Introduzione alla fisica dei sistemi biologici - Programma

Introduction

1. The physics behind Photo 51

• Photo 51
• Basics of X-ray diffraction
• Diffraction from a double helix

2. Life building blocks

• Proteins
• DNA
• From genes to proteins

Random walks and diffusion

3. Langevin equation

• Microscopic equilibrium
• Random walks
• Langevin equation

4. Diffusion equation

• Free Brownian particle
• Diffusion current
• Examples (1D step, diffusion limited respiration)
• Diffusion to a perfect absorber of generic shape

5. Smoluchowsky equation

• Smoluchowsky equation
• Boltzmann distribution

6. Kramers escape rate

• Kramers escape rate

Molecular motors

7. Translational motors

• Kinesin, dynein, myosin
• 1-state model
• Thermodynamic uncertainty relations
• Motor speed as a function of load and fuel
• 2 state model

8. Rotary motors

• The bacterial flagellar motor
• ATP synthase

Elasticity

9. Deflection of beams

• Stress and strain
• Shear forces and bending moments
• Beam deformation

10. Weakly deflected beams

• Euler-Bernoulli equation
• Deflection of cantilevers
• Bending of biological filaments

11. Fluctuating elastic filaments

• Elastic energy of a deformed beam
• Thermal fluctuations
• Persistence lengths of biological filaments

12. Buckling

• Euler buckling
• Buckling of spaghetti
• Buckling of microtubules

13. Entropic elasticity

• Thermodynamics of a polymer
• Force extension curve of single molecules
• Overstretching DNA
• Rubber bands

14. DNA packaging

• Viral DNA packaging
• Bending energy
• Measuring internal force
• Thermodynamics of viral packaging