Schedule
| Week | Date | Month | Topic | Reading | Lecturer | Notes |
|---|---|---|---|---|---|---|
| 1 | 22 | September | Equilibrium State | Bo Huang | ||
| 23 | September | Entropy | Chapter 7 | Bo Huang | ||
| 24 | September | Free Energies | Chapter 10 | Bo Huang | Homework 1 Assigned | |
| 26 | September | Discussion: protein conformation entropy | Chapter 10 | Michael Grabe | Paper: https://www.nature.com/articles/s41586-018-0699-5 | |
| 2 | 29 | September | Boltzmann distribution | Chapter 10 | Bo Huang | |
| 30 | September | Partition function | Chapter 10 | Bo Huang | ||
| 1 | October | Statistical mechanics of simple gases | Chapter 11 | Bo Huang | Homework #2 assigned | |
| 3 | October | Discussion: Modelling transcriptional regulation | Bo Huang | https://pubmed.ncbi.nlm.nih.gov/15797194/ | ||
| 3 | 6 | October | Chemical equilibria | Chapter 13 | Bo Huang | |
| 7 | October | Phase transitions | Chapter 16 | Bo Huang | ||
| 8 | October | Solvation and transfer between phases | Chapter 25 | Bo Huang | Homework #3 assigned | |
| 10 | October | Discussion: Liquid protein droplets in cells | Bo Huang | Paper: https://www.nature.com/articles/nature10879 | ||
| 4 | 13 | October | Polymers: Flory Huggins | Chapter 32 | Ignacia Echeverria | |
| 14 | October | Polymers: Phase Separation | Chapter 32 | Ignacia Echeverria | ||
| 15 | October | Polymers: Random Walk and Worm-like Chain | Chapter 32 | Ignacia Echeverria | ||
| 17 | October | Discussion: NPC | Ignacia Echeverria | |||
| 5 | 20 | October | Chemical Kinetics | Chapter 18 | Jed Pitera | |
| 21 | October | Chemical Kinetics; Discussion: transcriptional oscillatory networks | Jed Pitera | https://www.nature.com/articles/35002125 | ||
| 22 | October | Physical Kinetics | Chapter 19 | Jed Pitera | Homework #4 assigned | |
| 24 | October | Discussion: Diffusion in the cytoplasm | Jed Pitera | https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.101.248103 and https://doi.org/10.1088/1367-2630/15/7/075008 | ||
| 6 | 27 | October | Absorption & Saturation | Chapter 28 | Jed Pitera | |
| 31 | October | The math of chemotaxis | Handouts | Jed Pitera | ||
| 7 | 3 | November | QBC Retreat (no class) | |||
| 7 | November | Electrostatics: Water | Chapter 30 | Michael Grabe | ||
| 8 | 10 | November | Veterans Day (no class) | |||
| 14 | November | Electrostatics: Maxwell's Equations | Chapter 21 & 22 | Michael Grabe | ||
| 9 | 17 | November | Electrostatics: Force and Potential | Chapter 21 & 22 | Michael Grabe | Homework #5 Assigned |
| 21 | November | Electrostatics: Poisson Boltzmann Theory | Chapter 23 | Michael Grabe | ||
| 10 | 24 | November | Discussion: Electrostatics and membrane curvature | Michael Grabe | https://pubmed.ncbi.nlm.nih.gov/23153485/ | |
| 28 | November | Thanksgiving (No Class) | ||||
| 11 | 1 | December | Dynamics: Markov State Modelling | Michael Grabe | ||
| 5 | December | Dynamics: Markov State Modelling 2, Gillespie Algorithm | Michael Grabe | Homework #6 Assigned | ||
| 12 | 8 | December | Dynamics: Gillespie Algorithm 2 | Michael Grabe | ||
| 12 | December | Final Exam Date (discussion cancelled) | Michael Grabe | |||
| 15 | December | No class (previously tentative exam date) | Michael Grabe |
