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» Courses during the August Term

Course Schedule-I Term [Aug-Dec,2017]

» Courses during the January Term

 

 

Courses offered during August  Term


 

MB 201 (AUG) 2:0

Introduction to Biophysical Chemistry

RAGHAVAN VARADARAJAN

Basic thermodynamics, ligand binding and co-operativity in biological systems, kinetics, diffusion and sedimentation.

Tinoco, I, Sauer  K,  Wang J C
Physical Chemistry, Principles and Applications in Biological Sciences
Prentice Hall, New Jersey, USA, 1978.
Cantor,  C.R., and Schimmel P.R., Biophysical Chemistry, Vols. I-III,
W.H. Freeman and Co., San Francisco, USA, 1980.


MB 204 (AUG) 3:0

Molecular Spectroscopy and its Biological Applications

SIDDHARTHA P. SARMA AND MAHAVIR SINGH


Principles and biological applications of UV-Vis, fluorescence, vibrational and
circular dichroism spectroscopy. Mass spectrometry and basics of one- and two-dimensional NMR
spectroscopy with applications to peptide and protein structure determination.

Horst Friebolin, Basic One-and Two-Dimensional NMR Spectroscopy (Fourth
Edition), Wiley-VCH.
Claridge, T.D., W, High Resolution NMR Techniques in Organic Chemistry, Volume
27, Second Edition (Tetrahedron Organic
Chemistry) (Paperback Dec 5, 2008).


MB 205 (AUG) 2:0

Introduction to X-ray Crystallography.

 M. VIJAYAN  and  K. SUGUNA

Crystal morphology and symmetry.  Symmetry elements and symmetry operations, point groups, lattice space groups.  Production and properties of X-rays,   diffraction of X-rays by crystals, Laue equations, Bragg'sLaw, Fourier transformation and structure factor, reciprocal lattice, experimental techniques, rotating crystals and moving film methods.  Basic ideas of structure determination, Patterson and Fourier methods, chemical crystallography, structures of organic, inorganic compounds and minerals, powder diffraction.

Buerger M.J., Elementary Crystallography
Woolfson M.M., An Introduction to X-ray Crystallography.
Stout H. and Jenson L.H., X-ray Structure Determination, Macmillion, 1968.


MB 206 (AUG)  3:0

Conformational and  Structural aspects of  biopolymers.

 M. BANSAL,   N. SRINIVASAN AND ANAND SRIVASTAVA

Basic ideas on structure and conformation of simple molecules structural features  of  proteins, nucleic acids and carbohydrates, aspects of biomolecular forces .

Higher order structural organisation of  proteins and nucleic acid.

Ramachandran, G.N., and Sasisekharan, V.  Advances in Protein
 Chemistry, Vol. 23,  Academic Press, P. 283 (1968).
A.R. Leach, Molecular Modelling : Principles and Applications, Prentice Hall (2001).
Schulz and Schirmer, Principles of Protein Structure, Springer-Verlag (1979).


MB 207 (AUG) 2:0

DNA-Protein interaction, Regulation of gene expression, Nanobiology.

DIPANKAR CHATTERJI

Basic concepts on structural basis for macromolecular recognition; concept of charge in macromolecules; specific and non-specific recognition; symmetry in DNA-protein recognition; structural ensembles; co-operativity; specific examples; story of lambda; restriction enzyme recognition; t-RNA synthetase recognition; promoter-RNA polymerase interaction; inducers and repressors; action at a distance; single molecular paradigm; methods to follow nanobiology; DNA-protein recognition at the level of single molecules.

Genes IX,  Benjamin Lewin, Oxford.
Transcriptional Regulations I and II, McWright and Yamamoto, Cold Spring Harbor.
A Genetic Switch, Mark Ptashne, Cell Press.
Genes & Signals, Cold Spring Harbor Laboratory Ptaschne and Gann.
Selected papers.


MB 209 (AUG) 2:0

» More details on this course

Cellular Neurophysiology

S. K. SIKDAR AND RISHIKESH NARAYANAN

Membrane components and structures; membrane transport; passive and active electrical properties of the membrane-ionic  mechanisms of membrane and action potential; quantifying ionic hypothesis by voltage-clamp technique; Hodgkin Huxley formalism; structure-function aspects of voltage and chemically gated ionic channels; excitatory and inhibitory postsynaptic potentials; patch-clamp technique; recording and analysis of electrophysiological data;  measurement of Ca concentrations in single cells; cell membrane capacitance and exocytosis, confocal microscopy. Synaptic plasticity: short-term and long-term potentiation and depression; mechanisms underlying synaptic plasticity; dendritic structure; dendritic ion channels; active properties of dendrites; dendritic spikes and backpropagating action potentials; intrinsic plasticity; mechanisms underlying intrinsic plasticity.

Reference books:
Hille, B., Ionic channels of excitable membranes.  2nd Edition, Sinauer Associates, Sunderland, Massachussets.
Rudy, B., and Iverson, L.E. (Eds.) Methods in Enzymology, 207, 1992.
Kandel, E.R., Schwartz, J.H., & Jessel, T.M., Essentials of Neural Science and
Behaviour, Prentice Hall International, 1995.
Cowan, W.M., Sudhof, T.C.,  Stevens, C.F., Synapses, The Johns Hopkins University Press, First edition, 2003.
Stuart, G., Spruston, N., Hausser, M., Dendrites, Oxford University Press, Second edition, 2008.

 



Courses offered during January  Term

 


MB 303 (JAN) 3:0

Elements of Structural Biology.

B. GOPAL AND M.R.N.MURTHY

Elements of structural biology. Methods for determining structures of biological macromolecules, biophysical and biochemical methods to better understand structural data.

Reference books:
Kensal, E. Van Holde et al., Principles of Physical Biochemistry (Second Edition)
Pearson Education International
Cantor, C.R., and Schimmel  P.R., Biophysical Chemistry, Vols. I-III,
W.H. Freeman and Co., San Francisco, USA, 1980
Research papers and reviews.


MB 305 (JAN) 3:0

Biomolecular NMR Spectroscopy.

SIDDHARTHA P. SARMA

Basic theory of NMR spectroscopy.  Classical and theoretical descriptions of NMR spectroscopy.  Product operator formalism for description of multipulse homonuclear and heteronuclear NMR  experiments. Multidimensional NMR spectroscopy. Description  of basic homonuclear two dimensional  NMR experiments useful for structure determination of biological macro-molecules.   Experimental aspects of homonuclear NMR spectroscopy: data acquisition, processing and interpretation of 2D homonuclear spectra.  Principles of  heteronuclear NMR spectroscopy.  Analysis of 3D  and 4D heteronuclear isotope  edited NMR pulse sequences. Introduction to relaxation and dynamic  processes (chemical and conformational processes) that affect NMR experiments. Reference books:

Protein NMR Spectroscopy Principles and Practice
J. Cavanaugh, Fair Brother, A.G. Palmer III & N. Skelton (1995), Academic Press.
Spin Dynamics - .M.  Levitt (2000) John Wiley.
NMR of  Proteins & Nucleic Acids Kurt Wuthrich, John Wiley (1986).


MB 208 (JAN) 3:1

More details on this course

 Theoretical and computational neuroscience

RISHIKESH NARAYANAN AND ARUN SRIPATI

Need for and role of theory and computation in neuroscience; various scales of
modeling; ion channel models; single neuron models; network and multiscale models;
models of neural plasticity; oscillations in neural systems; central pattern
generators; single neuron oscillators; oscillators as nonlinear dynamical systems;
information representation; neural encoding and decoding; population codes;
hierarchy and organization of sensory systems; receptive field and map modeling;
case studies, computational laboratory and projects.

Prerequisites: MB209 (or basic exposure to ion channels and their functions), basic
knowledge of linear algebra, probability, statistics and ordinary differential
equations, and some programming knowledge.

Books and references

a.    Peter Dayan and L. F. Abbott, Theoretical Neuroscience: Computational and
Mathematical Modeling of Neural Systems, The MIT press, 2005.
b.   Christof Koch and Idan Segev (Eds), Methods in Neuronal Modeling: From Ions to
Networks, The MIT press, second edition, 1998.
c.    Eric De Schutter (Ed.), Computational modeling methods for neuroscientists, The
MIT press, 2009.
d.    Eugene Izhikevich, Dynamical systems in neuroscience: the geometry of
excitability and bursting, The MIT press, 2006.
e.    Kenji Doya, Shin Ishii, Alexandre Pouget, Rajesh PN Rao (Eds), Bayesian Brain:
Probabilistic Approaches to Neural Coding, The MIT press, 2007


MB 210 (JAN) 2:0

Peptides and Drug-Design

JAYANTA CHATTERJEE

Organic reaction mechanisms pertaining to peptide chemistry; synthesis and properties of alpha, beta and gamma  amino acids; conventional and contemporary ways of peptide and protein synthesis conformational features of small-peptides; synthesis and properties of cell-penetrating peptides; design of peptide mimics for drug-discovery.

Books and references:

a. Norbert Sewald and Hans-Dieter Jakubke, Peptides: Chemistry and Biology, Second Edition, Wiley-VCH Verlag GmbH & Co. KGaA, 2009.

b. Miguel Castanho and Nuno C. Santos (Eds), Peptide Drug Discovery and Development: Translational Research in Academia and Industry, Wiley-VCH Verlag GmbH & Co. KGaA, 2011.

c. Selected review articles.

 


MB 212 (JAN) 2:0

Electron microscopy and 3D image processing for Life sciences.

SOMNATH DUTTA

Objectives and basic principles of different types of microscopes. Different types of electron microscopies and their applications. Basic introduction of electron microscopy physics and optics. Principles of image formation, Fourier analysis, Contrast Transfer Function and point spread function. Advanced sample preparation, imaging, data collection techniques of bio-molecules by negative staining and cryo-electron microscopy. Theoretical, computational and practical aspects of various advanced 3D image processing techniques. Cryo-EM map interpretation and data analysis, validation, molecular docking (use of Chimera, VMD) and application of Molecular Dynamics Flexible Fitting (MDFF).

Books and references:

1. John J. Bozzola and Lonnie D. Russell (1992). Electron Microscopy (Jones & Bartlett Publishers).
2. Ray F. Egerton (2005). Physical Principles of Electron Microscopy: An Introduction to TEM, SEM, and AEM (Springer).
3. Elaine Evelyn Hunter and Malcolm Silver (1993). Practical Electron Microscopy: A Beginner's Illustrated Guide (Cambridge University).
4. John Kuo (2007). Electron Microscopy: Methods and Protocols (Methods in Molecular Biology) (Humana).
5. Earl J. Kirkland (2014). Advanced Computing in Electron Microscopy (Springer).
6. Gabor T. Herman and Joachim Frank (2014). Computational Methods for Three-Dimensional Microscopy Reconstruction (Birkhäuser Basel).
7. Joachim Frank (2006). Electron Tomography, (New York, Springer).
8. Joachim Frank (2006). Three-Dimensional Electron Microscopy of Macromolecular Assemblies (New York, Oxford U. Press).


MB 211 (JAN) 3:0

Multiscale Theory and Simulations of Biomolecular Systems

ANAND SRIVASTAVA

Theoretical and computational aspects of various advance sampling and free energy calculation methods. Maximum work theorem, Jarzinsky Equality (Free Energy Perturbation and Thermodynamic Integration as special case of Jarzinsky Equality), umbrella sampling, replica exchange, metadynamics, markov state model, etc). Continuum representation of solvent and calculation of electrostatic and non-electrostatic component of solvation free energy. Method development and application of multiscale coarse-graining methods such as forcematching, elastic network models, Inverse-Boltzmaan's method and relative entropy methods.

Prerequisites: Basic knowledge in statistical mechanics, thermodynamics and molecular simulation (and/or basic exposure to biomolecule conformations) Working knowledge of any one molecular dynamics tool.

Books and references:

a. Michael P. Allen and Dominic J. Tidesley, Computer Simulation of Liquids (Oxford Science Publications), 1981
b. Andrew Leach, Molecular Modeling: Principles and Application (Princet Hall), 2001.
c. Christophe Chipot (Ed.) and Andrew Pohorille (Ed.), Free Energy Calculations (Springer), 2008
d. Gregory A. Voth (Ed.), Coarse-Graining of Condensed Phase and Biomolecular Systems (CRC Press), 2008
e. Mark Tuckerman, Statistical Mechanics: Theory and Molecular Simulation (Oxford Graduate Texts), 2010
f. Ken Dill and Sarina Bromberg, Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience (Taylor and Francis), 2010
g. Gregory R. Bowman (Ed.), Vijay S. Pande (Ed.) and Frank Noé (Ed.), An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation: Advances in Experimental Medicine and Biology (Springer), 2013


 
 

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