Large scale simulation of protein mechanics and function.

The biomedical sciences are enjoying a wealth of data from innovative new techniques in structure determination, DNA sequencing at the level of entire genomes, and direct manipulation and observation of single molecules. Computational biologists seek to extend and refine these experimental advances through atomic level modeling, often in direct collaboration with experimental researchers. Systems that capture the interest of experimental and computational biologists today are membrane channels, bioenergetic proteins like ATPase, or the machinery of the expression system like the ribosome, all of which should be simulated in realistic environments. Combining expertise from the physical, computational and life sciences, computational biologists have developed for this purpose modeling tools for biomolecular systems of 100,000 atoms and more. They have also advanced mathematical modeling using stochastic and non-equilibrium statistical mechanical methods to bridge the still huge gap between simulation (10 ns) and physiological times (1 ms). This article demonstrates some of the progress achieved so far and the discoveries made.