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Introduction to Statistical Thermodynamics
of Soft and Biological MatterLecture 3
Statistical thermodynamics III
• Kinetic interpretation of the Boltzmann distribution. Barrier crossing.• Unfolding of single RNA molecule.• Diffusion. • Random walks and conformations of polymer molecules.• Depletion force.
Boltzmann distribution
• System with many possible states (M possible states) (different conformations of protein molecule) Each state has probability Each state has energy
Partition function:
Maxwell-Boltzmann distribution
Probability distribution for velocities:
Gas of N molecules: - velocity of a molecule
How to compute average…
If you want to derive the formula yourself…
Use the following help:
Example: fluctuations of polymer molecule
verify:- energy of polymer molecule
Probability distribution:
Equipartition theorem:
Example: Two state system
Probability of state:
Verify!
Kinetic interpretation of the Boltzmann distribution
- activation barrier
Reaction rates:
Kinetic interpretation of the Boltzmann distribution
- activation barrier
Detailed balance (at equilibrium):
Number of molecules in state 2 and in state 1
Verify!
Unfolding of single RNA molecule
J. Liphardt et al., Science 292, 733 (2001)
Optical tweezers apparatus:
J. Liphardt et al., Science 292, 733 (2001)
Two-state system and unfolding of single RNA molecule
Extension
Open state: Close state (force applied):
force extension
Diffusion
Robert Brown: 1828
Albert Einstein
Pollen grain (1000 nm)
Water molecules (0.3 nm):
Universal properties of random walk
0
L (step-size of random walk)
- random number (determines direction of i-th step)
One-dimensional random walk:
N-th step of random walk:
(N-1)-th step of random walk:
Verify!
Diffusion coefficient
From dimensional analysis:
Number of random steps N corresponds to time t:
Friction coefficient:
Diffusion coefficient and dissipation
Viscosity Particle size
Einstein relation:
Diffusion in two and three dimensions
One-dimensional (1D) random walk:
Two-dimensional (2D) random walk:
Three-dimensional (3D) random walk:
Conformations of polymer molecules
* Excluded volume effects and interactions may change law!
L – length of elementary segment
• Universal properties of random walk describe conformations of polymer molecules.
More about diffusion… Diffusion equation
Surface area: A
x
Flux:
c – concentration of particles
Solution of diffusion equation
verify this is the solution!
c(x,t)
x
The concentration profile spreads out with time
Pressure of ideal gasFree energy of ideal gas:
density:N – number of particlesV - volume
Pressure:
Osmotic forces: Concentration difference inducesosmotic pressure
Semi-permeable membrane(only solvent can penetrate)
Protein solution
Depletion force
R