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