Flash Animations -- January 09 - The new 3rd edition of Essential Cell Biology will use microtubule dynamics animation in their movie supplement!

Microtubule dynamics - Vesicle movements - Vesicles on dynamic microtubules - More cytoskeleton

Bacterial chemotaxis - Colon crypt

Microscopy and optics - including - laser, flim, fcs, CCD, scanning microscope, noisy image

Three dimensions - Interacting objects


Programming notes

winter 08/09 additions:

Three-way junctions - something like the pattern of tubular ER networks -- Three dimensional (red green pair)
Sliding attachments at the periphery -- fusion of sliding attachments - normalized forces -- standard model with choices

Rotate-able mobius strip - we think that ER sheets may sometimes take the form of a mobius strip. With surfaces.
Cross section through a mobius strip at different orientations (what ER might look like in an electron micrograph)
Red-green stereo pair with cross sections

Collisions - actionscript 3 program, my 2 Ghz iMac can handle ~400

Spreading in an incomplete hexagonal lattice - with backtrace!

Staining mechanism for cortical ER labeling by DiI -- from "Characterization of sea urchin egg endoplasmic reticulum in cortical preparations"  Dev. Biology 148: 398-401 (1991)

Animation of cAMP and cGMP changes during mouse oocyte maturation -- more parameters, graph result

Loop of Henle - Goldman equation

Hodgkin Huxley action potential

Predator prey animation - green=plants, white=rabbits, red=foxes
(foxes duplicate after eating 4 rabbits, rabbits after eating 10 plants) (foxes die if they haven't eaten for 250 frames, rabbits if they haven't eaten for 100 frames) To prevent extinctions - no plants are eaten when number < 6, no rabbits eaten or die if <3, no foxes die if <3).
Predator prey #2 - can specify plant growth rate, lifetime of rabbits, lifetime of foxes, how many plants eaten by a rabbit in order to reproduce, how many rabbits eaten by a fox in order to reproduce.

Stereo drawing - make your own fusion pair! Press mouse and hold in order to draw. Press "1" or "2" keys to change level. Red green version with drawing pointer in stereo!

Ray tracing for lens and image - Ray tracing from two points

Diffusion coefficient - how particles diffuse for a given diffusion coefficient (2 dimensions) - reference is "Random Walks in Biology by Howard Berg) - compare two species

Fraction of protonated and deprotonated acid as a function of pH (Henderson Hasselbach eqn)
Fraction of charged amino acids as a function of pH (double Henderson Hasselbach eqns)

Buffer - how the free concentration varies as buffer concentration / K is varied

Simple feedback system (michaelis menten with positive and negative hill coefficients: equations)

"Real time" - this animation monitors its own frame rate, and adjusts the number of calculations that it can does to maintain a frame rate of 10-12 frames per sec. Another animation adjusts the number of colliding balls it can handle at 10-12 frames per sec.

"Tree of life" - a kind of simulation of evolution

Animation of cdc2 activation in starfish oocytes - introduction (positive feedback loop on Myt1 and Cdc25) - Number display - Inactivation of Myt1 to a variable level

Two dimensional fourier transform of a disk (using FFT)

One dimensional fourier transform of a square pulse (black = real, blue = imaginary)
One dimensional power spectra for various signals

Back aperture plane demonstration: image of stripes / mask out pattern in back aperture plane
Real life image: mask out pattern in "back aperture plane"
Real life image: mask in / mask out disks and annuli

Load intensity image, decompose to real & imag, get real, imag, intensity FFT1 and FFT2

flow and flow lines (though this is not physical) - version 2 - move it around

gaussian chain - 1 free end - 2 free ends - circle

damped coupled oscillators in a plane - hexagonal lattice

more hex lattice 1 - 2 - 3 - 4

Photomultiplier tube

another hex lattice variation (try between 0 and 0.5)

Sum of two poisson processes (such as background plus signal in an image)

Microtome - simulation of the basic movements of a Leica ultramicrotome (red green stereo)

Bioluminescence (simulation of gonyaulax in the summer at Woods Hole) - in stereo!

Holiday greetings (snow)