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Hamad-Schifferli, Kim, Linda Griffith, Moungi Bawendi, and Robert Field, 20.110J Thermodynamics of Biomolecular Systems, Fall 2005. (Massachusetts Institute of Technology: MIT OpenCourseWare), (Accessed 09 Jul, 2010). License: Creative Commons BY-NC-SA

Thermodynamics of Biomolecular Systems

Fall 2005

Energy levels of the different conformations of a 4 bead polymer. (Image by Kim Hamad-Schifferli and MIT OCW.)

Course Highlights

This course features a complete set of lecture notes, exams, and assignments.

Course Description

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.


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.


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.


Grades for the subject will be based on a total of 550 points.

Activities Points
Three Exams (100 Points Each) 300 points
Final Exam 200 points
Homework 50 points


All examinations will be closed book. One double-sided 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 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.


1 Introduction to Thermo; 0th Law; Temperature; Work; Heat  
2 State Functions, 1st Law, Paths  
3 Joule and Joule-Thompson; Heat Capacity  
4 Reversible and Irreversible Processes  
5 Thermochemistry Problem set 1 due
6 2nd 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; Gibbs-Duhem  
12 ΔG0= -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 Self-Assembly Problem set 10 due
35 Special Topic (Coarse Grain/Monte Carlo Model)  
36 Course Review and Evaluations   Tell A Friend