- Introduction what is life, cells as building blocks of life;
- Basic facts about cells nuclear and cytoskeletal elements, biopolymer, membrane, molecular motors, DNA, Proteins and other major large and small molecules;
- Forces in the living world chemical forces, coulomb forces, Van der Waals interaction, electrostatic, hydrogen bonding, hydrophobic effect, entropic forces, depletion forces, excluded volume interaction;
- Random walk problems
- Physics of Polymers - what are polymers, biopolymers, polymerization, persistence length of polymers, size of polymers, radius of gyration, size of a Genome, polymer models - Freely joint chain, Self avoiding random walk, Worm-like chain; scaling laws, DNA loop formation;
- Brownian motion and diffusion active and passive transport, Fick's law, diffusion equation, diffusion with drift, applications of diffusion - modeling cell signaling problem, membrane transport, sedimentation
- Elements of Nonequilibrium Statistical Physics: Stochastic processes, Langevin dynamics, Fluctuation-Dissipation relation, Markov Process, Master equation, Fokker-Planck Equation, First-passage time
- Reaction kinetics; rate equations and dynamics - simple models of filament polymerization
- Dynamic of molecular machines- motors, ratchet models;
- Electrostatics and electricity in active systems: electrostatic potential, Bjerrum length, effect of screening, role of electricity in cells, action potential, nerve impulse propagation
- Life at low Reynolds number
- Physics of Membrane - structure, energetics and function;
- Biomechanics elasticity theory, bending of beam, buckling, torsion examples from biology
|