PH 360 Biophysics, August 2022

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.

  1. 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.
  2.  Biological Physics (BPN), Nelson, Student Edition, Chiliagon Press. It is quite cheap, if you want to buy the Kindle edition.
  3. An Introduction to Systems Biology, Alon, 2nd edition, CRC Press.
Class IDTentative class date (DDMMYY)TopicResources
102-08-22Introduction to biophysicsSyllabus, Lecture Note

Additional Reading:
1. Chapter 1 of PBoC
2. bionumbers book. Read the "Biological Numeracy" chapter.

Resources:
bionumbers
The Double Helix.
204-08-22Size and shape of cellsLecture Note

Additional Reading: PBoC chapter 2
311-08-22Temporal variations in cellsLecture Note

Additional reading: PBoC Chapter 3

News: Assignment 1 given. Due: 18/08/2022, in class.
416-08-22Thermal equilibrium in cellsLecture Note
518-08-22Two-state modelLecture Note
623-08-22Ligand-Receptor bindingLecture Note

Other resources:

1. Thermodynamic Ensemble

2. A recent paper that uses cooperativity to create logic gates
725-08-22Chemical equilibrium and chemical kineticsLecture Note
830-08-22Stochastic chemical kineticsLecture Material

Paper on Markov State Models
901-09-22Brownian motionLecture Note
1006-09-22Polymers as random walks Lecture Note

Relation between radius of gyration and diffusion
1108-09-22Beam Theory Lecture Note

Measurement of flexural rigidity of microtubule and actin (classic paper)
1213-09-22Chemotaxis Lecture Note + Berg-Purcell paper

Energetic costs of cellular computation
1315-09-22Cytoskeleton and beam theoryLecture Note
1420-09-22Midterm in class
1506-10-22Length regulation of cytoskeletal filamentsLecture Note
1611-10-22Biological Membranes I: Self AssemblyLecture Note
1713-10-22Biological Membranes II: MechanicsLecture Note 1

Lecture Note 2
1818-10-22Molecular MotorsLecture Note
1920-10-22Salty solutions Lecture Note
2025-10-22Ion ChannelsLecture Note
2127-10-22Spatiotemporal dynamics of bioelectricityLecture Note

Topological action potential

Topological action potential: Twitter version
2203-11-22Genetic circuits I: AutoregulationLecture Note
2310-11-22Genetic circuits II: Positive Autoregulation & FFLLecture Note + Jupyter Notebooks
2415-11-22Genetic circuits III: Feed forward loop and Toggle SwitchLecture Note
2517-11-22Genetic circuits IV: OptimizationLecture Note
2622-11-22Genetic circuits V: Kinetic ProofreadingLecture Note

Kinetic proofreading tutorial by: Rob Phillips and Daniel Zuckerman