PHYSICS SUBJECT BOARD – CORE COURSES

Integrated M.Sc. - Ph.D. Programme

P-101 / C-201 : Mathematical Methods

P-102 / C-203 : Numerical Methods and Algorithms in Chemical Physics

P-103 : Classical Mechanics

P-105 / C-202 : Quantum Mechanics – I

P-106 : Classical Electrodynamics – I

P-107 : Experimental Methods

+ All Core courses of Ph.D. Programme

Ph.D. Programme
P-202 : Numerical Methods – II

P-204 /C-103 : Statistical Mechanics – I

P-205 : Quantum Mechanics II / Advanced Quantum Mechanics

P-206 : Classical Electrodynamics – II

P-207 : Advance Experimental Methods

 CHEMISTRY SUBJECT BOARD – CORE COURSES

Integrated M.Sc. - Ph.D. Programme

C-101 : Physics & Chemistry of materials: Bulk to Nano

C-104 : Organic Chemistry (Elective for Ph.D.)

C-105 : Inorganic Chemistry (Elective for Ph.D.)

C-106 : Spectroscopy of atoms and molecules

C-203 / P-102 : Numerical Methods and Algorithms in Chemical Physics

+ All Core courses of Ph.D. Programme

Ph.D. Programme
C-201 / P-101 : Mathematical Methods

C-202 / P-105 : Quantum Mechanics - I

C-205 : Principles of NMR Spectroscopy (Elective for I.Ph.D.)

 BIOLOGY SUBJECT BOARD – BASIC COURSES

B-201 : Basic Cell Biology

B-202 : Cell Physiology and Cell signaling

B-203 / C-204 : Biophysics

B-204 : Basic Mathematics for Biologists

B-205 : Biological Thermodynamics

B-206 : Molecular Genetics

B-207 : Basic Immunology

 ELECTIVE COURSES

E-201 : Scientific Communication E-405 : Soft Matter: Equilibrium and Dynamics

E-202 : Error Analysis and Statistical Inference in

E-406 : Advanced Mathematical Physics
Experiments
E-203 : Computer Programming using Python
E-407 : Advanced continuum Mechanics
language

E-204 : Advanced Topics in Organic Chemistry and E-408 : Field Theory

Inorganic Chemistry
E-205 : Research Methodology
E-409 : Nonlinear Dynamics

E-206 : NMR Instrumentation E-410 : Intense laser matter interactions

E-207 : Biophysics E-411 : Solid State NMR

E-412 : Principles in Cancer & Cancer Stem cell

E-301 : Optics
biology

E-302 : Condensed Matter Physics E-413 : Fluorescence Methods in Cellular Biophysics

E-303 : Atomic & Molecular Physics E-414 : Mechanobiology

E-306 : Protein structure and synthesis E-415 : Advanced Mathematics

E-307 : Mechanisms of genome surveillance and E-416 : Electronic structure theory of matters
repair in biological systems

E-401 : Advanced Computational Methods E-417 : Magnetism

E-402 : Advanced Dynamics E-418 : Quantum Thermodynamics

E-403 : Advanced Statistical Mechanics / Statistical

E-419 : Biology of Sensory systems
Mechanics – II

E-404 : Phase Transitions, Ordering and Dynamics

Note:
1) Core / Basic courses from other disciplines may be taken as electives and the credits are allocated as
per the subject board guidelines under which the student is admitted / registered. The course work for
registration must be as per the requirement of respective subject boards.
2) The Research Methodology course is a compulsory 4 credit course that has to be taken by students
of all subject-boards.
P-101 / C-201: Mathematical Methods 4 Credits

 Linear vector space, series (convergence/divergence etc.)

 special functions such as Laguerre
 Hermite (besides Bessel and Legendre),
 spherical tensor operators (a bit of angular momentum here)
 Determinants and Matrix Algebra: Properties of determinants and matrices, Linear
transformation, Eigenvector-Eigenvalue problems, Similarity and unitary transformations
 Differential Equations: Separable, Exact, and First-order homogeneous linear differential
equations, Sturm-Liouville eigenvalue problem, Legendre polynomials and properties, Spherical
harmonics, Bessel equations and properties
 Vector Algebra: Gradient, Divergence, Curl, Gauss and Stokes theorem, Curvilinear coordinates,
Tensor analysis
 Complex Analysis : Cauchy-Riemann conditions, Analytic functions, Contour integrals, Taylor
and Laurent series, Singularities, Residue theorem, Gamma and Beta function, Method of
steepest descent, Stirling series, asymptotic series, Convergence tests
 Integral Transforms : Fourier series, Fourier transform, Laplace transform, Solution of initial
boundary-value problem, Convolution
 Error Analysis

P-102 / C-203: Numerical Methods and Algorithms in Chemical Physics 4 Credits

Part – 1 Foundation Topics

 Computers
 Linux - system commands.
 Fortran90 - basics, style, usage.
 Python - trends in modern programming.
 Numerical libraries - BLAS, LAPACK/Numpy, Scipy
 Examples from physical chemistry
 Equations of states: molar volume, heat capacity, virial coefficients
 Solving equations of chemical equilibria, balancing stoichiometric equations
 Principal coordinate system, moment of inertia
Math topics:
 Error analysis: Algorithms and error propagation
 Data analysis: Data modeling, principal component analysis
 Roots of equations: Newton-Raphson
 Numerical methods: Overview
Part - 2 Topics in Molecular Quantum Mechanics
 Time-independent variational problems
 Vibrational Schrödinger equation: Harmonic oscillator, Morse oscillator, diatomic
molecules, Dimensionless normal coordinates, potential energy surface fitting
 Electronic problems: Hückel molecular orbital method, Ground electronic state of
Helium atom, Hartree-Fock approximation
 NMR spectrum of AX spin system
  Math topics:
 Partial Differential Equations: Basis set representation
 Numerical integration: Gaussian quadrature, Monte Carlo
 Eigensolvers: Jacobi, inverse iteration, Lanczos
 Linear systems of equations: Least squares polynomial fitting, matrix inversion,
condition number, direct and iterative linear solvers
 Time-dependent problems
 Time-evolution of a non-stationary state, wave packets
 Bound states by imaginary time propagation
 Survival probability, correlation spectra
 Equation of motion of a harmonic oscillator, Coupled-rate equation for Lindemann-
Hinshelwood mechanism, Bloch equations
 Math topics:
 Ordinary differential equations: Euler’s method, Runge-Kutta, Predictor-Corrector
 Fourier series and Fourier transform. Fourier transform pairs in ab-initio quantum
chemistry
 Laplace transform, connection to integral equations
Part – 3 Topics in Molecular Classical Mechanics
 Introduction to Molecular Dynamics simulation
 Initialization of system, Force calculation from classical potential, Implementation of
periodic boundary condition, Integration schemes of Newtonian equation of motion.
Simple monoatomic liquids as the test system.
 Math topics:
 Ordinary differential equations: leap frog, verlet and velocity verlet
 Introduction to Monte Carlo simulation
 Initialization of system, Implementation of metropolis algorithm, Translational and
rotational monte carlo moves. Generation of Neighbor list (verlet and linked list).
Simple monoatomic liquids as the test system.
 Math topics:
 Probability and detailed balance, Sorting
 Calculation of static and dynamic property
Equation of state of a liquid, Pair correlation function and Static structure factor. self-
diffusion constant from Monte Carlo and Molecular Dynamics simulation. Handling
long range electrostatics using ewald summation.
 Math topics:
 Correlation functions and Histograms
 Fourier Transform.

P-103: Classical Mechanics 4 Credits

 One and Two-dimensional dynamical systems : Newton’s laws of motion, Harmonic
oscillator, Over-damped oscillator, Simple pendulum, Time period of oscillations, Fixed
points, simple bifurcations, Phase plane/space.
 Lagrangian formalism Elements of calculus of variations, Generalised coordinates,
Principle of least action, Euler-Lagrange equations, Constraints, Lagrangian for a free
particle and system of particles, Conservation laws, Mechanical similarity
  Central force fields and Collisions Motion in one dimension, Reduced mass, Motion in a
central field, Kepler’s problem, Elastic collisions, Scattering
 Small Oscillations : Free and forced oscillations, Vibrations of molecules, Damped
oscillations, Resonance, Parametric resonance, Regular perturbation theory, Anharmonic
oscillator, Motion in a rapidly oscillating field
 Hamiltonian formalism Hamilton’s equation, Poisson brackets, Canonical transformation,
Liouville’s theorem, Hamilton-Jacobi theory, Action-Angle variables Integrable and
NonIntegrable systems, Adiabatic invariants, and elements of time- dependent
perturbation theory.

P-105 / C-202: Quantum Mechanics - I 4 Credits

 Origins of the Quantum Theory: Radiation laws, particle aspects of light (photoelectric
effect, Compton scattering, pair-production, Bremsstrahlung, Frank-Hertz experiment),
wave aspects of matter (Davisson-Germer experiment), wave-particle duality, old
quantum theory with applications to simple potentials (Bohr atom, Ritz combination
principle, Wilson-Sommerfeld quantization rules), Bohr’s correspondence principle
 The Wave function: Wave-particle duality, Schroedinger equation, probability
interpretation of wave function, wave function in momentum space, Dirac-delta
function, time-independent Schrodinger equation: eigenvalues/eigenfunctions
 One-dimensional problems: Potential steps / wells / barriers, delta function potentials,
tunneling, harmonic oscillator (algebraic approach for harmonic oscillator)
 Structure of wave mechanics: Sturm-Liouville problem, vector space and operators,
degeneracy, time-dependence, operator methods
 Three-dimensional Systems: Angular momentum, ladder operators, spherical
coordinates, three-dimensional isotropic oscillator, central potentials (H atom), angular
momentum operator (matrix representation)
 Angular momentum algebra
 Approximation Methods: Variational theory, linear and nonlinear variational methods
(H2+, Helium, H, secular determinant), Rayleigh-Schroedinger perturbation (non-
degenerate zero-order case, degenerate zero-order case, matrix eigenvalues, cubic well,
quartic well, Stark effect, Van der Walls interaction), WKB method
 Time-Dependent Quantum Mechanics: Time-dependent Schroedinger equation, time-
dependent expectation values, semi-classical treatment of radiation, time-dependent
potential, periodic potential, transition frequencies, transition rules, sudden
approximation (adiabatic theorem), time-dependent perturbation theory, Fermi’s golden
rule. two-level systems, emission and absorption of radiation
 Many Particles: Identical particles, indistinguishability, Pauli exclusion principle, Slater
determinant, band structure of solids, quantum statistics, electron gas
 Atomic Spectra: Term symbols, fine structure of H, Zeeman effect, hyperfine splitting in
H, spin-orbit coupling, He atom, energy level diagrams, selection rules, radiation of
atoms (2p -> 1s transition, lifetime and linewidth, Einstein coefficients)
 Molecular Structure and Bonding: Molecular hamiltonian, Born-Oppenheimer
approximation, MOs as LCAOs, diatomic molecules (bond order, MO diagram), hybrid
orbitals, perturbation theory for molecular orbitals, Walsh diagrams, elements of
molecular spectroscopy, Hellmann-Feynman theorem
 Measurement and Interpretation: Determinism, locality, measurement, hidden
variables, EPR paradox, Bell’s Theorem, cat paradox, Cohenhagen interpretation
P-106: Classical Electrodynamics – I 4 Credits

 Single charged particles in E and B fields

 Electrostatic fields, potentials, energy and forces
 Analytical and numerical ways of solving electrostatic potential problems
 Idealized and real charge distributions and their potentials
 Current distributions and magnetic fields
 Magnetic materials
 Maxwell's equations, EM waves and their propagation in free space and in media.
 EM waves in confined spaces
P-107: Experimental Methods 8 Credits

 e/m Experiments. (1credit)

 Frank-Hertz experiment. (1credit)
 Michelson Interferometer. (1credit)
 Zeeman effect. (1credit)
 Plank Constant measurement. (1credit)
 Fiber coupling and profile mapping. (1credit)
 4-probe conductivity measurement. (1credit)
 Basic LabVIEW experiment. (1credit)

P-202: Numerical Methods - II 4 Credits

 Elements of Computer Programming: Flow-charts, Basic of C language (arrays, pointers,

functions), Add/Subtract/Multiply/division, Round of errors with some examples,
Data analysis using Matlab, python, gnuplot
 Linear algebra: Gauss elimination, Gram-Schmidt orthogonalization, Eigenvalue
problem, Examples using lapack.
 Differentiation and Integration: numerical schemes for differentiation (finite differences
and spectral methods) and integration (Trapezoidal, Simposon's 1/3, Gaussian
Quadratures).
 Ordinary Differential Equations: Euler, Runge-Kutta time integration and velocity verlet
scheme, Example elucidating Newton's equation of motion.
 Partial Differential Equation: Diffusion Equation, Advection equation, Advection-
diffusion equation, Laplace, Poisson equation, Helmholtz equation.
 Conjugate gradient method. Least square method of fitting data to different functions.
Linear, polynomial and non-linear functions (Levenberg-Marquardt algorithm),
Interpolation (Linear, polynomial, spline, etc.).
 Advanced topics: Introduction to Molecular Dynamics/Monte Carlo, Lattice Boltzmann
and Navier-Stokes Equations

P-204 / C-103: Statistical Mechanics - I 4 Credits

 Brief overview of Equilibrium Thermodynamics: Equilibrium states, Extensive and

intensive variables, Laws of thermodynamics, Entropy and free energy, Chemical
potential, Phase equilibria
 Ensembles in Statistical Mechanics: Introduction to microcanonical, canonical and grand
canonical ensembles, Partition functions and connections to thermodynamic quantities
 Fluctuations, correlations and response: Correlation functions for liquids and magnets,
Relation between fluctuations and response to external fields, Long range order
  Application of Statistical Mechanics to the Classical ideal gas, Rotational and vibrational
spectra, Heat capacity of crystals, Spin systems, Chemical reactions, Polymer chains.
 Quantum Statistics: Fermi and Bose statistics, Ideal Fermi gas and Ideal Bose gas,
recovering the classical limit, Fermi gases at low temperature, Bose-Einstein
condensation.
 Statistical Mechanics of Interacting Systems 1: Interactions as perturbations: High
temperature expansions, Virial expansions
 Statistical mechanics of interacting systems 2: Simple liquids and magnets: the lattice gas
model, Change of state, Mean field theory
 Applications of computer simulation: Introduction to Monte Carlo methods,
Connection with statistical mechanics, Simulations of model magnets Statistical
Mechanics of Interacting Systems 1: Interactions as perturbations: High temperature
expansions, Virial expansions.
 Statistical mechanics of interacting systems 2: Simple liquids and magnets: the lattice gas
model, Change of state, mean field theory.
 Applications of computer simulation: Introduction to Monte Carlo methods, Connection
with statistical mechanics, Simulations of model polymers and magnets

P-205: Quantum Mechanics – II / Advanced Quantum Mechanics 4 Credits

 Time dependant Quantum Mechanics

Time dependant Schroedinger equation, perturbation theory, transition probabilities
 Group theory and angular momentum algebra
Rotation groups: Rotation matrices D, Angular momentum addition: Clebsch-Gordon
coefficients, Wigner’s theorem, SU(2), SO(3), Wigner 3-j, 6-j, 9-j symbols, Racah coefficients.
 Second quantization
Quantization of fields, second quantization, Many fermion systems, interacting electrons, Wick’s
theorem
 Interaction of Radiation with Matter
Classical theory of interaction of matter and field, absorption and emission of light, light
scattering, interaction of monochromatic radiation, Radiation damping
 Density Matrices
Density operators and density matrices, Liouville equation, Bloch Equation
 Scattering theory
Elastic scattering: partial wave analysis, Born series and Born approximation, optical theorem;
wavepackets, flux, Green’s function, scattering matrix, semiclassical theory, Lippmann-
Schwinger equation
 Theories of reaction rates
Transition state theory: Rate of barrier crossing, RRKM theory and rate of unimolecular
reactions, Rate constants for bimolecular reactions
 Molecular energy transfer
Introduction to collisional energy transfer, state changing collisions, vibrational energy transfer,
electronic energy transfer
 Relativistic quantum mechanics
Elements of special relativity, relativistic Hamiltonian, Dirac matrices, origin of electron spin,
Dirac fields
P-206: Classical Electrodynamics - II 4 Credits

 Special relativity and relativistic kinematics

 Covariant (Lagrangian) formulation of electrodynamics
 Motion of charges and electromagnetic fields: Leinard Weichert potentials
 Charges in electromagnetic fields: radiation from an accelerated Charge,
Bremsstrahlung, Cherenkov, Synchrotron and Transition.
 Radiation reaction: energy loss mechanisms
 Electromagnetic fields propagating through matter: scattering, diffractionDispersion, causality
and Kramers-Kronig relation. Metamaterials: Negative index and hyperbolic media. Perfect
lensing. Optical pulses and beams: Fast and slow light. Goos-Hanchen and Feodorov-Imbert
shifts. Spin-orbit interaction with light
 Special topics: Lasers and nonlinear optics, novel optical phenomena, Plasmonics and nano-
optics

P-207: Advance Experimental Methods 12 Credits

 Study the hyperfine spectrum of Rb. (2 credits)

 Static and Dynamic Mechanical Analyses of polymer membranes (2 credits)
 Proton and hydroxyl ion transport studies on ion exchange
membranes using electrochemical impedance spectroscopy - Humidity
and Temperature dependency (2 credits)
 Magneto-Resistance Measurement on thin films (2 credits)
 Earth field NMR/ 300 MHz. (2 credits)
 Contact Angle Measurement (2 credits)

C-101: Physics & Chemistry of Materials: Bulk to Nano 4 Credits

Pre-requisites: P-105 / C-202

 Introduction to semiconductors: Metal, Semiconductor and Insulator, Formation of

Energy bands, carrier concentration and transport phenomena, electrochemical potential
& Fermi-Dirac statistics, metal-semiconductor contacts (ohmic & Schottky). P-N junction
characteristics, Transistors-Uni polar and bi-polar, Metal-oxide-semiconductor
characteristics, MOSFETs. Scaling down effects - properties at the nano-scale: change in
density of states due to confinement.
 Introduction to magnetism: Classifications - dia, para, ferro and anti-ferromagnetism.
Domain wall theory,Magnetic anisotropy, exchange interactions, Introduction to
meanfield approximation, periodic table of magnetic materials, magnons, and
demagnetization factor, Size effects in magnetism.
 Nano-materials & nano-probes : Synthesis of nanomaterials - top-down & bottom-up
approaches, characterization tools - optical and electron spectroscopy & microscopy, and
mechanical analysis, introduction to electrochemistry.
 Nanofabrication & Nano-devices: Basics of fabrication techniques: photo-lithography,
Ebeam lithography, etching techniques. Nano-devices–molecular electronics, resonant
tunneling devices, single electron transistors.
 Extra-components: Guest lectures, Lab tour & Student presentations (covering
important characterization methods / device physics).
C-104 : Organic Chemistry 4 Credits

1. Chemical bonding and molecular structure (2 lectures)

• Atomic and molecular orbitals
• Hybridization of atomic orbitals
• Introduction to frontier molecular orbitals
• Dipole moment and inductive effect
• Hyperconjugation and resonance structures
• pKa – Acidity and structure
• Aromaticity
2. Conformation and stereochemistry (3 lectures)
• Rotation & rigidity
• Rotation barriers
• Ring strain
• Optical activity, symmetry & chirality
• Enantiomers, diastereomers & meso-compounds
• R,S nomenclature
• Racemic mixture & resolution
• Stereoselectivity
• Prochirality
• Chiral compounds with no stereogenic centres
• The importance of being asymmetric
3. Organic reactions (8 lectures)
• Elimination and substitution reactions (Reaction rates and activation energy, α-eliminations,
β-elimations, SN1, SN2 reactions)
• Addition reactions
• Oxidations and Reductions
• Rearrangements
• Fragmentation
• Cross-coupling
• Metathesis
4. Reactive intermediates (3 lectures)
• Carbocations
• Carbanions
• Carbenes
• Carbynes
• Radicals
5. Retrosynthetic analysis (2 lectures)
• Planning a synthesis backwards
• Disconnection approach
• Synthons (donor & acceptor synthons)
• ‘Natural reactivity’ and ‘umpolung’
6. Concerted organic reactions & organic photochemistry (4 lectures)
• Introduction to pericyclic reactions
• Molecular orbitals of conjugated π-electron systems
• Electrocyclic reactions, cycloaddition reactions, group transfer reactions and sigmatropic
rearrangements
• Photoisomerization, di-π-methane rearrangement, de Mayo Reaction, Paterno-Büchi reaction,
Photoinduced Electron Transfer, Norrish
Type I and II
  Photochemistry in everyday life
7. Organic chemistry of Biomolecules (2 lectures)
• Amino acids & Sugars
• Peptides, Proteins & Nucleic acids

C-105 : Inorganic Chemistry 4 Credits

1. Chemistry of s- and p-Block Elements (8 lectures)

[a] Chemistry of compounds involving lithium and magnesium: synthesis, structure and reactivity
[b] Chemistry of boron: boranes, bonding of boranes, synthesis and reactivity, boron clusters,
carboranes and metallacarboranes
[c] Aluminum and silicon chemistry: synthesis and application
[d] Chemistry of compounds involving magnesium, boron, silicon, aluminum, germanium, tin, and
lead: synthesis, structure and reactivity

2. Transition Metal and Lanthanide Chemistry (8 lectures)

[a] Synthesis and structure of mononuclear and multinuclear transition metal complexes
[b] Theories of bonding: crystal-field and molecular orbital theory, effects of ligand-field
[c] Concepts of orbital symmetries for d-orbital splitting diagrams in different stereochemistry
[d] Spectroscopy of transition-metal complexes
[e] Magnetism of transition-metal complexes
[f] Supramolecular structures involving transition metal complexes
[g] Coordination complexes in applied chemistry
[h] Introduction of lanthanide chemistry
[i] Synthesis of organo-lanthanide complexes
[j] Applications of lanthanide complexes - magnetism and catalysis

3. Organometallic Chemistry (8 lectures)

[a] dn electron counting
[b] Elimination and addition Reactions involving transition metal complexes and their consequence on
catalytic process
[c] Syntheses and application of organometallic reagents
[d] Coupling reactions: Kumada coupling, Suzuki-Miyaura coupling, Hiyama coupling, Sonogashira
coupling, Negeshi coupling, Stille coupling, Buchwald-Hartwig Coupling, Heck reaction, Click
Reactions
[e] Homogeneous catalysis and catalysts: Alkene isomerization, hydrogenation, hydroformylation,
Monsanto acetic acid process.
[f] Alkene polymerization, cross coupling reactions, metathesis, C-H activation, and functionalization
C-106 : Spectroscopy of atoms and molecules 4 Credits
Pre-requisites: P-105 / C-202
1. Interaction of radiation with matter:
 Blackbody radiation, absorption and emission of radiation (semi – classical description)
 Review of time – dependent perturbation theory
 Einstein coefficients, relaxation phenomena
 Transition probabilities and spectral line shapes
2. Molecular symmetry and group theory:
 Symmetry operations, introduction to point groups
 Review of linear algebra, matrix representation of groups
  Quantum mechanics and group theory, selected applications
3. Atomic spectroscopy:
 One electron systems, many electron systems, selection rules
 Zeeman and Stark effect
4. Molecular spectroscopy:
 Rotational spectroscopy of diatomic and linear molecules, asymmetric tops
 Vibrational spectroscopy of diatomic and polyatomic molecules
 Symmetry and normal modes
 Light scattering and Raman spectroscopy
 Electronic spectroscopy of diatomic and polyatomic molecules
 Case study: H2, O2, NO, H2O, NH3 and C6H6 molecules
5. Spectroscopic Instrumentation and introduction to nonlinear optics:
 Spectrograph, monochromator and interferometers, detection of light
 Lasers as spectroscopic light sources
 Nonlinear optical mixing techniques, phase matching, quasi – phase matching, sum/difference
frequency and higher harmonic generation, optical parametric oscillators
6. Selected applications:
 Laser spectroscopy in molecular beams, double resonance spectroscopy
 Time resolved laser spectroscopy, pump – probe techniques
 Laser spectroscopy of collision processes

B-201: Cell Biology 3 Credits

This course will explore biological function at the level of the cell (as opposed to the level of the full
multicellular organism as in Developmental Biology or Genetics, the level of individual biomolecules as
in Biochemistry, or full ecosystems as in Ecological Biology or Population Genetics). A lot of interesting
biological phenomena is observed at this intermediate scale, and affects function across the different
levels. Of particular interest are processes of mechanical or biochemical regulation of cellular function,
which have been generating a lot of excitement in recent times. We will study these through a mix of
lectures and discussions of both classic and recent papers. Topics to be covered are presented below.

1. Basic processes of transcriptional, translational and post-translational regulation:

 Endocytosis, exocytosis and protein export
 RNA production, splicing and export
 Regulatory roles of non-coding RNA
 Biochemical processes in specific cellular organelles like the endoplasmic reticulum,
golgi, mitochondria, nucleus and nucleolus and the plasma membrane.
 Protein sorting in the cell – discovery of the Sec and SNARE proteins and their roles
in regulating subcellular trafficking.
2. Physical and chemical processes regulating cellular function:
 The cell cycle and its regulation
 Maintenance of pluripotency in stem cells; mechanobiology, effects of substrate stiffness and
mechanical forces on cell fate and development
 Chemical modifications of DNA and histone proteins regulating gene expression
(Epigenetics)
 Phosphorylation cascades that regulate chromatin function and DNA repair
 Nuclear architecture and its regulatory role in controlling gene expression
 Roles of membrane heterogeneity in regulating endocytosis and signaling
 Sources and use for noise in gene expression
3. Roles of the cytoskeleton and associated motor proteins:
  Structure of actin, microtubules, cytoskeletal intermediate filaments, nuclear
intermediate filaments (lamins)
 Discovery and function of molecular motor proteins like myosin, kinesin and
dynein.

B-202: Cell physiology and cell signaling 3 Credits

1. Diffusion, osmosis and cell volumes: Understand how electrolytes and non-electrolytes
change the cell volume in closed and open system under different experimental
conditions. Provide examples for each experimental condition, how intra-cellular and
extracellular permeants and impermeants change the flow-volume and ultimately the
cell-volume. Know the similarities and differences between diffusion and osmosis.
Provide examples to calculate the cell volume and osmotic pressure under different
experimental conditions. Understand the difference between, molarity, osmolarity,
equivalence and milli-equivalence. Explain why body fluids are measured in Osmolarity
or milli-equivalence.
2. Body fluid volume: Learn the composition of body fluids; Intra-cellular Fluid (ICF),
Extra-cellular Fluid (ECF), Interstitial Fluid (IS), Plasma volume (PV). Discuss how fluid
loss changes the body fluid composition and the cell volume (ex: vomition, diarrhoea,
sweating, etc.). Explain how body fluid volume could change the normal homeostasis
and cell signaling.
3. Membrane Transport system: Know the similarities and differences between diffusion,
facilitated diffusion, primary and secondary active transport, co-transport and counter
transport. Provide examples of each type of transport. Understand the energy source
which drives each type of transport. Understand the difference between pores, channels
and pumps.
4. Ionic equilibrium, current voltage diagrams and membrane potential: Explain how
chemical and electrical potential is getting developed in the cell and why cell maintains
negative membrane potential? Explain and derive Nernst potential equation.
Understand the importance of Na2+, K+,Cl-and Ca2+ions and Na2+/K+ pump in the
context of membrane potential. Provide examples to calculate membrane potential from
Nernst potential. Explain ionic current, conductance and permeability to understand the
current-voltage (I-V) relationship and membrane potential. Give introduction to patch-
clamp technique to measure the membrane potential and channel activity. Summarize
Nernst potential, membrane potential, chord conductance equation and the resting
membrane potential. Classify different types of ion channels
5. Generation and transmission of Action potential: Explain the resting membrane
potential, sub threshold potential, threshold potential and refractory period. Understand
the sequence of events in the action potential, ion channels involved and transmission of
action of potential. Explain the cable theory in comparison with neuronal signal
transmission. Explain how depolarization and repolarization in cardiac myocytes
measure as electro cardiogram (ECG).
6. Neuromuscular junction (NMJ) and central synapses: Learn the structure of a
neuromuscular junction and the sequence of events that lead to neurotransmission.
Understand end plate potential, miniature end plate potentials and spontaneous end
plate potentials. Understand the properties of acetylcholine receptor and their
importance in depolarization. Differentiate NMJ and central synapses.
7. Neurotransmitters in cell signaling: Learn different neurotransmitters involved in
central and peripheral nervous system. Understand the signaling mechanism how it
modulated ion channel and membrane proteins as a signaling molecules. Know
 differention channel blockers and its toxicological effect and pharmaceutical usage by in
modulating cell signaling.
8. Mitochondrial electron transport system and ATP production: Learn the structure and
mitochondrial membrane potential. Understand the electron transport process and the
respiratory enzyme complexes. Understand the mechanism of ATP synthesis using
proton gradient and mitochondrial energy metabolism. Understand the importance of
mitochondrial Ca2+signaling. Learn about mitochondrial uncoupling protein (UCP) and
mitochondrial calcium uniporter (MCU). Learn how UCP involved in hibernation. Learn
how to image mitochondria using fluorescent dye.
9. Ca2+signaling: Understand the important roles of calcium as a secondary messenger.
Learn about Ca2+ channels (voltage gated Ca2+channel, Store operated Ca2+ channel
(SOC), etc.) and pumps (SERCA and PMCA). Know more about endoplasmic reticulum,
intracellular and extracellular Ca2+signaling. Learn Ca2+ imaging techniques using
Fluo-4 and Fura-2.
10. Reactive oxygen species (ROS) signaling: Learn the mechanism of ROS generation in
mitochondria and plasma membrane. Understand the physiological and pathological
significance of ROS signaling.
11. Cell signaling pathways (cell survival and cell death signaling): Learn the basic
principles and classification of cell signaling pathways. Know about various types of
receptor and cell stimuli involved in cell signaling. Understand different cell signaling
pathways and proteins involved; PIP pathway, Akt /PI3K, MAP kinase, GPCRs, cAMP,
cGMP, PKA, PKC, PLC etc. Learn apoptotic and anti-apoptotic proteins and the
signaling mechanism. Differentiate apoptosis, necrosis and autophagy. Understand
different caspase proteins and their roles. Explain the relationship between Ca2+
signaling in apoptosis.

C-204 / B-203: Biophysics 4 / 3 Credits

1. Polymer statistics and intrinsically disordered proteins: Introduction to polymer chain

properties: defining radius of gyration, end-to-end distances, entropy etc. Intrinsically
disordered proteins: Definition of disorder, Types of IDPs, Functions of IDPs, Diseases
associated with IDPs
2. Systems Biology: Transcription Networks, Autoregulation, Feed Forward loop, Allostery,
Kinetic Proof Reading, Chemotaxis
3. Evolution: Basic Concepts
4. Single Molecule Biophysics: Introduction to fluorescence, FRET and smFRET, Optical
tweezers, Motor proteins, Super resolution microscopy

B-204: Basic Mathematics for Biologists 3 Credits

 Calculus: Limit, Differentiation, Integration

 Series: Convergence, divergence, Taylor series
 Determinants, Matrix Algebra
 Vector Analysis
 Error analysis
 Distribution functions, probability
 Simple differential equations
B-205 : Biological thermodynamics 3 Credits

 Introduction to Thermodynamics. Zeroth Law. Concept of different types of

thermodynamic systems. Temperature, work, and heat. Energy transformation.
 First law of thermodynamics. Energy conservations, thermodynamic states, and paths.
Concept of equilibrium. Reversible and Irreversible Processes. Heat engines. Maxwell
relations. Second law of thermodynamics. Entropy (Boltzmann and Clausius). Efficiency
of heat engine. Third law of thermodynamics.
 Thermodynamics and statistical thermodynamics. Maxwell’s demon, minus first law of
thermodynamics, and information theory. Concept of ensembles, partition functions,
Boltzmann distribution, and calculation of thermodynamic quantities from partition
function. Diffusion. Analysis of thermodynamic data. Multistate equilibrium.
 A mid-term test, on the laws of thermodynamics.
 Phase transition. Phase Equilibria. Clausius-Clapeyron Equation.
 Gibbs free energy: theory and applications. Chemical potential. Standard States and
Gibbs-Duhem equation. Ionic solutions. Equilibrium constant. Acids and bases. Redox
reactions. Chemical coupling. Glycolysis and citric acid cycle. Oxidative
phosphorylation and ATP hydrolysis. Osmosis, dialysis, and membrane potential.
Donnan equilibrium. Enzyme–substrate interaction. Protein stability and reaction. DNA
melting and polymerase chain reaction (PCR).
 Quiz on the theory and applications of Gibb’s free energy.
 Binding equilibria and reaction kinetics. Single-site model. Scatchard and Hill plots. Rate
constant and order of reaction. First and second order reactions. Transition state theory.
 Energy, information, and life. A discussion on non-equilibrium thermodynamics and
living systems.
 Oncogenes and tumour suppressor genes
 Maintenance of genore integrity and development of cancer
 Invasion and metastasis – epithelial to mesenchymal transition
 Cancer stem cells – Basics and how to target cancer stem cells
 Rationale treatment of Cancer
 Special emphasis on few important cancers which are prevalent in India – Breast cancer,
Oral cancer etc.

B-206 : Molecular Genetics 3 Credits

1. Model organisms
 Introduction to various models used for genetics studies
2. Principles of genetics
 Patterns of Inheritance
 Mutations and phenotypes
 Exception to Mendelian inheritance
3. Genome organization and genetic mapping
 Linkage and recombination
 Genetic mapping in model organism
 Methods for genetic and molecular mapping
4. Regulation of gene expression
 Regulation of transcription, alternative splicing, and translation
 Gene expression regulation in the Eukaryotic and prokaryotic system
 Epigenetic mechanisms such as imprinting
  The epigenetic mechanism in development and diseases
 Discovery tools to study gene regulation and epigenetics mechanisms
5. Genetics to study biological processes and diseases
 Methodologies used for genetic manipulation
 Forward and reverse genetics
 Dissection of gene function and genomics
 Genetics to study development
 Genetic regulation of behavior
 Genetics and evolution
 Detecting human disease alleles: molecular genetic diagnostics
 Model organisms in understanding human genetic diseases

B-207 : Basic Immunology 3 Credits

 Introduction to Innate Immunity, Innate Immune Cells and Inflammation

 Complement system
 Histocompatibility and Organ Transplantation
 Antigen Presentation
 Overview of Thymic Development, T Cell Subsets and Biology
 T cell Memory, Tissue Resident Memory and Vaccines
 Overview of B cell Development and Biology
 Affinity Maturation
 TCR and BCR Signaling
 Mast Cells and Allergy
 Autoimmunity
 Case Discussions and Landmark Papers in Immunology

E-304 : Molecular and nonlinear dynamics 4 Credits

Molecular Dynamics:
 Broad overview of Computer simulation and application of molecular dynamics simulation
 Basic linux primer, Primer on a programming language (Fortran), Plotting data using gnuplot
 Writing your first Molecular Dynamics code: Initialization of system, Force calculation from
classical potential, Implementation of periodic boundary condition, Integration schemes of
Newtonian equation of motion. Simple monoatomic liquids as the test system
 Using a software package for MD: GROMACS to simulate simple liquid
 Molecular force fields and overview of the existing bimolecular force fields, water models as case
study
 Implementation of Thermostats and Barostat in Molecular Dynamics simulation: Introduction to
Berendsen, Nose Hoover and Parrinello Rahman protocols for NVT and NPT simulation
 Handling Electrostatics in computer simulation: Implementation of Ewald summation and
Particle mesh ewald summation in computer simulation.

Nonlinear dynamics:
1. Introduction to 1D and 2D flows
 Fixed points and stability
 Linear stability analysis
 Bifurcations: saddle-node, transcritical, pitch-fork, imperfect bifurcations and catastropes, Hopf
bifurcation
 Phase plane: phase portraits, existence and uniqueness, Conservative and reversible systems,
 fixed-point and linearization.
 Limit cycle: Introduction, Poincare-Bendixon Theorem, Lienard systems, Relaxation oscillator,
weakly nonlinear oscillators
2. Oscillatory Reactions
 Chemical kinetics, mechanism, Lotka-Volterra, Brusselator, B-Z reaction, (Case studies using
numerical simulations)
3. Reaction-diffusion systems and pattern formation
 Turing Patterns: General theory, examples of model systems, (case studies using numerical
simulations)
4. Waves: traveling waves, solitons, spiral, target

E-418 : Quantum Thermodynamics 4 Credits

 Classical Thermodynamics: temperature, heat, work; first law; entropy and second law; specific
heats; heat engines, refrigerators and their efficiencies; entropy of mixing; chemical reactions and
entropy constants; Nernst and Nernst-Planck formulations of the third law; cooling rates;
dilution refrigerators.
 Classical Statistical Mechanics: microcanonical, canonical and grandcanonical ensembles; ideal
gases.
 Brief introduction to non-equilibrium stat mech, thermalisation.
 Quantum Statistical Mechanics: quantum ideal bose gas; specific heats and entropy.
 Quantum Thermodynamics of first kind: quantum modifications of classical thermodynamics;
third law in the light of QSM;; entropy constants for monatomic and di-atomic ideal gases; He3-
He4 mixtures and revision of entropy of mixing; chemical reactions revisited.
 Open Quantum Systems.
 Classical and Quantum Information
 Quantum Thermodynamics of the other kind: emergence of thermodynamic behavior in
quantum systems; quantum-work, quantum-heat and quantum-entropy; quantum first law;
many entropies and many second laws; quantum third law; quantum heat engines, refrigerators
and their efficiencies.

E-413: Fluorescence Methods in Cellular Biophysics 3 Credits

1. Basics of fluorescence - Jablonski diagrams, Stokes shifts, structures of fluorophores,

quantum yields, fluorescence instrumentation - fluorescence microscopy and
spectroscopy, light sources, filters, and detectors (PMTs, APDs and camera technologies
- CCD, EMCCD, CMOS, sCMOS etc.)
2. Forster Resonance Energy Transfer (FRET), Time-Correlated Single Photon Counting
(TCSPC), fluorescence lifetime, quenching - theoretical ideas, technical details behind
measurements and applications. Fluorescence polarization measurements - steady-state
and time-resolved fluorescence anisotropy - theory, instrumentation and technical
details.
3. Widefield microscopy, effects of objective numerical aperture on resolution, diffraction
limit of resolution of light microscopy, single molecule imaging of mRNA as an
example, basics of flow cytometry.
4. Confocal microscopy - point-scanning and spinning disk confocal microscopy; light
sheet microscopy; Total Internal Reflection Fluorescence (TIRF) microscopy;
considerations for temporal resolution; multiphoton microscopy.
5. GFP technology and dynamics measurements in live cells - Single Particle Tracking
(SPT), Fluorescence Correlation spectroscopy (FCS) - both APD and camera-based,
Fluorescence Recovery After Photobleaching (FRAP), live cell mRNA dynamics
 measurements
6. Super-resolution microscopy methods - stimulated emission depletion (STED),
structured illumination microscopy (SIM), stochastic optical reconstruction microscopy
(STORM), photo activated localization microscopy (PALM), point accumulation for
imaging in nanoscale topography (PAINT) and others.

E-204: Advanced Topics in Inorganic and Organic Chemistry 4 Credits

 First and Second Row Main Group Elements emphasizing with their low oxidation states:
Activation of Hydrogen by Lewis pairs, Hydrogenation and Dehydrogenation reactions
(catalytic-non catalytic) involving main group reagents. Boryl Lithium, Borylene, Boron
based nucleophile and Lewis Base. Classical and Non Classical Carbocation synthesis and
structure, Bonding of C2 molecule, Hyper coordinated carbon and some unusual carbon based
systems including carbenes.
 Heavier (3rd Row Elements and Beyond) Main Group Elements: Mg(I) Compound. Mg(I) as a
Reducing Reagents. Chemistry of compounds involving Low Valent Low- coordinate
Aluminum, Silicon, Germanium, Tin, Lead, Phosphorous, Arsenic, Antimony, and Bismuth.
Bonding description of disilenes and disilynes and its comparison with alkenes and alkynes.
 Recent Advances in Transition Metals: Compounds involving metal metal bonding (including
zinc) and its reactivity. Transition metal hydrides and fluorides. Some aspects of transition
metals in bio inorganic chemistry.
 New Strategy for the Installation of Organic Functional Group and Recent Trends in Organic
Synthesis: Application of Halonium ions (including fluoronium ion) in organic chemistry,
Cascade reactions, Flow reactions, Selective oxidation-reductions involving recent developed
reagents, application of boron and silicon compounds for selective functionalization, Modern
approach (without protection and deprotection of functional group strategy) for natural product
synthesis.

E-205 : Research Methodology 4 Credits

1. SKILLING STUDENTS TO:
 Sketch a Function
(Function and slope. Symmetries, Special pts, asymptotes, draw segments. Join up!)
 Write a CV
(First impression. Show professionalism! CV content. Fonts, topics, and sequencing.)
 Write a Letter
(Apply for postdoc. Ask to visit. Request to be cited.)
 Talk about research work
(10 minute talk, 1 minute talk, coffee conversation, the elevator pitch,140-character tweet.)
 Give a Research Talk
(Judge audience! 1 slide ~ 2 mins. Intro/Motivation/Methods/Results/Takeaways. Questions.)
 Write a Research Paper
(Abstract, Text, Fig Caps, Refs, Acknowledgements. Proof-reading. Good/Bad writing
examples.)
 Read a Research Paper
(Quick-read. Skim text, main refs. Go to Origins, trace Evolutions. Detailed reading.)
 Make Quantitative Estimates
(Memorize basic constants, sizes. Internal conversation. Compare others, on Log scale.)
2. METHOD OF SCIENCE
(Theoretical model, predict->Quantitative experimental test->Keep/ Modify
 model, predict->...Ideas of Bacon, Occam, Popper, Kuhn.)
3. RESEARCH ETHICS AND AVOIDING PLAGIARISM
(Dangers of copy-paste. Plagiarism. Proper citing. Indian Academy of Sciences
Report)
4. VISUAL REPRESENTATION OF RESEARCH DATA
(Optimal design of plots, charts, schematics, posters etc for graphic display of
empirical relationships in complex data.)

5. ERROR ANALYSIS OF RESEARCH DATA
(Random and systematic errors. Statistical errors and probability distributions.
Error propagation or addition of errors.)
6. STUDENT PRESENTATIONS
(Research Literature. 25+5 min talks,3 per class. Graded. Two cycles, if class-size
permits.)
7. LAB VISITS
(Students split up for Bio/ Chem/ Phys tours, guided by Senior PhD students)

E-206 : NMR Instrumentation 2 Credits

1. Proton NMR.
a) Chemical shifts: Chemical shift signatures of functional groups and abnormalities in chemical
shifts due to neighboring groups, paramagnetic shifts, etc.
b) Analysis and interpretation of peak intensities.
c) Analysis and interpretation of J-couplings: geminal, vicinal, and long range coupling
between protons.

2. Carbon NMR.
This part will cover the basics of 13C-detected or 13C-edited NMR experiments routinely used for
analyzing small molecules.
a) 1H-coupled and 1H-decoupled 13C NMR.
b) Polarization Transfer: Nuclear Overhauser Effect, INEPT.
c) Attached proton test (APT), the DEPT experiment.
d) C-X J couplings and interpretation (13C-1H, 13C-13C, 13C-19F).

3. Multidimensional NMR:
Correlation experiments
a) Basic of Multidimensional NMR
b) 1H-1H COSY 1H-1H NOESY, 1H-1H TOCSY
c) 13C-1H HSQC, 13C-1H HMBC, HOESY

Relaxation and Diffusion experiments

d) T1, T2, T1-rho relaxation experiments

e) DOSY
4. X-detected or edited NMR experiments

(X = 19F, 31P, 11B, 29Si, 15N, 207Pb, 117Sn, 2H)

 5. Solid state NMR experiments for small molecules and materials
X-Detected (spin ½)
Experiments with quadrupole nuclei.
1H Detected

6. Exercise on two small molecule structure interpretation

7. Pulse Programming and processing
• Pulses, phase, power levels, delays, acquisition, shaped-pulses, conditionals
• Multidimensional NMR: Loops, quadrature, data storage.
• Data processing: Fourier-transformation, apodization, zero-filling, phase-correction,
multidimensional processing.
• Practical training: (i) Writing and executing a simple pulse program: In this class, every student
will be given a simple program to code (example: onepulse, hahn-echo, inversion- recovery, etc)
and will be allowed to execute this program on the spectrometer while being monitored by the
instructor. (ii) Writing and executing a 2D pulse program: In this class, students will be given
simple 2D pulse programs to code (eg, COSY, NOESY, etc) and allowed to run these while being
monitored by the instruct
8. Current Topics of Research in small-molecule NMR
 The ‘PSYCHE’ pulse sequence
 Ultrafast multidimensional NMR.
 Non-uniform sampling and processing of non-uniformly sampled data.
 Multiple receivers and multiple acquisition.
 Structure activity relationship by NMR
9. Practical training on NMR instrument.
This is a practical session on 300 MHz NMR for the instrument operation and experimental setup.
 Brief over view of TCIS NMR facility.
 1H set up using topspin includes sample insertion, lock, shim, tuning & matching etc.
 13C NMR (coupled and decoupled).
 1H-1H COSY (correlation spectroscopy).
 1H-13C HSQC (Heteronuclear single quantum coherence spectroscopy).

 1H-13C HMBC (Heteronuclear Multiple Bond Correlation).

 X-Nuclei NMR setup (19F, 31P, 11B).

10. Instrumentation and general troubleshooting.
 NMR spectrometer functioning flow chart; Transmitter path and receiver path
 General troubleshooting

E-411: Solid State NMR 4 Credits

Pre-requisites: C-202 / P-105, C-205

 Principles of solid-state NMR: Spin interactions, anisotropy of interactions, Frame

transformations, magic-angle spinning, heteronuclear spin decoupling, cross
polarisation
 Sensitivity enhancement in spins-1/2: Cross polarisation, theory and pulse schemes,
transient oscillations, dipolar coupling information, spectral editing, adiabatic /ramped
CP, Scalar coupling transfers in solids.
 Resolution enhancement in spins-1/2: Decoupling, various pulse schemes, experimental
 strategies, refocussed and non-refocussed transverse relaxation times
 Distance and Geometry information via recoupling: Separated local field experiments,
pulse schemes based on symmetry of spin interactions, applications to
correlation/distances/bond and torsional angles/assignments
 Quadrupolar spins: Introduction to half-integer and integer spin quadrupolar nuclear
spins, comment on resolution and sensitivity issues, applications
 Solid-state NMR for bio-molecular applications.

E-414 : Mechanobiology 4 / 3 Credits

 Brief introduction to mechanical force: Basics of classical mechanics, mechanics of solids and fluids,
with examples from biology. Introduction to viscoelasticity and surface tension and how do they
operate at cellular and tissue level. Concept of scaling in biology. Biology by the numbers.
 How do the cells generate force? Cell as a chemical machine. Thermodynamics, rate-kinetics, and
mechanics. Effect of intercellular and intra-cellular forces at molecular- and meso-scale. Concept of
forced induced unfolding of proteins and DNA. Force-dependent reaction kinetics of slip and catch
bonds. Forces during cell division.
 Biology, Chemistry, and Physics of cellular force-bearing structures: Molecular and meso-scale
perspective. Acto-myosin network, Microtubules, Intermediate filaments, Different cell-cell
junctions, Extracellular matrix (ECM), Cell-ECM adhesions. Molecular motors.
 How can we measure forces at molecular and cellular level? Traction force microscopy, micropillar
assays, monolayer stress microscopy, atomic force microscopy, optical traps, molecular tension
sensors.
 Forces in tissue and organism development: Forces that shape a developing embryo. Forces in the
epithelium. How the cells build the tissue stiffness: molecular assembly and collective effect.
Epithelial constriction, invagination, bending, folding, and hydraulic fracture. Density-dependent
and independent jamming and unjamming of the epithelium. Force measuring techniques at tissue
level: current approaches and limitations.
 Effect of fluidic forces: Development of heart and blood vessel. Different flow types and their
biochemical effect. Rheology of blood. Introduction to microfluidics as the blood-vessel mimic.
 Mechanobiology of human diseases: Cardio-vascular diseases, aging, and cancer

E-415 : Advanced Mathematics 4 Credits

 Probability and Statistics:

Basic concepts: Combinatorics, Addition law of probailities, statistical inference. Dependent events:
Conditional probability, Bayes’ theorm, Bayesian interference with known priors, conjugate
priors. Random variables: Discrete and continuous random variables, distribution functions.
Probability distributions: Binomial and Poisson distribution, Normal distribution, Limit theorems:
Law of large numbers, central-limit theorem. Regression: Covariance, linear regression, reduction
of variables, resampling methods, bootstrapping
 Functional analysis:
Normed spaces: Linear space, linear maps and completeness, integrable functions. Hilbert space:
Cauchy inequality, quantum states as vectors in Hilbert space, Lebesgue integral, linear
operators on Hilbert space, linear functional space and dual vector space, spectral theorem,
Fourier series,
 Groups and group representations:
General group theory: Definitions, isomorphism, homomorphism, conjugate classes, cosets,
 invariant subgroups. Representation theory: Complete set of commuting operators, group
representations, Schur’s lemma. Finite and discrete groups: Examples including reflection groups
and lattices in relation with crystallography and molecular physics, permutation groups,
projection operators, Young diagrams. Lie groups, Rotation groups and Unitary groups: Lie algebra,
unitary groups, orthogonal groups, introduction to the representation theory of Lie algebra
(Poincare and Lorentz groups, SU(2) and SU(3) groups)
 Partial differential equations:
First-, second-, and third-order equations, Integral transform techniques, methods of
characteristics, classification of second-order PDE’s, hyperbolic, parabolic, and elliptic equations,
Green’s function methods for PDE’s, wave equation, diffusion equation, Laplace equation
 Complex analysis:
Review of complex analysis, analytic functions as mapping, conformal mapping, Cauchy’s
integral formula, general form of Cauchy’s theorem, calculus of residues, harmonic functions
 Special functions:
Gamma functions, Beta functions, Stirling’s series, Reimann Zeta function, Bessel functionsof the
first and second kind, Hankel functions, Legendre functions of the first and second kind,
physical interpretation of the generating function, spherical harmonics and irreducible tensor
operators, Wigner-Eckart theorm

E-416 : Electronic structure theory of matters 4 Credits

1. Bonds and Bands (4 lectures)

Qualitative molecular orbital theory, orbital interaction theory, perturbative molecular orbital
theory, Jahn-Teller distortion, from molecules to solids, Peierls distortion, Brillouin zone, Fermi
surface, Hückel and tight-binding methods, zero differential overlap, electronic structure theory –
literature survey.
2. Many Electron Wavefunctions and Operators (4 lectures)
Born-Oppenheimer approximation, diabatic and adiabatic states, conical intersections, Slater
determinant, configuration state functions, Slater-Condon rules for matrix elements, spin-adapted
wavefunctions, second-quantization, Feynman-Kac formula, Slater-Jastrow wavefunction.
3. Hartree-Fock Approximation (2 lectures)
Fock operator, self-consistent-field procedure, Koopman’s theorem, orbital relaxation, Roothan
equations, basis-set Ansatz.
4. Configuration Interaction (6 lectures)
Many-electron correlation, Brillouin’s theorem, natural orbitals, many-body perturbation, coupled-
cluster method, size-consistency, size-extensivity, Goldstone’s graphical method for many-body
perturbation, Wick’s theorem, linked graphs, Brueckner theory, quasi-particles, Green’s function
and self-energy, random-phase approximation, Bethe-Salpeter equation.
5. Stochastic Methods (1 lecture)
Quantum Monte-Carlo (quantum dots, jellium clusters), diffusion Monte-Carlo, Jastrow’s method.
6. Density Functional Theory (6 lectures)
Reduced density, pair density, Thomas-Fermi model, Fermi and Coulomb hole, self-interaction,
Hohenberg-Kohn theorems, Kohn-Sham equations, performance of various recipes, exchange-
correlation functionals.
7. Time-dependent Theories (2 lectures)
Excited states, time-dependent Hartree-Fock, Frenkel-Dirac variational theorem, Runge-Gross
theorem.
8. Application-Related Topics (5 lectures)
Structure relaxation, transition-state search (popular methods), potential energy surfaces, partial
atomic charges, density of states, solvent effects, energy derivatives as molecular response
properties.
E-417 : Magnetism 4 Credits

 Moments and Susceptibility

Local moments; Curie Law; Pauli paramagnetism; General formula for susceptibility
 Magnetic Moment of a Single Atom or Ion
Spin and Orbital effects; (A) Hund’s Rules; (B) Spin-orbit coupling; (C) Crystal fields
Transition Metals (C>B); Rare Earths (B>C)
 Exchange Interactions in Insulators
Direct (potential) exchange; Kinetic exchange; Superexchange; Dzyaloshinski-Moriya
interactions
 Local Moments in Metals and their Interactions
Anderson impurity Hamiltonian; Kondo limit and the Kondo effect; RKKY interactions; Kondo
Lattices
 The Hubbard Model
The atomic limit; Half-filling  the spin 1/2 Heisenberg model; Single hole: the Nagaoka result
 Magnetic States
Ferromagnets; Antiferromagnets: Neel and Resonating valence bond (RVB) states; Ferrimagnets;
Helimagnets; Spin glasses
 Magnetism in Metals
Itinerant magnetism

E-201: Scientific Communication 2 Credits

1. How to read a scientific paper

2. How to present work: students will do
 Short talks (10 mins) + poster sound – bites
 Journal club presentations of work published by others
 Presentations of own research aimed at both a specialist and a non - specialist
audience
3. Scientific Writing
 A journal article (bring drafts of current papers)
 A research proposal
 An article for the popular press
4. Video presentations
 An idea + experiment/demonstration in less than 4 minutes
 A description of personal research goals and interests (interview others)
5. Scientific literacy and ethics, including
 What constitutes ownership of an idea
 Proper referencing and credit attribution
 What constitutes plagiarism

E-202: Error Analysis and Statistical Inference in Experiment 2 Credits

1. Errors in experimental science: Errors as uncertainties. Inevitability of uncertainty.

Importance of knowing the uncertainties. Estimating uncertainties in repeatable
measurements.
2. How to report and use uncertainties: Best estimate ± Uncertainty. Significant figures.
Discrepancy. Comparison of measured and accepted values. Comparison of two
 measured numbers. Fractional uncertainties. Significant figures and fractional
uncertainties. Multiplying two measured numbers.
3. Propagation of uncertainties: Uncertainties in direct measurements. Sums and
differences, products and quotients. Independent uncertainties in a sum. Arbitrary
function of one variable. General formula for error propagation.
4. Statistical analysis of random uncertainties: Random and systematic errors. The mean
and standard deviation. The standard deviation as the uncertainty in a single
measurement. The standard deviation of the mean.
5. The normal distribution: Histogram and distributions. Limiting distributions. The
normal distribution. The standard deviation as 68% confidence limit. Justification of the
mean as the best estimate. Justification of addition in quadrature. Standard deviation of
the mean. Confidence.
6. Averaging data: Weighted averages
7. Rejection of data: The problem of rejecting data. Chauvenet’s criterion.
8. Least-square fitting: Maximum likelihood and Fitting data to a straight line.
9. The binomial distribution and the Poisson distribution: Probabilities in dice throwing.
Definition of the binomial distribution. Properties of binomial distribution. Definition of
the Poisson distribution. Properties of Poisson distribution
10. The χ 2 test for a distribution: Introduction to χ 2 . General definition of χ 2 . Degrees of
freedom and reduced χ 2 . Probabilities of χ 2 .
11. Some special topics: Use of covariance. Confidence limits on estimated parameters.

E-203: Computer Programming using Python language 2 Credits

1. Simple programs with input and output

2. Variables, operations, expressions, statements
3. Numbers, characters, strings
4. Tuples, lists, dictionaries, sets
5. Functions
6. Scoping
7. Conditionals
8. Iteration
9. Manipulating text
10. Files
11. Packages
12. Computing with random numbers Along the way, we will learn some simple
algorithms.

E-301: Optics 4 Credits

 Basic properties of EM field: Electro-magnetic field, Maxwell’s equations, boundary

conditions, energy law of EM field; Scalar waves, plane, spherical and harmonic waves,
phase and group velocity; Vector waves, EM plane wave, harmonic EM plane wave;
elliptic polarization, characterization of state of polarization, Stokes parameters,
Poincaré sphere representation; Reflection and refraction of plane waves, Fresnel
formulae, reflectivity and transmissivity, polarization on reflection, total reflection.
 Theory of interference and interferometers: Interference of two monochromatic waves,
wave-front and amplitude division interferometers, fringes with quasi monochromatic
sources, visibility of fringes, coherence; multiple beam interference and interferometers.
 Theory of diffraction: Huygens-Fresnel principle, Kirchhof’s diffraction theory,
 Fraunhofer and Fresnel diffraction; Fraunhofer diffraction at apertures and in optical
instruments, Fresnel diffraction at a straight edge.
 Interference and diffraction with partially coherent light: Polychromatic fields,
correlation function of light beams van-Cittert –Zernike theorem; polarization properties
of quasi monochromatic light, coherency matrix, degree of polarization.
 Optics of metals: Wave propagation in a conductor, reflection, refraction at a metal
surface, elementary electron theory
 Optics of crystals: Dielectric tensor of anisotropic medium, monochromatic wave in an
anisotropic medium, phase and ray velocity, Fresnel’s formulae, index ellipsoid, uniaxial
and biaxial crystals, measurements.
 Advanced topics: Beam shifts, cylindrical vector beams, optical angular momentum,
advances in microscopy.

E-302: Condensed Matter Physics 4 Credits

 Elementary excitations in solids

 Electrons in metals: Drude model
 Electrons in metals: Sommerfeld model
 Describing periodicity: Crystal lattices
 Electrons in periodic crystals: Bloch states & Bands
 Electrons in metals: Fermi surfaces
 Vibrations of periodic crystals: phonons
 Electrons & phonons: Scattering or binding
 From atoms to solids: Periodic Table
 Messing up periodicity: Defects in crystals

E-303: Atomic & Molecular Physics 4 Credits

 Interaction of one-electron atoms with electromagnetic radiation.

 One-electron atoms: fine structure, hyperfine structure and interaction with external
electric and magnetic fields.
 Two-electron atoms: Para and ortho states, Independent particle model, Excited states of
two-electron atoms.
 Many electron systems: Thomas-Fermi model, the Hartree-Fock method, LS- and jj-
couplings.
 The interaction of many-electron atoms with electromagnetic fields. Selection rules,
Atoms with several optically active electrons. Zeeman effect and quadratic Stark effect.
 Molecular structure. The Born-Oppenheimer separation for diatomic molecules, rotation
and vibration of diatomic molecules. Structure of polyatomic molecules.
 Molecular spectra: Rotational energy levels of diatomic molecules, Vibrational-rotational
spectra, electronic spectra, Electronic spectra and Hund’s cases, nuclear spin.

E-401: Advanced Computational Methods 4 Credits

Pre-requisites: P-202

 Programming primer - C Vs. Fortran Arrays, Memory allocation, Functions and

Subroutines, What NOT to do while handling arrays, Debuggers
 Advection equation - Finite difference, Spectral, Boundary conditions
 Diffusion equation - Finite difference, Spectral , Boundary conditions
 Examples of Advection-Diffusion equation - Inviscid and Viscous Burgers equation,
 Chemical reactions: Advection-Diffusion-Reaction equation (Fisher equation)
 Poisson equation - Matrix diagonalization , Fast solvers
 A "real" problem: 2D Navier-Stokes simulation in a box - Lid-driven cavity problem,
Introducting obstacles: Volume penalization
 A new approach to fluid dynamics: Lattice Boltzmann method - Boltzmann equation
and its discretization, From Boltzmann equation to Navier-Stokes: Chapman-Engskok
expansion, 2D Navier-Stokes with variety of boudary conditions
 MPI programming of Navier-Stokes and Lattice Boltzmann
 If possible: Invited presentations
 Rahul Pandit on Navier-Stokes simulations in 3d
 Mahendra Verma/Abhik Basu MHD simulations.
 Dhrubaditya Mitra on solar MHD simulations.
 Samriddhi Sankar Ray on Tigers in Burgers equations. (after Advection-
Diffusion)
 Rama Govindarajan on stability problems. (after Poisson equation)

E-402: Advanced Dynamics 4 Credits

Pre-requisites: P-101 / C-201 , P-202

 low-order systems of ordinary differential equations

 maps
 linear stability
 bifurcations
 routes to chaos
 Navier-Stokes and continuity equation, some simple shear flows
 Flow stability: Kelvin-Helmholtz, Rayleigh-Benard, Taylor-Couette
 Routes to turbulence
 Elastic instabilities

E-403: Advanced Statistical Mechanics / Statistical Mechanics - II 4 Credits

Pre-requisites: P-204 / C-103

 A quick summary of different ensembles. Non-interacting Classical Systems - magnetic systems,

ideal gas and Harmonic oscillator, Statistical mechanics for interacting systems: Cluster expansion.
 Interacting Magnetic Systems, Ising and Heisenberg Model, Mean Field Theory, Transfer Matrix
Method, Phase Transitions: Order Parameter, First and Second Order Phase Transitions, Landau-
Ginzburg Theory, Scaling, Critical exponents and Universality class, Generalized Homogeneous
function, Hyper Scaling relation, Kadanoff Construction, Renormalization Group Transformation,
Momentum Space RG.
 Linear Response, Fluctuation-Dissipation Theorem, Brownian Motion, Langevin Equation, Fokker-
Planck Equation

E-404: Phase Transitions, Ordering and Dynamics 4 Credits

Pre-requisites: P-204 / C-103

 Ordered Phases and Phase Transitions: Phenomenology; Models; Correlation Functions;

Mean field theory
  General Results on Ordering: Absence in 1-d; Peierls argument; Spin waves; Lower
critical dimension; Mermin-Wagner theorem
 Critical Phenomena: Fluctuations and their growth; Ornstein-Zernike theory; Scaling;
Universality; Upper critical dimension, Ginzburg criterion
 Renormalization Group: Basic idea; Real-space RG; Epsilon expansion; Multicriticality
Specific Systems: XY Model; Polymers
 The framework of time-dependent statistical mechanics: Linear response theory,
fluctuation-dissipation theorem, Kubo formulae
 Brownian motion: Langevin and Fokker-Planck approaches
 Microscopic stochastic dynamics: Kinetic Ising models; Master equation
 Coarse-grained stochastic dynamics: Generalised Langevin equations; Fluctuating
hydrodynamics of broken-symmetry systems; dynamics of critical phenomena
 Field-theoretic methods and models: Functional integrals for statistical dynamics;
dynamical renormalization group; application of these techniques to selected models at
and away from thermal equilibrium.

E-405: Soft Matter and Biological Physics 4 Credits

Pre-requisites: P-204 / C-103, P-403

Polymers, Glass Formation and Jamming

 Polymers: Introduction to polymers; Ideal polymer chains; Real Chains: Excluded
Volume; Polymer Solutions; Electrostatics; Polyelectrolytes; Networks and gelation;
Polymer Dynamics; Rheology of Polymers; Protein Folding
 Glass Formation and Jamming: Glass transition phenomenology; Crystal nuclation and
glass forming ability; Description of dynamics; Mode Coupling Theory; Energy
landscape approach; Spin glasses; Random First Order Transition theory; Dynamic
Heterogeneity; Jamming; Glassy Rheology

E-406: Advanced Mathematical Physics 4 Credits

Pre-requisites: P-101 / C-201

 Vectors in 3-d; addition, products; transformation under rotations; active and passive
transformations; invariants; compact formulation via isotropic tensors; vectors in diverse
dimensions; polar and axial vectors in 3-d;Euler angles.
 Vector fields and vector calculus; div and curl; various identities of vector calculus;
electrodynamics as illustration of 4-d; electrodynamics in diverse dimensions;
applications to fluid dynamics and elasticity; line, surface and volume integrals.
 Gauss’s theorem, Stoke’s theorem, Green’s theorem, Helmholtz theorem and Alfven’s
theorem; coherence in quantum optics.
 Matrices; nilpotent and idempotent matrices; diagonalisation; upper and lower
triangular matrices; orthogonal, unitary and Hermitian matrices; normal matrices;
LUdecomposition; direct product matrices; eigenvalues and eigenfunctions; generalized
eigenvectors; geometric and algebraic multiplicities; defective matrices ; left and right
eigenvectors; Schur canonical form; Jordan canonical form; Singular value
decomposition; Schmidt decomposition.
 Tensor calculus
 Group theory; rotations and translations; generators and their algebra; unitary
unimodular groups in physics; Lorentz and Poincare groups; group representations
 Transformations and symmetries; coordinate transformations; invariances and
 symmetries; Noether’s two theorems
 Finite groups; order of the group, order of the element, periods, rearrangement theorem,
multiplication tables, subgroups and cosets; Lagrange’s theorem; quotient group;
conjugacy classes; group characters;
 Permutation groups and their properties; cyclic groups and their properties; the
continuous groups SO(2), SO(3), SU(2) and SU(N)
 10.Representations of groups
 Probability theory; discrete and continuous random variables; mean, variance and
higher moments; dependent and independent random variables - joint, marginal and
conditional probabilities; uniform distribution, gaussian distribution; uniform
distribution on group manifolds; Bayesian approach to probability.

E-407: Advanced Continuum Mechanics 4 Credits

Pre-requisites: P-101 / C-201

 Hydrostatics, Surface tension, continuity equation, Euler equation, Bernoulli’s theorem.

Vorticity equation, inviscid, simple vertical flows, shear stress, simple channel flow.
Navier-Stokes, non-dimensionalisation, Stability theory
 The elastic continuum, broken symmetry. Simple elastic free energies of meso-phases
and solids. Defects, Volterra constructions, Defect dynamics and elasticity. Time
dependent elastic moduli. Elements of plasticity.

E-408: Field Theory 4 Credits

Pre-requisites: P-105 / C-202, P-101 / C-201, P-205

 Resume of classical mechanics, resume of quantum mechanics, path integral formulation

of quantum mechanics, connections to classical statistical mechanics.
 Relativistic quantum mechanics: spin, Klein paradox, antiparticles. Inevitability of many
particles even in single particle descriptions. Dirac sea. Simple relativistic processes.
 Fermi sea, particles and holes, nonrelativistic many-body systems, ‘relativistic’
behaviour in non-relativistic systems, graphene.
 Point particles to fields. Classical fields in Lagrangian and Hamiltonian formulations,
symmetries and conservation laws.
 Electromagnetic and Gravitational fields. Elasticity as field theory. Hydrodynamics and
Field theory, Field theory of liquid crystals.
 Quantisation of scalar fields. Overview of Quantum Electrodynamics. Why atoms
radiate? Casimir effect. Examples from Quantum Optics.
 BCS theory of superconductivity. Pions and superconductivity. Higgs bosons and
superconductivity.
 Asymptotic freedom in QCD. Kondo effect - asymptotic freedom in condensed matter
physics.
 Singular potentials in QM as a guide to renormalisation. Scaling and critical phenomena.

E-409: Nonlinear Dynamics 4 Credits

The course will consist mainly of homework and project work, with few lectures. The book
"Nonlinear dynamics and chaos" by Steven Strogatz will be broadly followed and home-
work assignments will be based on this.
Apart from this, each student (or pair of students) will be assigned a Separate project on a
particular aspect of NLD.
E-410: Intense laser matter interactions 4 Credits
Pre-requisites: E-301 / E-303

 Conditions for producing a Laser – Population inversions, Gain and Gain Saturation
 Laser Oscillation above Threshold
 Requirements for obtaining Population inversions
 Laser Pumping requirements and techniques
 Laser Cavity Modes
 Stable Laser Resonators & Gaussian Beams
 Introduction to the Theory of Field-Induced Atomic Transitions
 Multiphoton Stimulated Bremsstrahlung
 Multiphoton Compton Scattering and Ponderomotive Forces in an Inhomogeneous
Light Field
 Free-Electron Lasers

E-412 : Principles in Cancer & Cancer Stem cell biology 3 Credits

 Normal Cell Vs. Cancer Cell

 How are tumours derived?
 Carcinogens and Tumourigensis
 Cell immortalization
 How do viruses cause cancer
 Oncogenes and tumour suppressor genes
 Maintenance of genore integrity and development of cancer
 Invasion and metastasis – epithelial to mesenchymal transition
 Cancer stem cells – Basics and how to target cancer stem cells
 Rationale treatment of Cancer
 Special emphasis on few important cancers which are prevalent in India – Breast cancer,
Oral cancer etc.

E-419 : Biology of Sensory systems 3 Credits

Will be updated soon…

E-307 : Mechanisms of genome surveillance and repair in biological systems 2 Credits

Will be updated soon…