Doctoral Dissertations

Date of Award


Degree Type


Degree Name

Doctor of Philosophy


Computer Engineering

Major Professor

Gregory D. Peterson, Chris D. Cox

Committee Members

Seddik M. Djouadi, Donald W. Bouldin, Michael L. Simpson


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.

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