Lambda Repressor Protein
This image is from an animation of the lambda repressor protein simulated in water by William Swope and Jed Pitera at IBM. I used Maya to render the frames. You can watch the clip here. I worked with this data while working on the documentary entitled "Exploring Time." The animation was meant to demonstrate the way that visualization methods shed light on the behavior of molecules at timescales imperceptible to the human eye.
This image is from a paper entitled: "Reciprocal Linkage between Self-organizing Processes is Sufï¬cient for Self-reproduction and Evolvability" published by MIT Press in 2006, authored primarily by anthropologist Terrence Deacon. It includes several still images from an animation I worked on about the formation of the Autocell. I worked with Professer Deacon and Greg Niemeyer, among others at UC Berkeley, to visualize a theory about the origin of natural selection on pre-cellular Earth. The basic idea behind the project was that "autocatalysis" is a form of natural selection. Autocatalysis refers to the following scenario: a hypothetical molecule A catalyzes the formation of another molecule B from whatever raw constituents are available, and B catalyzes A from the same raw constituents. So, if A and B form an autocatalytic cycle, they will likely appear more frequently than molecule C, who forms only under certain rare circumstances. If A and B happen to self-assemble into a shell or barrier, this barrier may further select for the formation of A and B. The shell or "autocell" may even carry A and B into new environments and help spread the system. This theory is corroborated by various natural phenomena, including autocell sized pits in Martian meteors.
These animations, produced with George Oster of UC Berkeley, try to show the sequence of chemical interactions that result in the rotation of the F0 protein complex of the protein ATP Synthase , which in turn provides the mechanical energy required to synthesize ATP. Almost all life stores energy as Adenosine Tri-Phosphate, or ATP. The F0,F1 rotary complex or ATP-synthase, sits in the mitochondrial membrane, as shown on top. To the left is an illustration of the sequence of reactions above the motor, in the F1 portion, showing the interaction between the asymmetrical "axle" and the alpha/beta hexamer. The purple molecules are ATP. See more animations of this process here.
Polymerase Chain Reaction
Above is a short clip depicting Polymerase Chain Reaction- a series of chemical reactions designed to selectively replicate a segment of DNA by powers of two. download the M.E.L. scripts I used to make this animation:
Here are the steps (illustrated below): 1. DNA denatured by heating to 95 C. 2. Cool the solution to 68 C. Single strand nucleotide sequences flanking the segment of interest (primers) anneal to the parent strands. 3. Heat the solution to 72 C, and the enzyme DNA Polymerase catalyzes synthesis of daughter strands (the first generation daughter strands stretch too far; they go to the end of the parent strands. 4. denature the DNA again by heating to 95 C. 5. cool the solution to 68 C again, and complimentary primers anneal to the first generation daughter strands ( DNA is directional, so the primers run in opposite directions). 6. heat the DNA to 72 C and the desired segment is isolated four fold. Repeat 3-6 to get desired amount.
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