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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

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