Title

Solving molecular distance geometry problems in OpenCL

Document Type

Conference Proceeding

Department or Administrative Unit

Computer Science

Publication Date

5-24-2012

Abstract

We focus on the following computational chemistry problem: Given a subset of the exact distances between atoms, reconstruct the three-dimensional position of each atom in the given molecule. The distance matrix is generally sparse. This problem is both important and challenging. Our contribution is a novel combination of two known techniques (parallel breadth-first search and geometric buildup) and its OpenCL parallel implementation. The approach has the potential to speed up computation of three-dimensional structures of molecules - a critical process in computational chemistry. From experiments on multi-core CPUs and graphic processing units, we conclude that, for sufficient large problems, our implementation shows a moderate scalability.

Comments

This article was originally published in 2012 13th International Conference on Optimization of Electrical and Electronic Equipment (OPTIM). The full-text article from the publisher can be found here.

Due to copyright restrictions, this article is not available for free download from ScholarWorks @ CWU.

Journal

2012 13th International Conference on Optimization of Electrical and Electronic Equipment (OPTIM)

Rights

Copyright © 2012, IEEE

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