DOI
https://doi.org/10.25772/Z2F8-6156
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