Defense Date

2011

Document Type

Thesis

Degree Name

Master of Science

Department

Engineering

First Advisor

James McCollum

Abstract

The finite state projection algorithm provides modelers a new way of directly solving the chemical master equation. The algorithm utilizes the matrix exponential function, and so the algorithm’s performance suffers when it is applied to large problems. Other work has been done to reduce the size of the exponentiation through mathematical simplifications, but efficiently exponentiating a large matrix has not been explored. This work explores implementing the finite state projection algorithm on several different high-performance computing platforms as a means of efficiently calculating the matrix exponential function for large systems. This work finds that general purpose graphics processing can accelerate the finite state projection algorithm by several orders of magnitude. Specific biological models and modeling techniques are discussed as a demonstration of the algorithm implemented on a general purpose graphics processor. The results of this work show that general purpose graphics processing will be a key factor in modeling more complex biological systems.

Rights

© The Author

Is Part Of

VCU University Archives

Is Part Of

VCU Theses and Dissertations

Date of Submission

April 2011

Included in

Engineering Commons

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