A special purpose array processor architecture for the molecular dynamics simulation of point-mutated proteins

• Authors: Karl-Heinz Zimmermann
• Venue: Journal of VLSI Signal Processing Systems - Special issue on signal processing and neural networks for bioinformatics
• Year: 2003

Point mutation of amino acids is a means used by biotechnologists to improve the performance of proteins. To study a point-mutated polypeptide, one requires its global minimum energy conformation. This conformation can be determined by molecular dynamics via Langevin's equations of motion. Molecular dynamics simulations belong to the most difficult problems to parallelize in a scalable manner. We provide a method for defining a special purpose 3D array processor architecture for the molecular dynamics simulation of point-mutated polypeptides. The architecture is derived from a spatial decomposition of a known conformation of the point-mutated polypeptide or the native conformation of the given protein. By using an approximation scheme for the deterministic forces, the interprocessor communication can be kept local. The architecture affords a simple distributed load balancer and is scalable. The computational workload of the array processor architecture to perform molecular dynamics simulations under realistic conditions is addressed. An example architecture is given by point-mutated penicillin amidase.