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

Volume

5

fYear

1995

fDate

3-6 Jan 1995

Firstpage

123

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;

fLanguage

English

Publisher

ieee

Conference_Titel

System Sciences, 1995. Proceedings of the Twenty-Eighth Hawaii International Conference on

Conference_Location

Wailea, HI

Print_ISBN

0-8186-6930-6

Type

conf

DOI

10.1109/HICSS.1995.375344

Filename

375344