F8510 - Physics of biopolymers

1. Electrostatic interactions in vacuum: Coulomb law, superposition principle, interactions of charges, dipoles, rotating dipoles, and induced dipoles, van der Waals interaction  - Slides

2. Electrostatic interactions in aqueous solutions: Poisson-Boltzmann equation, Debye-Hückel theory, Debye screening length, Gouy-Chapman theory, fluctuating charges -Slides

3. Interactions of big uncharged particles: Hamaker constant, Derjaguin approximation, solution for particles with different geometries - Sldies

4. Entropic interactions: directional entropic forces, ideal chain and its deformations, membrane fluctuations - Slides

5. Depletion interaction, hydrophobic interaction, DLVO theory, hydrogen bond, salt bridge, π-interaction - Slides

6. Polymers in aqueous solutions: Flory-Huggins theory, polymer mixtures - Slides

7. Protein folding: native contacts, funneling, helix-coil transition, swelling, crowding

8. Biopolymer models: ab initio, all-atom description, molecular mechanics, coarse-grained simulations

9. Radial distribution function, matter arrangement, structure factor

10. Solvation of molecules and ions: water – structure and properties, cavitation energy, Born solvation energy)

C9926 – Problems and issues of molecular modelling

1. Thermostats - flying ice cube; Equipartition theorem; hot solvent cold solute; stochastic thermostats and dynamics

2. Long-range interactions - cut off; charge neutrality of the system; dipole in the system

3. Forcefiled - parametrisation; mixing rules; polarization catastrophe; implicit solvent

4. External field - perpetum mobile

C9925 - Introduction to soft matter models of membranes and proteins

1. Introduction to coarse grained models

2. Ideal chain approximation

3. Ideal thin membrane

4. Interaction of uncharged membrane and proteins

5. Interaction of charged membrane and proteins I

6. Interaction of charged membrane and proteins II

7. Thermodynamic principles of self assembly

8. Langmuir adsorption and grand canonical ensemble

9. Dynamics and transport

10. Advanced Monte Carlo

NBCM147 - Interactions of proteins and membranes – introduction to soft matter

Short lecture on membrane structure and function

plus lipid biochemistry