title: Efficient SDH Computation In Molecular Simulations Data.
abstract: Analysis of large particle or molecular simulation data is integral part of the basic-science research community. It often involves computing functions such as point-to-point interactions of particles. Spatial distance histogram (SDH) is one such vital computation in scientific discovery. SDH is frequently used to compute Radial Distribution Function (RDF), and it takes quadratic time to compute using naive approach. Naive SDH computation is even more expensive as it is computed continuously over certain period of time to analyze simulation systems. Tree-based SDH computation is a popular approach. In this paper we look at different tree-based SDH computation techniques and briefly discuss about their performance. We present different strategies to improve the performance of these techniques. Specifically, we study thedensity map(DM) based SDH computation techniques. A DM is essentially a grid dividing simulated space into cells (3D cubes) of equal size (volume), which can be easily implemented by augmenting a Quad-tree (or Oct-tree) index. DMs are used in various configurations to compute SDH continuously over snapshots of the simulation system. The performance improvements using some of these configurations is presented in this paper. We also present the effect of utilizing computation power of Graphics Processing Units (GPUs) in computing SDH.
authors.affiliation: Department of Computer Science and Engineering, University of South Florida, Tampa, Florida - 33620 ytu@cse.usf.edu.
authors.forename: Yi-Cheng
authors.initials: YC
authors.lastname: Tu
authors.affiliation: Department of Mathematics, Wuhan University of Technology, 122 Luosi Road, Wuhan, Hubei, 430070, P. R. China chensp@whut.edu.cn.
authors.forename: Shaoping
authors.initials: S
authors.lastname: Chen
authors.affiliation: Department of Physic, University of South Florida, Tampa, Florida - 33620 pandit@cas.usf.edu.
authors.forename: Sagar
authors.initials: S
authors.lastname: Pandit
authors.affiliation: Department of Computer Science and Engineering, University of South Florida, Tampa, Florida - 33620 akumar8@cse.usf.edu.
authors.forename: Anand
authors.initials: A
authors.lastname: Kumar
authors.affiliation: Department of Computer Science and Engineering, University of South Florida, Tampa, Florida - 33620 vgrupcev@cse.usf.edu.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Grupcev
keywords: Molecular Simulation; Protein Structure; Radial Distribution Function; Spatial Distance Histogram; Structural Biology