BS - MS Dual Degree Program

Guidebook of

Curriculum

2012-13

Contents

Sr. Particulars

1.

Objectives

2. General Pattern

3. Details of Courses Biology Chemistry Mathematics Physics Inter Disciplinary Courses

I. Objectives This model of education (sponsored by DST) is concept-based & inquiry-driven, as opposed to the more traditional content-based models. There is a strong emphasis on the interdisciplinary nature of today's science, and recognition of the importance of research experience while doing UG studies. The courses offered for the UG program form part of a comprehensive program that will enable the students to understand the basic laws of nature and develop necessary skills to apply them to any desired area or discipline. The students get trained for a career in basic sciences or any related applied science or technology.

II. General Pattern The courses offered during the first two years (semesters I to IV) of course work are meant as basic courses from the four streams, common and mandatory for all students and therefore are introductory in nature. These courses are meant to give a flavor of the various approaches and analyses as well as to prepare them for advanced courses in later years of study. In addition there will be interdisciplinary courses for computational skills, scientific computing, mathematical methods etc.

In the third and fourth years (semesters V to VIII), students can choose advanced courses based on their interest. The courses offered in the first two years would help them to make an informed judgment to determine their real interest and their aptitude for a given subject. Students also have the freedom to choose advanced courses from more than one discipline to achieve interdisciplinary expertise.

One of the novel features of the curriculum is a Lab Training/Theory project, equivalent to a course of 3 credits, in which the student will work in a lab with one faculty or do a theory project with one faculty. This is meant to help the student to be trained by the in-house expertise or facility which will form a good basis for the project work in the fifth year. Only one such course per semester is permitted.

The fifth year will be devoted to a thesis by research which completes the requirements of the program

III. Details of courses The list of courses offered from each discipline with brief contents and text books is given below. Other relevant details like objectives, prerequisites, topic in detail, pattern of assessment, books for study and reference etc. will be prepared by the course instructor and communicated to the students well in advance.

BIOLOGY

Semester I

BIO101 Introductory Biology I (3 credits) Contents

This course introduces students to Biology. It asks fundamental questions such as what is life and what are its salient features of life. This course aims at understanding organization of life at different levels. Contents include the hierarchical levels of organization in Biology; Shapes and sizes of life forms; Comparative organization of life forms; Organizational themes in plants and animals; Variation and diversity of life - bacteria, protists, fungi, plants and animals. The chemical basis of life: Water, carbon, and the molecular diversity of life, structure and function of biological macromolecules. References:

1. Campbell and Reece (2005) Biology, 7th edition. 2. Raven, Johnson, Losos and Singer (2005) Biology, 7th edition. 3. Alberts, Bray, Hopkin, Johnson, Lewis, Raff, Roberts and Walters (2003)

Essential cell biology, 2nd edition. 4. Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith

Roberts, Peter Walter. (2007). Molecular Biology of the Cell. 5th

Edition.

BIO 121 Biology Lab I (2 credits) This practical course will cover basic concepts in biology, cell biology and cell culturing techniques with an emphasis on 3D's in biology – draw, describe and differentiate. Practicals include: Basics of microscopy; Field trip; Microscopy of samples; Micrometry of different cells; Staining of bacteria, fungi, Plant cells, Blood cells and Bone marrow; Osmosis; Mitosis; Crude cultures – Bacteria and Protozoa; Pure culture techniques; Sterilization and media preparation; Streaking of bacteria; Enumeration of bacteria

Semester II

BIO102 Introductory Biology II (3 credits) Contents

This course mainly discusses the molecular mechanisms of various processes of life. It starts with discussion on Cells as the unit of life. Contents include, Cell types, from single cell to multi-cellular organism; Cell architecture; macromolecular trafficking within and between cells; Bioenergetics, Cellular respiration and photosynthesis: Respiration and associated metabolism, light and dark reactions of photosynthesis; Reproductive biology: DNA replication, cell division in prokaryotes, meiosis & mitosis in eukaryotes. Mendelian, Genetics, Microbial genetics, Viruses and Human Genetics. Recombinant DNA technology and its applications. Books:

1. Campbell and Reece (2005) Biology, 7th edition. 2. Raven, Johnson, Losos and Singer (2005) Biology, 7th edition. 3. Alberts, Bray, Hopkin, Johnson, Lewis, Raff, Roberts and Walters (2003)

Essential cell biology, 2nd edition. 4. Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith

Roberts, Peter Walter. (2007). Molecular Biology of the Cell. 5th

Edition.

BIO 122 Biology Lab II (2 credits) This practical course will cover biochemical, genetic and molecular basis of life. Practicals include: Glucose estimation; Lipid estimation; Amino acid Paper chromatography; Protein estimation; Enzyme assay and Kinetics; Human genetic traits and blood grouping; DNA isolation; DNA estimation; Transformation; Plasmid isolation; Agarose gel electrophoresis; Restriction digestion and Ligation; PCR demonstration; ATC PTC demonstration; Animal handling, inoculation, dissection.

Semester III

BIO 201 Introductory Biology III - Ecology & Evolution (3 credits) Contents

This is an introductory course that provides a broad overview of concepts in

ecology and evolution. Topics covered will include: Introduction: An overview

of biological processes; Population ecology; Life history evolution;

Community ecology; Species interaction; Behavioral ecology; Ecosystem

dynamics; Population genetics; Macroevolution and diversity of life.

Text Books:

1) Molles (2006). Ecology: Concepts and Applications, 4th Edition, McGraw Hill; 2) Templeton, AR. (2006). Population Genetics and Microevolutionary Theory. Wiley-Liss; 3) Hartl, DL and Clark, AG. (1997). Principles of Population Genetics. Sinauer Associates; 4) Futuyma, D. (2005) Evolution, Sinauer Associates. BIO 221 Biology Lab III (2 credits) This practical course will cover basic concepts in ecology and evolution. Practicals include: Evolution of Ethnocentrism; Isolation of organisms; Global Population Dynamics Database; Plant Biodiversity field work; Growth curve (Factorial design 3 pH × 2 temperatures); Effect of nutritional selection on bacterial growth; Chemical ecology and its impact on diatom diversity; Behavioral Ecology.

SEMESTER IV BIO 202 Introductory Biology IV – Biology of systems (3 credits) Contents

This course introduces integrative themes in biology. Using broad biological systems and building from the previous Introductory Biology courses, it attempts to demonstrate how hierarchical levels of organization and complexity are manifest in Biology. Mathematical modeling and network approaches are also introduced. The course content includes: comparative organization; signal transduction & signaling networks; gene expression & gene regulatory networks; integrative themes in developmental biology and the immune system; neurobiology & behavior and modeling/network approaches in systems biology.

Text Books:

Alberts, B. et al. (2008). Molecular Biology of the Cell. 5th Ed. Garland.

Alon, U. (2007). An Introduction to Systems Biology. 1st Ed. Chapman and Hall.

Semester V

BIO 310 Biostatistics (4 credits) Contents

This course is application oriented with a focus on the statistical techniques for biologists. Topics covered will include: inter alia hypothesis testing, experimental design, correlation and regression analysis, analysis of variance, multivariate analysis & elementary time-series analysis. At the end of this course the students are expected to be familiar with statistical procedures to a) design experiments, b) perform preliminary data analysis, and c) initiate complex statistical analysis as needed. Text Books: Sokal RR and Rohlf HA (1995). Biometry: the principles & practice of

statistics for biological research, 3rd Edition, WH Freeman & Co.;

Zar JH, (1998). Biostatistical analysis, 4th edition, Prentice Hall.

BIO 311 Advanced Cell Biology (4 credits)

Contents

This course covers a wide range of advanced cell biology topics such as, DNA, chromosomes and genome, DNA replication, repair and recombination, membrane structure, transport, intracellular compartments, protein sorting and vesicular traffic, energy conversion: mitochondria and chloroplasts, cell cycle and cell division, mechanisms of cell communi- cations, the cytoskeleton, cell junctions, adhesion, extracellular matrix and cell motility.

Text Books:

1) Molecular Biology of the Cell by Alberts, Johnson, Raff, Lewis et al.

(2007) 5th Ed. Garland Science;

2) Molecular Biology of the Gene by James Watson et al., (2007) 6th Ed.

Benjamin Cummings;

3) Molecular Cell Biology by Lodish, Berk, Kaiser et al. (2007) 6th Ed. W. H.

Freeman.

BIO 312 Animal Physiology I (4 credits)

Contents

The course aims at imparting in-depth knowledge of the physiological processes with emphasis on the human cardio-vascular system and blood; skeletal and smooth muscle systems; excretion and regulation of the body fluids; gaseous exchange, transport and tissue respiration; gastrointestinal physiology and physiology of digestion, endocrines and reproduction. The course will also include lab-work on the regeneration in hydra, various organ systems in a teleost fish and rat model, isolated goat tracheal chain preparation for assay of acetylcholine, evaluation of blood pressure of rat, and study of histological preparations of various tissues. Text Books:

1) Guyton, A.C. et al. (2008). Textbook of Medical Physiology. 11th Ed. W.B.

Saunders Co.

2) Randall, D. et al. (2002). Eckert Animal Physiology, 5th Ed. Freeman.

3) Kronenberg, et al. (2008) Williams Textbook of Endocrinology. W. B. Saunders Co.

BIO 410 Advanced Biochemistry I (4 Credits)

Contents

Water and life, Biomolecules: Structural & functional aspects of Proteins, Nucleic Acids, Lipids and Carbohydrates, Protein folding, dynamics and interaction, binding of macromolecules, Thermodynamics of ligand: receptor interactions, Mechanisms of Enzyme Action, Techniques of Protein and Nucleic acid Purification: Chromatography, electrophoresis, Ultracentrifugation, nucleic acid fractionation

Text Books:

1) Metzler DE (2003), Biochemistry: The chemical reactions of living cells,

Volumes I & II, 2nd Edition, Academic Press.

BIO 332 Immunology I (3 Credits) Contents

The lymphoid system and organs, Cell migration and inflammation, antibody structure, Genetics of antibody generation, B-lymphocyte development and activation, T-lymphocyte development and activation, Innate Immune system – dendritic, natural killer cells, macrophages, Major Histocompatibility complexes; The humoral vs. cellular immunity; Recognition of self vs. non-self, autoimmunity- the breakdown of self- recognition.

Text Books:

1) Kindt TJ, Osborne BA, Goldsby RA (2006), Kuby Immunology, 6th Edition

W.H. Freeman & Company.

BIO 334 Neurobiology I (3 Credits) Contents

The course introduces neuroscience as a specialized discipline. Course content includes: evolution and organization of the nervous system; electrical properties of neurons; ionic basis of membrane potentials and the action potential; development of the nervous system; synaptic transmission;

experience-dependent synaptic refining & plasticity; neurobiology of sensory systems; motor functions of the spinal cord; the autonomic nervous system; introduction to learning and memory.

Text Books :

1) Kandel E, et al. (2000). Principles of Neural Science, 4th Ed. McGraw-Hill

Medical;

2) Bear M, et al. (2006). Neuroscience. 3rd Ed. Lippincott Williams & Wilkins;

3) Sanes D, et al. (2005). Development of the Nervous System. 2nd Ed.

Academic Press.

BIO 335 Animal Behaviour (3 credits)

Contents

This course is an introduction to practices and theories in the study of animal behavior. Topics covered include: research methods, behaviours to do with learning, foraging, territoriality, movement, reproduction and communication. The classes revolve around discussions of scientific papers, and the students are expected to carry out individual projects spanning the semester on a species and question of their choice.

Text Books:

1) Krebs, J.R. and Davies, N.B. (1993) An introduction to behavioural

ecology. Blackwell Publishing, 3rd ed. 2) Dugatlin, L. A. (2004) Principles of animal behavior. W. W. Norton & Co. 3) In addition, reading assignments will be from Ecology, Evolution and

Behaviour Journals.

Semester VI

BIO 320 Genetics (4 Credits) Contents

Mendelian and Non-Mendelian Genetics; The Chromosomal basis of

inheritance; Genomes, genomics and the Dynamic Genome; The Genetics of Bacteria & Bacteriophages; Genetic screens for functional genomics; Gene isolation and manipulation; Techniques that revolutionized modern genetics; The utility of the following Model Organisms will be discussed: Eschereschia coli, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster & Mus Musculus. Text Books

1) Griffiths, AJ et al. (2008), Introduction to Genetic Analysis, 9th

Edition, WH Freeman & Co.

BIO 321 Plant Biology I (4 Credits) Contents This course would cover up the basic and advanced knowledge of plant biology. It will embrace information's of plant Cells, water transport; mineral Nutrition; photosynthesis- light & carbon reactions; ecological considerations; solute transport; transporter genes; phloem translocation; respiration; lipid metabolism; growth & development; phytochrome and light control of plant development, blue light response, plant hormones and development, stress physiology. Text Books:

1) Lincoln Taiz and Eduardo Zeiger (2006), Plant Physiology, 4th

edition Sinauer Associates

2) Bob Buchanon, Wilhelm Gruissem and Russel Jones (2007) Bio- chemistry & Molecular Biology of Plants, IK international Pvt. Ltd.

BIO 412 Microbiology (4 credits) Contents

Microbial diversity: Cultural and culture independent methods, taxonomy, functional anatomy of prokaryotic and eukaryotic microbial cells. Microbial physiology: Unique pathways for fermentation, biodegradation and biosynthesis. Microbial growth kinetics. Development and differen- tiation in microorganisms: spores, cysts, biphasic growth, Dictyostelium development, myxobacterial development, Biofilms and signaling among microbial cells. Microbial genetics. Principles of disease and epidemio- logy: Mechanisms of pathogenicity, host parasite interactions, Antimi- crobial drugs, disease transmission dynamics, public health and prophy- laxis. Microbial biotechnology and bioengineering: Types of bioreactors, design of bioreactor, operation, downstream processing, development of new products, scale up. Text Books:

1) Tortora GJ, Funke BR and Case CL (2004) Microbiology: An

Introduction. 8th edition, Pearson Education. 2) Birge EA (2006) Bacterial and bacteriophage genetics. Springer.

3) Nicklin J, Khan N and Killington R (2006) Microbiology. 3rd edition, Taylor and Francis.

4) Mansi ME, Bryce CFA (2007) Fermentation microbiology and

biotechnology. 2nd edition, Taylor and Francis.

BIO 351 Biology and Disease (3 credits)

Prerequisite BIO 311

Contents

This course integrates the biology (cell, molecular and physiology) taught so far, to develop insights into the biology revealed by disease conditions, and teach technology development and translation prompted by the disease condition. Cancer and neurodegenerative disorders will be used as the disease models. It will cover a range of topics from the biology of cancer/neurodegeneration, molecular mechanisms to disease etiology, screening, diagnosis and treatment. Text Books:

1) Kleinsmith L, (2005), Principles of Cancer Biology, 1st Ed. Benjamin

Cummings;

2) Weinberg R, (2006). The Biology of Cancer, 1st Ed. Garland Science; 3) Weinberg RA, (1999). One Renegade Cell: The Quest For The Origin Of

Cancer (Science Masters), 1st Ed. Basic Books; 4) Beal MF, Lang AM, Ludolph AC, (2005). Neurodegenerative Diseases:

Neurobiology, Pathogenesis and Therapeutics, 1st University Press;

5) Chesselet M, (2001). Molecular Mechanisms of Neurodegene- rative Diseases (Contemporary Clinical Neuroscience), Humana Press.

Ed. Cambri

BIO 352 Animal Physiology II (3 credits)

Prerequisite BIO 312

Contents Thermoregulation in ectothermic and endothermic animals; physiology of circulation, respiration, excretion, ionic balance in sub-mammalian vertebrates; physiology of reproduction among different groups of animals; metamorphosis in amphibians; circulation, ionic balance and excretion, respiration, digestion, moulting, nervous and neuroendocrine system, reproduction and life cycle of insects; vision in invertebrates; special topic – parasitism. Text Books:

1) Randall, D. et al. (2002). Eckert Animal Physiology, 5th Ed. Freeman.

2) Hill, R.W. et al. (2008). Animal Physiology. 2nd Ed. Sinaur Associates;

3) Guyton, A.C. et al. (2008), Textbook of Medical Physiology. 11th Ed. W.B.

Saunders Co.

4) Withers, P.C. et al. (1992) Comparative Animal Physiology. 1st

Ed., Brooks Cole.

BIO353 Immunology II (3 Credits) Prerequisite BIO 332 Contents Host-pathogen interactions; Subversion of the host immune responses by intracellular parasites; Ontogeny and function of dendritic cells; Auto antibodies in health and disease; Molecular interactions between the T cell receptor and MHC molecules; Immune synapse; Polyspecificity of T cell receptor recognition; Molecular mimicry and epitope spreading; T cell memory; Peripheral tolerance and regulatory lymphocytes; Animal models of immune dysregulation; Interactions between the immune and the nervous systems. Text Books:

1) Kindt TJ, Osborne BA, Goldsby RA (2006), Kuby Immunology, 6th Edition

W.H. Freeman & Company; 2) In addition, reading assignments for this course will be from recently

published papers from the primary literature.

BIO 354 Neurobiology II (3 credits) Prerequisite BIO 334 Contents Neurobiology of sensory perception; motor control; sexual dimorphism of brain; brain imaging - EEG, PET, CT, fMRI; neurodegenerative disorders; neural basis of behavior, arousal and sleep; circadian rhythms; emotions and the limbic system; higher functions of the brain, learning and memory, perception and cognition, anxiety and depression Text Books:

1) Kandel, E. et al. (2000). Principles of Neural Science, 4th Ed. McGraw-Hill Medical;

2) Bear, M. et al. (2006). Neuroscience - Exploring the brain, 3rd Lippincott Williams & Wilkins;

Ed.

3) Guyton, A.C. et al. (2008). Textbook of Medical Physiology, 11th Ed. W.B.

Saunders Co.

4) Purves, D. et al. (2008). Neuroscience, 4th Ed. Sinauer Associates.

Semester VII

BIO 322 Biophysics (4 Credits) Contents Laws of Physics and chemistry - thermodynamics and biophysical chemistry of macromolecules, Biological reactions and interactions - function aspects of various bio-molecules particularly ion channels, ATP synthases and motor proteins. Biophysical techniques; Chromatography, electrophoresis, diffusion, sedimentation, light scattering; Chemical kinetics - Absorption Spectro- scopy, Circular dichroism, Emission spectroscopy, light microscopy, electron microscopy, crystallography, Nuclear Magnetic Resonance, Mass spectrometry. Text Books:

1) Van Holde KE, Johnson C, and Ho PS (2005). Principles of Physical

Biochemistry, 2nd Edition, Prentice-Hall. 2) Cantor CR, Schimmel PR (1980) Biophysical Chemistry: Part 1 - The

Conformation of Biological Molecules, 1st ed., WH Freeman. 3) Cantor CR, Schimmel PR (1980) Biophysical Chemistry: Part 2 - The

Study of Biological Structure and Function. 1st Edition, WH Freeman.

BIO 411 Ecology I (Basic ecology) (4 credits)

Contents

This course will cover the basic theoretical framework of ecology. Topics covered will include: Introduction - history, philosophy and practice of ecology; Ecology of individual organisms - physiological ecology; population ecology - population growth and regulation, evolution of life- history, species interactions, trophic interactions; Community ecology - community structure & properties, succession & disturbance; Ecosystem ecology – biodiversity, productivity and energy flow, biogeochemistry. Text Books:

1) Begon M, Townsend CR, Harper JL (2006). Ecology: from individuals to ecosystems. 4th edition, Blackwell Publishing.

2) Ricklefs RE, and Miller (2000). Ecology. 4th edition, Freeman and Co.

3) Gurevitch J, Schener SM, and Fox GA (2006). The Ecology of Plants. 2nd Edition, Sinaeur and Associates.

BIO 417 Advanced Biochemistry II (4 Credits) Contents

Advanced enzyme kinetics and energy metabolism, Metabolic processes and

pathways such as Glycolysis, glycogen metabolism, membrane transport,

Citric acid cycle, electron transport, amino-acid metabolism, carbohydrate

metabolism, photosysnthesis, lipid and nucleotide metabolism will be discussed

in detail. Text Books:

1) Metzler DE (2003), Biochemistry: The chemical reactions of living cells,

Volumes I & II, 2nd Edition, Academic Press; 2) Readings will also be assigned from current articles from the primary

literature.

BIO 420 Developmental Biology (4 Credits) Contents

This course deals with how a single-celled embryo develops into a complex multi cellular individual with all its complexity. It deals with early development and axial specification; Pattern formation; Development of germ cell layers; growth and differentiation; Metamorphosis, regeneration and aging; Plant development; Stem cell biology and tissue repair; Principles of experimental embryology; Development mechanisms of Evolutionary change. Text Books:

1) Gilbert SF, (2010). Developmental Biology, 9th

Associates.

Edition, Sinauer &

2) Wolpert L, et al. (2006). Principles of Development, 3rd Edition, Oxford University Press.

BIO 431 Epigenetics (3 credits)

Contents

This course deals with all that goes between genotype to phenotype. Imprinting in plants and animals; X-inactivation; Gene regulation host defense, tissue specific effects; Molecular mechanisms – DNA methylation, histone modification, euchromatin vs. heterochromatin, RNA silencing, micro RNA, RNAi - mediated gene regulation; Methods of detecting epigenetic mechanisms; interplay of epigenetic mechanisms in development, differentiation, regeneration and aging.

Text Books:

1) Allis & Reinberg (2007). Epigentics. 1st Edition, Cold Spring Harbor

Laboratories Press.

BIO 433 Mathematical Biology (3 credits) Contents

This course is an introduction to mathematical modeling in biology. Topics covered will include: Phase-plane analysis of (nonlinear) ODEs; Introduction to modeling in neuroscience (including a classification of neural models based on bifurcations); Enzyme kinetics, including a derivation of Michaelis-Menten through a slow-fast analysis; Elementary geometric singular perturbation theory; Reduction strategies for larger dimensional systems; Modeling, ecological and evolution systems; Stochastic models, enzymes, channels and pumps. Students will be expected to be comfortable with a programming environment of their choice: Matlab, C, FORTRAN or XPPAut. Text Books:

1) Ellener SP, and Guckenheimer J. (2006). Dynamic Models in Biology. Princeton University Press.

2) Keener J, Sneyd J, Mathematical Physiology (2001), Springer.

3) Dayan P, Abbott LF, Theoretical Neuroscience (2005), 1st Edition, MIT Press;

4) Edelstein-Keshet, Mathematical Models in Biology (2005), 1st

Edition, SIAM: Society for Industrial and Applied Mathematics.

BIO 452 Plant Biology II (3 Credits) Prerequisite BIO 321 Contents The objective of this course is to understand the value of applied plant biology. Topics such as plant cell, tissue & organ culture, biotechnology in crop improvement; transgenic plants, production of phytochemicals, neutraceuticals, bio-fuels; phytoremediation; pharmacognosy, molecular farming; secondary metabolites, common diseases of plants and plant/ pathogen interaction, molecular mechanisms, quantitative genetics, molecular markers and plant breeding, seed technology and site visits to plant biotech companies are covered in this course. Text Books:

1) Rainer Fischer and Stefan Schillberg (2004). Molecular Farming, Wiley VCH Verlag GMBH & Co.

2) Indra K. Vasil and Trevor A. Thorpe (2005). Plant Cell and Tissue

culture, Springer.

3) MK Razdan (2002). Introduction to Plant Tissue Culture, 2nd

Edition, Oxford and IBH.

Semester VIII

BIO 421 Bioinformatics & Computational Biology (4 credits) Contents This course covers a range of computational methods, which address a broad spectrum of problems in functional genomics, including; sequence analysis (alignment, motif discovery and gene annotation), pattern recognition/discovery in expression data, phylogenetic trees, phylogeny, and alignment. Also included in this course are topics in computational modeling of biological processes, data-mining, algorithm development, statistical and mathematical analyses. Perl and BioPerl will be used to implement algorithms and will be covered as necessary; no prior programming knowledge is required. Text Books:

1) R. Durbin, S. R. Eddy, A. Krogh, and G. Mitchison (1999). Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press;

2) D. Gusfield (2007). Algorithms on strings, trees, and sequence: computer science and computational biology (2007), Cambridge Univ. Press.

BIO 422 Evolution (4 credits) Contents

Population genetics: Hardy-Weinberg principle and the deviations from it, Wright's F-statistics; Quantitative Genetics: Additive genetic variance, Fisher's fundamental theorem, Adaptive landscape; Life-history evolution; Selection: multilevel selection, sexual selection, experimental evolution; Application: Aging, evolutionary psychology, evolutionary medicine, evolution and society. Text Books:

1) Nicholas H. Barton, Derek E.G. Briggs, Jonathan A. Eisen, David B. Goldstein, Nipam H. Patel (2007). Evolution. Cold Spring Harbor Laboratory Press.

BIO 423 Ecology II (Advanced ecology) (4 credits) Prerequisite BIO 411

Contents This course will cover current topics in Ecology by readings and discussions from the primary literature. The broad focus will be on: History, Philosophy & Practice of Ecology; Physiological Ecology; Behavioural Ecology; Evolutionary Ecology; Ecological Genetics; Population Ecology; Molecular Ecology; Community structure; Biodiversity and Climate Change.

Text Books:

1) Ricklefs RE, and Miller (2000). Ecology. 4th edition, Freeman and Co.

2) Gurevitch J, Schener SM, and Fox GA (2006). The Ecology of Plants. 2nd Edition, Sinaeur and Assciates;

3) Krebs JR and Davis NB (1997). Behavioural Ecology, 4th

Blackwell Science; Edition,

4) In addition readings from the primary literature will be assigned from journals: Ecology; Ecology Letters; Journal of Ecology; Annual Reviews in Ecology Evolution and Systematics; Evolution; Oikos; Oecologia; Molecular Ecology; American naturalist.

BIO 451 Human Genetics (3 Credits) Contents Single locus, complex multi-factorial traits and inheritance; population genetics, linkage disequilibrium, and mapping; cytogenetics, molecular genetics, biochemical genetics, clinical genetics, epigenetics, gene- environment interactions; genetic counseling and gene therapy; Myths and realities of the genetic basis and inheritance of intelligence, behavior, diseases; Model systems for Human Genetics. Text Books:

1) Lewis R (2009), Human Genetics, 9th Edition, McGraw-Hill.

2) Cummings M, (2008), Human Heredity: Principles and Issues, 8th

Edition, Brooks Cole.

BIO 454 Structural Biology (3 Credits)

Contents

Structure-function relationship of bio-polymers (proteins, nucleic acids, lipids and membranes); DNA – replication and recombination; Protein synthesis - translation; Protein folding and degradation; Enzyme function; Cell motility and transport; Structural aspects of cell-cell interactions; Methods of structure determination (X-ray, NMR), structure prediction, determining the structure of major macromolecular machines in action (Case studies: ribosome, the polyketide synthase, motor proteins etc) and challenges in structural biology. Text Books:

1) Liljas A. et al. (2009), Structural Biology, paperback Edition, World Scientific Publishing Company.

BIO 490 Introduction to Mathematical Modeling (3 credits) Contents

This course will cover approaches in the formulation and analysis of mathematical models in physics, chemistry & biology. Topics covered will include dimensional analysis; differential equations; probability and optimization; modeling using ordinary and partial differential equations; stochastic models; numerical methods and function fitting; principal component analysis (PCA) and single value decomposition (SVD); wavelets, neural networks; time series analysis of data; topics in climate modeling. Extensive use will be made of simulations.

Text Books:

1) Gershenfeld N. (1998). The Nature of Mathematical Modeling. Cambridge University Press.

2) Ermentrout B. (2002) Simulating, analyzing, and animating dynamical systems: A guide to XPPAUT for researchers and students. Society for Industrial and Applied Mathematics (SIAM).

BIO491 Literature review (3 credits)

Contents

This main objective of this course is to familiarize students with the primary scientific literature. This will include use of database search tools; reading, analyzing, and critically evaluating the scientific literature; and, effectively summarizing, communicating (oral-written) this information. Course content will include: Introduction to the scientific literature: what is the scientific literature? Primary, secondary and tertiary scientific literature; Reading & evaluating the scientific literature, searching the scientific literature; Conducting a literature review; Scientific writing: plagiarism and referencing, format and style; Oral presentations.

Text Books:

1) Reading assignments for this course will be from a variety of scientific journals.

CHEMISTRY

Semester I

CHM: 101 Introductory Chemistry I - Physical Chemistry (3 credits)

Contents

Basic principles of physical chemistry like thermodynamics, chemical kinetics, kinetic theory of gases, quantum mechanics, and chemical bonding. Text Books:

1) Physical Chemistry a Molecular Approach: Donald A. McQuarrie and John D. Simon, Viva Books (1997).

2) Physical Chemistry: P. W. Atkins, 7th edition Oxford University Press. CHM: 121 Chemistry Lab I (2 credits) Contents

Acid-base titrations using pH meter and conductivity methods; potentio-metric titration; heat of neutralization; kinetic studies of ester hydrolysis; activation parameter calculations; enzyme kinetics; colligative properties of solutions; and polarimetry. Text Books:

1) Experiments in Physical Chemistry: C. W. Garland, J. W. Nibler, D. P.

Shoemaker, 8th edition, McGraw Hill Higher Education.

2) Atkin's Physical Chemistry: P. Atkins, J. de Paula, 8th edition, W.H. Freeman.

Semester II

CHM: 102 Introductory Chemistry II - Inorganic Chemistry (3 credits) Contents Atomic structure, periodic table and the concept of periodicity; chemical bonding; acids-bases; oxidation and reduction; representative chemistry of Transition metals and main-group elements. Text Books:

1) Inorganic Chemistry: Shriver and Atkins, 4th edition, Oxford University Press. 2) Concepts and Models of Inorganic Chemistry: D. McDaniel and Alexander, 3rd edition, Wiley.

CHM: 122 Chemistry Lab II (2 credits)

Contents

General chemistry experiments; acid-base, complexometric & iodometric titrations; synthesis and characterization of coordination complexes; soap making; synthesis of alums and polyoxometalates; spectrophotometric estimation; photochemical reduction of metal complexes.

Semester III CHM: 201 Introductory Chemistry III - Organic Chemistry (3 credits) Contents Chemical Bonding: VSEPR theory; hybridization/LCAO; molecular orbital theory. Arrow pushing concepts; inductive effects; hyper conjugation; acidity and basicity of organic molecules, pKa concept; stereo chemistry: conformational analysis, optical activity. Organic reactions: nucleophilic substitution; elimination; addition; electrophilic aromatic substitution. Basic characterization of organic molecules; chemistry of life; polymer chemistry.

Text Books : 1) Organic chemistry: J. Clayden, N. Greeves, S. Warren, P. Wothers, 1st

Edition, Oxford University Press. 2) Organic Chemistry: T. W. Graham Solomons, Craig B. Fryhle, 9th

Edition, Wiley.

Semester IV

CHM: 202 Introductory Chemistry IV - Fundamentals of Spectroscopy (3 credits)

Contents

Light-matter interaction; rotational spectroscopy; vibrational spectroscopy; Raman spectroscopy; electronic spectroscopy; nuclear magnetic resonance spectroscopy; electron spin resonance spectroscopy. Text Books:

1) Fundamentals of molecular spectroscopy: C. N. Banwell and E. M.

McCash, 4th edition, Tata McGraw-Hill, 1994. 2) Introduction to spectroscopy: D. L. Pavia, G. M. Lampman, G. S. Kriz and

J. R. Vyvyan, 4th edition, Brooks Cole, 2008. 3) Spectrometric identification of organic compounds, R. M. Silverstein, F.

X. Webster, 7th edition, Wiley, 2005.

CHM: 221 Chemistry Lab III (2 credits) Contents Synthesis and characterization of a wide range of aliphatic and aromatic substances; techniques such as reflux, distillation, vacuum filtration, purification and determination of yield and purity; stereospecific addition reactions, elimination reactions, condensation reactions, electrophilic and nucleophilic substitution reactions, rearrangements, multi-step organic synthesis, synthesis of fluorescent molecules and organic dyes.

Semester V

CHM 320 Symmetry and Group Theory (4 credits) Contents Symmetry elements, point group and its applications; Great Orthogonality Theorem; reducible & irreducible representations; Mulliken symbol; character table; direct product; application of direct product concept to spectroscopy as well as in quantum mechanics; Projection operator and its application to symmetry adapted linear combination (SALC); construction of molecular orbital correlation diagram of simple and complex molecules; Hückel ð molecular orbital for conjugated system. Text Books:

1) Chemical Applications of Group theory: F. A. Cotton, 3rd edition, Wiley Interscience, 1990. 2) Molecular symmetry & group theory: R. L. Carter, John Wiley & Sons,

1998; 3) Symmetry and Spectroscopy: D. C. Harris and M. D. Bertolucci, Dover

publications, 1978.

CHM: 311 Physical Organic Chemistry (4 credits) Contents

Structure and bonding, valence bond theory, qualitative MO theory; bonding and structures of reactive intermediates; solution and solvent properties and non-covalent binding forces, conformational analysis of acyclic and cyclic systems, stereo electronic effects and stereo chemical concepts, aromaticity and electronic effects on structure, structural effects on stability and reactivity, kinetic postulates (Hammond postulate, Curtin- Hammett principle, Marcus theory etc.,); reaction kinetics; kinetic isotope effects and isotopic labeling experiments; linear free energy relationships. Organic reaction mechanisms: substitution reactions at aliphatic and aromatic centers; reactions involving additions and eliminations; physical organic considerations of thermal pericyclic reactions; and sigma tropic rearrangements. Text Books:

1) Modern Physical Organic Chemistry: E. Anslyn, E. Dougherty, University Science Books, 2006.

2) March's Advanced Organic Chemistry: M. B. Smith, J. March, 6th

edition, Wiley Interscience. 3) Advanced Organic Chemistry Part A, Structure and Mechanism: R. J.

Sundberg, F. A. Carey, 4th Edition, Kluwer/Plenum Press.

4) Physical Organic Chemistry: N. Isaacs, 2nd Edition, Addison-Wesley- Longman.

CHM: 312 Main Group Chemistry (4 credits) Contents General chemistry- the covalent bond: VSEPR theory, Valence bond theory, MO theory. Acids and bases. Chemistry of the main group elements: general trends, hydrogen, alkali metals, alkaline earths, chemistry of group 13-16 elements, inorganic chains, rings, cages, and clusters; chemistry of halogens; the noble gases; main group organometallic chemistry. Text Books:

1) Advanced Inorganic Chemistry by F. A. Cotton, G. Wilkinson, C. A. Murillo and M. Bochmann, 6th Ed. Wiley, 2003.

2) Chemistry of the Elements by N. N. Greenwood and A. Earnshaw, 2nd Ed. Butterworth- Heinemann, 2005.

3) Organometallics by Christoph Elschenbroich, 3rd Ed. Wiley-VCH, 2006.

CHM: 331 Self-assembly in Chemistry (3 credits) Contents Introduction to self-assembly and supramolecular chemistry; types of self-assembly and non-covalent interactions, pre-organization; Crown ethers, Cryptand, metallo-supramolecules; self-complementary two, three and multiple hydrogen bonding systems; liquid crystals; mesogens self-organization; anionic, cationic and neutral micelles, critical micelle concentration; bolaamphiphilies; self-assembly in DNA; protein and peptides; drug delivery applications. Text Books

1) Comprehensive Supramolecular Chemistry, Pergamon, vol.1-10, 1999. 2) Core concepts in Supramolecular chemistry and Nano-chemistry: J. W.

Steed, 1st edition, Wiley.

3) Introduction to Soft mater Synthetic and Biological Self-Assembly Materials: I. W. Hamley, Wiley revised edition.

CHM: 332 Separation Principles and Techniques (3 credits)

Contents

Theory of separation; chomatogrophic Separations; Chomatogrophic techniques: GC, GC-MS, HPLC; Bio-Separations Electrophoresis, Centrifugation DNA/Protein separations/purifications; Polymer separations-Green Separation Process Separation using Zeolite and Polymer membranes; Chiral separations, Molecular recognition, Molecule imprinting, Polymer separations.

Text Books :

1) An Introduction to Separation Sciene : B.L. Karger, L.R. Snyder, C. Horvath, 1st edition, Wiley Interscience.

2) Handbook of Separation Process Technology: R.W. Rousseau, Wiley Interscience.

3) Separation Process Principles: J.D. Seader, E.J. Henley, 2nd edition, Wiley.

CHM 340 Advanced Organic Chemistry Lab (3 credits) Contents

Classical name reactions, oxidations, reductions, rearrangements, and multi-step reactions; purification techniques such as column chromato- graphy; characterization using IR, UV, NMR and mass spectrometer.

Semester VI

CHM: 310 Quantum Chemistry (4 credits) Contents

Schrödinger equation; exact solutions for: a particle in a box; harmonic oscillator; rigid rotor and hydrogen atom; approximate methods like perturbation and variational methods; molecular orbital and valence bond theories; Hartree-Fock approximation.

Text Books:

1) Quantum Chemistry: Donald A. McQuarrie, 2nd Science Books, 2007.

edition, University

2) Quantum Chemistry: Ira N. Levine, 6th edition, Prentice Hall, 2008. 3) Modern Quantum Chemistry: Introduction to Advanced Electronic

Structure Theory: A. Szabo, N. Ostlund, Dover Publication, 1996.

CHM: 321 Organic Synthesis I (4 credits) Prerequisite CHM 311

Contents

Nucleophilic substitution, Interconversion of carboxylic acid derivatives; protecting and deprotecting functional groups; protection of hydroxyl-, amino-, carbonyl-, and carboxylic acid-groups. Electrophilic additions, cyclizations, reductions. Formation of carbon-carbon single bond via enolates:1,3-Dicarbonyl and related compounds, Direct alkylations of simple

enolates, imines and hydrazone anions; enamines; aldol conden- sation, Mannich reaction, Claisen condensation, Robinson annulations; organometallic reagents; reagents and procedures for alcohol oxidation, oxidation procedures to caroboxylic acids, Allylic oxidation of alkenes Text Books:

1) Advanced Organic Chemistry, Part B: Reactions and Synthesis: F. A.

Carey, R. J. Sundberg, 5th Edition, 2007, Springer.

2) Organic chemistry: J. Clayden, N. Greeves, S. Warren, P. Wothers, 1st Edition, 2001, Oxford University Press.

CHM: 322 Transition Metal Chemistry (4 credits) Contents Introduction to coordination compounds; nature of metal ligand bonding; stability of coordination compounds; inorganic spectroscopy; organometallic chemistry; catalysis; bioinorganic chemistry.

Text Books:

1) Advanced Inorganic Chemistry: Cotton, Wilkinson, Murillo and Bochmann, 6th edition, Wiley Interscience.

2) Chemistry of the Elements: Greenwood and Earnshaw, 2nd edition, Butterworth-Heinemann.

3) Inorganic Chemistry: J. E. Huheey, E. A. Keiter, R. L. Keiter, 4th edition, Prentice Hall.

CHM 334 Physical Chemistry of Solutions (3 credits) Contents Thermodynamic description of mixtures, electrolytes in solution, thermo- dynamic description of electrochemical cells, ionic liquids, polymer and gel electrolytes, chemical sensors, biosensors, fuel cells, impact on biochemistry, phase equilibria. Text Books:

1) Physical Chemistry: Gordon M. Barrow, 5th edition, McGraw Hill college, 1996.

2) Physical Chemistry: P. W. Atkins and Julia de Paula, 8th edition, W. H. Freeman, 2006.

3) Physical Chemistry: I. N. Levine, 6th edition, McGraw Hill Science, 2008.

CHM 351 Bioorganic Chemistry (3 credits) Contents Basic structure of nucleic acids, proteins, lipids and carbohydrates; biological functions and biosynthesis of precursors: amino acids, nucleotides, fatty acids, lipids and secondary metabolites; primary and secondary metabolism; bioenergetics; coenzymes and cofactors; peptide antibiotics and their biological activities. Text Books:

1) Lehninger Principles of Biochemistry, M. Cox and D. Nelson, 5th Edition, 2008, W. H. Freeman and Company.

2) Biochemistry, D. Voet and J. G. Voet, 3rd Edition, 2004, John Wiley & Sons.

3) Bioorganic Chemistry: Nucleic Acids, Edt. S. M. Hecht, 1st Edition, 1996, Oxford University Press, USA.

4) Bioorganic Chemistry: Peptides and Proteins, Edt. S. M. Hecht, 1st Edition,

1998, Oxford University Press, USA. CHM: 360 Advanced Inorganic Chemistry Lab (3 credits)

Contents

Synthesis of inorganic compounds such as coordination complexes, organometallic, main group compounds; characterization & investigation by spectroscopic methods such as IR, UV and NMR techniques; quantitative estimation by redox, complexometric and precipitation titrations, spectrophotometric analysis and solvent extraction.

Semester VII

CHM 410 Advanced Molecular Spectroscopy (4 credits)

Contents

Fundamentals of lasers and laser systems; advanced Raman spectroscopy; electronic spectroscopy; advanced laser spectroscopic techniques, appli- cation of lasers in various fields of chemistry, environmental and medical application of lasers. Text Books:

1) High Resolution Spectroscopy: J. M. Hollas, 2nd Edition, Wiley, 1998.

2) Laser fundamentals: William T. Silfvast, 2nd

University Press, 2008.

Edition, Cambridge

3) Laser Chemistry: Spectroscopy, Dynamics and Applications: H. H. Telle,

A. G. Urena, R. J. Donovan, 1st edition, Wiley, 2007.

CHM 411 Organic Synthesis - II (4 credits)

Contents

Formation carbon-carbon bonds: palladium-catalyzed coupling reactions: multicomponent reactions; Domino, cascade and tandem reactions; retrosynthestic analysis; saturated heterocycles and stereoelectronics & aromatic heterocyclic: structures, reactions and synthesis; asymmetric synthesis: chemistry of natural products.

Text Books:

1) Advanced Organic chemistry, Parts A and B: F. A. Carey and R. J.

Sundberg, 5th edition, Springer.

2) March's Advanced Organic Chemistry: M. Smith and J. March, 6th

edition, Wiley-Interscience.

3) Organic Synthesis, the Disconnection Approach: S. G. Warren, 2nd

edition, Wiley.

4) Organic chemistry: J. Clayden, N. Greeves, S. Warren, P. Wothers, 1st edition, Oxford University Press.

5) Classics in Total Synthesis: Targets, Strategies, Methods: K. C. Nicolaou, E. J. Sorensen, Wiley-VCH, 1996.

CHM 412 Advanced Inorganic Chemistry (4 credits)

Contents

Reactions mechanisms of transition metal complexes, electron transfer and Marcus theory; inorganic photochemistry; metal clusters and organometallic chemistry. Text Books:

1) Inorganic Chemistry: J. E. Huheey, E. A. Keiter, R. L. Keiter, 4th

edition, Prentice Hall. 2) Reaction Mechanisms of Inorganic & Organometallic Systems: R. B.

Jordan, 3rd edition, Oxford University Press.

3) Organometallics: C. Elschenbroich, 3rd edition, Wiley-VCH.

CHM: 430 Advanced Physical Chemistry Lab (3 credits) Contents Advanced instrumentation techniques: spectrophotometry; fluorimetry, differential scanning calorimetry (DSC); thermal gravimetric analysis (TGA); cyclic voltametry (CV); as well as its application to study a variety of chemical problems; quantum chemistry-, symmetry and group theory- based computational experiments. CHM: 431 Chemical Biology (3 credits) Contents Chemical & enzymatic methods to synthesize nucleic acids, and peptides; biomolecular interactions: protein-nucleic acid, protein-small molecule, nucleic acid-small molecule. Combinatorial approaches to drug discovery; high-throughput screening; chemical glycomics; & biophysical techniques. Text Books: 1) Nucleic Acids in Chemistry and Biology, Edt. M. Blackburn, M. Gait, D.

Loakes & D. Willaims, 3rd Edition, 2006, RSC Publishing.

2) Chemical Biology: A Practical Course, H. Waldmann and P. Janning, 1st

Edition, 2004, Wiley-VCH. 3) Chemical Biology: From small molecules to systems biology and drug design, Edt. S. L. Schreiber, T. Kapoor and G. Wess. Volume 2, 2007, Wiley-VCH. CHM: 432 Solid State Chemistry (3 credits) Contents Crystal structure, crystal diffraction by X-rays, neutrons and electrons, electronic properties and band theory of solids, magnetic properties, dielectric & optical properties, superconductivity, mechanical properties, thermal analysis, materials synthesis. Text Books:

1) Basic Solid State Chemistry: A. R. West, 2nd edition, Wiley, 1999. 2) Solid State Chemistry and its applications: A. R. West, Wiley, 1987. 3) New Directions in Solid State Chemistry: C. N. R. Rao and J. Gopalakrishnan, Cambridge University Press, 1997.

CHM: 436 Molecular Modeling and Simulation (3 credits)

Contents

Model systems and potentials, force fields, statistical mechanical applications, molecular dynamics (MD), Brownian dynamics, Langevin dynamics, different Monte Carlo techniques, special MD techniques, advanced simulation techniques and applications, introduction and application of different MD programs (AMBER, CHARMM, GROMAS), quantum chemical modeling, semi-empirical methods, ab initio methods, density functional methods, application on optimization and transition state determination, intrinsic reaction coordinate calculation, introduction to quantum chemistry programs (Gaussian, GAMESS), introduction to combined QM/MM Methods. Text Books: 1) Computer Simulation of Liquids: M. P. Allen, D. J. Tildesley, Oxford University Press, 1989. 2) Introduction to Computational Chemistry: F. Jensen, 2nd edition, Wiley, 1998.

Semester VIII

CHM: 420 Structural Methods and Analysis (4 credits) Contents

Principles and applications of infrared, ultraviolet, fluorescence, electron spin resonance, nuclear magnetic resonance spectroscopy and mass spectrometry. Text Books:

1) Fundamentals of molecular spectroscopy: C. N. Banwell and E. M. McCash, 4th edition, Tata McGraw-Hill.

2) Introduction to Organic Spectroscopy: L. M. Harwood, T. D. W. Claridge, 1st

edition, Oxford University Press.

3) Electron Spin Resonance Analysis and Interpretation: P. H. Reiger, 1st

edition, RSC Publishing.

4) Mass Spectrometry Basics: C. G. Herbert, R. A. W. Johnstone,1st edition, CRS Press.

CHM: 421 Polymer Chemistry (4 credits) Contents Basic concepts, molecular weight distribution, linear, branched, cross- linked, grafted- polymers, polymer crystallization, glass transition, solution and melt viscosity, polymer rheology, step-polymerization, addition polymers, radical, cationic, anionic living polymerization, block copolymers, liquid crystalline polymers, ring opening polymerization, physical and reactive blends, nano-composites and synthetic-natural fiber composites, concepts of conducting polymers and their applications in opto-electronics and sensors, one and 3D dimensional nano-materials, stereochemistry, NMR FT-IR, mass spectrometry of polymers. Text Books:

1) Principles of Polymerization: G. Odian, 4th edition, Wiley Interscience.

2) Text Book of Polymer Science: F. W. Billmeyer Jr., 3rd edition, John Wiley & Sons.

3) Polymers: Chemistry and Physics of Modern Materials: J. M. G. Cowie, 3rd

edition, CRC Press.

CHM: 422 Statistical Thermodynamics (4 credits) Contents Canonical, Microcanonical and Other Ensembles, Fluctuation, Bose- Einstein and Fermi-Dirac Statistics, Non-interacting ideal monatomic, diatomic gases & solids, Partition Function, Liouville Equation, Chemical Equilibrium, Distribution Functions, Debye Hückel Theory, Statistical Mechanical theory of Phase Transition, Time Correlation Function Formalism Text Books:

1) Statistical Mechanics: D. A. McQuarrie, 2nd edition, University Science

Books, (Viva Books, Indian edition 2003). 2) An In t roduct ion to S ta t i s t ica l Thermodynamics: T. L . Hill,

Dover Publications, New York, 1986. 3) Introduction to Modern Statistical Mechanics: D. Chandler, Oxford

University Press, 1987.

CHM 423 Medicinal Chemistry (4 credits) Contents Principles of drug discovery; biochemistry of disease; drug action at receptors; how does the message get received? How does a receptor change shape? Drug development: quantitative structure-activity relation- ships (QSAR); drug metabolism; prodrugs and drug delivery systems. Text Books:

1) Foe's Principles of Medicinal Chemistry: T. L. Lemke and D. A. Williams, 6th

edition, Lippincott Williams & Wilkins.

2) An Introduction to Medicinal chemistry: G. Patrick, 3rd edition, Oxford University Press.

3) The Organic Chemistry of Drug Design and Drug Action: R. Silverman, 2nd

edition, Academic Press.

CHM: 433 Photochemistry (3 credits) Contents The laws of photochemistry; Primary processes in photochemical reactions; Fluorescence & phosphorescence; Quenching phenomenon; Fluorescence Resonance Energy Transfer (FRET); Dimerization reaction; Excimer and exciplex; Energy transfer processes; Diffusion controlled rate constants; Some typical photochemical reactions; Quantum yield of a reaction; Photosensitized reactions; Photochemical equilibrium; Flash photolysis; Pulse radiolysis. Text Books:

1) Modern Molecular Photochemistry: N. J. Turro, 1st edition, University

Science Books, 1991.

2) Principles of Fluorescence Spectroscopy: J. R. Lakowicz, 3rd edition,

Springer, 2006. 3) Fundamentals of Photochemistry: K. K. Rohatgi Mukherjee, Revised edition, New age International, 1986. CHM: 435 Bioinorganic Chemistry (3 credits)

Contents

Metal ions in biology; inorganic chemistry of biological systems; dioxygen carriers and its reactions, blue copper proteins and photosynthesis, metal-sulfide proteins. Text Books: 1) Bio-inorganic Chemistry: I. Bertini, H. B. Gray, S. J. Lippard, J. S.

Valentine, 1st edition, Viva.

2) Inorganic Chemistry: J. E. Huheey, E. A. Keiter, R. L. Keiter, 4th edition, Prentice Hall. 3) Inorganic Electronic Structure & Spectroscopy: E. I. Solomon & A. B. P.

Lever, 1st edition, Wiley Interscience.

MATHEMATICS

Semester I

MTH: 101 Introductory Mathematics I - Linear Algebra (3 credits) Contents Definition and examples of Fields, Solving a system of Linear Equations, Matrices, Row and Column operations, Invertible matrices, Elementary Matrices and revisit to solving linear equations.

Vector Space and examples, Subspace, Special example of Rn and its

coordinates, Sum and intersection of subspaces, Solution space of linear equations, Linear independence of vectors, Basis and Dimension, Coordinates with respect to different basis. Linear Transformations (LT) between two vector spaces, Representing LT by a Matrix, Rank-Nullity Theorem, Linear Operators (LT on same space) and square matrices, Algebra of Linear operators, Base Change and Similarity of matrices. Determinant and its properties, Inverse of a matrix, Eigen value and Eigen vector, Characteristic Polynomials, Diagonalisation and Triangulation of Matrices, Cayley Hamilton Theorem, Minimal Polynomial of a Matrix. Inner Product Spaces, Cauchy-Schwartz Inequality, Orthogonal basis, Grahm orthogonalisation process, Orthogonal Group. Text Books: 1) Linear Algebra: Kenneth Hoffman and Ray Kunze, Second Edition, Prentice-Hall India. 2) Linear Algebra Problem Book: Paul R. Halmos, Dolciani Mathematical Expositions, The Mathematical Association of America. 3) Linear Algebra and its Applications: Gilbert Strang, Brooks Cole.

Semester II

MTH: 102 Introductory Mathematics II - Single variable calculus (3 credits) Contents Set Theory, Real Numbers, Complex Numbers and properties, Finite, Countable and Uncountable sets, Euclidean Spaces, Sequences and Series, Convergence and various Tests, Limit and Continuity of functions of one variable, Differentiation, Chain Rule, Mean Value Theorems, Taylor Expansion, Applications, Integration, Fundamental Theorem of Calculus, Change of variables and applications. Text Books:

1) Calculus: T. M. Apostol, Vol.-I, 2nd Edition, Wiley; 2) Calculus: Michael Spivak, 4th Edition, Cambridge University Press.

Semester III MTH: 201 Introductory Mathematics III - Probability & Statistics

(3 credits) Contents Axiomatic definition of probability, Theorems on probability, Conditional probability and independence, Bayes' theorem, Random variables, their properties, Some standard discrete & continuous variables, Mathematical expectation, variance, moments, moment generating function, Chebyshev's inequality, Functions of a random variable, their distributions & moments, Joint, marginal and conditional distributions, independence of random variables, Law of large numbers, Central limit theorem, Sampling distributions. Estimation of parameters: Maximum likelihood and method of moments, Properties of best estimates, Testing of hypotheses: Neyman-Pearson Lemma, standard tests for one and two sample problems. Text Books:

1) A First Course in Probability: Sheldon Ross, 6th Edition, Prentice-Hall;

2) Introduction to probability models: Sheldon Ross, 8th Edition, Academic Press, Inc. 3) An Introduction to Probability and Statistics: Vijay, K. Rohatgi, A. K. Md. E.

Saleh, 2nd Edition, Wiley-Interscience. 4) Probability and Statistics in Engineering: William W. Hines, Douglas C. Montgomery, David M. Goldman, Connie M. Borror, 4

th Edition, Wiley. 5) Introduction to Probability Theory and Its Applications, William Feller, Vol-

1, 3rd Edition, Wiley.

Semester IV

MTH: 202 Introductory Mathematics IV – Multivariable Calculus (3 credits) Contents Vector functions of one variable and their derivatives, Functions of several variables, partial derivatives, chain rule, gradient & directional derivative, Tangent planes and normals, Maxima, minima, saddle points, Lagrange multipliers, exact differentials. Repeated and multiple integrals with application to volume, surface area, moments of inertia. Change of variables. Vector fields, line and surface integrals. Green's, Gauss and Stokes' theorems and their applications.

Text Books: 1) Calculus: T. M. Apostol, Vol. II, 2nd Edition, Wiley, 1969. 2) Calculus and Analytic Geometry: G. B. Thomas and R. L. Finney, 6th/9th Edition, Narosa/Addison Wesley/Pearson, 1985/1996.

3) Calculus- Concepts and Contexts: James Stewart, 4th Edition, Brookes Cole.

Semester V

MTH: 310 Analysis (4 credits) Prerequisite MTH 102

Contents: Real & Complex Number System, Metric Spaces, Compact & Connected metric spaces, Complete Metric spaces and completion, Numerical sequences and series, Concept of Limit of a sequence, Continuous functions, Differentiable functions, Mean Value Theorems, Riemann Integration, Sequences and Series of Functions, Uniform Convergence, Stone Weierstrass Theorem. Text Books:

1) Principals of Mathematical Analysis: Walter Rudin, 3rd Edition, McGraw- Hill.

2) Mathematical Analysis: T. M. Apostol, 2nd Edition, Addison-Wesley.

3) Introduction to Topology & Modern Analysis: George F. Simmons, Krieger Publishing Company. 4) Calculus on Manifolds: Michael Spivak, W. A. Benjamin.

MTH: 311 Algebra- Group Theory (4 credits)

Prerequisite MTH 101

Contents Definition of Groups & Homomorphisms, Examples, Lagrange's Theorem, Normal subgroups and Quotient Groups, Group Action, Cayley's Theorem, The Class Equation, Sylow Theorems, Direct Products, Semidirect Products, Nilpotent Groups and Solvable Groups. Rings and examples, Polynomial Rings.

Text Books:

1) Abstract Algebra: D. S. Dummit and R. M. Foote, 2nd Edition, Wiley.

2) Topics in Algebra: I. N. Herstein, 2nd Edition, Wiley.

3) Algebra: Serge Lang, Revised 3rd Edition, Springer 4) Algebra: Thomas W. Hungerford, Springer.

MTH: 312 Discrete Mathematics (4 credits)

Contents

Set Theory: Definition of set, Relations, Equivalence relations and equivalence classes, Principle of mathematical induction, Posets, Chains and well-ordered sets. Combinatorics: Principles of addition and multiplication, Arrangements, Permutation and combinations, Multinomial theorem, Partitions and allocations, Pigeonhole principle, Inclusion-exclusion principle, Generating functions, Recurrence relations.

Graph Theory: Graphs and digraphs, Eulerian cycle and Hamiltonian cycle, Adjacency and incidence matrices, Vertex coloring, Planarity, trees, Spanning trees, Minimum spanning trees. Text Books: 1) Discrete Mathematics with Applications to Computer Science, J.P. Tremblay and R.P. Manohar, McGraw Hill, 1989. 2) Introductory Discrete Mathematics, V. K. Balakrishnan, Dover, 1996. 3) Graph Theory, F. Harary, Narosa, 1995.

4) Discrete Mathematics and applications: Kenneth Rosen, 6th McGraw-Hill.

5) A course in combinatorics: J. H. Van Lint and R. M. Wilson, 2nd

Edition, Cambridge University Press.

Edition,

MTH: 313 Graph Theory (4 credits) Contents The Basics: graphs, paths & cycles, connectivity, trees & forests, bipartite graphs, contraction and minors, Euler tours, Hamilton Cycle; Matching, Covering and Packing: matching in bipartite graphs, matching in general graphs, packing and covering; Connectivity: 2-connected graphs and subgraphs, the structure of 3-connected graphs, Menger's Theorem; Planar Graphs: topological prerequisites, drawing, Kuratowski's theorem, algebraic planarity criteria, plane duality; Coloring: coloring maps and planar graphs, coloring vertices, coloring edges, perfect graphs; Flows: flows in networks, k-flows for small k, flow-coloring duality, Tutte's flow conjectures; Infinite graphs; Ramsey Theory for Graphs; Random graphs. Text Books:

1. Graph Theory, 3rd edition, Reinhard Diestel, Springer. 2. Introduction to Graph Theory, Gary Chartrand and Ping Zhang, Tata McGraw- Hill Edition. MTH: 469 Mathematical Biology (3 credits) Contents An introduction to modeling and analysis of biological systems. The focus of the course is two-fold: classical models in mathematical biology, and the biophysical bases of construction of new models. The course will cover a wide variety of topics, some examples of which are: phase-plane analysis of (nonlinear) ODEs, Introduction to modeling in neuroscience (including a classification of neural models based on bifurcations), enzyme kinetics, including a derivation of Michaelis-Menten through a slow-fast analysis, elementary geometric singular perturbation theory, some reduction strategies for larger dimensional systems, modeling: ecological and evolution, stochastic models, enzymes, channels and pumps, pattern formation, cell cycle modeling, systems biology. Text Books: 1) Mathematical Models in Biology: Leah Edelstein-Keshet, SIAM: Society for Industrial and Applied Mathematics 2) Mathematical Physiology, 1 & 2: James Keener and James Sneyd, Springer. 3) Theoretical Neuroscience: Peter Dayan and L. F. Abbott, The MIT Press. 4) Nonlinear Dynamics & Chaos: With applications to Physics, Biology, Chemistry and Engineering, Steven H. Strogatz, Westview Press.

Semester VI MTH: 320 Complex Analysis (4 credits)

Contents

Algebra of complex numbers, Analytic functions, Polynomials, Rational functions, Sequences, Series, Power series, Abel's Limit theorem. Exponential and trigonometric functions, Conformality, Analytic functions in regions, conformal mappings. Linear transformations, cross ratio, Cauchy's theorem in a disc, Cauchy's integral formula, The calculus of residues. Riemann Zeta function, Riemann mapping theorem. Text Books:

1) Complex Analysis: Lars Alhfors, 3rd Edition, McGraw Hill; 2) Functions of One Complex Variable I: John B. Conway, Graduate Texts in Mathematics, Springer 3) Complex function Theory: Donald Sarason, American Mathematical Society. MTH322 Topology (4 credits) Prerequisite MTH310 Contents: Topological Spaces, Examples, Continuous maps, Quotient Spaces, Connectedness, Compactness, Countability and separation axioms, Tychonoff Theorem, Uryshon's Lemma, Tietz Extension Theorem, Metrization Theorems, Fundamental Group of Topological Spaces. Text Books: 1) Topology: James R. Munkres, Prentice-Hall; 2) Basic Topology: M. A. Armstrong, Springer; 3) Introduction to Topology and Modern Analysis: George F. Simmons, Krieger Publishing House.

MTH: 324 Vector Space and Modules (4 credits) Prerequisite MTH311 Contents Vector Space, Basis, Linear Transformations, Representing LT by a Matrix, Algebra of Linear operators, Base Change and Similarity of matrices. Determinant and its properties, Inverse of a matrix, Eigen value and Eigen vector, Characteristic Polynomials, Diagonalisation and Triangulation of Matrices, Cayley Hamilton Theorem, Minimal Polynomial of a Matrix. Inner Product Spaces, Cauchy-Schwartz Inequality, Orthogonal basis, Grahm Orthogonalisation process, Orthogonal Group. Modules, Structure Theory of Module over PID, Jordan and Rational canonical form. Text Books:

1) Linear Algebra: Kenneth Hoffman and Ray Kunze, 2nd Edition, Prentice- Hall

India. 2) Algebra: M. Artin, Prentice-Hall India. 3) Linear Algebra Problem Book: Paul R. Halmos, Dolciani Mathe- matical Expositions Number 16, The Mathematical Association of America.

4) Linear Algebra and its Applications: Gilbert Strang, 4th Edition, Brooks Cole.

5) Advanced Linear Algebra: Steven Roman, Graduate Texts in Mathematics, Springer. 6) Further Linear Algebra: T. S. Blyth and E. F. Robertson, Springer. MTH341 Group Theory and Applications (3 credits)

Prerequisite MTH311

Contents Sylow's Theorem, Direct and Semidirect Product, Classification of groups of order

p2 and p3, Solvable Groups, p-groups. Generators and relations, Presentation of a group, Free Groups, Free Products, HNN extension.Linear Groups GLn and SLn, Flags, Borel subgroups and parabolic

subgroups, Simplicity of PSLn.

Text Books: 1) Groups and Representation: J. L. Alperin and R. B. Bell, Graduate Texts in Mathematics, Springer. 2) A Course in the Theory of Groups: Derek J. S. Robinson, Graduate Texts in Mathematics, Springer.

MTH363 Theory of Algorithms (3 credits) Prerequisite: MTH 312

Contents Algorithm analysis, order arithmetic, time & space complexities, average & worst case analysis, lower bounds. Algorithm design techniques: divide and conquer, search and traversals, dynamic programming, backtracking. Sorting and searching algorithms (insertion sort, quick sort, heap sort, merge sort). Graph Algorithms: Connectivity, shorter path, spanning trees, topological sorting. Algorithms for set union-find problems. Text Books: 1) Design and Analysis of Algorithms, A.V. Aho, J.E. Hopcroft, J.D. Ullman, Addition and Wesley, 1976. 2) Fundamentals of Computer Algorithms, E. Horowitz and S. Sahni, Galgotia Publishers, 1984. 3) Data Structures and Algorithms, K. Melhorn, Vol. 1 and 2, Springer Verlag, 1998. 4) Introduction to Algorithms, Cormen, Leiserson and Rivest, Prentice Hall- India, 2002. 5) Combinatorial Optimization: Algorithms and Complexity, C.H. Papadimitriou and K.Steiglitz, Prentice Hall-India, 1992.

Semester VII

MTH: 410 Measure Theory & Integration (4 credits) Prerequisite MTH310 Contents Theory of Function of one variable, Measurable Sets, Lebesgue Measure, Measurable Functions, Riemann Integral and Lebesgue Integral, Convergence Theorems, Differentation and Integration. Text Books :

1) Real Analysis: H. Royden, 3rd Edition, Prentice-Hall. 2) Measure Theory: Paul R. Halmos, Graduate Texts in Mathematics,

Springer.

3) Real & Complex Analysis: Walter Rudin, 3rd Edition, McGraw-Hill.

MTH: 413 Differential Topology (4 credits)

Prerequisite MTH 310 Contents

Rn and Euclidian Spaces, Topological Manifolds, Function of several Variable, Continuity and Differentiability of functions of several variables, Differentiable manifolds, Tangent Spaces, Inverse Function Theorem, Submanifolds, Local immersion theorem, local submersion theorem, differential forms, Integration on Manifolds, Stokes' Theorem, de Rham's theorem. Text Books: 1) An Introduction to Differentiable Manifolds and Riemannian Geometry: William M. Boothby, Academic Press. 2) Foundations of differentiable manifolds and Lie groups: Frank W. Warner, Graduate texts in Mathematics, Springer. 3) Introduction to Smooth Manifolds: John M. Lee, Graduate texts in Mathematics, Springer.

MTH 414 Field Extensions and Galois Theory (4 credits) Prerequisite MTH311

Contents Fields, Field Extension, Irreducible Polynomials, Degree of extension, Algebraic Extension, Finite Extension, Splitting Field & Algebraic Closure, Separable extension, Normal Extension, Galois Extension, Main theorem of Galois Theory, Applications, Quadratic and Cyclotomic extension. Text Books: 1) Abstract Algebra: D. S. Dummit and R. M. Foote, 2nd Edition, Wiley. 2) Galois Theory of Algebraic Equations: Jean-Pierre Tignol, World Scientific Publishing Company. 3) Field Theory: Steven Roman, Graduate Texts in Mathematics, Springer.

4) Algebra: Serge Lang, Revised 3rd Edition, Springer.

MTH: 443 Representation Theory of Finite Groups (3 credits)

Prerequisite MTH 311

Contents Revision of Modules & Group Actions, G-Modules and Representations, Character Theory and orthoganility relations, Simple and Semisimple modules, Simple and Semisimple Rings, Wedderburn's Theorem, Revisit to Character Theory, Character Table of Cyclic groups, Abelian groups, Quaternion groups, S3; S4, Dihedral groups, GL2(Fq) along with some topics form below: (i) Induced Representations and Induced Characters, (ii) Representations of GL2(Fq) and SL2(Fq), (iii) Young Tabluex and Representation Theory of Sn, (iv) Real Characters, Orthogonal and Symplectic Characters, Schur index, (v) Rationality Questions, (vi) Weyl Duality.

Text Books: 1) Linear Representations of Finite groups: J. P. Serre, Graduate Texts in Mathematics, Springer.

2) Representation and Characters of Groups: G. James and M. Liebeck, 2nd

Edition, Cambridge University Press. 3) Representations of Finite and Compact Groups: B. Simon, American Mathematical Society. 4) Representation Theory: A first Course: W. Fulton and J. Harris, Graduate Texts in Mathematics, Springer. MTH: 344 Commutative Algebra (3 credits) Prerequisite MTH311

Contents Rings, Prime and Maximal ideal, Modules, Nakayama Lemma, Ring of fractions, Localization, Chain Conditions, Noetherian and Artinian Rings, Noether Normalisation and Hilbert Nullstellansatz. Text Books: 1) Introduction to Commutative Algebra: M. F. Atiyah and I. G. Macdonald, Westview Press. 2) Steps in Commutative Algebra: R. Y. Sharp, Cambridge University Press. 3) Commutative Algebra with a view towards Algebraic Geometry: David Eisenbud, Graduate Texts in Mathematics, Springer.

MTH: 491 Recent Trends in Mathematics (3 credits)

Contents

This is to familiarize students with the areas of Mathematics where current research is going on. This course consists of guest lectures held under Mathematics Seminar Series. Text Books: 1) Books, articles and research papers recommended by the speakers.

Semester VIII

MTH420 Functional Analysis (4 credits)

Prerequisite MTH410

Contents

Hilbert Spaces, Normed Linear Spaces, Banach Spaces, Hahn-Banach Theorem, Open Mapping Theorem, Closed Graph Theorem, Banach Fixed Point Thereom, Compact Operators, Spectral Theorem. Text Books: 1) Introduction to Topology and Modern Analysis: George F. Simmons,

Krieger Publishing House. 2) A course in Functional Analysis: John B. Conway, Graduate Texts in

Mathematics, Springer. 3) Functional Analysis: B. V. Limaye, Halsted Press; 4) Introductory Functional Analysis with Applications: Erwin Kreyszig,

Wiley.

MTH421 Number Theory (4 credits)

Prerequisite MTH321

Contents

Solving Polynomials, Algebraic Numbers and Integers, Integral Bases, Dedekind Domains, Ideal factorization, Ideal Class Group, Finiteness of Class Group, Dirichlet's Unit Theorem. Text Books:

1) Number Fields: Daniel A. Marcus, Universitext, Springer; 2) Problems in Algebraic Number Theory: M. RamMurty and Jody Esmonde, Graduate Texts in Mathematics, Springer; 3) Algebraic Number Theory: Serge Lang, Graduate Texts in Mathematics, Springer.

MTH422 Applicable Mathematics - Cryptography (4 credits) Contents Classical Cryptography; Shannon's Theory; Block Ciphers: Data Encryption Standard and the Advanced Encryption Standard. Cryptographic Hash Functions; The RSA Cryptosystem and Factoring Integers; Public-key Cryptography and Discrete Logarithms; Signature Schemes; Pseudo-random Number Generation; Identification Schemes and Entity Authentication; Key Distribution; Key Agreement Schemes; Public-Key Infrastructure; Secret Sharing Schemes Text Books:

1) Cryptography: Theory & Practice: Douglas R. Stinson, 3rd Chapman and Hall/CRC.

Edition,

2) Introduction to Cryptography: Johannes. A. Buchmann, Undergraduate texts in Mathematics, Springer. 3) Handbook of Applied Cryptography: Alfred J. Menezes, Paul C. van Oorschot and Scott A. Vanstone, CRC Press. MTH 448 Computer Algebra (3 credits) Prerequisite MTH311, MTH321 Contents: Computation with finite groups using GAP, computation with multivariable polynomials using Grobner Basis. Text Books: 1) An introduction to Grobner bases: W. Adams, American Mathematical Society.

MTH455 Algebraic Topology (3 credits)

Prerequisite MTH311, MTH322

Contents: Fundamental groups of topological spaces, Covering spaces, Axioms of singular homology theory, Excision, Mayer-Vietoris sequence, Jordan curve theorem, Quotient spaces, CW complexes, Cohomology theory, cup products, cohomology rings, Universal coefficient theorems, Kunneth theorem, Eilenberg-Zilber theorem, Kunneth theorem for cohomology, Poincare duality, Cap products, Lefschetz duality, Alexander duality. Text Books: 1) Elements of Algebraic topology: James R. Munkres, Westview Press. 2) Algebraic Topology: Allen Hatcher, Cambridge University Press. 3) Topology and Geometry: G. E. Bredon, Graduate Texts in Mathematics,

Springer. 4) An introduction to algebraic topology: Joseph J. Rotman, Graduate Texts in Mathematics, Springer. 4) A basic course in algebraic topology: W. Massey, Graduate Texts in

Mathematics, Springer. MTH470 Mathematical Modeling (3 credits) Contents

Formulation and analysis of mathematical models in physics, chemistry and biology. Mathematical methods include dimensional analysis, differential equations, probability and optimization. Simulations will be used extensively. The essential ideas necessary will be developed during the course, and students are expected to participate in designing and constructing models, and analyzing them. Text Books: 1) The Nature of Mathematical Modeling: Neil Gershenfeld, Cambridge University Press. 2) Simulating, Analyzing, and Animating Dynamical Systems: A Guide to XPPAut for Researchers and Students: Bard Ermentrout, Society for Industrial Mathematics. MTH 490 Trends in Mathematics (3 credits)

Contents

Lectures by guest faculty and internal faculty on current research in Mathematics. Text Books Papers, Books etc. will be recommended at the time of the lecture by the Instructors.

PHYSICS

Semester I

PHY101 World of Physics I (3 credits)

Contents

An exposure to mathematical methods, classical mechanics, classical electrodynamics and quantum mechanics with applications. Text Books:

1) University Physics- H D Young & R A Freedman-11th edn-Pearson Edn 2006.

2) Mechanics- Berkeley Physics Course-Vol I- Tata McGraw Hill (2008). 3) Electricity & Magnetism- Berkeley Physics Course-Vol II- Tata McGraw Hill (2008). 4) Quantum Physics- Berkeley Physics Course- Vol IV- Tata McGraw Hill (2008).

PHY121 Physics Lab I (2 credits)

Experiments: 1. Simple Pendulum, 2. Torsional Pendulum: Modulus of rigidity, 3. Young's modulus, 4. Coefficient of friction: Euler's relation, 5. Faraday's and Lenz's law of electromagnetic induction, 6. Magnetic field measurement, 7. Measuring techniques for inductance and capacitance, 8. Solar cell: I-V characteristics and efficiency

Course material will be provided at the beginning of semester.

Semester II

PHY102 World of Physics II (3 credits) Contents

An exposure to statistical mechanics, condensed matter physics, physics of materials, astrophysics, atomic molecular and optical physics and dynamical systems with recent trends and applications. Text Books: 1) Statistical Physics- Berkeley Physics Course-Vol V- Tata McGraw Hill (2008). 2) Concepts of Modern Physics by A.Beiser. Tata McGraw Hill Education 6th edn 2006.

3) Modern Physics- Kenneth Krane- 2nd edn –John Wiley( 2002). 4) Introduction to Modern Physics- J D Walecka- World Scientific (2008).

Semester III PHY201 Classical Physics (3 credits)

Contents

An introductory course on classical mechanics and classical electro- dynamics. The classical mechanics part comprises of Lagrangian for simple systems, Harmonic oscillator, small oscillations and rotational dynamics etc. The electrodynamics course would offer an introduction to the concepts of electro and magneto statics, introduction of Coulomb's law, Ampere's and Faraday's law, Lenz's law, Maxwell's equations and electromagnetic waves. Text Books: 1) Classical mechanics- R D Gregory - Cambridge University Press (2008).

2) Mechanics-L D Landau & E M Libshitz- 3rd edn Elsevier (2007).

3) An Introduction to Electrodynamics - D. J. Griffiths, 3rd Ed., Pearson (2006). PHY221 Physics Lab III (2 credits) Experiments: 1. Thermal expansion coefficient, 2. Thermal conductivity, 3. Stefen's law, 4. Thermistors, 5. Newton's rings, 6. Diffraction using a grating, 7. Malu's law, 8. Resolving power of telescope and prism,

Semester IV PHY202 Quantum & Statistical Physics (3 credits) Contents

An introductory course to quantum mechanics and statistical physics, Motivation and postulates of quantum physics, vector space and operators, uncertainty principle, harmonic oscillator and square wells and some elementary concepts of atoms and molecules etc. The statistical physics part will deal with laws of thermodynamics, temperature, entropy, thermodynamic potentials, random walk, ensembles and probability distribution. Text Books:

1) Principles of Quantum Mechanics – R Shankar, 2nd Ed., Springer (2008). 2) Fundamentals of Statistical and Thermal Physics – Frederick Reif, McGraw Hill (1985).

PHY222 Physics Lab IV (2 credits)

Experiments: 1. Particle-size determination using a laser source, 2. Determination of Brewster angle and refractive index, 3. Determination of numerical aperture and divergence of a given laser beam, 4. The Cornu's method: determination of Elastic constants, 5. Determination of Rydberg's constant, 6. Determination of the specific charge e/m for electron, 7. Michelson-Morley's experiment, 8. Electron diffraction, 9. Hall effect, 10. Determination of band gap.

Semester V

PHY310 Mathematical Methods (4 credits)

Contents

Vectors & Tensors, Matrices, Group Theory, Sequences and Series, Complex Variables, Differential Equations, Orthogonal Functions, Legendre Polynomials, Bessel Functions, Fourier Series and Fourier Transform, Laplace Transform, Green's function . Text Books:

1) Essential Mathematical Methods for Physicists, Weber & Arfken, 5th

edition Academic Press – Elsevier (2005). 2) Mathematical Methods for Physics and Engineering – K F Riley, M P

Hobson & S J Bence, 3rd Ed., Cambridge University Press (2006). PHY311 Classical Mechanics (4 credits)

Contents

Euler Lagrange equation- Brachistochrone - Lagrange's equation from variational principle- integrals of motion- conservation theorems & symmetries– Hamiltonian- canonical equations - Poisson brackets- Symplectic formulation-Canonical transformations- Hamilton Jacobi theory- Action angle variables Central force motion- integrals- Kepler problem- scattering -Small oscillations- normal modes- linear triatomic molecule-lattice vibrations Continuous systems- classical fields, Classical perturbation theory- nonlinear oscillators-Hamiltonian chaos. Text Books: 1) Classical Mechanics- A contemporary approach-J V Jose & E J Saletan- Cambridge University Press (2006).

2) Classical Mechanics – H Goldstein, C Poole & J Safko-- 3rd ed. Pearson (2008). 3) Classical Dynamics of Particles and Systems – S T Thornton and J B Marion, Brooks/Cole (2004). PHY312 Classical Electrodynamics (4 credits) Contents Electrostatics and magnetostatics in dielectric media, solution of Laplaces eqn in free space and in dielectric media, magnetic vector potential, ferro- magnetism and the B-H curve, Maxwell's equations, Gauge transfor- mations, EM waves, reflection, refraction, transmission coefficients.

Text Books:

1) Classical Electrodynamics – J D Jackson, 3rd Ed., Wiley Eastern Ltd.

(1962).

2) An Introduction to Electrodynamics – D J Griffiths, 3rd Ed., Prentice Hall

(2006). PHY330 Advanced Physics Lab I (3 credits) Experiments: 1. Multi-frequency excitation and imaging, 2. Diffusion measurements, 3. Measurement of Stokes parameter of light, 4. Velocity distribution of atoms in a gaseous phase & temperature dependence of the velocity. PHY 333 Symmetries in Nature (3 credits) Contents Spatial transformations-rotations, translations, reflections, dilations, Moving frames and space time symmetry, Classification of physical quantities according to transformation properties, Symmetries and classical conservation laws, Symmetry applied to waves and wave functions: examples from optics, atomic and molecular physics. Quantum numbers, degeneracy, selection rules, Crystal symmetry and its constraints on physical properties, Symmetry breaking by bifurcation, Continuous phase transitions and broken symmetry. Text Books:

1) Elements of Group theory for physicists- A W Joshi-4th edn New Age Int Pub (2007). 2) Symmetry- H Weyl- Princeton Univ Press (1983). 3) Group Theory and Quantum Mechanics- M Tinkham- Courier Dover Pub (2003). PHY337 Classical Optics (3 credits) Contents Nature of light, propagation of light, interaction of light with matter, reflection, refraction, interference, diffraction, polarization, Optical properties of metals and semiconductors in bulk and at nano scale. Text Books:

1) Optics – Eugene Hecht, 4th Ed., Dorling Kindersley (india) Pvt Ltd (2006). 2) Optical Properties of Solids Anthony Mark Fox, Oxford University Press

(2001).

PHY351 Gravitation & Cosmology (3 credits) Prerequisite PHY 310 Contents The course will cover advanced special relativity, basic general relativity and cosmology. Gravitation: four vectors and SR concepts in four vector notation, introduction to action principle and SR dynamics from action principle, Development of tensor algebra and calculus leading up to curvature, Einstein's equation from action principle and its basic properties including the weak field limit of Newtonian gravity, Schwarzschild solution and classical tests of relativity; basic ideas of black hole physics, introduction to gravitational waves. Cosmology: Some basic introductions to contents and scales of universe, Friedmann metric and its basic kinematic properties , Dynamics of the FRW universe; basic solutions., Thermal history of the universe starting from BBN leading up to CMBR, Introduction to more advanced topics like inflation, structure formation, dark energy etc. Text Books:

1) The classical theory of fields- L D Landau & E M Libshitz- 3rd edn Elsevier

(2007). 2) Theoretical Astrophysics Vol 1- T Padmanabhan-Cambridge University Press (2005).

Semester VI PHY321 Quantum Mechanics I (4 credits) Prerequisite PHY 310 Contents Postulates and uncertainty principle, vector space and operators, represen- tations and transformations, Schroedinger, Heisenberg and interaction pictures of quantum dynamics, harmonic oscillator, hydrogen atom, angular momentum, approximation methods, symmetry & conservation laws . Text Books:

1) Principles of Quantum Mechanics – R Shankar, 2nd Ed., Springer (2008) 2) Quantum Mechanics (Vol. 1) – C Cohen Tannoudji, B Dau and R Laloe, John Wiley & Sons (2005). 3) Modern Quantum Mechanics – J J Sakurai, Revised Edition, Addison- Wesley Publishing Co. (2009).

PHY322 Statistical Mechanics (4 credits)

Prerequisite PHY311

Contents Hamiltonian dynamics & Liouville's equation, microcanonical, canonical and Grand canonical ensembles, free energy & thermodynamic relations, B-E and F-D statistics and indistinguishable particles, phase equilibrium, phase transitions, diffusion and other transport processes, non equilibrium systems, master equation and Fokker-Planck equation. Text Books:

1) Statistical Mechanics – K Huang, 2nd Ed., John Wiley &Sons (2005)

2) Statistical Mechanics – R K Pathria, 2nd Ed., Elsevier (2008). PHY323 Advanced Physics Lab II (4 credits) Experiments: 1. Spin-spin and spin-lattice relaxation, 2. Cross-polarization transfer, 3. Dynamic light scattering, 4. Selection rules of atomic transition and Zeeman splitting of atomic levels. PHY334 Astronomy & Astrophysics (3 credits) Contents

Physics of Stars: Stellar structure and composition, evolution; compact stellar objects, Active Galactic Nuclei: Radio galaxies, quasars, Galaxies and Galaxy Clusters: Galaxy structure and classification; Phenomena in galaxy clusters (X-ray gas; gravitational lensing; radio sources), Cosmology: High red shift Universe, Cosmic microwave background, Structure Formation. Text Books: 1. Sparke, L. S.; Gallagher III, J. S. (2000). Galaxies in the Universe: An Introduction. Cambridge University Press. 2. Verschuur, G.L.; Kellermann, K.I. (1988). Galactic & Extragalactic Radio Astronomy. Springer-verlaag. 3. Phillips, A.C. (1999). The Physics of Stars (Manchester Physics Series). John Wiley & Sons.

PHY352 Fluid Dynamics (3 credits)

Prerequisite PHY 310

Contents This course will be an introduction to the basics of fluid dynamics with an emphasis on astrophysical and geophysical applications. Applicability of the fluid approximation, conservation laws, and a build up towards the Navier Stokes equations. approximations to the full Navier Stokes equations and their realms of applicability, viscous and inviscid flows, applications to astrophysical situations such as the solar wind, and accretion disks around black holes geophysical applications of fluid dynamics. Text Books: 1) The Physics of Fluids and Plasmas, Arnab Rai Choudhuri- Cambridge University Press (2004). 2) An Invitation to Astrophysics, T. Padmanabhan- World Scientific (2006).

3) Geophysical Fluid Dynamics, Joseph Pedloski- 2nd edn Springer (1987). PHY353 Relativity and Electrodynamics (3 credits) Prerequisite PHY312 Contents Special relativity, relation to Maxwell's equations, covariant formulation of electrodynamics, elements of general relativity. Text Books: 1) Radiative Processes in Astrophyscis- Rybicki & Lightman, John Wiley & Sons

2) Classical Electrodynamics 3rd Eds, J.D. Jackson, Wiley Eastern PHY355 Statistical Methods in Data Analysis (3 credits) Contents Review of random variables, probability distributions with examples from real world, measures of central moments and deviation, stationery and ergodic process. Least squares fitting of linear and non-linear models, parametric and non-parametric estimation, confidence limits, hypothesis testing, Markov chains. case studies. Text Books: 1) Probability, Random Variables & Stochastic Processes, A. Papoulis and S

Unnikrishnan Pillai, 4th Edition, McGraw Hill, 2002. 2) Numerical Recipes, by Press, Teukolsky, Vetterling & Flannery, 3rd

edition, Cambridge University Press.

Semester VII

PHY410 Condensed Matter Physics (4 credits)

Prerequisite PHY 310 Crystal structures, Bravais lattice, diffraction and Bragg law and Laue equation etc, Bloch function, Bands, weak binding and strong binding theory of band formation, Drude - Sommerfeld theory of conduction, semi classical theory of conduction, Hartree-Fock approximation and exchange interaction, magnetic phase transitions. Text Books: 1) Solid State Physics – N W Ashcroft and N D Mermin, Brooks/Cole Publishers (2009).

2) Introduction to Solid State Physics – C Kittel, 8th Ed., John wiley & Sons (2005). 3) Advanced Solid state Physics – Philip Phillips, Overseas Press (2008). 4) Principles of Condensed Matter Physics – P M Chaikin and T C Lubensky, Cambridge University Press (2004). PHY413 Electronics (4 credits) Contents

Introduction to semiconductors, Band Gap, P-N Junctions, Diodes, BJT, Field Effect Transistors, Transistor characteristics, electronic transport, Amplifiers, Photo electric devices, Digital circuits, concept of logic gates and Fabrication. Text Books: 1) The Art of Electronics - P.Horowitz and W.Hill, Cambridge University

Press- 2nd edn (2001). 2) Electronic Principles - A.P. Malvino, McGraw Hill Higher Education (2007). 3) Electronic Devices & Circuits- J. Millman & C.E. Halkias, McGraw Hill (2008). PHY414 Computational Physics (4 credits) Contents Introduction to programming, advanced numerical techniques, Solutions to ordinary and partial differential equation; Solutions to eigenvalue problems Monte-Carlo techniques, Density functional theory, Molecular dynamics.

Text Books: 1) Computational Physics by Jos Thijssen (Cambridge Univ Press, 1997). 2) An introduction to computational physics by Tao Pang (Cambrdige Univ Press, 2006). 3) Computational physics: Problem Solving with Computers by Rubin H. Landau et. al. (Wiley VCH, 2007). 4) Monte Carlo Simulations in Statistical Physics – K Binder and D W

Heermann, 4th Ed., Springer Berlin.

PHY430 Advanced Physics Lab III (3 credits) Experiments: 1. Doppler broadening of spectral lines, 2. Doppler- free spectroscopy, 3. Study of spin exchange, 4. Structure determination of small molecules/biomolecules using NMR technic PHY 441 Physics of Information & Quantum Computation (3 credits) Contents Statistical Physics, Thermodynamics, and Information, Computability and Turing Machine, Computational Complexity, Classical computers and Moore's law, Quantum bits and Quantum Circuits, Quantum Teleportation, Quantum Algorithms, Quantum Simulation, Decoherence, Quantum Error Correction, Physical realization of Quantum Computers. Text Books: 1. Quantum Computation and Quantum Information, M. A. Nielsen and I. L. Chuang, Cambridge University Press. 2. An introduction to Quantum Computing, P. Kaye, R. Laflamme and M. Mosca, Oxford Unviserity Press. 3. Preskill's lecture notes on Quantum Information and Quantum Computation, http://www.theory.caltech.edu/people/preskill/ ph229. PHY443 Physics at Nano scale (3 credits) Contents Overview, nanotechnology in nature, Clusters –clusters to solids, effect on structure, ionization potential, melting etc. Electronic Structure of Semiconductor Nanoparticles: Effective Mass Approximation, size dependent optical properties, Metal Nanoparticles: Surface Plasmon Resonance, Mie theory, Stability of metal particles, metamaterials Magnetism at Nanoscale: Magnetism in small and nanoparticles, super- paramgnetism, introduction to spintronics, spin valve, magnetic tunnel junction, memory elements Synthesis of Nano materials: Physical, chemical, biological and hybrid methods Analysis of nanomaterials: Various Diffraction,

microscopy and spectroscopy techniques. Text Books: 1) Optical Properties of Semiconductor Nanocrystals – S. V. Gaponenko, Cambridge Studies in Modern Optics (1997). 2) Nanoscale Materials in Chemistry – Ed. By Kenneth J. Klabunde, John Wiley & Sons Inc. (2001). 3) Nano technology: Principles and Practices by Sulabha K. Kulkarni, Capital Publishing Company, N. Delhi (2009, revised reprint).

PHY445 Quantum Mechanics II (3 credits) Prerequisite PHY 321

Contents

Perturbation theory, applications to interaction of classical fields with atomic systems, adiabatic and sudden approximations, scattering theory, Coupling of charges and spins to the scalar and vector potential, gauge transformations, Identical particles and statistics, Occupation number representation and creation and annihilation operators, oscillator coherent states, Radiation field as a set of quantised harmonic oscillators and its coupling to atoms. Dirac equation and its main consequences, special topics- Bell,s inequalities, entanglement, geometric phases, super symmetric quantum mechanics. Text Books: 1) Quantum Mechanics (Vol I and II) – C Cohen Tannoudji, B Dau and R Laloe, John Wiley & Sons (2005). 2) Modern Quantum Mechanics – J J Sakurai, Revised Edition, Addison- Wesley Publishing Co (2009). 3) Quantum Mechanics: A Modern Development – L E Ballentine, World scientific (2006).

Semester VIII

PHY421 Atomic Molecular and Optical Physics (4 credits) Prerequisite PHY 321 Contents

Interaction of atoms with photons, Perturbation by an oscillating electric

field, Rotating wave approximation, Transition probabilities, Induced and

spontaneous emission, Einstein coefficients, Selection rules, Lifetimes of

excited states, Line profiles of spectral lines, Interaction of monochro-

matic radiation with atoms, Concepts of Pi and Pi/2 pulses, Rabi

oscillations, Bloch sphere, Laser cooling and trapping of neutral atoms,

Magnetic trapping of Neutral atoms, Electrodynamic trapping of ions,

Quantum information processing with trapped ions, Atom interferometry,

Advanced experimental techniques in atomic and molecular physics.

Text Books: 1) Quantum Optics – M O Scully and M S Zubairy, Cambridge University Press (1997). 2) Optical coherence and Quantum Optics – L Mandel and E Wolf, Cambridge University Press (1995). 3) Laser Cooling and Trapping – H Metcalf and P V der Straten, Springer (1994).

4) Laser spectroscopy – W Demtroeder, 4th edn Springer (2008).

5) Quadrupole Ion trap Mass Spectrometry – R E March and J F J Todd, 2nd

edn John Wiley & Sons(2005).

PHY422 Nuclear & Particle Physics (4 credits)

Prerequisite PHY 321, PHY 445

Contents Introduction, Particles & Nuclei, Properties of nuclei- classification- fermions & bosons-leptons-mesons-quarks-gluons-intermediate bosons structure of subatomic particles-scattering- form factors, Symmetries & Conservation laws, Additive conservation laws- Angular momentum & isospin- invariance under partial rotation- charge independence of hadronic forces- isospin invariance, PC & CPT- parity- intrinsic parity- conservation and break down of parity- CC & time reversal- neutral kions- break down of CP invariance.

Text Books:

1) Subatomic Physics – E M Hanley and A Garcia, 3rd Ed., World Scientific (2007).

2) Introduction to Elementary Particles – D Griffiths, 2nd edn John Wiley &

Sons, Inc. (2008).

3) Introduction to High Energy Physics – D H Perkins, 4th Ed., Cambridge University Press. (2000).

PHY423 Advanced Physics Lab IV (4 credits) Experiments: 1. Synthesis of a superconducting/ferroelectric compound and determination of its lattice parameters, 2. Normal to superconducting state transition studied using a 4-probe resistivity technic, 3. Structural transition in a ferroelectric compound studied using temperature dependant powder x-ray diffraction technic, 4. Implementation of simple quantum algorithm.

PHY 444 Material Science (3 credits) Contents

Historical perspectives, Types of materials, bond types and structure, defects in solids, phase diagrams, synthesis and analysis of materials, materials for electronics, energy, etc. Materials and waste management (environment). Text Books: 1) The Nature and Properties of Engineering Materials – J D Jastrzebski, John Wiley & Sons. 2) Materials Science and Engineering: An introduction-William D. Callister, John Wiley. PHY 452 Nuclear Magnetic Resonance (3 credits) Contents Principles of NMR spectroscopy and spin-dynamics in general will be discussed. Contents include: Spin Angular Momentum, Coupling of Angular Momenta, Transformation under Rotations, Irreducible Tensors, Nuclear Magnetism, and NMR Hamiltonians, Fourier Transform NMR, Single & Multi-Spin Coherent Dynamics, Motion and Relaxation, Characterization of Molecular Structure and Dynamics, Selected Experiments in High-Resolution NMR, Powder distribution, Cross-Polarization, Magic Angle Spinning, Average Hamiltonian, Spin-decoupling, Symmetry Sequences, Materials Characterization, Selected Experiments in SSNMR.

Text Books: 1. Elementary Theory of Angular Momentum, M. E. Rose, Dover Publications, 1995. 2. Principles of Nuclear Magnetic Resonance in One and Two Dimensions, R.R. Ernst, G. Bodenhausen, and A. Wokaun, Oxford University Press, 2004. 3. Spin Dynamics: Basics of Nuclear Magnetic Resonance, M. H. Levitt,

John Wiley&Sons Ltd, 2007. 4. Solid-State NMR Spectroscopy: Principles and Applications, Melinda J. Duer, Blackwell Science, 2002. PHY453 Dynamical Systems (3 credits) Prerequisite PHY 311

Contents Classification, phase flow, equilibria, stability analysis, discrete systems, 1-d and 2-d systems, bifurcation structure, higher dimensional systems, limit cycle, quasiperiodicity, strange attractors, Lyapunov exponents, fractals, applications. Text Books: 1) Dynamical Systems – C Robinson- CRC Press (1998). 2) Differential equations, Dyanmical systems- M W Hirsh, S Smale & R L

Devaney- Academi Press- 2nd edn (2004). 3) Chaos and Nonlinear Dynamics – R C Hilborn, Oxford University Press. 4) Nonlinear differential equations and Dynamical systems- F Verhulst Springer (2006).

PHY 454 Advanced Condensed Matter Physics (3 credits) Prerequisite PHY 410

Contents Second quantization, Interacting electron gas, Local magnetic moments and the Kondo problem, Bosonization, Electron-Lattice interactions and superconductivity, Phase transitions, Critical phenomena, Static and dynamic renormalization groups and methods of momentum shell calculations.

Text Books: 1) Advanced Solid state Physics – Philip Phillips, Overseas Press (2008). 2) Principles of Condensed Matter Physics – P M Chaikin and T C Lubensky, Cambridge University Press (2004). 3) Statistical Mechanics of Phase transitions – J M Yeomans,Oxford Univ Press (1992). 4) Introduction to Phase Transitions and Critical Phenomena – HE Stanley, Oxford Univ Press (1971). 5) Nonlinear Dynamics Near and Far from Equilibrium – JK Bhattacharjee and S Bhattacharya, Hindustan Book Agency (2007).

Interdisciplinary Courses IDC101 Introduction to Computation (3 credits)

Contents

This course aims to provide students with an understanding of the role computation can play in problem solving. It also aims to help students, regardless of their computing background, to feel confident of their ability to write programs that allow them to accomplish useful goals. We work with the Python™ programming language. The course also intends to familiarize students with the Linux operating system. The course starts with basic computing concepts like flow control, variable types, looping constructs. Then we cover data structures such as arrays and associative arrays. We teach the idea of modular programming and how it works in the context of Python. Random numbers are introduced as they are useful in many scientific applications. File I/O is covered. We discuss namespaces and Python's rules for scoping. We introduce regular expressions as they are useful for text processing. Next, we introduce them to classes and object-oriented programming (OOP). Finally, we introduce complexity and discuss how we can measure the time efficiency of programs. Besides lecture notes, the online Python documentation at http://www.python.org/doc/ will be used.

Text Books: 1) M. Lutz, Learning Python, 3rd Edition (O'Reilly Media, Inc., 2007), ISBN 0596513984 IDC102 Scientific Computing (3 credits)

Contents

This course aims to provide students with a basic understanding in scientific computing. A large part of the course focuses on numerical analysis. We cover methods to solve linear systems using LU factorization, Gaussian elimination, and Gauss-Jordan elimination. The students also implement these algorithms using Python and numpy (a package for numerical analysis). We also cover methods for linear least squares analysis where methods related to data fitting are covered. Included are normal equations method, Householder transformations, Givens rotations and QR-factorizarion. Numerical calculation of selected eigenvalues of a matrix using power iteration, inverse power iteration, and power iteration with shifts. Estimation of eigenvalues and igenvectors using Rayleigh iteration. Calculation of all eigenvalues of a matrix using QR-iteration. Text Books: 1) M. T. Heath, Scientific Computing: An Introductory Survey (McGraw Hill, 2002), 2nd ed.

IDC 201 Mathematical Methods (2 credits) Contents

This course aims to train students in basic mathematics that an undergraduate student of natural sciences is expected to know. The topics included are : Linear algebra and vector calculus, Transformation laws, gradient, divergence, curl, tensors – Fourier series and transforms, Fourier series, even and odd functions, cosine and sine– Ordinary differential equations, Basic concepts, geometric meaning, exact ODEs– Laplace transforms, Transform and its inverse, transforms of integrals, derivatives Text Books:

1) Erwin Kreyzig, Advanced Engineering Mathematics, Wiley, 8th edition. 2) G B Arfken and H J Weber, Mathematical methods for physicists,

Academic Press, 6th edition (2007).

Distribution of Courses: The distribution of courses in the four years of course work is given below. The course code for courses from each stream will have three letters indicating the discipline followed by three digits.

Semester BIOLOGY CHEMISTRY

PHYSICS MATHE -

IDC HSS

T C-3

L C-2

T C-3

L C-2

T C-3

L C-2

T C-3

C- 2/3

C- 1/2

I 101 121 101 121 101 121 101 101 101

II 102 122 102 122 102 - 102 102 102

III 201 221 201 - 201 221 201 201 201

IV 202 - 202 221 202 222 202 202 202

C-4 C-3 C-4 C-3 C-4 C-3 C-4 C-3

V 310 311 312 322

301-P 332 334 335

320 311 312

331 332 340-L

310 311 312

301-P 330-L 333 337 351

310 311 312 313

301-P 469

VI 320 321 412

302-P 351 352 353 354

310 321 322

334 351 360-L

321 322 323-L

302-P 334 352 353 355

320 322 324

302-P 341 363

VII 410 411 417 420

401-P 431 433 452

410 411 412

430-L 431 432 436

410 413 414

401-P 430-L 441 443 445

410 413 414

401-P 344 443 491

VIII 421 422 423

402-P 451 454 490 491

420 421 422 423

433 435

421 422 423-L

402-P 444 452 453 454

420 421 422

402-P 448 455 470 490

IX & X PROJECT

T- Theory course, L- Lab course, P- Project course, C- Credits