Molecular Thermodynamics
M W F 9:00-10:30 BH 215

Bo Huang: (Course Director)
Michael Grabe:
Jed Pitera:
Andrew Pohorille:
Sy Redding:

TA: David Bauer:


Textbook: Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience, 2nd Edition, by Ken Dill and Sarina Bromberg

Grade: 50% homework, 50% final exam.

Homework is assigned during class and due the following Monday before the lecture.

Final exam: take home, problem set handed out on Mar 17th, due on Mar 24th.

What are the stable states of biomolecules? How do molecules interact? What forces drive molecules to bond and associate, to adsorb, to permeate through membranes, to undergo chemical reactions, to undergo conformational changes? These questions are addressed by statistical thermodynamics, a collection of principles and models that when combined with thermodynamics, aim to explain molecular forces and flows.

The revamped molecular thermodynamic course will now be more closely connected to real biological systems than ever before. Each week, the course will focus on one topic, with Monday and Wedensday lectures giving the theoretical background and Friday discussing a chosen paper or a biological questions that the statistics mechanical principles and be applied to.


  Week 1 (Jan 9, 11, 13) Entropy and free energy (BH)
  Week 2 (Jan 18, 20) Boltzmann distribution (BH)
  Week 3 (Jan 23, 25, 27) Chemical equilibria (SR)
  Week 4 (Jan 30, Feb 1, 3) Chemical kinetics (JP)
  Week 5 (Feb 6, 8, 10) Polymer (BH)
  Week 6 (Feb 13, 15, 17) Electrostatics (BH/MG)
  Week 7 (Feb 22, 24) Water and solution (MG)
Week 8 (Feb 27, Mar 1, 3) Diffusion and adsorption (JP)
  Week 9 (Mar 6, 8, 10) Protein folding (AP)
  Week 10 (Mar 13, 15, 17) Single-molecule dynamics (SR)
  Week 11 (Mar 24) Final due





Notes and papers
Week 1 9-Jan Entropy and fundamental theromdynamics eq (chp 5, 6) BH  
  11-Jan Free energy (chapter 8) BH  
13-Jan Discussion: protein conformation entropy BH Tzeng 2012
2 16-Jan No lecture on Martin Luther King Day  
  18-Jan Boltzmann distribution and partition function BH  
  20-Jan Discussion: lipid droplets in cells BH Li 2012
3 23-Jan Chemical equilibria SR  
  25-Jan Chemical equilibria SR  
  27-Jan Chemical equilibria SR  
4 30-Jan Chemcial kinetics JP
  1-Feb Chemcial kinetics JP  
  3-Feb Discussion: transcription regulator oscillatory network JP Elowitz&Leibler
5 6-Feb Polymer - random walk polymer BH  
  8-Feb Polymer - worm-like chain BH  
  10-Feb Discussion: chromatin packaging BH Lieberman Aiden
(Mirny 2011)
6 13-Feb Electrostatics BH  
  15-Feb Electrostatics BH  
  17-Feb Discussion: electrostatics in enzyme function MG Suydam 2006
7 20-Feb No lecture on President's Day    
  22-Feb Water and solution MG  
  24-Feb Water and solution MG Levy_2006
8 27-Feb Diffusion JP  
  1-Mar Adsorption JP  
  3-Mar Discussion: target searching on DNA JP Bonnet 2008,
(Berg 1981)
9 6-Mar Protein folding AP  
  8-Mar Protein folding AP  
  10-Mar Protein folding AP Kubelka 2008
10 13-Mar Single-molecule dynamics SR  
  15-Mar Single-molecule dynamics SR  
  17-Mar Single-molecule dynamics SR  
11 24-Mar Final due