Doctoral Dissertations
Date of Award
8-2006
Degree Type
Dissertation
Degree Name
Doctor of Philosophy
Major
Computer Engineering
Major Professor
Gregory D. Peterson, Chris D. Cox
Committee Members
Seddik M. Djouadi, Donald W. Bouldin, Michael L. Simpson
Abstract
The ability to accurately and efficiently simulate computer models of biochemical systems is of growing importance to the molecular biology and pharmaceutical research communities. Exact stochastic simulation is a popular approach for simulating such systems because it properly represents genetic noise and it accurately represents systems with small populations of chemical species. Unfortunately, the computational demands of exact stochastic simulation often limit its applicability. To enable next-generation whole-cell and multi-cell stochastic modeling, advanced tools and techniques must be developed to increase simulation efficiency. This work assesses the applicability of a variety of hardware and software acceleration approaches for exact stochastic simulation including serial algorithm improvements, parallel computing, reconfigurable computing, and cluster computing. Through this analysis, improved simulation techniques for biological systems are explored and evaluated.
Recommended Citation
McCollum, James Michael, "Accelerating Exact Stochastic Simulation of Biochemical Systems. " PhD diss., University of Tennessee, 2006.
https://trace.tennessee.edu/utk_graddiss/1829