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 for non-commercial purposes.
Syllabus: Syllabus-Aug2025
Class team: PH 360: Aug-Dec 2025
Additionally, the suggested readings for this course are the following textbooks.
- Physical Biology of the Cell (PBoC), Phillips et.al. Garland Science, 2nd edition.
- Biological Physics (BPN), Nelson, Student Edition, Chiliagon Press.
- An Introduction to Systems Biology, Alon, 2nd edition, CRC Press.
| Class ID | Class date | Topic | Details | Resources |
|---|---|---|---|---|
| 1 | 05-08-2025 | Introduction | 1. What is biophysics? 2. How do we model biological phenomena? 3. Biological units. 4. Estimation techniques. | Lecture Note |
| 2 | 07-08-2025 | Introduction to biophysical models | 1. Estimating 30 s 2. Rules of estimation 3. Image analysis of E.coli growth 4. Estimating E.coli doubling rate using Bionumbers 5. Resource allocation during cell division | Lecture Note + E. coli growth images + Codes |
| 3 | 19-08-2025 | Thermal equilibrium in cells | 1. Body temperature 2. Laws of thermodynamics 3. Entropy 4. Maximum entropy distributions 5. Applications | Lecture note PBoC Ch 5.3, 5.4, 5.5, 5.5.1 |
| 4 | 21-08-2025 | Ligand-receptor binding | 1. Boltzmann distribution 2. Two-state systems 3. Ligand-receptor binding 4. DNA-protein binding | Lecture Note |
| 5 | 26-08-2025 | Cooperative binding | 1. Regulation of gene expression 2. Gibbs ensemble 3. Ligand-receptor binding revisited 4. Cooperative binding of oxygen to hemoglobin | Lecture Note |
| 6 | 28-08-2025 | Chemical kinetics | 1. The law of mass action 2. Well-mixed mass action kinetics 3. Rate equations 4. Michaelis-Menten kinetics 5. Population growth kinetics | Lecture Note + Code |
| 7 | 02-09-2025 | Negative autoregulation | 1. What is systems biology? 2. Response time 3. Network motifs 4. Autoregulation as a network motif 5. Rapid response through auto regulation | Lecture Note |
| 8 | 04-09-2025 | Positive autoregulation + Feedforward loop | 1. Positive autoregulation 2. Delayed response 3. Bistability 4. FFLs | Lecture Note |
| 9 | 09-09-2025 | Feedforward Loop + Toggle switch | 1. C1-FFL 2. Logic gates 3. I1-FFL 4. Toggle switch 5. Nullcline analysis | Lecture Note |
| 10 | 11-09-2025 | Stochastic Chemical Kinetics | 1. Markov processes 2. Markov state models 3. Master equation 4. Chemical master equation 5. Doob-Gillespie algorithm | Lecture Note + Python Notebooks |