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Efficient molecular dynamics simulat...

Cho, Eunjung.

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Efficient molecular dynamics simulation on reconfigurable models with multigrid method.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Efficient molecular dynamics simulation on reconfigurable models with multigrid method./
Author:	Cho, Eunjung.
Description:	117 p.
Notes:	Source: Dissertation Abstracts International, Volume: 69-04, Section: B, page: 2410.
Contained By:	Dissertation Abstracts International69-04B.
Subject:	Computer Science. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3308460
ISBN:	9780549564201

Efficient molecular dynamics simulation on reconfigurable models with multigrid method.
Cho, Eunjung.

Efficient molecular dynamics simulation on reconfigurable models with multigrid method. - 117 p.

Source: Dissertation Abstracts International, Volume: 69-04, Section: B, page: 2410.

Thesis (Ph.D.)--Georgia State University, 2008.

In the field of biology, MD simulations are continuously used to investigate biological studies. A Molecular Dynamics (MD) system is defined by the position and momentum of particles and their interactions. The dynamics of a system can be evaluated by an N-body problem and the simulation is continued until the energy reaches equilibrium. Thus, solving the dynamics numerically and evaluating the interaction is computationally expensive even for a small number of particles in the system. We are focusing on long-ranged interactions, since the calculation time is O(N2) for an N particle system.

ISBN: 9780549564201Subjects--Topical Terms:

626642
Computer Science.

Efficient molecular dynamics simulation on reconfigurable models with multigrid method.
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020 $a 9780549564201
035 $a (MiAaPQ)AAI3308460
035 $a AAI3308460
040 $a MiAaPQ $c MiAaPQ
100 1 $a Cho, Eunjung. $3 2100975
245 1 0 $a Efficient molecular dynamics simulation on reconfigurable models with multigrid method.
300 $a 117 p.
500 $a Source: Dissertation Abstracts International, Volume: 69-04, Section: B, page: 2410.
500 $a Adviser: Anu G. Bourgeois.
502 $a Thesis (Ph.D.)--Georgia State University, 2008.
520 $a In the field of biology, MD simulations are continuously used to investigate biological studies. A Molecular Dynamics (MD) system is defined by the position and momentum of particles and their interactions. The dynamics of a system can be evaluated by an N-body problem and the simulation is continued until the energy reaches equilibrium. Thus, solving the dynamics numerically and evaluating the interaction is computationally expensive even for a small number of particles in the system. We are focusing on long-ranged interactions, since the calculation time is O(N2) for an N particle system.
520 $a In this dissertation, we are proposing two research directions for the MD simulation. First, we design a new variation of Multigrid (MG) algorithm called Multi-level charge assignment (MCA) that requires O(N) time for accurate and efficient calculation of the electrostatic forces. We apply MCA and back interpolation based on the structure of molecules to enhance the accuracy of the simulation. Our second research utilizes reconfigurable models to achieve fast calculation time. We have been working on exploiting two reconfigurable models. We design FPGA-based MD simulator implementing MCA method for Xilinx Virtex-IV. It performs about 10 to 100 times faster than software implementation depending on the simulation accuracy desired. We also design fast and scalable Reconfigurable mesh (R-Mesh) algorithms for MD simulations. This work demonstrates that the large scale biological studies can be simulated in close to real time. The R-Mesh algorithms we design highlight the feasibility of these models to evaluate potentials with faster calculation times. Specifically, we develop R-Mesh algorithms for both Direct method and Multigrid method. The Direct method evaluates exact potentials and forces, but requires O(N2) calculation time for evaluating electrostatic forces on a general purpose processor. The MG method adopts an interpolation technique to reduce calculation time to O(N) for a given accuracy. However, our R-Mesh algorithms require only O( N) or O(logN) time complexity for the Direct method on N linear R-Mesh and Nx N R-Mesh, respectively and O(r)+O(logM) time complexity for the Multigrid method on an Xx YxZ R-Mesh. r is N/M and M = XxYx Z is the number of finest grid points.
520 $a Index words. Molecular Dynamics Simulation, Multigrid, Reconfigurable Model, Reconfigurable Mesh Algorithm, FPGA.
590 $a School code: 0079.
650 4 $a Computer Science. $3 626642
650 4 $a Biology, Bioinformatics. $3 1018415
690 $a 0984
690 $a 0715
710 2 $a Georgia State University. $3 1018518
773 0 $t Dissertation Abstracts International $g 69-04B.
790 $a 0079
791 $a Ph.D.
792 $a 2008
793 $a English
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3308460