Handling External Events Efficiently in Gillespie's Stochastic Simulation Algorithm

Gillespie's Stochastic Simulation Algorithm (SSA) provides an elegant simulation approach for simulating models composed of coupled chemical reactions. Although this approach can be used to describe a wide variety biological, chemical, and ecological systems, often systems have external behaviors that are difficult or impossible to characterize using chemical reactions alone. This work extends the applicability of the SSA by adding mechanisms for the inclusion of external events and external triggers. We define events as changes that occur in the system at a specified time while triggers are defined as changes that occur to the system when a particular condition is fulfilled. We further extend the SSA with the efficient implementation of these model parameters. This work allows numerous systems that would have previously been impossible or impractical to model using the SSA to take advantage of this powerful simulation technique.

Name thesis:degree_name

Master of Science

Level thesis:degree_level

Thesis

Discipline thesis:degree_discipline

Engineering

Year dc:date.available

2010

Author dc:creator

• Geltz, Brad

Contributors dc:contributor

• James McCollum

• Stochastic simulation
• Modeling biochemical systems
• Gillespie algorithm
• Systems biology
• Efficient event handling
• Engineering

Statement dc:rights

• © The Author

Identifier

https://scholarscompass.vcu.edu/etd/168

OAI identifier oai:identifier

oai:scholarscompass.vcu.edu:etd-1167