Dr. Aniruddha Chakraborty

Course Details                                                                                 <<back

This course will provide the relevant foundations of non-equilibrium thermodynamics required to understand biological processes at the subcellular level.
The biological cell can be considered as open thermodynamic system far from equilibrium that enzymatically controls various different reactions and transport processes across internal and the cytoplasmatic membrane. So understanding open thermodynamic system far from equiibium - 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 biomolecules 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 books:

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.



Text books:

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.