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 |
| 11 | 16-09-2025 | Brownian motion and diffusion | 1. Random walk 2. Brownian motion 3. Derivation of the diffusion equation from the master equation. 4. Derivation of the Smoluchowski equation. | Lecture Note |
| 12 | 18-09-2025 | Molecular transport in biological systems | 1. How do we measure diffusion coefficients? 2. Anomalous diffusion. 3. Non-diffusive transports | Lecture Note |
| 13 | 23-09-2025 | Guest lecture + Chemotaxis | 1. Lecture on Phototaxis of Chlamydomonas phototaxis by Prof. Prerna Sharma 2. Discussion of the physics of chemoreception by Berg and Purcell | Lecture Materials |
| 14 | 25-09-2025 | Mid-term exam | ||
| 15 | 07-10-2025 | Polymers as random walks | 1. Freely-jointed chain model of polymers. 2. Kuhn length 3. Radius of gyration. 4. The concept of persistence length. | Lecture Note |
| 16 | 09-10-2025 | Beam theory-1 | 1. Polymers and cytoskeletal filaments as slender rods. 2. Beams, ribbons, and membranes 3. Bending rigidity of a beam. 4. Persistence length as a measure of bending rigidity | Lecture Note |
| 17 | 14-10-2025 | Beam theory-2 + Basics of lipid self-assembly | 1. Buckling of beams under stress. 2. Lipids as ampiphiles 3. Nomenclature of lipids 4. Thermodynamics of equilibrium self-assembly | Lecture materials |
| 18 | 16-10-2025 | Guest lecture | 1. Liquid-liquid phase separation by Prof. Shibananda Das 2. Partial differential equations by Soumyadeep Mondal | |
| 19 | 21-10-2025 | Basics of membrane mechanics | 1. Geometric criteria for lipid assemblies. 2. Cell membranes as an self-assembled structure of lipids. 3. Membrane deformation and associated free energies. 4. Bending of membranes and height fields. | Lecture note |
| 20 | 23-10-2025 | Molecular motors | 1. What are molecular motors? 2. Functions of molecular motors. 3. Simple theory of molecular motors. | Lecture materials |
| 21 | 28-10-2025 | Salty solutions | 1. Ionic equilibrium 2. DNA condensation in bacteriophage 3. Salty solution 4. Debye-Huckel theory 5. DNA packaging revisited | Lecture note |
| 22 | 30-10-2025 | Ion channels | 1. Osmosis 2. Nernst equation 3. Ligand-gated ion channels 4. Allostery | Lecture note |
| 23 | 04-11-2025 | Biological electricity - I | 1. Membrane as an electrical circuit 2. Membrane potential 3. Ion channel conductivity 4. Patch-clamp experiments 5. Voltage-gated ion channels | Lecture note |
| 24 | 06-11-2025 | Biological electricity - II | 1. Neuron as a cable 2. Cable theory 3. Propagation of depolarization waves 4. Pattern formation | Lecture materials |