Computer Science ETDs

Author

Mark Fleharty

Publication Date

7-1-2010

Abstract

Dendrimers are branched molecules that often have chemical properties similar to proteins and other large organic molecules. Dendrimers presently have applications as reactive surfaces for catalysis, and as hosts for drug delivery. Computer simulations of dendritic molecules are difficult due to their relatively large size and the tendency of atoms within a dendrimer to come within very close proximity to each other. The large number of steric interactions makes modeling of dendrimers difficult due to unphysically high energies that arise when a modeler attempts to construct a starting dendrimer from which to minimize its energy. Here we present Dendmol, a code that uses rigid body mechanics and a Monte Carlo method to set up the initial conditions for a dendrimer and present our findings. We found that this method is able to rapidly find conformations of dendrimers that can be readily placed into molecular mechanics, and molecular dynamics codes for further study of the dendrimer.

Language

English

Keywords

dendrimer, optimization, monte carlo, dendmol

Document Type

Thesis

Degree Name

Computer Science

Level of Degree

Masters

Department Name

Department of Computer Science

First Advisor

Luan, Shuang

First Committee Member (Chair)

Evans, Deborah

Second Committee Member

Stefanovic, Darko

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