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.
- Biological Physics (BPN), Nelson, Student Edition, Chiliagon Press.
- An Introduction to Systems Biology, Alon, 2nd edition, CRC Press.
| Class ID | Tentative class date (DDMMYY) | Topic | Details | Resources |
|---|---|---|---|---|
| 1 | 03-08-23 | Introduction to Biophysics | 1. What is biophysics? 2. How do we model biological phenomena? 3. Scope of the course. | Syllabus Lecture Notes and Slides |
| 2 | 08-08-23 | How do we estimate biological numbers? | 1. Useful estimation techniques. 2. Database of biological numbers. 3. Examples. | Lecture Note |
| 3 | 11-08-23 | How do cells estimate? | 1. How do cells measure size? 2. How do cells measure time? 3. Introduction to mathematical modeling. | Lecture Materials |
| 4 | 17-08-23 | Thermal equilibrium in cells | 1. Are cells in thermal equilibrium? 2. Boltzmann formula for entropy. 3. Maximum Entropy Principle. 4. Applications in Biophysics | Lecture note |
| 5 | 22-08-23 | Two state models | 1. Boltzmann distribution 2. Two-state models 3. Ligand-Receptor binding 4. Gene Regulation | Lecture note |
| 6 | 24-08-23 | Ligand-Receptor Binding | 1. Cooperative Binding 2. Gibbs Ensemble 3. Concentration dependence of chemical potential 4. Dimoglobin 5. Hemoglobin | Lecture note |
| 7 | 31-08-23 | Chemical Equilibrium and Chemical Kinetics | 1. Grand Canonical Ensemble. 2. The Law of Mass Action 3. Well-mixed mass action kinetics 4. Linear stability analysis 5. Examples | Lecture materials |
| 8 | 05-09-23 | Introduction to Systems Biology | 1. What is systems biology? 2. Gene regulatory networks 3. Network motifs 4. Negative autoregulation | Lecture notes |
| 9 | 07-09-23 | Systems Biology II | 1. Positive autoregulation 2. Bistability | Lecture materials |
| 10 | 08-09-23 | Systems Biology III | 1. Positive autoregulation contd. 2. Feed forward loops | Lecture materials |
| 11 | 12-09-23 | Systems Biology IV | 1. Coherent feed forward loops 2. Incoherent feed forward loops 3. Toggle switch | Lecture materials |
| 12 | 14-09-23 | Stochastic Chemical Kinetics | 1. Markov state models 2. Principle of detailed balance 3. Doob-Gillespie algorithm 4. Demonstrations | Lecture materials |
| 13 | 21-09-23 | Salty solutions | 1. Ionic equilibrium 2. DNA packaging 3. Charge screening in salty solutions | Lecture notes |
| 14 | 05-10-23 | Ion channels | 1. Osmosis 2. Ion channels 3. Ion Pumps 4. MWC model | Lecture note |
| 15 | 10-10-23 | Self-assembly | 1. Lipids and lipid diversity 2. Self assembly 3. Frustration 4. Glassy landscape 5. Asseembly rules | Lecture note |
| 16 | 12-10-23 | Brownian motion and diffusion | 1. Random walk 2. Central limit theorem 3. Master equation 4. Smoluchowski equation 5. Stokes-Einstein relation | Lecture note |
| 17 | 17-10-23 | Application of diffusion equation | 1. Fick's laws 2. Solution of diffusion equation 3. Theory of FRAP | Lecture note |
| 18 | 19-10-23 | Understanding proteins | 1. Amino acids 2. Protein structure 3. Anfinsen's experiment | Prof. Anand Srivastava's lecture note |
| 19 | 26-10-23 | Protein Structure / Function | Anand Srivastava lecture note | |
| 20 | 31-10-23 | Phase separation in biology | Anand Srivastava lecture note | |
| 21 | 02-11-23 | Intrinsically disordered proteins | Anand Srivastava lecture note | |
| 22 | 07-11-23 | Beam theory | 1. Examples of beams 2. Geometry of curves 3. Persistence length | Lecture note |
| 23 | 09-11-23 | Buckling of beams and membrane elasticity | 1. Buckling of beams 2. Thermodynamics of buckling 3. Membrane elasticity | Lecture note |
| 24 | 14-11-23 | Membrane deformations | 1. Laplace-Young law 2. Free energy of bending 3. Free energy to form vesicles 4. How to measure membrane elastic moduli? 5. Energetics of reticulated membranes | Lecture note |
| 25 | 16-11-23 | Pattern formation 1 | 1. How to form gradients? 2. Turing's model of morphogenesis 3. Linear stability analysis | Lecture materials |