Document Type
Thesis - Open Access
Award Date
2008
Degree Name
Master of Science (MS)
Department / School
Mechanical Engineering
Abstract
An efficient working model for the computer simulation of motion behaviors associated with molecular dynamics is presented. This model has been developed through a seamless integration between computational molecular dynamics, multibody dynamics, mathematical numerics, and computer science. Thus an efficient and effective rigid molecular modeling technique and O(n) simulation procedure has been produced as result of the integration. As computer simulation of molecular dynamics emerges as an effective method for nano phenomenon analysis, an efficient means to perform these simulations would greatly ease any computational burdens that may be presented for a researcher. Traditional methods for molecular dynamics simulations rely on a computationally demanding method for forming and solving the system equations of motion. The methods that can be used to simulate a system with n degrees of freedom requires an Order n3 (O(n3)) number of calculations to produce and solve the systems equations of motion. This load can become extremely demanding as the degrees of freedom (n) increases; an example of this is a protein folding simulation which can include millions of bodies with as many as 6 degrees of freedom per body. Obviously, the heavy computational loads produced by a traditional O(n3) algorithm for such a scenario will overwhelm any powerful computer system. The method presented and developed in this thesis requires an O(n) number of operations to perform a typical simulation, instead of the traditional O(n3) burden normally encountered. This method can significantly decrease the load on the computing system when large multi-body molecular systems are presented.
Library of Congress Subject Headings
Molecular dynamics -- Computer simulation
Format
application/pdf
Number of Pages
125
Publisher
South Dakota State University
Recommended Citation
Ries, Andy, "An Efficient O(N) Algorithm for Computer Simulation of Rigid Body Molecular Dynamics" (2008). Electronic Theses and Dissertations. 1471.
https://openprairie.sdstate.edu/etd2/1471
