Molecular Thermodynamics
M W F 9:00-10:30 BH 209

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

TA: Sasha Dickinson:


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 16th, due on Mar 23th.

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 8, 10, 12) Entropy and free energy (BH)
  Week 2 (Jan 17, 19) Boltzmann distribution (BH)
  Week 3 (Jan 22, 24, 26) Chemical equilibria (SR)
  Week 4 (Jan 29, 31, Feb 3) Chemical kinetics (JP)
  Week 5 (Feb 5, 7, 9) Diffusion and adsorption (JP)
  Week 6 (Feb 12, 14, 16) Electrostatics (MG)
  Week 7 (Feb 21, 23) Water and solution (MG)
Week 8 (Feb 26, 28, Mar 2) Protein folding (AP)
  Week 9 (Mar 5, 7, 9) Polymer (BH)
  Week 10 (Mar 12, 14, 16) Single-molecule dynamics (SR)
  Week 11 (Mar 23) Final due





Notes and papers
Week 1 8-Jan Entropy and fundamental theromdynamics eq (chp 5, 6) BH  
  10-Jan Free energy (chapter 8) BH  
12-Jan Discussion: protein conformation entropy BH Tzeng 2012
2 15-Jan No lecture on Martin Luther King Day  
  17-Jan Boltzmann distribution and partition function BH  
  19-Jan Discussion: lipid droplets in cells BH Li 2012
3 22-Jan Chemical equilibria SR  
  24-Jan Chemical equilibria SR  
  26-Jan Chemical equilibria SR  
4 29-Jan Chemcial kinetics JP
  31-Jan Chemcial kinetics JP  
  2-Feb Discussion: transcription regulator oscillatory network JP Elowitz&Leibler
5 5-Feb Diffusion JP  
  7-Feb Adsorption JP  
  9-Feb Discussion: target searching on DNA JP Bonnet 2008,
(Berg 1981)
6 12-Feb Electrostatics MG  
  14-Feb Electrostatics MG  
  16-Feb Discussion: electrostatics in enzyme function MG Suydam 2006
7 19-Feb No lecture on President's Day    
  21-Feb Water and solution MG  
  23-Feb Water and solution MG Levy_2006
8 26-Feb Protein folding Ap  
  28-Feb Protein folding AP  
  2-Mar Protein folding AP Kubelka 2008
9 5-Mar Polymer - random walk polymer BH  
  7-Mar Polymer - worm-like chain BH  
  9-Mar Discussion: chromatin packaging BH Lieberman Aiden
(Mirny 2011)
10 12-Mar Single-molecule dynamics SR  
  14-Mar Single-molecule dynamics SR  
  16-Mar Single-molecule dynamics SR  
11 23-Mar Final due