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 07 Jul, 2010). License: Creative Commons BYNCSA
Energy levels of the different conformations of a 4 bead polymer. (Image by Kim HamadSchifferli 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.
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: 047121504X.
Dill, Ken A., and Sarina Bromberg. Molecular Driving Forces: Statistical Thermodynamics in Chemistry and Biology. New York, NY: Garland Science, 2003. ISBN: 0815320515.
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



