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» 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.

Reference Books:
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


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.

Reference Books:
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.


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.

Reference Books:
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.


Basic ideas on structure and conformation of simple molecules, structural features  of  proteins, nucleic acids,carbohydrates and lipids. Aspects of biomolecular forces. Higher order structural organisation of  proteins and nucleic acid.

Reference books:
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).
Wolfram Saenger. Principles of Nucleic Acid Structure (19840).

MB 305 (AUG) 3:0

Biomolecular NMR Spectroscopy


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 214 (AUG) 3:0

» More details on this course

Neuronal Physiology and Plasticity


Neuronal and synaptic physiology: exquisite insights from simple systems, history of technical advances: electrophysiology imaging and computation history of conceptual advances: excitable membranes action potentials ion channels oscillations synapses behavioral neurophysiology complexities of the mammalian neuron dendritic structure dendritic ion channels active properties of dendrites dendritic spikes and backpropagating action potentials heterogeneity diversity and degeneracy in the nervous system hippocampus as an ideal system for assessing learning and memory synaptic plasticity: short-term plasticity long-term potentiation and depression mechanisms underlying synaptic plasticity intrinsic plasticity mechanisms underlying intrinsic plasticity issues in the credit-assignment problem on mechanisms behind learning and memory.

Reference books:
1. "Foundations of Cellular Neurophysiology" by Daniel Johnston and Samuel Wu, MIT Press 1995.
2. "Neuroscience" by Dale Purves George J. Augustine David Fitzpatrick William C. Hall Anthony-Samuel LaMantia Richard D. Mooney Michael L. Platt Leonard E. White Oxford University Press 2017.
3. "The Hippocampus Book" by Per Andersen Richard Morris David Amaral Tim Bliss and John O'Keefe. Oxford University Press 2006.
4. "Dendrites" by Greg Stuart Nelson Spruston and Michael Hausser. Oxford University Press 2016.
5. "Synapses" by W. Maxwell Cowan Thomas C. Südhof Charles F. Stevens The Johns Hopkins University Press 2003.
6. "The synaptic organization of the brain" by Gordon Shepherd Oxford University Press 2004.
7. "Rhythms of the Brain" by Gyorgy Buzsaki Oxford University Press 2006.

Courses offered during January  Term


MB 207 (JAN) 2:0

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

Amit Baidya

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 303 (JAN) 3:0

Elements of Structural Biology.


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 316 (JAN) 3:1

Relaxation Theory and Applications to Solution State Biomolecular NMR Spectroscopy


Chemical shift and dipolar coupling Hamiltonians, Redfield theory - derivation of the Redfield master equations for predicting relaxation rates and key assumptions, relaxation in homonuclear and heteronuclear two-spin IS systems, T1 relaxation, T2 relaxation, cross-relaxation, relaxation interference, a brief introduction to the origins of biomolecular dynamics and the concept of the conformational free energy landscape, utilizing relaxation rates for understanding biomolecular dynamics: the model-free approach, exchange-mediated relaxation: the chemical shift timescale and fast, slow and intermediate timescale exchange processes, experiments for estimating exchange parameters

Prerequisities: MB305 or knowledge of basic NMR theory, product operator formalism and its use in analysis of 2D and 3D NMR pulse sequences

Reference Books:
1) Arthur G. Palmer III, Wayne J. Fairbrother, John Cavanagh, Nicholas J. Skelton and Mark Rance, Protein NMR Spectroscopy,: Principles and Practice (Second Edition) 2) Josef Kowalewski and Lena Maler, 'Nuclear Spin Relaxation in Liquids: Theory, Experiments, and Applications' (Second Edition)

MB 208 (JAN) 3:1

More details on this course

Theoretical and computational neuroscience


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.

Reference Books
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 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).

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) 3:1


Advanced Methods in Bio-Molecular Simulations

Theoretical and computational aspects of various advance sampling and free energy calculation methods (maximum work theorem, Jarzinsky equality, umbrella sampling, replica exchange, metadynamics, markov state model, etc). Continuum representation of solvent and calculation of electrostatics and non-electrostatics component of solvation free energy. Method development and application of multiscale coarse graining methods such as force-matching, elastic network models, Inverse Boltzmann¿s and relative entropy methods.

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

Reference Books

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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