Jawaharlal Nehru Centre for Advanced Scientific Research

SCHEME OF INSTRUCTION

2003-2004

JAWAHARLAL NEHRU CENTRE FOR ADVANCED SCIENTIFIC RESEARCH (A Deemed University) JAKKUR, BANGALORE - 560 064

PREFACE The Jawaharlal Nehru Centre for Advanced Scientific Research, a deemed University, offers the following degree programmes : (i)

Ph.D - Chemistry and Physics of Materials, Evolutionary and Organismal Biology, Molecular Biology and Genetics, Engineering Mechanics, Theoretical Sciences, Theoretical Condensed Matter Physics, Statistical Mechanics, Materials.

(ii) Integrated Ph.D – Chemistry and Materials Science. (iii) M.Sc by Research – Evolutionary Biology, Molecular Biology and Genetics, and Engineering Mechanics. This booklet contains information about the courses offered by the Centre during the academic year 2003 -2004. Selected students conduct high quality research with state-of-the-art facilities.

JM...Molecular Biology and Genetics Unit JT...Theoretical Sciences Unit The course numbers follow the two alphabets; this is followed by the level of the course and the credit hours. For example, JE 202 is a 200 level course offered by the Evolutionary and Organismal Biology Unit of the Centre. Under this system of instruction each course carries a ‘credit’ rating relating the weekly work load for the semester. One credit is assigned to one hour of lecture per week per semester or three continuous hours of academic work per week in a semester in a Laboratory/Workshop. For example : a)

a credit rating of 2:0 indicates (2x1)+(0x3)=2 hours of lecture and no additional academic work per week in the term;

b)

a credit rating of 0:3 means (0x1)+(3x3)=no lecture and 9 hours of academic work per week in the term in a Laboratory/ Workshop.

c)

A credit rating of 2:1 indicated (2x1)+(1x3)=2 hours of lecture and 3 hours of other academic work per week in the term.

The students undergoing Degree programmes are offered: a) b) c)

Courses identified by the Centre to give a broad base in the main field of study. Dissertation project to lay emphasis on application of knowledge to their problems. Advanced courses chosen by the student in consultation with the Faculty Advisor.

Each course is listed under the appropriate Unit. The Units in the Centre are represented by two alphabets : JC...Chemistry and Physics of Materials Unit JE...Evolutionary and Organismal Biology Unit

Each degree programme has a course requirement of a prescribed no. of credits. For individual requirements, the students are advised to approach the Chair of the respective units. Some of the courses offered by the Indian Institute of Science are generally recommended for students of M.Sc. (by research), Integrated Ph.D as well as regular Ph.D students. The academic performance of every student admitted to the Centre will be evaluated by the Eight Point Scale Grading System.

JF... Engineering Mechanics Unit 1

2

The following table indicates the qualitative assessment and point values of the grades in the Eight Point Scale Grading System: GRADE

Qualitative Assessment

Point Value of Grade

S

Outstanding

8

A

Excellent

7

B

Very Good

6

C

Good

5

D

Satisfactory

E

Fail

4 (Pass Grade) 0

All students who join the Centre are expected to have proficiency in English and those who need help can approach the Chair of the respective units in which they are admitted.

COURSE REQUIREMENTS FOR DIFFERENT PROGRAMMES

Integrated Ph.D Programme Minimum number of credits for completion of programme for those with Bachelor’s degree Candidates registered for Ph.D With Master’s degree

...

12 Credits

With Bachelor’s degree in Engineering/ Technology Qualification

...

18 Credits

...

12 Credits

Candidates registered for M.Sc (by research) With BE/B.Tech/MBBS degree

3

... 64 Credits

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COURSES (Offered at the Centre)

March, Norman H & Mucci, Joseph F, Chemical Physics of Free Molecules. (Plenum Press, 1993) Griffiths D.J. - Introduction to Electro dynamics (Prentice Hall, 2000) S. Balasubramanian and K.S. Narayan

JC 201 (AUG) 3:0 JC 202 (AUG) 3:0

Fundamental Concepts in Chemical Physics Mathematics Orientation : Vector analysis & calculus, matrices (representation and diagonalization), partial differential equation, common solutions, series equations, Fourier transformation, Review of concepts and solutions of standard quantum mechanics, harmonic oscillator, 1D, 2D, 3D potential well problems, spherical harmonics, Hydrogen atom. Maxwell’s equations, light propagation and dispersion in media, boundary value problems, electrostatics, and other electromagnetism basics. Ideal gas, equations of state, non-ideal case, statistical thermo-dynamics elements, gas-liquid, phase diagrams, phase transitions. Bonding concepts, trends in periodic table, diatomic molecules, Hartree-Foch, B-O approximation, variational approach, molecular orbital treatment of H2+, Huckel theory treatment of pi electron in ethene, Franck-Condon principle. Suggested Reading: E. Kreyszig “Advanced Engineering Mathematics”, 8th Edition (John Wiley, 1999) G.B Arfken and H.J. Weber, “Mathematical methods for physicists”, Indian Edition (Academic Press, 1995) P.W. Atkins “Physical Chemistry”, 3 rd edition (Oxford, ELBS, 1987) Shaum Series-Advanced Mathematics, Vector Analysis McQuarrie, Physical Chemistry (Viva Books Pvt. Ltd., 2001) 5

Experimental Techniques for Materials X-ray, electron and neutron diffraction, Scanning probe microscopy, X-ray photoelectron spectroscopy, Nuclear Magnetic Resonance, Electron Spin Resonance, Neutron Scattering, Reflection Measurment, Kramer-Kronig transformation, UV-vis and Infra-red Absorption, Fourier Transform Spectroscopy, Raman Scattering, Ellipsometry, Photoluminescence. Course assignments will include solving and interpreting typical data from each of these techniques. Prerequisites : M.Sc degree in Chemistry / Physics / Materials Science, II year Int. Ph.D Programme. Suggested Reading: S.W. Lovesey, Theory of Neutron Scattering from Condensed Matter (Clarendon Press, Oxford, 1990) Light Scattering in Solids I-VIII edited by M Cardon and G. Guentherodt, Vols. 8,50,51,54,66,68,75 of Topics in Applied Physics (Springer-Verlag, Heidelberg, 19821999) Infrared and Raman Spectroscopy-Methods and Applications, edited by B Schrader (VCII, Weinheim, 1995) X-ray diffraction procedures, H.P Klug and L.E. Alexander, (Wiley, 1974) 6

Electron Diffraction Techniques, J.M. Cowley (Oxford University Press, 1992)

JC 302 (JAN) 2:1 Introduction to Surface Science and Thin Films

Solid State Spectroscopy, H. Kuzmany (Springer-Verlag, 1998) G.U. Kulkarni and N. Chandrabhas

JC 204 (JAN) 1:0 Special Course in Chemistry and Physics of Materials: Term papers in contemporary research topics and presentation. JC 205 Seminar Course : Satisfactory / Unsatisfactory grades ( in the second and third year) JC 301 (AUG)-(JAN) 2:0 Photonics : Properties, Materials and Devices Linear optics, electro-optics, elementary principles in communication, wave guides, fiber optics, photorefractive materials, photonic materials

Thin Films and Surfaces: Techniques of thin film deposition (inorganic and organic), characterization of thin films by X-ray diffraction, optical and electron microscopy and other methods. Structure of surfaces: Reconstructions, adsorption induced modifications; scanning probe microscopy, photoelectron spectroscopy and other vacuum techniques, electronic structure and reactivity of surfaces. Prerequisites : M.Sc degree in Chemistry, Physics or Materials Science/II Year Int. Ph.D Programme. Suggested Reading: Ohring, M., The Materials Science of Thin Films, (Academic Press, New York 1992). Francobe, M.H., Physics of Thin Films, Vol. 16(1992) and Vol. 17 (1993) Editors: Francobe, M.H., and Vossen, J.L., (Academic Press, New York). Briggs, D. & Seah, M.P., Practical Surface Analysis (2 nd Edn., Volumes 1&2), (John Wiley, 1990) Woodruff, D.P. & Delchar, T.A., Modern Techniques of Surface Science, (Cambridge Univ. Press, 1994)

Suggested Reading:

Ert, Z. and Kippers, J., Low Energy Electrons and Surface Chemistry (2nd Edn.), (VCH, 1985)

Yariv., Quantum Electronics

Clarke, L.J., Surface Crystallography

Joannopoulos, John D etal, Photonic Crystals : molding the Flow of Light (Princeton Univ. Press, 1995)

G.U. Kulkarni and A.R. Raju

K.S. Narayan 7

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JC 303 (JAN)-(AUG) 2:0 Selected topics in materials science Contemporary topics covering review articles appearing in Reviews in Materials Science, MRS Bulletin, Current topics in Solid State Materials etc., Combinde CPMU Faculty JC 304 (AUG) 3:0 Chemistry of Materials Recent advances in physical and chemical aspects of materials will be discussed. This includes synthesis and Characterization of new materials based on organic and inorganic-zeolites, micro-and meso-porous materials, supramolecular organization, nano-scale particles, Giant Magneto Resistance (GMR), Superconductivity, Organic solid state devices, semiconductor hetero structures, glasses, liquid crystals will be described extensively. Characterization techniques based on EXAFS,. Tunnelling microscopy and spectroscopy will be discussed. This course will have a student seminar component and a term paper. Prerequisites: Advanced research students (II year Ph.D, II/III year Integrated Ph.D) as well as others who have taken preliminary courses in the above areas. Suggested Reading: Mostly recent journals pertaining to Materials/Solid State Chemistry/Solid State Physics.

JE 201 (AUG) 3:0 Population and Quantitative Genetics Population Genetics : Historical development of classical population genetic theory, Hardy-Weinberg equilibrium for one and two loci and sex-linked loci: basic models of viability selection, mutation and migration; selection mutation and selection-migration balance; variable selection intensities; in breeding, assortative mating and random genetic drift; evolution in sub- structured populations. Quantitative Genetics : Phenotypic variance and its partitioning; estimating the components of phenotypic variance, average effects of alleles and heritability; responses to selection; genetic correlations; maintenance of quantitative variation in populations Prerequisites : M.Sc.degree in some area of biology; basic knowledge of Mendelian genetics. Suggested Reading: Danial, L. Hartl & Andrew G. Clark, Principles of Population Genetics, (Sinauer Associates, 1989 (2nd Ed.)) Genetics (Sinauer, Sunderland, Mass., USA, 1989 (2nd Ed.)) Falconer, D.A., Quantitative Genetics (Longman New York, USA 1981, 2nd Ed.) Provine W.B., The Origins of Theoretical Population Genetics, (University of Chicago Press, Chicago, IL USA, 1971) Amitabh Joshi

S. Natarajan and A.R. Raju 9

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JE 202 (AUG) 3:0 Chronobiology

Introduction to Population Dynamics

Introduction to biological rhythms; Daily, lunar and annual rhythms; Rhythmic phenomena in plants, animals and humans; Zeitgeber and biological rhythms; Light and temperature relations; Drosophila eclosion clock as a case study, Entrainment, free-run, transients and phase-shifts; Circadian rhythms and photo-periodism; Models and mechanisms of endogenous time-keeping; Ecology and evolution of circadian rhythms; Medical applications of chronobiology. Prerequisites:

JE 203 (JAN) 3:0

M.Sc. degree in any scientific discipline.

Introduction to systems analysis, positive and negative feedback; Phase spaces, trajectories and equilibria; Models of single species population growth; Basic models of competition and predator-prey interactions; Models of metapopulation structure and dynamics; Empirical studies of single-and multi-species population dynamics; Empirical studies of metapopulation dynamics in single and multi species systems. Prerequisites : M.Sc. degree in any area of biology, mathematics or statistics; knowledge of basic calculus.

Suggested Reading:

Suggested Reading :

Course material from various sources, including the primary literature will be provided as needed.


Buenning, E., The Physiological Clock (Springer Verlag, Heidelberg, New York, 1973).

Amitabh Joshi and Faculty

Edmunds, L.N., Cellular and molecular bases of biological clocks (Springer Verlag, New York, 1988). Goldbeter, A., Biochemical oscillations and cellular and rhythms (Cambridge University Press, Cambridge, 1996). Winfree A.T., The timing of biological clocks (Scientific American Library: An imprint of Scientific American Books, Inc., New York 1987) M.K. Chandrashekarana and Vijay Kumar Sharma

JE 204 (AUG) 3:0 Basic Quantitative Tools in Biology A. Mathematics Basic algebra : functions, equations and their manipulations, matrix manipulation Basic analytical geometry : coordinate geometry, straight lines. Basic Trigonometry : trigonometric functions and their manipulation.

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Basic calculus: limits, differentiation and integration, differential equations. B. Statistics

fitness: Evolution of aging; Evolution of host/ habitat specialisation; Density-dependent selection and fitness tradeoffs; Evolution of sexual reproduction; Laboratory natural selection and the design of evolutionary experiments.

Basic Probability : Combinatories, random variables and distributions, probability, Binomial, / Poisson and Normal distributions.

Suggested Reading:

Basic Estimation : Sampling, estimators, confidence intervals, logic of hypothesis testing.


Prerequisites : M.Sc. Degree in any area of biological sciences.

Amitabh Joshi

Prerequisites: Population and Quantitative Genetics

Suggested Reading : R. Ellis & D. Gulick Calculus with Analytic Geometry, (Harcourt Brace Jovanovich, 1986) R.S. Paul & E.G. Haeussler Jr. Algebra for college students, (Reston Publ. Co., 1985) R.V. Hogg & E.A. Tanis. Probability and Statistical Inference. (MacMillan Publ. Co., 1983) L. Ott. An Introduction to Statistical methods and Data Analysis. (PWS-KENT Publ. Co., 1988)

JE 302 (JAN) 3:0 Chronobiology: Advanced Aspects Phase response curves, analysis of periodicity, parameters of circadian rhythm, multi-oscillator view of circadian rhythm, models in circadian rhythm studies, circadian rhythms and photoperiodism in plants and animals, circannual rhythms and bird migration, circadian rhythms in humans, chronobiology in human health and welfare, genetic basis of circadian rhythms. Prerequisites : M.Sc. degree in any scientific discipline.

Amitabh Joshi and Vijay Kumar Sharma Suggested Reading: JE 301 (JAN) 3:0 Evolutionary Genetics of Fitness Theoretical and empirical approaches to studying adaptive evolution: Genetic architecture of fitness components; Lifehistory evolution and trade-offs among components of 13

Buenning, E., The Physiological Clock (Springer Heidelber, New York, 1973). Edmunds, L.N., Cellular and molecular bases of biological clocks (Springer Verlag, New York 1988)

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Goldbeter, A., Biochemical oscillations and cellular rhythms (Cambridge University Press, Cambridge 1996) Winfree, A.T., The timing of Biological clocks (Scientific American Library: An imprint of Scientific American Books, Inc., New York, 1987). Aschoff. J. (Ed) Circadian clocks (North Holland, Amsterdam 1965) Chovnik (Ed.) Biological Clocks, Cold Spring Harbor Symposium Quant. Biol. 25, 1960. Primary literature (research papers) will be provided. M.K. Chandrasekharan and Vijay Kumar Sharma JF 201 (AUG) 3:0 Mathematical Methods Ordinary differential equations, phase plane (and Poincare maps), Fourier transforms, basic linear algebra, introduction to partial differential equations, introduction to perturbation methods, complex analysis. The emphasis will be on applying the methods being taught to physical situations. Each part of the course will include simple solutions by numerical methods, followed by assignments. Prerequisites : M.Sc / B.E Suggested Reading:

Bender, Carl M & Orszag, Steven A, Advanced Mathematical Methods for Scientists and Engineers (Springer Verlag, 1999) Kumar N., Deterministic Chaos: Complex Change out of Simple Necessity: (Univ. Press, 1995) Rama Govindarajan JF 301 ( JAN) 3:0 Advanced Topics in Fluid Dynamics Content : This course will be conducted in a discussion format. The instructors will give a brief description of each topic. This will be followed up by detailed study of related literature by the students and presentations in the class. Some of the topics are: Insect flight dynamics, flow visualisation techniques, measurement techniques, diffusion in stratified media, some well-known instabilites, two-fluid stability, atmospheric boundary layers, wavelet transforms. The idea is to expose students to research areas and tools of a wider range than their thesis topic. The emphasis will be on areas of interest to members of the Unit. Prerequisites : M.Sc/B.Tech K.R. Sreenivas and Rama Govindarajan JM 201 (AUG) 2:0 Introduction to Genetics

Kreyszig, E, Advanced Engineering Mathematics, (John Wiley & Sons, 1999)

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Principles of genetic transmission, genetic analysis, genotype, phenotype, complementation, mitosis, metosis, meiosis, genetic linkage and epistatis, Gene interactions mapping, 16

basic organization of an eukaryotic chromosome, variation in chromosome structure and number, beginings of the molecular genetics. Prerequisites : Masters degree in any scientific discipline.

Voet, Donald and Voet, Judith G, Biochemistry (John Wiley, 1995) Nelson, David L & Cox Michael M, Lehninger, Principles of Biochemistry, (Macmillan Press, 2000) Stryer Lubert, Biochemistry (W.H. Freeman & Co., 1995)

Suggested Reading : Hemalatha Balaram Griffiths, A.J.F, Miller, J.H., Suzuki, D.T., Lewontin, R.C. and Gelbart, W.M. An Introduction to Genetic Analysis (W.H. Freeman and Company, New York, U.S.A, 2000) Klug, W.S. and Cummings, M.R., Essentials of Genetics (Prentice Hall, New Jersey, U.S.A, 1996). Hartl, D.L. and Jones, E.W., Genetics- Principles and Analysis (Jones and Bartlett Publishers, Boston. U.S.A) Anuranjan Anand

JM 202 (AUG) 3:0 Basic Biological Chemistry Biomolecules, 3-D structure of proteins and DNA, protein folding, mechanism of enzyme action rates of reactions, enzymes, catalysis, complete metabolism: carbohydrate, lipid, amino acid and nucleotide Prerequisites : M.Sc in Life Science or Chemistry

JM 203 (AUG) 3:0 Molecular Biology DNA structure, Genome Structure and complexity, Mechanism of transcription in prokaryotes, complexity and beauty of eukaryotic transcription, DNA replication in prokaryotes and eukaryotes, Mechanism of DNA repair in prokaryotes and eukaryotes, Translational regulation in prokaryotes and eukaryotes. A short introduction to Genetic Engineering. In addition to the regular course lectures, 6-7 guest lectures will be arranged. Each student will be asked to present two seminars on the selected papers, during the tenure of the course. Prerequisites : M.Sc degree in any area of biology and / or Organic Chemistry. Suggested Reading :

Suggested Reading :

Watson.et. al, Molecular Biology of the gene, (Benjamin Cumming, 1988)

Cantor, Charles R & Schimmel, Paul R, Biophysical Chemistry Vol. I, II and III (W.H. Freeman & Co., 1980)

Stryer. L, Biochemistry IV, (W.H. Freeman & Co., 1995)

Creighton Thomas E, Proteins : Structures and Molecular Properties, (W.H. Freeman & Co., 1993) 17

Alberts, Bruce et al. Molecular Biology of the cell, (Garland, 1994) Lewin. B, Genes V/IV, (Oxford Univ. Press, 1994) 18

Sambrook, J et al, Molecular Cloning : a Laboratory Manual 3v., (CSHLP, 1989) Ausubel. Fredrick M., et. al, Current Protocols in molecular Biology 3V, (John Wiley, 1996). Watson and Tooze, A short course in Genetic Engineering. Tapas Kumar Kundu JM 204 (AUG) 2:0 Basics in Immunology

JM 205(AUG) 2:0C Signal Transduction in Biological Systems Principles of signal transduction, receptors, second messengers and ion channels in bacteria, yeast, Dictyostelium and mammals, Mammalian signalling mechanisms through protein kinases, second messenger generating systems and ion channels. Signal transduction during fertilization. Sensory transduction and gene regulation in Dictyostellium Prerequisites : M.Sc in Life Sciences

General properties of the immune system. Cells and tissues of the immune system. Antigens and anitbodies. Organisation and expression of immunoglobulin genes. Bcell, maturation activation and differentiation.

Suggested Reading : Recent papers and reviews in the field.

T-cell maturation, activation and differentiation. Major histo-compatibility, complex Antigen processing and presentation. Immune effector mechanisms. Infection and vaccines.

Namita Surolia

Prerequisites: M.Sc in Biology

Gene Expression and Development

Suggested reading : Kuby Janis, Immunology, (W.H. Freeman & Co., 1997) Abbas, Abdul K, et al, Cellular and Molecular immunology, (W.B. Saunders, 1997) Benjamin and Lescowitz, A short course.

JM 206 (AUG) 3:0

General aspects of animal and microbial development; maternal information; inducation; developmental genetics; mammalian development with emphasis on mouse development, regulation of gene expression during development. Prerequisites : M.Sc in Life Sciences or M.B.B.S

Janeway and Travers, Immunobiology, (Elsevier, 1999)

Suggested Reading :

Ranga Uday Kumar

Slack, J.M.W., From egg to embryo, (Cambridge Univ. Press, 1991) Scott F. Gilbert, 2nd Ed. Developmental Biology, (Sinauer Associates, 1997) 19

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Eric Davidson, Gene Activity in Early Development, 3rd Ed. Maneesha Inamdar

worms and humans; Molecular basis of chromosome wide regulatory phenomenon; strategies of genetic mapping in humans; methods of mutation detection. Suggested Reading :

JM 207 (JAN) 2:0 Advance Course in Regulation of Gene Expression. This course will deal with the recent advancement of our understanding in regulation of gene expression in prokaryotes, parasites and eukaryotes. The direct applications of these studies will also be discussed; for example, the role of chromatin remodeling in regulation of gene expression and its application to design drugs or understanding of the regulation of plasmodium falciparum gene expression to combat drug resistance will be discussed. Active participation of the students by means of seminar presentation is expected. Each student will be asked to present three or more seminars on selected topics during the tenure of the course. Prerequisities : Basic understanding of molecular biology Suggested Reading : Recent papers and reviews in the field. Tapas Kumar Kundu and Namita Surolia JM 301 (JAN) 3:0 Advanced molecular Genetics The logic and techniques of genetic analysis; illustrations of application of genetic analysis to specific complex biological systems; genetics of morphogenesis with examples from phage, bacteria and Drosophila, sexual development in flies 21

Human Genetics: Problems and Approaches F. Vogel and A.G. Motulsky Strickberger, M.W., Genetics Annual Review of Genetics (Series) Anuranjan Anand, Usha Vijayraghavan (IISc) Parag Sadhale (IISc) JT 201 (JAN) 3:0 Introduction to Condensed Matter Physics This course will cover fundamentals in solid state physics, Special emphasis will be placed on methods of calculating the electronic properties (nearly free electron approach, tight binding approximation, density functional theory) and vibrational properties (Harmonic approximation, anharmonic effects) of solids. Specific applications to both bulk and surface systems will be discussed. Origin or electronic, optical and magnetic phenomena in solids will be dealt. Prerequisites : Knowledge of Elementary Quantum Mechanics. Suggested Reading : Kittel, C., Introduction to solid State Physics, (6th and 7th Edn.) (Wiley Eastern Limited, 1996)

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Ashcroft, N.W. & Mermin, N.D., Solid State Physics (Saunders College, Philadelphia / CBS Publishing Asia Limited, 1976) Ohring M., The Materials Science of Thin Films (Academic Press, New York 1992) Francobe, M.H. Physics of Thin Films, Vol.16 (1993) Editors: Francobe, M.H., and Vossen, J.L., (Academic Press, New York) Handbook of Thin Film Process Technology, Editors; Glocker, D.A. Shah, S.I. (Institute of Physics publishing, Bristol, 1995) Briggs, D.& Seah, M.P., Practical Surface Analysis (2 nd Edn., Volumes 1 & 2), (John Wiley, 1990) Woodruff, D.P. & Delchar, T.A., Modern Techniques of Surface Science, (Cambridge Univ. Press, 1994) Ertl. Z. and Kuppers, J., Low Energy Electron and Surface Chemistry (2nd Edn.), (VCH, 1985) Ibach, H. and Mills, D.L., Electron Energy Loss Spectroscopy and Surface Vibrations, (Academic Press, 1982)

General Principles of Numerical calculation: Error,(in) stability, condition numbers, scaling of an algorithm. Representation of a problem on a computer: Grids, basis sets, dimensions, units, etc. Interpolation, Derivatives, Integration Linear algebra: Matrices, solutions of linear algebraic equations and singular value decomposition Root finding and nonlinear sets of equations Minimization of functions of several variables: Steepest descent, Conjugate gradient Eigenvalue problems: Lanczos, conjugate gradient, inverse iteration Ordinary and Partial differential equations: Runge-Kutta method, initial and boundary value problems Fitting and modeling of data

Clarke, L.J., Surface Crystallography.

Special Techniques: Fast Fourier Transform, Monte Carlo Methods, Molecular Dynamics, Genetic algorithm, Fast multipole (Greengard-Rokhlin algorithm), Ewald summation

Umesh V. Waghmare and Shobhana Narasimhan

Prerequisites : JF 201 Mathematical Methods or equivalent; some exposure to computers

Somarjai G.A., Chemistry in Two Dimensions; Surfaces

JT 202 (JAN) 3:0 Computational Methods An introduction to computers and Programming Unix, FORTRAN or C, mathematica, visualization tools, parallel programming. 23

Suggested Reading : (a) Programming Reference: Fortran: Rajaraman, (C++: Deitel and Deitel, The Mathematical Book: Wolfram) (b) Dahlquist, Bjorck and Anderson, Numerical Analysis : (1) Numerical Methods 24

(2) Gould, H and Tobochnik, J, An Introduction to Computer Simulation Methods: Applications to Physical Systems

Stone, A.J. , “The theory of intermolecular forces”, (Clarendon Press, Oxford, 1996)

(3) Allen, M.P & Tildesley, D.J., Computer Simulations of Liquids (Clarendon Press, 1987)

Leach, A.R., “Molecular Modelling: principles and applications”, (Addison-Wesley Longman Ltd, 1997)

Umesh V. Waghmare

Cotton, F.A., “Chemical applications of group theory”, (John Wiley, 1999) JT 203 (JAN) 3:0

Swapan K. Pati and S. Balasubramanian

Advanced Theoretical Chemistry JT 204 (Aug) 3:0 Basic formalism of quantum theory; various representations, Schroedinger equation, Angular momentum, spin, spinorbit coupling, Many particle systems, One/two centre integrals, variational method, perturbation theory, Closed/ Open shell molecules; Hartree-Fock method; Basis-sets, Ionization potential, electron affinity, Koopman’s theorem, Orbital picture, bonds, Hybridization and geometry, Valence bond, Molecular orbital, Huckel theory, semiempirical LCAO-MO theories for molecules and polyenes; correlation and configuration interactions, Multipole moments of molecules, polarizabilities, response to electromagenetic field, intermolecular interactions Prerequisites : Basic quantum mechanics

Statistical Mechanics Brief overview of the phenomena and types of experiments that statistical mechanics is concerned with. Elements of probability theory and the central limit theorem. The basis and postulates of equilibrium statistical mechanics; the ensembles and their equivalence; the statistical basis of thermodynamics; chemical potential; simple phase diagrams in field as well as density variables; first-order and continuous transitions. The simple noninteracting problems: independent spins in a magnetic field and the ideal gases (Boltzmann, Fermi, and Bose).

Suggested Reading : Levine, I.N., “Quantum Chemistry”, 5th edition (Prentice Hall, 1999) Szabo, A. and Ostlund, N.S., “Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory”, (Dover Publication, 1996)

Elements of interacting systems: lsing models (exact solution in one dimension, mean-field theory, and Landau theory) and their relation with classical nonideal gases. Random walks, Brownian motion, and the lengevin equation Suggested Reading:

Salem, L., “Molecular Orbital Theory of Conjugated System”, (Benjamin, New York) 25

Texts: Huang, K, Statistical Mechanics 1987) 26

(John Wiley, New York,

Reif, F., Fundamentals of Statistical and Thermal Physics (McGrawHill, New York, 1965)

JT 302 (JAN) 3:0 Topics in Condensed Matter Theory

Reference Books: Bhattacharjee, J.K., Statistical Mechanics: Equilibrium and Nonequilibrium Aspects (Allied, New Delhi 1996) D. Chandler, Introduction to Modern Statistical Mechanics (Oxford, Univ. Press, New York 1987) H.B. Callen, Thermodynamics and an Introduction to Thermostatistics (Wiley, New York 1985) L.D. Landau and E.M. lifshitz: Statistical Physics (Pergamon, New York, 1969) Srikanth Sastry

Review of one-electron band theory, effects of electronelectron interactions: Hatree-Fock approximations, semi empirical methods, introduction to exact many-body methods. Exchange and correlation effects, density functional theory. Anharmonic effects and electron-phonon interactions: phonons in metals, mass renormalization, polarons. Impurities, imperfections and noncrystalline solids, solid surfaces. Optical properties of metals and insulators, excitonic effects. Hubbard model, Heisenberg model, spin-wave analysis and Bosonizations. Chargedensity, spin-density and bond-order waves, metal-insulator transitions and Kondo effects. Cooper pairs, BCS and Landau-Ginzburg theories. Suggested Reading

JT 301 (JAN)-(AUG) 2:0 Computational methods for Electronic Structure Density Functional Theory; Tight-binding and pseudopotential methods; Car-Parrinello, Conjugategradient and Lanczos algorithms; O(N) methods based on density matrix; Methods for electronic structure of disordered systems. Suggested Reading :

“Solid State Physics”, N.W. Ashcroft and N.D. Mermin (Saunders College, 1976) “Quantum Theory of Solids”, C. Kittel (John Wiley, 1987) “Principles of Condensed Matter Physics”, P.M. Chaikin and T.C. Lubensky (CUP, 1995) Shobhana Narasimhan and Swapan K. Pati JT 303 (JAN) 3:0

Payne, et, al., Rev. Mod. Phys. 64m p 1045 (1992) W. Harrison, Electronic Structure Parr and Yang, Density Functional Theory of Atoms and Molecules. Umesh V. Waghmare 27

Quantum Mechanics II Time dependent perturbation theory. Fermi golden rule. Transitions caused by a periodic external field. Dipole transitions and selection rules. Decay of an unstable state. Born cross section for weak potential scattering. Adiabatic 28

and sudden approximations. WKB method for bound states and tunneling. Scattering Theory: Partial wave analysis, low energy scattering, Scattering length, Born Approximation, optical Theorem, Levinson’s Theorem, Resonances, Elements of Formal Scattering Theory. Minimal coupling between radiation and matter, Diamagnetism and Paramagnetism of atoms, Landau levels and Aharonov Bohm Effect. Addition of Angular Momenta, Clebsch Gordon Series, Wigner Eckart Theorem, Lande’s g factor. Many particle systems: Identity of particles, pauli principle, exchange interaction, bosons and fermions. Second Quantization, Multielectron atoms, Hund’s rules. Binding of Diatomic Molecules. Introducation to Klein Gordon and Dirac equations, and their non relativistic reducation, g factor of the electron. Suggested Reading: Landau, L.D. and Lifshitz E.M., Quantum Mechanics, (Pergamon, New York, 1974) Baym, G., Lectures on Quantum Mechanics, (Benjamin, New York 1973) Bethe, H.A. and Jackiw, R., Intermediate Quantum Mechanics, (Benjamin, New York., 1968) Swapan K. Pati

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