Title :
Solving molecular distance geometry problems in OpenCL
Author :
Istvân Lőrentz;Răzvan Andonie;Levente Fabry-Asztalos
Author_Institution :
Electronics and Computers Department, Transilvania University, Braş
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.
Keywords :
"Complexity theory","Vectors","Geometry","Proteins","Equations","Computers"
Conference_Titel :
Optimization of Electrical and Electronic Equipment (OPTIM), 2012 13th International Conference on
Print_ISBN :
978-1-4673-1650-7
DOI :
10.1109/OPTIM.2012.6231916