... in which we meet our hero for the first time.
Instead of nothingness broken only by void seasoned with sprinkles of empty, or my favorite quotation from my favorite philosopher, or pictures of my imaginary cat, I introduce to you my bread and butter: Molecules![*]
[*] Well, I could have used tin can openers. Or bunnies. They can dance, too. But molecules are more sciency, and that's what that page is about. If you insist on cute and fluffy, you can watch dancing bunnies here.
The dancing molecules are all from the Glycolysis and TCA pathways (converting yummy sugar to energy, which is kinda neat). Since these molecules are quite central in (hard)core metabolism, I see them quite often on my screen. This is what it looks like when I close my eyes some nights. See the pyruvate crowding the poor lactate? Notice how succinate always teams up with citrate against fumarate?
A variation of the boid algorithm I hacked up in Processing and put on the interwebs using processing.js. You might not see anything if your lousy browser is to uncool for HTML5 and too boring for the mighty <canvas>.
The animation is quite simple and controlled by only a couple of parameters. The molecules (boids) want to flock together with their neighbors (coherence), but when they get too close, they move away again (separation). Which molecules they regard as their neighbors is controlled with the radius - the smaller the radius, the smaller the groups they form. I added a little gravity drawing them to the center of the canvas. The interplay of these 3 basic tendencies (vectors) results in quite unpredictable and interesting behavior. You can play with the controls, the molecules won't mind. Only the initial state is slightly randomized (molecules are seeded with random speed vectors at the very beginning). The rest is completely deterministic. Try to predict some behavior and the response to changing parameters[*].
[*] This is what Systems Biology has to put up with all day long --- different components and their interactions producing complex behavior, capable of adaptation to varying environments and disturbances. This is interesting as well as "interesting", because, well, each tiny cell in itself is just too damn complicated, intricated, convoluted (and a whole lot of other words) to be easily predictable. For example, we try to find vectors that describe the fluxes of metabolites through the complex network of chemical reactions that make up a cell. Each describes a particular phenotype, some are stable on some levels (like the orbiting flocks in my initial parameter set), some are more interesting than others, and some are simply not viable (molecules shooting away into outer space).
There's a speed limit (Max Speed) and a minimum of gentleness is preserved (Max Force) (these basically cap the respective vectors), which is kind of cheating, but it keeps everything under control.
Pretty useless, isn't it? Have fun!
Parameter Control Console