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अखिल भारतीय आयुर्विज्ञान संस्थान, नई दिल्ली
All India Institute Of Medical Sciences, New Delhi

M.Sc. Biophysics Syllabus

M.Sc. Biophysics Syllabus

PAPER I
Cell biology: Organization and structure of prokaryotes and eukaryotes, nucleus, cytoplasm, plasma membrane, mitochondria-structure, function respiratory chain and ATP synthesis, endoplasmic reticulum, golgi apparatus, membranes, ribosomes, peroxisomes, lysozomes, transcription and translation, transport of proteins, cancer and its molecular genetics, oncogenes, tumor suppression gene
Molecular biology: central dogma, genetic code, gene and operon, structure of DNA and RNA, plasmids, selectable markers, agarose gel, PCR, cloning PCR products, expression vectors, cell free translation, c- DNA libraries, genomic libraries, DNA micro arrays, DNA sequencing
Bioinformatics: Introduction, repositories, databases, pairwise sequence based alignment, relationship between sequence and structures, structural bioinformatics, genomics, proteomics, human genome project, software packages
Numerical methods: Introduction to numerical methods, solutions to non-linear algebraic equations by the method of iteration and Newton aphson method, numerical integration by trapezoidal rule and simpson’s rule, numerical solution of ordinary differential equations by picard’s method of successive approximation, Euler’s method and Runge-Kutta method

Dynamics of non-linear processes: Physico-mathematical foundations of the dynamics of non-linear processes, phase plane method, different modes of excitations, nearly sinusoidal oscillations, building up of oscillations, effect of third harmonic distortion, Liapounov criteria of stability, limit cycles

PAPER II

Elementary crystallography: Introduction, symmetry in crystals, lattices and unit cells, crystal systems, Bravais lattices, elements of symmetry- rotation axis, mirror planes and center of inversion, point group symmetry- monoaxial point groups, polyaxial point groups, translational symmetry- screw axis and glide planes, space group, equivalent points, X-ray diffraction and Bragg equation 
X-ray diffraction methods: scattering factor, structure factor expression, reciprocal lattice, Ewald’s sphere, electron density equation, phase problem, Patterson function, molecular replacement method, isomorphous replacement, refinement programs and interpretation of results, methods of data collection of crystal containing small molecule and large molecule, factors affecting the measurement of integrated intensities, photographic methods, diffractometers, area detectors and image plates.
Proteins : Purification, structure and function: twenty amino acids: structure and function, the peptide bondprimary structure of a protein: methods of sequence determination, forces determining protein structuresecondary structure of a protein: β strands, β sheets (parallel and anti parallel), β turns, α helix, 3.10 helix and π helix (differences), tertiary structure of a protein: protein folds-all alpha helix motifs (Lone helix, helix-turn-helix, four helix bundle and eight helix bundle), protein folds-all β sheet motifs (β sandwich, β barrel, greek Key topology and β propellars), protein folds- α / β motifs (Tim barrel, Rosman fold, α/β horseshoe), quaternary structure of a protein: macromolecular assemblies, domains and domain swapping, membrane proteins, purification methods, studies of proteins with MALDI-TOFenzymes and enzyme kineticsG-proteins and G-protein coupled receptors(GPCRs), proteins as targets for rational structure based drug design
Principles of nucleic acid structure: nucleotide structure and properties: Introduction to DNA, RNA, bases, sugars, phosphates, structure of nucleotide, nucleosides and polynucleotides and their nomenclature scheme. tautomerisation and ionization. genetic code. stereochemistry: nucleoside, torsion angles, sugar confirmation, NMR study, DNA structure: different types of DNA and their structure, DNA motifs, DNA repeats and their significance, function and stability, spectroscpic study of DNA: dye binding, interaction, denaturation, and renaturation of DNA, thermal denaturation and Tm value, RNA: structure and properties, different forms of RNA and their significance, alkaline hydrolysis of RNA, how it differs from DNA, role of 2’OH group, structure of phenylalanine tRNA, enzymes involved in molecular biology: DNA polymerase, RNA polymerase, reverse transcriptase, restriction endonuclease. DNA interaction: protein, dye, drugs and carcinogens, DNA replication: DNA polymerization, mutation, and DNA repair, DNA transcription: RNA synthesis, types of RNA polymerase, DNA polymorphism: repeats of DNA and their significance, single nucleotide polymorphism, c-DNA, cloning and expression and purification
Membrane Biology: Lipid structure and their organization, comparison of different membrane models, diffusion and permeability, different types of transport systems across membranes, liposome and its applications
Peptides-design, synthesis and applications: Introduction to peptides, peptide design, synthesis of peptides (solution phase and solid phase), protection and deprotection of amino and carboxyl group, unnatural amino acids, conformation of peptides, purification and crystallization of peptides, determination of structure of small molecules (briefly), application of peptides
PAPER III

Mathematical methods and their applications in biological systems: Ordinary differential equations of the first degree and first order (variable separable method, linear equation), linear differential equations of the second order with constant coefficients, the Laplace Transform, Inverse Laplace transform, application of Laplace transform to solutions of differential equations, Fourier series and their applications.

Quantum biology and its uses: Classical mechanics, Newton, Lagrange and Hamilton’s equations, Schrodinger’s equation and its complete solution for S.H.O, central force and angular momentum
Quantum chemistry: Atomic orbital models, the wave equation, molecular orbitals, the LCAO method, the overlap method, coulomb and resonance integrals, the hydrogen molecule, charge distributions, approximate methods.
Theoretical modeling of biomolecular systems: Basic principles of modeling, modeling by energy minimization technique, concept of rotation about bonds, energy minimization by basic technique for small molecules, Ramachandran plot, torsional space minimization, energy minimization in cartesian space, molecular mechanics-basic principle, molecular dynamics basic principles
Spectroscopic techniques: Introduction to spectroscopy, basic principles, instrumentation and applications of UV-VIS absorption, infrared, Raman, atomic absorption, fluorescence, circular dichroism, Laser spectroscopy, nuclear magnetic resonance, electron spin resonance, acoustic spectroscopy; solvent perturbation; difference spectroscopy; Fourier transform techniques; applications of Laser; mass spectroscopy.
 

         

 

 

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