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Flash animations
These animations were written in Flash 8 with actionscipt 2.0 and require a recent flash player. If the animations don't work in your browser and you would like to see them, please install the most recent flash player on your computer.
Microtubule dynamic instability - This shows
slow growth and rapid depolymerization of the plus end, as well as microtubule
release and depolymerization from the minus end. Things to try: during mitosis,
the catastrophe frequency increases, resulting in shorter, more dynamic microtubules.
You can see this by changing the catastrophe frequency from 0.042 to 0.15 for
instance (you can change the parameters while the animation is running). Another
microtubule phenomenon is treadmilling. You can see this by changing the "minus
end depolym"
rate from 0.8 to 0.12 (the same as the growth rate). References for parameters:
PNAS 94: 5078, J Cell Biol 162: 963.
-- Programming limitation:
once the microtubule is released, a new microtubule in its place can be nucleated.
However, that new microtubule can't be released until the previously released
microtubule has disappeared.
-- Two
of them! In this case, microtubules are captured by the chromosomes, and
when all the chromosomes are connected, the chromosomes move towards the poles,
then the poles move apart, then the microtubule dynamics goes to interphase
values.
-- Under construction: pauses during microtubule growth (e.g. J
Cell Biol 145:
993); first attempt at tip
complexes.
Version with variable
length scale
Vesicle binding and movement on microtubules - This is something like the fish melanophore. The blue vesicles (pigment granules) move randomly until they "hit" a microtubule. They move first in the outward (+) direction. They can fall off either spontaneously or when they reach the end of the microtubule. The default spontaneous rate of fall off ("fall off parameter") is 0.1, meaning that for every time step, there is a 10% chance that they will fall off. You can change this number during the animation. Once the vesicle falls off, it moves randomly until it hits another microtubule. Then it will move in the inward (-) direction, until it spontaneously falls off or reaches a certain set distance from the center. The vesicles continue to alternate directions after they fall off and re-bind. In the fish melanophore, the cAMP level determines the distribution of the pigment granules. By pressing the up or down arrows, you can switch the cell between the high and low cAMP states. Another version - no minus end directed movement in the high cAMP state.
Chemotaxis - bacteria travel in a straight line, tumble to sample the environment, then set off in a new direction that is towards the food gradient. In this animation, bacteria move towards mouse cursor or can be switched to move away from the cursor. The "tumble frequency" is how often the bacteria stop moving in a line in order to check which direction to move in - 0.15 means that there's a 15% chance every time step that they will tumble. If the tumble frequency is 1.0, they won't ever move. The "decision frequency" is just how long they tumble. 0.3 means that there is a 30% chance that they will make their decision for every time step. If it is 0, they will never come out the tumble stage, and if it is 1, they will decide but won't tumble at all. The "bias" has to do with what variation they move towards the mouse. If the bias is 0, the bacteria will move directly towards the mouse. When it is at 180, they will move in a random direction ± 90° to the left or right of the mouse. When it is at 360, they won't have any net movement towards the mouse at all.
Cdc2 activation (from Slepchenko, B.M., and Terasaki, M. 2003. Cyclin aggregation and robustness of bio-switching. Mol. Biol. Cell 14: 4695-4706)
Membrane traffic - From Heinrich, R., and Rapoport, T.A. Generation of nonidentical compartments in vesicular transport systems. J. Cell Biol. 168: 271-280 (2005).
Nuclear transport - from Smith, A.E., Slepchenko, B.M., Schaff, J.C., Loew, L.M., and Macara, I.G. Systems analysis of Ran transport. Science 295: 488-491 (2002). Steady state system -- It should take around 5-10 seconds to display the first time point. The simulation comes to steady state after ~100 seconds. You can get data points by pausing the animation, putting cursor in a text box, select all, copy and paste into Excel or similar.
Collisions - 40 balls, one of them green, collide against walls and each other (current flash player in March 2007 can't handle much more than 40 at a time). Collisions between balls makes them red, until they hit the wall and turn black - 10 balls - 40 balls. Each ball collision makes the two balls slightly more green. (the physics of collision paths is not quite perfect, but it is close).
Image formation by a lens -- Image
formation by the eye
Snell's law
Total internal reflection - this shows light going
from glass to water, as in a microscope. The two cases of the electric field
perpendicular to the plane of incidence and parallel to the plane of incidence
are shown. The intensities were calculated according to the Fresnel equations.
The brightness of the light rays for the two polarization directions can be
toggled with the up and down arrow keys. Total internal reflection is at angles
greater than 63. Note also the Brewster angle at 42, where the reflected light
is all perpendicular. Reflection and transmission intensities for air
to glass - air to water
Dispersion (not that great, it only shows red and
blue because more colors overlap too much) --
wave fronts and refraction - how to explain Snell's
law
wavelets and refraction - another way to explain
Snell's law, using Huygens wavelets
The Principle of Least Time (first attempt) - running
vs swimming
Constructive / destructive interference
Phase delay
Transmission through a polarizer
Elliptical polarization
Differential interference contrast (DIC) -
preliminary version - move the specimen and change the bias.
Spectrum
Poisson process
Gaussian process
Random walk with statistics - random angle movement - up
down left or right - up down random but always
left or right on alternating rows
Continuous random walk - up down left or right - up
down random, randomized rows are single direction (resulting in "super-diffusive
motion)
Centrioles during meiosis (from a journal club on Shirato, Tamura, Yoneda, and Nemoto, Development 133: 343 (2006).
Quantitative microinjection method
How to write a random walk program in Flash
Source files - microtubule dynamics - vesicles on microtubules - chemotaxis - snare - collisions