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
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
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!
