Title :
A parallel algorithm for calculating the potential energy in DNA
Author :
Conery, John S. ; Peticolas, Warner L. ; Rush, Thomas, III ; Shanmugam, Kesavan ; Dominguez, Jost
Author_Institution :
Dept. of Comput. & Inf. Sci., Oregon Univ., Eugene, OR, USA
Abstract :
The Dreiding force field is a seven-term equation that describes the potential energy in a molecule as a function of the relative positions of bonded atoms and electrostatic interactions between atoms that do not share a bond. For large molecules such as DNA, with several thousand atoms, the O(n2) nonbonded terms can require a significant amount of computation. We present a data-parallel algorithm that takes time O(n) on n processors. We compare the execution time of our algorithm on a MasPar MP-I with an efficient sequential program running on an SGI workstation
Keywords :
DNA; bioelectric phenomena; biology computing; molecular biophysics; parallel algorithms; DNA; Dreiding force field; MasPar MP-I; SGI workstation; bonded atoms; data-parallel algorithm; deoxyribonucleic acid; electrostatic interactions; execution time; long polymeric structure; molecule; nonbonded terms; parallel algorithm; potential energy; sequential program; seven-term equation; Bonding forces; Chemistry; DNA computing; Equations; Information science; Nuclear magnetic resonance; Parallel algorithms; Potential energy; Raman scattering; Spectroscopy;
Conference_Titel :
System Sciences, 1995. Proceedings of the Twenty-Eighth Hawaii International Conference on
Conference_Location :
Wailea, HI
Print_ISBN :
0-8186-6930-6
DOI :
10.1109/HICSS.1995.375344
