» Courses during the August Term
Course Schedule-I Term [Aug-Dec,2016]
» Courses during the January Term
Courses offered during August Term
MB 201 (AUG) 2:0
Introduction to Biophysical Chemistry
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
SIDDHARTHA P. SARMA AND MAHAVIR SINGH
Principles and biological applications of UV-Vis, fluorescence,
circular dichroism spectroscopy. Mass spectrometry and basics of
one- and two-dimensional NMR
spectroscopy with applications to peptide and protein structure
Horst Friebolin, Basic One-and Two-Dimensional NMR Spectroscopy
Claridge, T.D., W, High Resolution NMR Techniques in Organic
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.
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.
MB 209 (AUG) 2:0
» More details on this course
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.
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.
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).
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
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.
Sewald and Hans-Dieter Jakubke, Peptides: Chemistry and Biology,
Second Edition, Wiley-VCH Verlag GmbH & Co. KGaA, 2009.
Castanho and Nuno C. Santos (Eds), Peptide Drug Discovery and
Development: Translational Research in Academia and Industry,
Wiley-VCH Verlag GmbH & Co. KGaA, 2011.
MB 212 (JAN) 2:0
Electron microscopy and 3D image processing for Life sciences.
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).
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
Theoretical and computational aspects of various advance sampling and free energy
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
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.
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
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