Thermodynamics of Biomolecular Systems

Lecture Notes

MB = Prof. Moungi Bawendi
KHS = Prof. Kimberly Hamad-Schifferli
LGG = Prof. Linda G. Griffith

LEC #

TOPICS

LECTURERS

1

Introduction to Thermo; 0th Law; Temperature; Work; Heat (PDF)

MB

2

State Functions, 1st Law, Paths (PDF)

MB

3

Joule and Joule-Thompson; Heat Capacity (PDF)

MB

4

Reversible and Irreversible Processes (PDF)

MB

5

Thermochemistry (PDF)

MB

6

2nd Law; Entropy (Boltzmann and Clausius) (PDF)

MB

7

ΔS for Reversible and Irreversible Processes (PDF)

MB

8

Equilibrium; Maxwell Relations; Free Energy (PDF)

MB

9

Chemical Potential; Phase Equilibrium (PDF)

MB

10

Chemical Equilibrium; Equilibrium Constant (PDF)

MB

11

Standard States; Gibbs-Duhem (PDF)

MB

12

ΔG0= -RTlnK; Example (PDF)

MB

Hour Exam 1

13

Boltzmann Distribution (PDF)

KHS

14

Thermo and Boltzmann Distribution (PDF)

KHS

15

Occupation of States (PDF)

KHS

16

Third Law (PDF)

KHS

17

Phase Equilibria, Single Component (PDF)

KHS

18

Phase Equilibria II; Clausius Clapeyron (PDF)

KHS

19

Regular Solutions; Mixing Energy; Mean Fields

KHS

20

Nonideal Solutions

KHS

21

Solvation; Colligative Properties (PDF)

LGG

Hour Exam 2

22

Osmotic Pressure and Phase Partitioning (PDF)

LGG

23

Surface Tension (PDF)

LGG

24

Polymer 1 - Freely Jointed Chain (PDF)

LGG

25

Polymer 2 - Chain Conformation (PDF)

LGG

26

Polymer 3 - Rubber Elasticity (PDF - 2.2 MB)

LGG

27

Electrolyte Solutions (PDF)

LGG

28

Electrolytes at Interfaces; Debye Length (PDF)

LGG

29

Titration of Polyelectrolytes (PDF)

LGG

30

Thermodynamics of DNA Hybridization (PDF - 1.5 MB)

LGG

31

Cooperativity (PDF)

KHS

Hour Exam 3

32

Cooperativity, Part 2

KHS

33

Cooperativity, Part 3

KHS

34

Driving Forces for Self-Assembly

KHS

35

Special Topic (Coarse Grain/Monte Carlo Model)

36

Course Review and Evaluations

Recitations

Many recitation problems are from the following textbooks:

[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.

SES #

PROBLEMS

1

Problem 2.1 in:  Gaskell, David R. Introduction to the thermodynamics of materials. Washington, DC: Taylor & Francis, 1995. ISBN: 9781560324324.

SAB 2.10, 2.18, 2.19

2

Systems: Seltzer water demo

Example 2.1 in:
  Tinoco, Ignacio, Jr. Physical Chemistry: Principles and Applications in Biological Sciences. 4th ed. Upper Saddle River, NJ: Prentice Hall, 2001. ISBN: 9780130959430.

3-4

SAB 2.28, 2.31

Recitation Problems 3-4 (PDF)

5

SAB 3.16, 3.23

6

SAB 4.12, 4.14

9

DB Examples 1.15, 1.17 and Problem 1.2

10

Derivations for <ε>, S, A, μ, P

DB Example 10.5

11

Recitation Problem 11 (PDF)

12

SAB 3.24

Example 1 in:
  Levine, Ira N. Physical Chemistry. New York, NY: McGraw-Hill, 1994. ISBN: 9780070375284.

Find the melting point of ice at 100 atm. Δfus
 H = 79.7 cal/g, Ρliq=1.000 g/cm3, Ρice = 0.917 g/cm3.

SAB Example 6.4

15

Recitation Problem 15 (PDF)

16

Recitation Problem 16 (PDF)

17-18

DB 32.6, 10.11

Problem 2.13 in:
  Boal, David H. Mechanics of the Cell. Cambridge, UK: Cambridge University Press, 2002. ISBN: 9780521796811.

Recitation Problems 17-18 (PDF)

19

Recitation Problem 19 (PDF)

20

Recitation Problem 20 (PDF)