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Statistical Thermodynamics of Biomolecular Systems (BE.011J) >> Content Detail



Study Materials



Readings

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The table below provides information on the course's lecture (L) and exam (E) sessions.

Text Readings

All Text Readings are in Amazon logo Dill, K., and S. Bromberg. Molecular Driving Forces. New York, NY: Routledge, 2002. ISBN: 9780815320517.

Additional References

van Holde = Amazon logo van Holde, K. E., W. C. Johnson, and P. S. Ho. Principles of Physical Biochemistry. Upper Saddle River, NJ: Prentice Hall, 1998. ISBN: 9780137204595.

Eisenberg = Amazon logo Eisenberg, D., and D. Crothers. Physical Chemistry with Applications to the Life Sciences. Menlo Park, CA: Benjamin/Cummings, 1979. ISBN: 9780805324020.

Kittel = Amazon logo Kittel, C., and H. Kroemer. Thermal Physics. 2nd ed. New York, NY: W.H. Freeman, 1980. ISBN: 9780716710882.

SES #TOPICSTEXT READINGSADDITIONAL REFERENCES
L1Introduction

Purpose of Stat Mech

Probability
Ch. 1 (Ex. 1.1-1.6)
L2ProbabilityCh. 1, 2
L3Equilibrium StatesCh. 2 (Through Ex. 2.2)
L4Equilibrium States – Lattice Model for Diffusion

Rubber Elasticity
Ch. 2
L5Introduction to Conservation Laws (1st Law, Quantization, 2nd Law)Ch. 3
L6Boltzmann’s Law and Entropy as an Extensive Property

Law of Increased Entropy
Ch. 6 (Through Ex. 6.2)Kittel, Ch. 2
L7More Boltzmann’s Law

Partition Functions
Ch. 6
L8Simulations

PCR
E1Quiz I
L9Thermodynamic Systems

Intensive/Extensive Properties

Fundamental Equations for Energy and Entropy

Definitions of Thermodynamic Driving Forces (Part 1) Thermodynamic Forces

Homogeneous Functions

Definition of Equilibrium, Temperature, Pressure
Ch. 7 (To Ex. 7.4)
L10Introduction to Chemical Potential - Thermo Cycles - First Law Relations between Heat, Work, EnergyCh. 7
L11Reversible and Irreversible ProcessesCh. 7
L12Introduction to Free Energy

Helmholtz Free energy
Ch. 8
L13Enthalpy

Gibbs Free Energy
Ch. 8Kittel Problem, 9.4

van Holde, Ch. 2
L14Fundamental Equations and their Natural Variables

Heat Capacities

Equilibrium Temperature
Ch. 8
L15Thermodynamic Cycles

Carnot Cycle and Inequality

Heat Engines

Path Dependence
Ch. 8Kittel, Ch. 8
L16Partial Molar PropertiesCh. 9
L17Partial Molar Properties IICh. 9Eisenberg, Ch. 7
L18Simulations

Monte Carlo
E2Quiz II
L19Boltzmann Distribution LawCh. 10
L20Partition FunctionsCh. 10
L21Prediction of Thermodynamic Properties from Partition Functions

Ensembles
Ch. 10Eisenberg, Ch. 14
L22Quantum Partition FunctionCh. 10, 11
L23EquipartitionCh. 11
L24Equipartition (cont.)Ch. 11
L25Chemical Equlibria

Le Chatelier’s Principle (Ex. 8, Pressure Denaturation of Proteins)

van’t Hoff
Ch. 13 (To Ex. 13.18)van Holde, Ch. 3
L26Solid-liquid-gas EquilibriumCh. 14
L27Solutions and Mixtures

Polymers
Ch. 15, 31
L28Solvation – Osmotic PressureCh. 16
L29Solvation – Protein/Macromolecule Adsorption at InterfacesCh. 16van Holde, Ch. 2
L30Polymer ChainCh. 31
E3Quiz III
L31Polymer Chain IICh. 32
L32Polymer Chain IIICh. 33
L33CooperativityCh. 26
L34Cooperativity (cont.)Ch. 28
L35Protein Foldingvan Holde, Ch. 2
L36Review

 








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