements capture. Introduction to the Unified Modelling Language. Use case, class
and sequence diagrams; associations and multiplicity; operations. Benefits of the UML approach to code
implementation. Medical informatics examples.

BE2-HEE2 Electrical engineering II

DR E. DRAKAKIS
Integrated technology: historic milestones; lithography; passive components; BJT technology; MOSFET
technology; BiCMOS technology; state-of-the-art bioengineering examples. The BJT: structure and
operation, deviations from ideality,
-equivalents, HF small-signal model. The MOSFET: structure and
operation, deviations from ideality,
-equivalent, HF small-signal model. Basic IC building blocks: Current-
mirrors, voltage- and current-references (VT-based, VBE-based and Bandgap), single-stage amplifiers,
common-emitter/source, common-base/gate, common-collector, response of a cascade of single-stage
amplifiers, DC- and AC- load lines for BJT- and MOS-based amplifiers, importance of selection of operating
point for undistorted amplification, BJT and MOS Differential-Pairs: large-signal behaviour, CMRR, slew,
OP-AMPs and OTAs, transistor-level topology synthesis by means of simpler blocks.

BE2-HFLM Fluid mechanics

DR J. SIGGERS
The continuum approximation, Eulerian and Lagrangian description of fluid, definitions of fundamental
kinematic and thermodynamic fluid properties, state relations for gases, flow visualisation in two-
dimensional (planar or axisymmetric). Pressure force acting on a surface, hydrostatic pressure, gage
pressure, buoyancy force on a submerged or floating body (Archimedes' laws), stability of submerged or
floating body, rigid-body motion of fluid: simple examples. Control volumes, statement of the Reynolds
Transport Theorem, and its application to conservation of mass and linear momentum. Conversion
between inertial and non-inertial frames, the Bernouilli equation: derivation and application. The
differential equations of fluid flow (to understand though not reproduce derivation): (i) the continuity
equation and incompressible case, the momentum equation for general stress tensor, simplification in the
case of inviscid and Newtonian fluid. Examples of exact solutions of equations.

BE2-HHMT2 Heat and mass transport II

DR D. O’HARE
Chemical kinetics: rates of reactions, reaction order, integrated rate laws, Arrhenius’ equation, transition
state theory, reaction mechanisms, multistep reactions, the steady state approximation, enzyme kinetics,
applications in pharmacokinetics, experimental approaches to chemical kinetics. Thermodynamics: phase
equilibria, the phase rule, phase diagrams. Statistical thermodynamics Bulk properties from molecular
energetics, Boltzmann distribution. Application of Boltzmann’s distribution to thermodynamic properties:
the partition function. Statistical definitions of entropy. Diffusion Random walks, tracer diffusion. Mean
free path and average diffusion distance., thermodynamic driving forces for diffusion. Steady state
diffusion. Time dependent diffusion and Fick’s second law. Experimental techniques for studying diffusion
Bioengineering 11

in biomedical engineering: radiolabels and fluorescence techniques, capillary electrophoresis, photon

correlation spectroscopy, electrochemical methods (rotating disc voltammetry, chronoamperometry),
fluorescence recovery after photobleaching. Diffusion-convection and diffusion reaction problems.

BE2-HSAS Signals and systems

DR A.A. BHARATH
Introduction to signals and systems: Definition of a signal, system, inputs and outputs, deterministic and
random/stochastic signals, continuous and discrete time signals, periodic signals; Examples in
bioengineering; Typical signals such as sinusoidal, exponential, step, impulse, ramp. Simple operations on
signals: time translation, dilation/contraction; scaling and addition, component-wise product, convolution
of two signals and correlation, inner product, norm. Reminder on complex numbers, Euler formula, root of
unity; signal vector spaces with inner products. Fourier representations: Fourier series of continuous and
discrete periodical signals, relationship to finite dimensional spectral representation. Fourier integral
representation, Fourier forward and inverse transforms, duality between time and frequency domains.
Examples of Fourier analysis in bioengineering. Properties of Fourier transform: Parseval relation,
convolution property, continuous discrete duality, discrete time Fourier representations. Sampling and
digital signals: sampling theorem, Nyquist frequency, continuous signal reconstruction, discrete sampling,
decimation, numerical Fourier transform. LTI systems: linear and nonlinear, time varying and time
invariant systems; representation as linear time invariant differential equations, mechanical and electrical
LTI systems.

BE2-HMDP Mechanics design project

DR A.M.J. BULL
Large group-project with peer assessment. Engineering for orthopaedics, three-dimensional design (using
SolidWorks design software), technical presentation skills/report writing skills, clinical issues related to
the specific design brief (brief changes every year and is different for each group). Basic concepts in
biomaterials, materials used in orthopaedics. Fracture fixation devices—materials, design features, bone
properties. Commercial Issues in medical device design—CE Mark/FDA. Practical orthopaedic imaging—
MRI, CT, X-ray, nuclear imaging. Formal design process. Group dynamics.

BE2-HMEW Mechanics workshop

DR A.M.J. BULL
Mechanical workshop skills.

BE2-HAMSS Atomic, molecular and semiconductor structure

DR S. SCHULTZ, DR M. TANG
Review of basics of atomic and molecular structure, Quantum theory of atomic structure : wave particle
duality, Compton scattering, PE effect, Schrodinger’s equation, Energy bands, Introduction to
Semiconductors: conductors, insulators, semi-conductors; crystal structure of group IV materials; doping,
donor and acceptor impurities, holes and electrons; p-type and n-type semiconductors; effective mass and
mobility, conductivity; drift and diffusion currents. Energy band: density of states, Fermi-Dirac probability
function; hole and electron densities, energy band diagram for intrinsic and doped semiconductors;
energy band diagram under external electric field. p-n junction: built-in voltage, depletion zone; junction
under external electric field; calculation of current in a p-n junction. Bipolar junction transistor (BJT):
emitter, base and collector of a BJT; emitter, base and collector currents; current gain in a BJT. Molecules:
types of molecular bonds, chemical bonds (more links to quantum theory), spectroscopy, rotations etc,
molecular bonding, applications of spectroscopy, including MR.

BE2-HSDM Solid mechanics

DR A. BULL, DR S.D. MASOUROS,
Revision of Newtonian mechanics, revision of Free body diagrams , Pin-jointed structures
M,Q,N diagrams in beams (Shear force & Bending moment diagrams)
a. For various supports and loading (incl. beam-frames)
b. Solution using the superposition method
12 Undergraduate syllabuses

Strength of materials (stress and strain)

a. a.Define stress, strain and shear – Introduction to stress-strain graphs,
b. The stress element (3D and 2D),
c. Stresses in oblique planes – Equilibrium of cubic element – coordinate transformations,
d. Principal stresses – Mohr’s circle – stress invariants,
e. Strain (similar analysis to stress – principal strains) – Strain gauges
Statically determinate and indeterminate systems
a. Deformations in axially loaded bars (determinate and indeterminate problems),
b. Thermal strains,
c. Introduction to solution methods for general indeterminate problems
Stress-strain relationships (material properties)
a. Behaviour in small (Hooke’s Law) and large (yield, strength, toughness) strains,
b. Viscoelasticity, friction, hardness,
c. Generalised Hooke’s Law (tri-axial stress state),
d. Elastic constants,
e. Tensor notation – introduction to anisotropic behaviour,
f. Plane stress – plane strain
Uniformly loaded thin shells
a. Pressurised thin-walled sphere and cylinder – hoop and axial stresses,
b. Thin rotating ring or cylinder – Resisted thermal expansion
Failure theories – Strength of materials (con’d)
a. Failure theories (von Mises, Tresca) – Safety factor,
b. Other factors affecting strength of materials {(fatigue, creep, stress relaxation), stiffness, wear,
corrosion, stress concentration}
Bending (simple theory)
a. Normal stresses due to bending,
b. Various cross sections (I, T, C, U) – moments of area (and theorems),
c. Combined bending and axial load,
d. Unsymmetrical bending,
e. Shear stresses in bending,
f. Slope and deflection in bending (incl. 4th order diff. eq.),
g. Statically indeterminate beams
Torsion (simple theory) – Combined Loading
a. Solid circular shafts (torsion formula),
b. Thin-walled, hollow circular shafts,
c. Combined bending, torsion and axial load (superposition)
Buckling
a. Buckling of columns – Euler’s theory – Critical load for various supports,
b. Eccentric loading in columns
Additional topics
a. Helical springs,
b. Equilibrium equations (2D Cartesian coordinates),
c. Strain – compatibility equations.

BE2-HCTRL Control systems

DR E. BURDET
Definition and properties of the bilateral and unilateral Laplace transform: differentiation, integration,
convolution and final value theorems, inverse Laplace transform, transfer function of a linear system,
solution of a linear differential equation using the Laplace transform, block diagrams and graphical
programming of LTI systems. Role of feedback: BIBO stability, analysis with poles and Routh-Hurwitz
criterion, examples of linear dynamical systems with open- and closed-loop. Time domain analysis:
temporal response of first and second order systems, steady state response, dominant pole
approximation, transient specification, time domain design, PID control. Frequency response: Bode plot,
Bioengineering 13

example on first and second order systems, decomposition of system into first and second order factors.
From transfer function to frequency response and back, relationships between time domain and frequency
domain analysis and design. Simple low-pass filters: average filter in time and in space, high-pass filters:
derivative and gradient filters, ideal filter, implementation in time and frequency domains, applications in
bioengineering, main characteristics of filters in time and frequency domain. Butterworth low-pass filters.

BS-821 Project management

For more information on this module please see BS 821 project management in the Business School
section.

THIRD OR FOURTH YEAR

Third year and fourth year MEng students also have options available in the humanities department and
within the Business School. In addition, module options are available to MEng students in the
Departments of Electrical and Electronic Engineering, Mechanical Engineering, Computing and materials.
The availability of these options is subject to review, and do have certain prerequisites. They currently
include the following:

BE3-HIPR Image processing

DR A.A. BHARATH
Introductory lecture: applications of image processing in medical imaging, and bioengineering. Basic
concepts: organisation of primate visual system, colour and monochrome images, representation of
images, discrete image models. Binary images: thresholding, binary image processing, image moments,
methods of structural representation. Image transforms: the Fourier transform, the two-dimensional DFT,
general linear transforms, inner product representations, the inverse of a linear transform, separable
general linear transforms. The Hadamard transform, the Haar transform, the Karhunen-Loeve (KL)
transform, applications of image transforms: compression, image enhancement, image analysis.
Neighbourhood operators: types of neighbourhood operators, linear neighbourhood operators.
Smoothing, enhancement, edge detection, filter banks, feature extraction, implementation issues, non-
linear operators, applications. Image segmentation applications, cell nuclei classification, rendering three-
dimensional data, quantification, types of segmentation, thresholding, region based approaches, feature
space segmentation, detailed example, supervised segmentation, the discriminant function, unsupervised
segmentation, clustering and k-means algorithm, edge detection. Image registration: types of
transformations, rigid-body transformations, affine transformations, image distortion, intensity
distortions, rigid-body registration using geometric features, registration using points, iterative closest
point, Voxel similarity measures, optimisation, interpolation and sampling. Optional Topic—Motion:
finding incidence of motion, block matching, object tracking, Kalman filtering, particle filtering, the
condensation algorithm, demonstration of particle filter, optical flow.

BE3-HBIMG Biomedical imaging

DR R. DICKINSON, MS E. KULUMA
X-ray imaging: Nature and generation of X-rays: electron interaction with matter. Xray spectrum,
Characteristic X-rays. Interaction of X-rays with matter, attenuation and Beer’s law, effect of tissue density
and photon energy. Image formation, gamma characteristic, theoretical contrast, image mottle and
geometric blurring. Beam hardening. Image quality; parameters and measurement. exposure times, Dose
and Contrast/Noise. Equipment; Tube, Filters, Anti-scatter grid, Collimator. Safety. Standard radiological
safety checks. X-ray CT: Basic principle of CT. The central slice theorem, backprojection algorithm: Choice
of reconstruction filter. Scanning configurations and implementation: Spiral CT. Image Quality parameters
and artefacts. Image manipulation:, archiving, DICOM. Ultrasonic imaging: Ultrasound propagation in
tissue, generation, piezo-electric effect, transducer construction. Beam patterns. Fresnel and Fraunhofer
diffraction.. Pulsed A-Mode systems. Envelope detection. TGC. B-Mode imaging. Scanning geometries:
rectilinear, curvilinear., beam steering. B-mode processing. Dynamic range compression, scan conversion.
Doppler shift. Continuous Wave Doppler. Pulsed Doppler. Range cell and resolution. Magnetic resonance
Imaging: NMR signals, gyromagnetic ratio, spin populations,. Types of magnet. Block diagram of MR
14 Undergraduate syllabuses

system; field strengths, coils. T1 and T2, free induction decay, spin dephasing, T2*. Basic pulse sequences:
saturation recovery, inversion recovery, spinecho; contrast mechanisms. Imaging: gradients, slice
selection, frequency and phaseencoding, FOV, scan-time, multiple slices, k-space. Image Artefacts,
Overview of MR Clinical Techniques. MR Safety I: Projectile effect, pacemakers, controlled areas, EM field
effects on other equipment. Optical imaging: Optical imaging: Interaction of light with tissue.
Microscopy: principles and limitations, wide-field, confocal microscopy, optical sectioning. Fluorescence
imaging: single-photon and multiphoton excitation. Indicators for fluorescence microscopy. Optical
coherence tomography, Other novel optical imaging techniques. Endoscopy: minimally invasive surgery,
confocal endoscopy.

BE3-HPMDA Physiological monitoring and data analysis

DR M. BOUTELLE AND OTHERS
An advanced course focused on four core aspects of biological and clinical measurement. The
measurement topics are supported by example papers from the recent literature that illustrates the
benefits of using time domain data to understand physiological and pathological processes. In vivo
statistics of measurement: Significance testing, data rejection, error propagation, calibration, noise and
filtering. Supported by problem classes. Biopotential measurement: Instrumentation and signal analysis of
ECG, EEG, ECoG and cellular patch-clamp measurements. Physical measurement in vivo: The underlying
principles and instrumentation for the measurement of pressure, temperature, respiratory flow and blood
flow (including clearance and optical methods). Chemical measurement: Consideration of electrochemical
and optical methods of measurement of ions (including ion selective electrodes and confocal fluorescent
imaging), nutritional markers, dissolved gases, biosensors, immunoassay.

BE3-HMIB Modelling in biology

DR M. BARAHONA
Introduction and background: linear vs. nonlinear. Phase plane analysis. Stochastic and deterministic
models. One-dimensional systems: fixed point analysis; global and local stability; bifurcations. Two-
dimensional systems: oscillations and limit cycles. Hopf bifurcation and Poincaré-Bendixson theorem.
Three- and higher dimensional systems: chaos. The Lorenz system. Modelling of neuronal activity:
Hodgkin-Huxley equations. Examples throughout the course drawn from: population dynamics,
biochemical networks, ecological models, neuronal modelling, physiological systems.

BE3-HHEDM Health economics and decision making1

PROFESSOR N. BOSANQUET
Health Systems. What are key criteria for success? Case Studies UK/US/Europe/Asia. The NHS Plan and
the Wanless Report. The Reform phase. The international tool-kit of health reforms. The Changing health
Environment. The expected and unexpected shifts in the demand for health. Economic decision
techniques. CBA/CEA/CUA. Case study of NICE in England. The expensive economics of hospitals and of
doctors. The impacts of competition. Models for decision-making by health care firms. Porter/PIMS. The
Core Competence models. The product life cycle: how short can it get? Developing strategy. Case Studies
in corporate strategy. Pharmaceuticals—GSK, Astra Zeneca, US majors Pharma industry in Asia. Medical
equipment/devices. GE, Johnson and Johnson. Smith and Nephew. Medtronic. Health Futures.
Demands/needs from an ageing population. The outlook for health supply. How will health systems
change with more limited public funding?

BE3-HBIP Final year BEng project

DEPARTMENT OF BIOENGINEERING STAFF AND OTHERS
All three terms are spent on an extended research project. Projects are available in many different areas.
They are assessed by an interim report, a jointly written project report and a poster presentation.

1
The syllabus of this course is subject to change.
Bioengineering 15

BE3-HBMX Biomechanics
PROFESSOR C. ROSS ETHIER, DR D. OVERBY
At the successful completion of the module, students will be able to: identify key mechanical constituents
of cells and the extracellular matrix; understand how forces are transmitted between cells and their
surroundings; understand and manipulate the lumped parameter, tensegrity and actin foam models of
cellular biomechanics; be familiar with the anatomy and biomechanics of the respiratory system, including
the lungs and the associated structures; understand the role of surface tension and surfactant in lung
biomechanics; understand and be able to use models of mass transfer at the single alveolar and whole
lung level; understand the major determinants of blood rheology and the implications for blood flow in the
large arteries; be able to quantify steady and unsteady blood flow features in the large arteries;
understand the unique flow features of blood flow in capillaries; understand the composition and
mechanical properties of the arterial wall; be able to describe the mechanics of elastic wave propagation
in arteries, including factors that influence wave speed and reflection; describe the mechanics of all major
tissues of the body; calculate joint reaction force; estimate muscle force; discuss relationship between
muscle performance and anatomical and physiological constraints; be able to determine the movement of
body segments based on kinematic data; calculate segment and joint angles; calculate segment velocity
and acceleration; calculate joint forces from kinematic and kinetic data; be able to estimate muscle forces
from equilibrium equations; compute stresses in bone from static force balances using surrounding tissue
components; understand the mechanical factors that control the performance and growth of bone.

BE4-MAMI Advanced medical imaging

DR D. MCROBBIE AND OTHERS
X-ray imaging: Fluoroscopic/fluorographic imaging: image intensifiers, special techniques, DSA,
interventional radiology. Mammography: breast screening, risk vs benefit considerations. Digital
radiography: digital fluoroscopy. Fluorography, storage media, computed radiography, direct digital
radiography, PACS. Advanced image quality: MTF, evaluation of contrast/details thresholds, square wave
and edge response functions, ROC analysis, figure of merit. Performance assessment: Quality assurance,
test objects, phantoms. Radiation protection: risks and hazards, patient dose, occupational dose,
shielding, room design, the critical examination, dose reduction measures, measurement of patient dose,
dose surveys. Radiation protection legislation: Guidance, codes of practice, basic safety standards, EU
directives. X-ray CT Technology: Continuous rotation systems, slip rings, detector systems, relationship
between detector system and image quality, resolution enhancement techniques, flying focal spot, quarter
wave shift, third and fourth generation trade-offs. Image Reconstruction From Projections: Algebraic
interpretation, Central slice theorem, convolution backprojection, reconstruction filters, effect of filters on
image quality, image reconstruction artefacts, spatial sampling and aliasing. Iterative reconstruction, ART
and SIRT algorithms; ML reconstruction and EM algorithms. Spiral CT: pitch factor, interpolation,
reconstruction, multiple slice systems. Quantitative and functional CT: dynamic CT, bone densitometry, CT
angiography, CT fluoroscopy. CT Image Quality: noise, uniformity, slice width, spatial resolution, MTF,
figure of merit, test objects, artefacts. CT dosimetry: dose profile, CTDI, practical measurement, patient
dosimetry, scattered radiation, radiation protection issues, daily and monthly QA tests. Ultrasonic Imaging
Transducer Design and Construction: The piezoelectric effect, transducer construction and characteristics,
crystal thickness and resonance, damping, matching layer. Focussing techniques: lens, curved elements,
mirrors. Focal zone characteristics: DOF, PMI, focal area, far and near field characteristics. Transducer
arrays: Linear, linear phased, annular. Electro-acoustic modelling. U/S Field Theory: Beam Formation,
lateral and axial resolution, beam steering, focussing and apodization. Advanced Doppler Techniques:
Spectral Analysis, DFT, autocorrelation techniques. Colour haemodynamic systems. Velocity vector
analysis and display, digital RF signal processing. Doppler Signal Quantification: empirical, curve fitting
methods, mathematical methods, quantitative blood flow rate measurements, vessel compliance
measurements. Therapeutic Techniques: Bioeffects, thermal interactions/cavitation, transducer array
design, beam focussing, clinical studies: lithotripsy, ablation, hyperthermia, physiotherapy. three-
dimensional Ultrasound: Position sensing, image data acquisition, interpolation techniques, editing
procedures, volume and surface rendering techniques, display modes, ultrasound tomography.
16 Undergraduate syllabuses

Ultrasound RF Analysis: Radiofrequency signal data, signal analysis: bulk properties, structural
organisation parameters. Systems Architecture: Equipment types, system design, QA protocols, Acoustic
output measurements, preventative maintenance protocols, first line maintenance. Contrast Agents and
Harmonic Imaging: Nature of contrast agents, areas of clinical application, fundamental and harmonic
imaging, stimulated acoustic emissions, drug delivery. Dosimetry and Safety: Thermal, non-linear and
cavitation effects. Cellular effects. Cooling mechanisms in vivo. Ultrasound field measurements, thermal
and mechanical indices, operating parameters, International safety regulations. Magnetic Resonance
Imaging NMR phenomenon. Reference frames, resonance and Bloch equations. MR Hardware: Magnet
design and constraints, superconductivity, gradient coil design, gradient performance, eddy currents and
shielding. Components of Receiver chain: coil design, coil loading, quadrature and array coils, SNR vs field
strength. Advanced pulse sequences: CPMG, Stimulated echoes. Fast Imaging Sequences: k-space,
segmented sequences, FLASH, turbo-FLASH, Fast spin-echo, Echo-planar, sequential scanning. Clinical
Scanning Techniques: Contrast agents, paramagnetic ions, positive and negative contrast agents, fat
suppression, chemical shift, chemical and motion artefacts, gating, STIR, in and out-phase techniques,
chemical selection, spatial saturation. MR Angiography: Physics of flow effects, in-flow, phase effects,
gradient moment rephasing, time-of-flight MRA, phase-contrast MRA, two-dimensional and three-
dimensional techniques, TONE, MIP, quantitative velocity measurement, Fourier encoding. Advanced
contrast mechanisms: BOLD effect, diffusion, perfusion, magnetisation transfer. MR Spectroscopy:
chemical shift, common nuclei for investigation, spectral features, line widths, technical requirements,
localisation methods, CSI. MR Image Quality: SNR and resolution, assessing image quality, test objects,
parameters, test materials. MR Safety II: Bioeffects and safety, biological effects of static, time-varying
fields, magneto-hydrodynamic effect, neuro-muscular stimulation, heating, SAR, exposure limits and units.
Pacemakers, implants, standards, guidance and organisational issues, siting and environmental issues.

BE3-MABM Advanced biological modelling

DR M. BARAHONA
Optimisation. Introduction to optimisation: definitions and concepts, standard formulation. Convexity.
Combinatorial explosion and computationally hard problems. Least squares solution: pseudo-inverse;
multivariable case. Applications: data fitting. Constrained optimisation: linear equality constraints:
Lagrange multipliers; linear inequality constraints: linear programming. Simplex algorithm. Applications.
Gradient methods: steepest descent; dissipative gradient dynamics; improved gradient methods. Heuristic
methods: simulated annealing: continuous version; relation to stochastic differential equations. Neural
networks: general architectures; nonlinear units; back-propagation; applications and relation to least
squares. Combinatorial optimisation: ‘hard’ problems, enumeration, combinatorial explosion. Examples
and formulation. Heuristic algorithms: simulated annealing (discrete version); evolutionary (genetic)
algorithms. Applications. Discrete-time systems (maps): Linear difference equations: general solution;
auto-regressive models; relation to z-transform and Fourier analysis. Nonlinear maps: fixed points;
stability; bifurcations. Poincaré section. Cobweb analysis. Examples: logistic map in population dynamics
(period-doubling bifurcation and chaos); genetic populations. Control and optimisation in maps.
Applications: management of fisheries. Advanced topics (background lectures + journal papers + class
discussion + mini essay) Networks in biology: graph theoretical concepts and properties; random graphs;
deterministic, constructive graphs; small-worlds; scale-free graphs. Applications in biology, economics,
sociology, engineering. Nonlinear control in biology: recurrence plots and embeddings; projection onto
the stable manifolds; stabilisation of unstable periodic orbits and anti-control. Applications to
physiological monitoring.

BE3-MCNS Computational neuroscience

DR S. SCHULTZ, DR K. HARRIS
Definition and Scope: What is Computational Neuroscience? Electrical properties of neurons: the cell
membrane, integrate-and-fire and conductance-based neuron models, spike rate adaptation,
refractoriness. The Hodgkin and Huxley model. Axons and dendrites: the cable equation, multi-
compartment neuron models. Synapses: synaptic physiology, synaptic models. Neural circuits: the
“connectome”. Systems – visual information processing in the retina, thalamus and visual cortex. Visual
Bioengineering 17

perception. Vision in flying insects: optic flow processing. Simple and complex cells. Sparse coding in the
visual system; natural scene statistics. Linear filter models of visual processing. The somatosensory
system: spinal cord, ventral posterior nucleus, somatosensory cortex, the sense of touch. Somatotopic
maps. The motor system: spinal mechanisms, motor cortex and voluntary movement, the cerebellum.
Sensorimotor control systems. The hippocampal system and memory. Neural network models: Firing rate
models. Feedforward networks: the perceptron, multilayer networks. Coordinate transformations.
Recurrent networks: linear and nonlinear recurrent networks, the Hopfield network, associative memories.
Adaptation and learning: supervised and unsupervised learning. Networks of integrate-and-fire neurons.
Spike train statistics: variability of inter-spike intervals. Receptive fields and sensory information
processing. Reverse correlation and spike-triggered analysis methods; constructing simple and complex
V1 receptive fields. Information
theory and the neural code. Spike timing and spike count codes. Population coding. Population firing rate
and “labelled line” codes. The neural code and perception. ROC analysis. Decoding neural spike trains.

BE3-MSYNB Synthetic biology

DR G. BALDWIN, PROFESSOR R.I. KITNEY, PROFESSOR P. FREEMONT, DR R. ENDRES
(The syllabus of this course is subject to change)
This lecture course is taught jointly between Biochemistry and Bioengineering, and consists of
two phases. In the first phase, students from both Departments are taught separately, and in the
second phase, they are taught jointly. This syllabus contains only the material presented to
Bioengineering students.
PHASE 1 Biochemistry for Bioengineers: DNA structure and the central dogma of molecular biology;
Molecular biology: Cloning techniques and manipulating DNA, Plasmid vectors, Restriction enzymes, PCR.
RNA transcription: Turning genes on and off and controlling the flow of information. Enzyme kinetics:
Principles of enzyme kinetics and binding curves. Structure and function: An overview of three-
dimensional macromolecular structure and interactions. Practicals: Essential microbiology, plating and
propagating bacterial strains – overexpression of a restriction endonuclease and plasmid DNA
preparation; restriction enzyme digestion of DNA; Electrophoresis of DNA. Computer Practical: Modelling
of a biological system - simplification and abstraction; choice of models; choice of modelling tools –
differential equations and graphical representations; Analysis – data representation.
PHASE 2 Joint Programme. Transcriptional control in biological systems; examples of biological systems;
systems analysis of biological systems. The biological system will then be analysed
from a system perspective to understand how the components interact to give the observed biological
behaviour.
A series of practicals, group exercises, round-table discussions and team projects will then be conducted
centered around the theme of biobricks.

BE4-MBMI Brain-machine interfaces

DR S. SCHULTZ, DR K. HARRIS
Introduction: history of Brain-Machine Interfaces (BMIs). Motivations for BMI development. Tetraplegia
and "Locked In" Syndrome as example application domains. Non-invasive BMIs: electro-encephalography
- physics, applications and bandwidth limitations. Magneto-encephalography. Functional magnetic
resonance imaging for "brain reading". Functional electrical stimulation. Transcranial magnetic
stimulation. Cochlear implants. Invasive BMIs: micro-electrode based neural interface technology. Nerve-
cuff electrodes and peripheral nervous system applications. Applications to spinal cord injury. Central
nervous system applications. Retinal prostheses - electrical microstimulation and optoelectronic
approaches. Other modalities and crossmodal prostheses. Cortical visual prostheses. Motor system
neuroprosthetics. ‘Mind control' of a robot arm. Signal processing and neural decoding algorithms for BMI
applications. Performance measurement. Brain plasticity and BMIs. Deep brain stimulation: applications
to Parkinsons Disease and absence seizures. The electrode-tissue interface: gliosis and scarring.
Biocompatibility issues. Regulatory and ethical issues. Prospects for the future.
18 Undergraduate syllabuses

BE4-MNMC Neuromuscular control

DR E. BURDET
Introduction: A system level approach of human motor control considering the biological mechanics,
sensorics and neural control; feedforward and feedback; summary of linear control; force and impedance;
measurement systems. Muscle mechanics and control: sarcomere properties; regulation of myosin
binding; force regulation by firing rate; length-tension and force-velocity relationship; elastic energy
storage; muscle stiffness and damping. One-joint system and reflexes: Exteroceptors and proprioceptors;
muscle sensory receptors; spinal organization; reflexes; geometrical measurement of muscle-tendon
parameters, combination of elastic elements; joint control. Multi-joint multi-muscle system: Direct and
inverse kinematics; differential kinematics; rigid-body dynamic model; transformation of force and
impedance; intersegmental analysis; redundant muscle systems to optimize biomechanical constraints.
Multi-joint control and motor learning: A model of force and impedance in movements; evidence of
internal dynamic model; nonlinear adaptive control of arm movements; joint-level control of force; multi-
muscle control of force and impedance. Application in Sports and Rehabilitation Showcases of sports
biomechanics, post-stroke rehabilitation treatment; gait rehabilitation devices and strategies; arm
rehabilitation devices and modalities; effectiveness of robot-aided therapies.

BE4-MCBMX Cellular biomechanics

DR D. OVERBY
Cellular Biology strand: overview of how mechanical forces impact biological function, introduction to
signalling mechanisms, receptors, overview of cell architecture, cytoskeleton, coupling of the cytoskeleton
to the cell membrane, focal adhesion molecules, cell-cell and cell-matrix coupling, overview of
extracellular matrix.
Measurement strand: Introduction to measurement techniques on a cellular level. Advanced methods for
measuring mechanical properties of individual cells: magnetic bead cytometry, magnetic bead twisting,
AFM, optical tweezers, microfabricated devices. Determining the mechanical properties of individual
molecules: AFM and steered molecular dynamics.
Mechanical strand: mechanical models of the cell, models of molecular mechanics Role of pre-stress in
cellular biomechanics, Cellular biomechanics in whole tissue.
Molecular Strand: conversion of mechanical stimuli into biochemical signals, mechanical effects on gene
expression, mechanotransduction at focal adhesions, mechanosensitive molecules and force-dependent
changes in molecular conformation, role of stretch-activated ion channels, membrane deformations and
cytoskeleton.
Case studies in mechanobiology: Red cell membrane biomechanics;vascular endothelium and control of
arterial calibre; Osteoclasts and osteoblasts and control of bone density; Outer hair cells and acoustic
transduction; Chondrocytes and control of cartilage composition; Trabecular meshwork and regulation of
intraocular pressure; Cardiac myocytes and electrical-mechanical coupling in the heart.

BE4-MOBMX Orthopaedic biomechanics

DR S. SHEFELBINE
Introduction: History of biomechanics; Anatomical definitions (planes, movements). Musculoskeletal
tissues (bone, tendon, muscle, ligament, cartilage). Muscle: structure, function; models of muscle (Hill,
etc.); musculoskeletal force analysis, inverse dynamics, optimization routines; gait analysis; Bone
mechanics, strength, structure, function; growth (and deformities) diseases (osteoporosis, osteogenesis
imperfecta, osteomalacia); fracture healing; distraction osteogenesis; modelling and remodelling.
Cartilage structure, function; osteoarthritis, rheumatoid arthritis; treatments and therapies. Joints
structure, function (specific joints), mechanics, tribiology; implants (knee, hip, shoulder). Ligaments and
Tendons: structure, function, mechanics; problems with, surgical repair; Musculoskeletal biomaterials:
tissue differentiation; tissue engineering; Spine biomechanics: structure, function, tissues; problems with
spine and treatments; Clinical considerations and perspective. Evolution of bone.
Bioengineering 19

BE4-MMLNC Machine learning and neural computation

DR ALDO FAISAL
Syllabus in preparation

BE3-MMGP Third year group project

DEPARTMENT OF BIOENGINEERING STAFF AND OTHERS
All three terms are spent on an extended research project. Projects are available in many different areas.
They are assessed by an interim report, a jointly written project report and a
poster presentation.

BE4-MMIP Final year MEng project

DEPARTMENT OF BIOENGINEERING STAFF AND OTHERS
All three terms are spent on an extended research project. Projects are available in many different areas.
They are assessed by an interim report, a written dissertation and an oral presentation.

Department of Mechanical Engineering options1

ME3-HFFM Fundamentals of fracture mechanics
ME3-HMSD Machine system dynamics
ME3-HSAN Stress analysis
ME3-HSPAP Structure properties and applications of polymers
ME3-HFMX Fluid mechanics
ME3-HTRB Tribology
ME3-HCCM Computational continuum mechanics

Department of Electrical and Electronic Engineering options1

E.3.01 Analogue integrated circuits and systems
E.3.02 Instrumentation
E.3.05 Digital system design
E.3.07 Digital signal processing
E.3.09 Control engineering
E.3.11 Advanced electronic devices
E.3.12 Optoelectronics
E.3.16 Artificial intelligence

Department of Computing options1

Comp.493 Intelligent data analysis and probabilistic inference
Comp.341 Introduction to bioinformatics

Department of Materials options1

MSE.315 Biomaterials and artificial organs
MSE.4XX Advanced Biomaterials

1 Please check the relevant departmental sections for syllabus details. Availability of some modules
subject to change.