2.772
Thermodynamics of Biomolecular Systems
See description under subject 20.110[J] .
Fall 2005
Topics
- Introduction to Thermo; 0 th Law; Temperature; Work; Heat
- State Functions, 1 st Law, Paths
- Joule and Joule-Thompson; Heat Capacity
- Reversible and Irreversible Processes
- Thermochemistry
- 2 nd Law; Entropy (Boltzmann and Clausius)
- ΔS for Reversible and Irreversible Processes
- Equilibrium; Maxwell Relations; Free Energy
- Chemical Potential; Phase Equilibrium
- Chemical Equilibrium; Equilibrium Constant
- Standard States; Gibbs-Duhem
- ΔG 0 = -RTlnK; Example
- Boltzmann Distribution
- Thermo and Boltzmann Distribution
- Occupation of States
- Third Law
- Phase Equilibria, Single Component
- Phase Equilibria II; Clausius Clapeyron
- Regular Solutions; Mixing Energy; Mean Fields
- Nonideal Solutions
- Solvation; Colligative Properties
- Osmotic Pressure and Phase Partitioning
- Surface Tension
- Polymer 1 - Freely Jointed Chain
- Polymer 2 - Chain Conformation
- Polymer 3 - Rubber Elasticity
- Electrolyte Solutions
- Electrolytes at Interfaces; Debye Length
- Titration of Polyelectrolytes
- Thermodynamics of DNA Hybridization
- Cooperativity
- Cooperativity, Part 2
- Cooperativity, Part 3
- Driving Forces for Self-Assembly
- Special Topic (Coarse Grain/Monte Carlo Model)
- Course Review and Evaluations
Readings
- Silbey, R., R. Alberty, and M. Bawendi. Physical Chemistry . New York, NY: John Wiley & Sons, 2004. ISBN: 9780471215042.
- Dill, Ken A., and Sarina Bromberg. Molecular Driving Forces: Statistical Thermodynamics in Chemistry and Biology . New York, NY: Routledge, 2002. ISBN: 9780815320517.
- [SAB] Silbey, R., R. Alberty, and M. Bawendi. Physical Chemistry . New York, NY: John Wiley & Sons, 2004. ISBN: 9780471215042.
- [DB] Dill, Ken A., and Sarina Bromberg. Molecular Driving Forces: Statistical Thermodynamics in Chemistry and Biology . New York, NY: Routledge, 2002. ISBN: 9780815320517.
- LEC #: 1 · TOPICS: Introduction to Thermo; 0 th Law; Temperature; Work; Heat · READINGS: SAB 1.1-1.4, 1.8-1.9, 2.1
- LEC #: 2 · TOPICS: State Functions, 1 st Law, Paths · READINGS: SAB 2.2-2.6
- LEC #: 3 · TOPICS: Joule and Joule-Thompson; Heat Capacity · READINGS: SAB 2.7-2.9
- LEC #: 4 · TOPICS: Reversible and Irreversible Processes · READINGS: SAB 2.10, 3.1
- LEC #: 5 · TOPICS: Thermochemistry · READINGS: SAB 2.11-2.13
- LEC #: 6 · TOPICS: 2 nd Law; Entropy (Boltzmann and Clausius) · READINGS: SAB 3.2
- LEC #: 7 · TOPICS: ΔS for Reversible and Irreversible Processes · READINGS: SAB 3.3-3.5
- LEC #: 8 · TOPICS: Equilibrium; Maxwell Relations; Free Energy · READINGS: SAB 4.1-4.2, 4.9
- LEC #: 9 · TOPICS: Chemical Potential; Phase Equilibrium · READINGS: SAB 4.3-4.4, 4.6-4.7
- LEC #: 10 · TOPICS: Chemical Equilibrium; Equilibrium Constant · READINGS: SAB 5.1-5.4
- LEC #: 11 · TOPICS: Standard States; Gibbs-Duhem · READINGS: SAB 4.8
- LEC #: 12 · TOPICS: ΔG 0 = -RTlnK; Example · READINGS: SAB 8.1-8.2
- LEC #: 13 · TOPICS: Boltzmann Distribution · READINGS: DB 6
- LEC #: 14 · TOPICS: Thermo and Boltzmann Distribution · READINGS: DB 10 (first half)
- LEC #: 15 · TOPICS: Occupation of States · READINGS: DB 10 (second half)
- LEC #: 16 · TOPICS: Third Law · READINGS: SAB 3.8
- LEC #: 17 · TOPICS: Phase Equilibria, Single Component · READINGS: SAB 6.1-6.2
- LEC #: 18 · TOPICS: Phase Equilibria II; Clausius Clapeyron · READINGS: SAB 6.3
- LEC #: 19 · TOPICS: Regular Solutions; Mixing Energy; Mean Fields · READINGS: DB 15
- LEC #: 21 · TOPICS: Solvation; Colligative Properties · READINGS: DB 16
- LEC #: 22 · TOPICS: Osmotic Pressure and Phase Partitioning · READINGS: DB 16
- LEC #: 23 · TOPICS: Surface Tension · READINGS: DB 14
- LEC #: 24 · TOPICS: Polymer 1 - Freely Jointed Chain · READINGS: DB 31
- LEC #: 25 · TOPICS: Polymer 2 - Chain Conformation · READINGS: DB 31
- LEC #: 26 · TOPICS: Polymer 3 - Rubber Elasticity · READINGS: DB 32
- LEC #: 31 · TOPICS: Cooperativity · READINGS: DB 26
- LEC #: 32 · TOPICS: Cooperativity, Part 2 · READINGS: DB 28
Spring 2004 · Statistical Thermodynamics of Biomolecular Systems (BE.011J)
Topics
- Introduction
- Probability (cont.)
- Equilibrium States
- Introduction to Conservation Laws (1st Law, Quantization, 2nd Law)
- Boltzmann’s Law and Entropy as an Extensive Property
- More Boltzmann’s Law
- Simulations
- Reversible and Irreversible Processes
- Introduction to Free Energy
- Enthalpy
- Fundamental Equations and their Natural Variables
- Thermodynamic Cycles
- Partial Molar Properties
- Partial Molar Properties II
- Boltzmann Distribution Law
- Partition Functions
- Prediction of Thermodynamic Properties from Partition Functions
- Quantum Partition Function
- Equipartition
- Equipartition (cont.)
- Chemical Equlibria
- Solid-liquid-gas Equilibrium
- Solutions and Mixtures
- Solvation: Protein/Macromolecule Adsorption at Interfaces
- Polymer Chain
- Polymer Chain II
- Polymer Chain III
- Cooperativity
- Cooperativity (cont.)
- Protein Folding
Readings
- All Text Readings are in Dill, K., and S. Bromberg. Molecular Driving Forces . New York, NY: Routledge, 2002. ISBN: 9780815320517.
- van Holde = 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 = Eisenberg, D., and D. Crothers. Physical Chemistry with Applications to the Life Sciences . Menlo Park, CA: Benjamin/Cummings, 1979. ISBN: 9780805324020.
- Kittel = Kittel, C., and H. Kroemer. Thermal Physics . 2nd ed. New York, NY: W.H. Freeman, 1980. ISBN: 9780716710882.
- SES #: L2 · TOPICS: Probability · TEXT READINGS: Ch. 1, 2
- SES #: L3 · TOPICS: Equilibrium States · TEXT READINGS: Ch. 2 (Through Ex. 2.2)
- SES #: L5 · TOPICS: Introduction to Conservation Laws (1st Law, Quantization, 2nd Law) · TEXT READINGS: Ch. 3
- SES #: L10 · TOPICS: Introduction to Chemical Potential - Thermo Cycles - First Law Relations between Heat, Work, Energy · TEXT READINGS: Ch. 7
- SES #: L11 · TOPICS: Reversible and Irreversible Processes · TEXT READINGS: Ch. 7
- SES #: L16 · TOPICS: Partial Molar Properties · TEXT READINGS: Ch. 9
- SES #: L17 · TOPICS: Partial Molar Properties II · TEXT READINGS: Ch. 9 · ADDITIONAL REFERENCES: Eisenberg, Ch. 7
- SES #: L19 · TOPICS: Boltzmann Distribution Law · TEXT READINGS: Ch. 10
- SES #: L20 · TOPICS: Partition Functions · TEXT READINGS: Ch. 10
- SES #: L22 · TOPICS: Quantum Partition Function · TEXT READINGS: Ch. 10, 11
- SES #: L23 · TOPICS: Equipartition · TEXT READINGS: Ch. 11
- SES #: L24 · TOPICS: Equipartition (cont.) · TEXT READINGS: Ch. 11
- SES #: L26 · TOPICS: Solid-liquid-gas Equilibrium · TEXT READINGS: Ch. 14
- SES #: L28 · TOPICS: Solvation – Osmotic Pressure · TEXT READINGS: Ch. 16
- SES #: L29 · TOPICS: Solvation – Protein/Macromolecule Adsorption at Interfaces · TEXT READINGS: Ch. 16 · ADDITIONAL REFERENCES: van Holde, Ch. 2
- SES #: L30 · TOPICS: Polymer Chain · TEXT READINGS: Ch. 31
- SES #: L31 · TOPICS: Polymer Chain II · TEXT READINGS: Ch. 32
- SES #: L32 · TOPICS: Polymer Chain III · TEXT READINGS: Ch. 33
- SES #: L33 · TOPICS: Cooperativity · TEXT READINGS: Ch. 26
- SES #: L34 · TOPICS: Cooperativity (cont.) · TEXT READINGS: Ch. 28
- SES #: L35 · TOPICS: Protein Folding · ADDITIONAL REFERENCES: van Holde, Ch. 2
- Dill, K., and S. Bromberg. Molecular Driving Forces . New York, NY: Routledge, 2002. ISBN: 9780815320517.
- Hill, T. L. An Introduction to Statistical Thermodynamics . New York, NY: Dover, 1987. ISBN: 9780486652429.
- 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, D., and D. Crothers. Physical Chemistry with Applications to the Life Sciences . Menlo Park, CA: Benjamin/Cummings, 1979. ISBN: 9780805324020.
- Kittel, C., and H. Kroemer. Thermal Physics . 2nd ed. New York, NY: W.H. Freeman, 1980. ISBN: 9780716710882.
- McQuarrie, D. A. Statistical Mechanics . New York: Harper Collins, 1976.
- Atkins, P. W. Physical Chemistry . San Francisco: W. H. Freeman, 1997.
Prerequisites & course information
Same subject as 20.110[J] Prereq: ( Biology (GIR) , Calculus II (GIR) , Chemistry (GIR) , and Physics I (GIR) ) or permission of instructor U (Fall) 5-0-7 units. REST
Sources
- Course catalogue ↗2026–2027
- MIT OpenCourseWare ↗Fall 2005
- MIT OCW syllabus ↗
- MIT OCW calendar ↗
- MIT OCW readings ↗
- MIT OpenCourseWare ↗Spring 2004
- MIT OCW readings ↗
- MIT OCW syllabus ↗
- MIT OCW calendar ↗
- Historical MIT OpenCourseWare offering. Named reading entries and schedule topics are automatically extracted from the linked source pages.
- Historical MIT OpenCourseWare offering. Named reading entries and schedule topics are automatically extracted from the linked source pages.
Catalogue variants
- Thermodynamics of Biomolecular Systems · 5-0-7 units. REST · Undergraduate