Multi-scale Behavior in Chemical Reaction Systems: Modeling, Applications, and Results

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dc.contributor.authorTurner, Jesse Hosea IIIen_US
dc.date.accessioned2018-06-19T17:13:02Zen_US
dc.date.available2018-06-19T17:13:02Zen_US
dc.date.issued2008-08en_US
dc.date.noteAugust 2008en_US
dc.descriptionThis work was also published as a Rice University thesis/dissertation: http://hdl.handle.net/1911/22206en_US
dc.description.abstractFour major approaches model the time dependent behavior of chemical reaction systems: ordinary differential equations (ODE's), the tau-leap algorithm, stochastic differential equations (SDE's), and Gillespie's stochastic simulation algorithm (SSA). ODE's are simulated the most quickly of these, but are often inaccurate for systems with slow rates and molecular species present in small numbers. Under ideal conditions, the SSA is exact, but computationally inefficient. Unfortunately, many reaction systems exhibit characteristics not well captured individually by any of these methods. Therefore, hybrid models incorporating aspects from all four must be employed. The aim is to construct an approach that is close in accuracy to the SSA, useful for a wide range of reaction system examples, and computationally efficient. The Adaptive Multi-scale Simulation Algorithm (AMSA) uses the SSA for slow reactions, SDE's for medium-speed reactions, ODE's for fast reactions, and the tau-leap algorithm for non-slow reactions involving species small in number. This article introduces AMSA and applies it to examples of reaction systems involving genetic regulation. A thorough review of existing reaction simulation algorithms is included. The computational performance and accuracy of AMSA's molecular distributions are compared to those of the SSA, which is used as the golden standard of accuracy. The use of supercomputers can generate much larger data sets than serial processors in roughly the same amount of computational time. Therefore, multi-processor machines are also employed to assess the accuracy of AMSA simulations.en_US
dc.format.extent143 ppen_US
dc.identifier.citationTurner, Jesse Hosea III. "Multi-scale Behavior in Chemical Reaction Systems: Modeling, Applications, and Results." (2008) <a href="https://hdl.handle.net/1911/102095">https://hdl.handle.net/1911/102095</a>.en_US
dc.identifier.urihttps://hdl.handle.net/1911/102095en_US
dc.language.isoengen_US
dc.titleMulti-scale Behavior in Chemical Reaction Systems: Modeling, Applications, and Resultsen_US
dc.typeTechnical reporten_US
dc.type.dcmiTexten_US
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