Dr. Aniruddha Chakraborty

Course Details:

This course will provide the relevant foundations of non-equilibrium thermodynamics required to understand biological processes at the sub-cellular level. The biological cell can be considered as open thermodynamic system far from equilibrium that enzymetically controls various different reactions and transport processes across internal and the cytoplasmetic membrane. So understanding open thermodynamic system far from equilibrium - is necessary for learning ‘biological cell’. In this course enzymatic free energy and signal transduction processes will be discussed in detail. It will be shown that all the biological molecular machines, also pumps and motors can be considered to be effective chemo-chemical free energy transducers.The role of internal dynamics of bio-molecules on the activity control of enzymes and the action of molecular machines will be discussed at the end.

Module 1: Statistical Description of Matter

Molecular structure, irreversibility of macroscopic process, origin of irreversibility, statistical ensembles, probability & entropy, Law of large numbers, relativity of thermodynamic equilibrium.

Module 2: Thermodynamic State

Thermodynamic variables, Clausius entropy, Temperature & Thermodynamics Forces, Energy Transformations, Free energy & bound energy, Open systems, Rate of Thermodynamic processes.

Module 3: Origins & Evolution of Life

Structure of cell, Origin of the cell machinery, Photosynthetic revolution, metabolic pathways – enzymes.

Module 4: Molecular Biology of the Cell

Membranes, channels & pumps, Phophorylation, microfilaments, microtubules, regulation of enzyme activity, receptors, cell cycle.

Module 5: Chemical Reactions

Theory of reaction rates, transport across membranes, protolysis reactions, redox reactions, electron & proton transport, enzymatic catalysis, competitive & non competitive inhibition, Allosteric control of enzymatic activity, oscillations in enzymatic reactions.

Module 6: Biological Free Energy Transduction

Isothermal machines, chemochemical machines, flus-force dependence, signal transduction.

Module 7: Lack of Thermodynamic equilibrium

Intramolecular dynamics of Biomolecule, enzymes in a multitude of conformational states, Coupled enzymatic processes, biased Maxwell’s demon, Molecular Machines, actomyosin motor.

Text Book:

The Thermodynamic Machinery of Life, M. Kurzynski , Springer, 2006.

Reference Books:

1. Cells, Gels and the Engines of Life, G. H. Pollack, Ebner & Sons, 2001.

2. Introduction to Modern Statistical Mechanics, D. Chandler, Oxford University Press, 1987.

3. Biological Thermodynamics, D. T. Haynie, Cambridge University Press, 2008.

4. Non-Equilibrium Thermodynamics, S. R. De Groot & P. Mazur, Dover, 2011.

5. The Machinery of Life, D. S. Goodsell, Springer, 2009.

6. Life Itself: Its Origin and Nature, F. Crick, Simon and Schuster, 1981.