M W F 9:00-10:30 BH 215
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.
Aim: 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-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
|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|
|3-Mar||Discussion: target searching on DNA||JP||Bonnet 2008,
|10-Mar||Protein folding||AP||Kubelka 2008|