Biological Physics (2018)
Vijay Krishnamurthy, Sriram Ramaswamy and Shashi Thutupalli

Time: Mon & Fri 1715-1845 (First meeting on Fri 3 Aug 2018)
Location:  Auditorium, Ground Floor, Physics Department, IISc

Prerequisites: Mechanics and Statistical physics at 1st-year graduate student level
Evaluation: Mid-semester & end-semester exams

References:

• Philip Nelson, Biological Physics: Energy, Information, Life (W. H. Freeman, 2014)
• R Phillips, J Kondev, J Theriot, H Garcia, Physical Biology of the Cell (Garland Science 2013)
• W Bialek, Biophysics: Searching for Principles (Princeton University Press 2012)
• Relevant papers

Course Outline and Lectures:
1. Phenomena
       - Lectures 1 & 2

• The living state as a physicist sees it
• Molecular, Cell & Developmental Biology, Neurobiology, Ecology & Evolution
• What a cell does:  metabolism, maintenance, replication, motility, sensing & signaling and death
• What a cell contains:  various classes of biomolecules, DNA, RNA, proteins, lipids, carbohydrates
• Scales and numbers in cell biology

       - Lecture 3

• Biological information; genes, stability and mutation
• Mendel, Timofeeff
• Luria-Delbruck

2. Statistical mechanics in biology
       - Lecture 4

• Random walks, Langevin equation, Fokker-Planck
• Examples: Brownian motion, molecular motors as biased random walks

       - Lecture 5 & 6

• Diffusion
• Examples: permeation, feeding by diffusion and size, membrane potentials & Nernst, Berg-Purcell, Morphogen gradients

       - Lecture 7

• Master equation
• chemical kinetics: protein synthesis and degradation, Michaelis-Menten kinetics, Berg-von Hippel

       - Lecture 8

• Entropic forces, water: self-assembly

3. Molecular devices

• Polymerases, motors, synthases, enzymes, ion pumps, mitochondria

4. Metabolism

• Bioenergetics, glycolysis: aerobic and anaerobic, ATP synthesis

5. Macromolecular assemblies

• Polymers: entropic elasticity, force-extension relations, folding, melting
• Microtubules, catastrophe, actin, treadmilling, polymer networks
• Membranes: bending elasticity, shape, budding, domains, rafts, pumps

6. Replication

• Copying errors, kinetic proofreading
• Monod's experiments
• Cell division: cytokinetic ring, mitotic spindle

7. Sensing & signalling

• Mechanical, optical and chemical signals
• Receptors, MWC model, pathways
• Electrical transport across membranes: neurons, nerve impulses

8. Motility

• Crawling: treadmilling
• Swimming: Purcell
• Collective motility: active hydrodynamics

9. Patterns

• Genetic circuits
• Networks
• Cell & Developmental patterns

• Population dynamics