Date of Award:

12-2011

Document Type:

Dissertation

Degree Name:

Doctor of Philosophy (PhD)

Department:

Computer Science

Committee Chair(s)

Bart C. Weimer (Co-Chair), Donald H. Cooley (Co-Chair)

Committee

Bart C. Weimer

Committee

Donald H. Cooley

Committee

Nicholas S. Flann

Committee

Gregory J. Podgorski

Committee

John R. Stevens

Abstract

The term "metabolism" refers to the chemical processes occurring in a living organism to convert the food consumed into the energy needed to maintain a living state. Metabolism consists of two states, namely, a dynamic state and a steady state. In the dynamic state, the rate of chemical conversion of a substance is proportional to the amount of substance available, whereas in the steady state this rate is constant and independent of the amount of substance present (Chapter 4 Figure 1). Like all other fields of engineering, metabolic engineering involves the analysis and synthesis of metabolism. Molecular biological tools for synthesis have advanced far ahead of the tools for analysis.

Bioinformatics is an inter-disciplinary field that applies computer science and information technology to biology. Bioinformatics has stepped in to bridge the gap between analysis and synthesis in metabolic engineering. There are several bioinformatics tools available to perform analysis of metabolism at steady state because in this state, the complex kinetics can be ignored due to the fact that the rate of a reaction is constant. However, studying metabolism at dynamic state gives more information about the processes and kinetics involved. Once the kinetics of a process is known, adjusting the parameters that will affect the rate of metabolite conversion becomes possible. Thus, a reaction can be modified to be faster or slower or be blocked based on the needs of the given situation in the process of metabolic engineering.

The focus of this doctoral research was on analysis of dynamic state metabolism. The goals were achieved by developing two software tools: 1) Metabolome Searcher and 2) DynaFlux. These two tools aid in filling the gap between the analysis and synthesis phases of metabolic engineering.

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Comments

Publication made available electronically December 21, 2011.

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