Venue: Lecture Hall 4, Room # F0-11, Department of Physics
Time: Tuesdays & Thursdays 2-3.30
This page will serve as a resource for the PH 360 course at the Department of Physics, IISc. Course content will be updated periodically.
This course will be taught using lecture notes prepared by Sumantra Sarkar. The lecture notes are free to use at your own peril.
Additionally, the suggested readings for this course are the following textbooks.
- Physical Biology of the Cell (PBoC), Phillips et.al. Garland Science, 2nd edition. It is quite expensive. Five copies of PBoC will be reserved at the library as reading room facility for this course.
- Biological Physics (BPN), Nelson, Student Edition, Chiliagon Press. It is quite cheap, if you want to buy the Kindle edition.
- An Introduction to Systems Biology, Alon, 2nd edition, CRC Press.
| Class ID | Tentative class date (DDMMYY) | Topic | Resources |
|---|---|---|---|
| 1 | 02-08-22 | Introduction to biophysics | Syllabus, Lecture Note Additional Reading: 1. Chapter 1 of PBoC 2. bionumbers book. Read the "Biological Numeracy" chapter. Resources: bionumbers The Double Helix. |
| 2 | 04-08-22 | Size and shape of cells | Lecture Note Additional Reading: PBoC chapter 2 |
| 3 | 11-08-22 | Temporal variations in cells | Lecture Note Additional reading: PBoC Chapter 3 News: Assignment 1 given. Due: 18/08/2022, in class. |
| 4 | 16-08-22 | Thermal equilibrium in cells | Lecture Note |
| 5 | 18-08-22 | Two-state model | Lecture Note |
| 6 | 23-08-22 | Ligand-Receptor binding | Lecture Note Other resources: 1. Thermodynamic Ensemble 2. A recent paper that uses cooperativity to create logic gates |
| 7 | 25-08-22 | Chemical equilibrium and chemical kinetics | Lecture Note |
| 8 | 30-08-22 | Stochastic chemical kinetics | Lecture Material Paper on Markov State Models |
| 9 | 01-09-22 | Brownian motion | Lecture Note |
| 10 | 06-09-22 | Polymers as random walks | Lecture Note Relation between radius of gyration and diffusion |
| 11 | 08-09-22 | Beam Theory | Lecture Note Measurement of flexural rigidity of microtubule and actin (classic paper) |
| 12 | 13-09-22 | Chemotaxis | Lecture Note + Berg-Purcell paper Energetic costs of cellular computation |
| 13 | 15-09-22 | Cytoskeleton and beam theory | Lecture Note |
| 14 | 20-09-22 | Midterm in class | |
| 15 | 06-10-22 | Length regulation of cytoskeletal filaments | Lecture Note |
| 16 | 11-10-22 | Biological Membranes I: Self Assembly | Lecture Note |
| 17 | 13-10-22 | Biological Membranes II: Mechanics | Lecture Note 1 Lecture Note 2 |
| 18 | 18-10-22 | Molecular Motors | Lecture Note |
| 19 | 20-10-22 | Salty solutions | Lecture Note |
| 20 | 25-10-22 | Ion Channels | Lecture Note |
| 21 | 27-10-22 | Spatiotemporal dynamics of bioelectricity | Lecture Note Topological action potential Topological action potential: Twitter version |
| 22 | 03-11-22 | Genetic circuits I: Autoregulation | Lecture Note |
| 23 | 10-11-22 | Genetic circuits II: Positive Autoregulation & FFL | Lecture Note + Jupyter Notebooks |
| 24 | 15-11-22 | Genetic circuits III: Feed forward loop and Toggle Switch | Lecture Note |
| 25 | 17-11-22 | Genetic circuits IV: Optimization | Lecture Note |
| 26 | 22-11-22 | Genetic circuits V: Kinetic Proofreading | Lecture Note Kinetic proofreading tutorial by: Rob Phillips and Daniel Zuckerman |