HamadSchifferli, Kim, Linda Griffith, Moungi Bawendi, and Robert Field, 20.110J Thermodynamics of Biomolecular Systems, Fall 2005. (Massachusetts Institute of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed 09 Jul, 2010). License: Creative Commons BYNCSA
This course features a complete set of lecture notes, exams, and assignments.
This subject deals primarily with equilibrium properties of macroscopic and microscopic systems, basic thermodynamics, chemical equilibrium of reactions in gas and solution phase, and macromolecular interactions.
Syllabus
About the Course
20.110/2.772 was first taught in 2002 with the aim of providing a foundation in the thermodynamic principles used to describe biomolecular behavior and interactions such as those that lead to assembly of cell membranes, binding of growth factors to cells, annealing of cDNA sequences to oligonucleotides on microarray chips, and separation of complex mixtures of biomolecules for atomic analysis. Many of these problems, as well as related problems in nanotechnology and polymer science, are illuminated by a statistical thermodynamics approach. As the course evolved to become the foundational thermodynamics subject for the Biological Engineering S. B. degree and for many students in Biology, we found that our original syllabus did not include the appropriate treatment of classical thermodynamics required to solve practical problems in biochemical thermodynamics. Further, it became clear that a revision of the 20.110/2.772 syllabus to begin with classical thermodynamics provide a fortuitous overlap with parts of the 5.60 syllabus. Chemistry, Mechanical Engineering, and Biological Engineering thus developed a common syllabus for the first half of the term, with each subject then diverging into significantly different emphases in the latter part of the term (5.60 concludes with chemical kinetics, and 20.110/2.772 with biomolecular structure and interactions). A pilot version of the combined syllabus was taught in Spring 2005 by Professors Silbey, Griffith, and Irvine as 20.110/2.772, and the current syllabus is slightly revised from the pilot.
Acknowledgements
The material for first half of 20.110/2.772 that overlaps with 5.60 has evolved over a period of many years, and therefore several faculty members have contributed to the development of the course contents. The following are known to have assisted in preparing the lecture notes available on OCW:
Emeritus Professors of Chemistry: Robert A. Alberty, Carl W. Garland, Irwin Oppenheim, John S. Waugh.
Professors of Chemistry: Moungi Bawendi, John M. Deutch, Robert W. Field, Robert G. Griffin, Keith A. Nelson, Robert J. Silbey, Jeffrey I. Steinfeld.
Professor of Bioengineering and Computer Science: Bruce Tidor.
Professor of Chemistry, Rice University: James L. Kinsey.
Professor of Physics, University of Illinois: Philip W. Phillips.
Required Texts
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.
Grading
Grades for the subject will be based on a total of 550 points.
Grading criteria.
Activities 
Points 
Three Exams (100 Points Each) 
300 points 
Final Exam 
200 points 
Homework 
50 points 
Exams
All examinations will be closed book. One doublesided sheet of notes is allowed for the first exam; two for the second exam, three for the third exam, and four for the final.
Homework
Homework will be due on the sessions specified in the calendar section. Late homework will not be accepted. The two lowest homework grades will be dropped. Graded homework will be returned in recitation. Recitation problems are available in the recitation section. Students who can work all practice and homework problems easily without looking at notes or asking for help usually perform well on exams. You are encouraged to work in study groups, but must turn in only your own work.
Calendar
Course calendar.
LEC # 
TOPICS 
KEY DATES 
1 
Introduction to Thermo; 0^{th} Law; Temperature; Work; Heat 

2 
State Functions, 1^{st} Law, Paths 

3 
Joule and JouleThompson; Heat Capacity 

4 
Reversible and Irreversible Processes 

5 
Thermochemistry 
Problem set 1 due 
6 
2^{nd} Law; Entropy (Boltzmann and Clausius) 

7 
ΔS for Reversible and Irreversible Processes 
Problem set 2 due 
8 
Equilibrium; Maxwell Relations; Free Energy 

9 
Chemical Potential; Phase Equilibrium 

10 
Chemical Equilibrium; Equilibrium Constant 
Problem set 3 due 
11 
Standard States; GibbsDuhem 

12 
ΔG^{0}= RTlnK; Example 


Hour Exam 1 

13 
Boltzmann Distribution 

14 
Thermo and Boltzmann Distribution 
Problem set 4 due 
15 
Occupation of States 

16 
Third Law 

17 
Phase Equilibria, Single Component 
Problem set 5 due 
18 
Phase Equilibria II; Clausius Clapeyron 

19 
Regular Solutions; Mixing Energy; Mean Fields 

20 
Nonideal Solutions 
Problem set 6 due 
21 
Solvation; Colligative Properties 


Hour Exam 2 

22 
Osmotic Pressure and Phase Partitioning 

23 
Surface Tension 

24 
Polymer 1  Freely Jointed Chain 
Problem set 7 due 
25 
Polymer 2  Chain Conformation 

26 
Polymer 3  Rubber Elasticity 

27 
Electrolyte Solutions 
Problem set 8 due 
28 
Electrolytes at Interfaces; Debye Length 

29 
Titration of Polyelectrolytes 

30 
Thermodynamics of DNA Hybridization 
Problem set 9 due 
31 
Cooperativity 


Hour Exam 3 

32 
Cooperativity, Part 2 

33 
Cooperativity, Part 3 

34 
Driving Forces for SelfAssembly 
Problem set 10 due 
35 
Special Topic (Coarse Grain/Monte Carlo Model) 

36 
Course Review and Evaluations 
