**Class Notes**

**1/6 Molecular Motions in the Cell A****1/8 Molecular Motions in the Cell B and Slides****1/13 Molecular Motions in the Cell C and Slides****1/15 No class****1/20 Fluid Flow on the Scale of a Cell A and Slides****1/22 Fluid Flow on the Scale of a Cell B and Slides****1/27 Reaction Kinetics****1/29 No class****1/30 Matlab Tutorial Slides and Handout****2/5 Auto Tutorial**

Brownian Motion

Random walks and 1-D diffusion

Calculation of a probability distribuion from a random walk

Single molecule studies of repressor diffusion on DNA and Dynein on a microtubule

Fick's Law and the diffusion equation

Steady-state and time-dependent (Gaussian) solutions

Coordinate systems (cartesian, cylindrical, spherical)

Diffusion-limited binding in solution

Binding to membrane receptors on the cell surface

Flux as an external force

Lateral diffusion in a membrane (Saffman-Delbruck)

Single molecule measurement of lateral diffusion

Diffusion-limited binding on a cell surface

Brownian ratchets

Protein translocation as a Brownian ratchet

Scaling arguments and dimensionless numbers

Life at low Reynold's Number

Turbulent versus laminar (time-reversible) flow

Why can't a bacterium swim like Flipper?

Diffusion-advection equation

Peclet Number: convection versus advection

Can a bacteria get more food by swimming?

Can a cilia enhance food uptake by sweeping fluid against the cell surface?

Evolution of the volvocine green algae flagellum

Cilia and embriogenesis (Hensen's node and symmetry breaking)

Elementary mass action kinetics

De-dimensionalizing equations: protein dimerization example

Timescales: protein degradation example

Using timescales to simplify equations

Michaelis-Menton kinetics revisited

Defining an ODE function in an M-file

Solving first-order ODEs

Solving systems of first-order ODEs

Solving higher order ODEs