Title page for ETD etd-05082009-031719


Type of Document Master's Thesis
Author Liu, Zhen
Author's Email Address zhenliu@vt.edu
URN etd-05082009-031719
Title Stochastic Simulation Methods for Solving Systems with Multi-State Species
Degree Master of Science
Department Computer Science
Advisory Committee
Advisor Name Title
Cao, Yang Committee Chair
Murali, T. M. Committee Member
Sandu, Adrian Committee Member
Keywords
  • StochSim
  • rule-based modeling
  • multi-state
  • SSA
  • hybrid method
Date of Defense 2009-05-06
Availability unrestricted
Abstract
Gillespie's stochastic simulation algorithm (SSA) has been a conventional method for stochastic modeling and simulation of biochemical systems. However, its population-based scheme faces the challenge from multi-state situations in many biochemical models. To tackle this problem, Morton-Firth and Bray's stochastic simulator (StochSim) was proposed with a particle-based scheme. The thesis first provides a detailed comparison between these two methods, and then proposes improvements on StochSim and a hybrid method to combine the advantages of the two methods. Analysis and numerical experiment results demonstrate that the hybrid method exhibits extraordinary performance for systems with both the multi-state feature and a high total population.

In order to deal with the combinatorial complexity caused by the multi-state situation, the rules-based modeling was proposed by Hlavacek's group and the particle-based Network-Free Algorithm (NFA) has been used for its simulation. In this thesis, we improve the NFA so that it has both the population-based and particle-based features. We also propose a population-based method for simulation of the rule-based models.

The bacterial chemotaxis model has served as a good biological example involving multi-state species. We implemented different simulation methods on this model. Then we constructed a graphical interface and compared the behaviors of the bacterium under different mechanisms, including simplified mathematical models and chemically reacting networks which are simulated stochastically.

Files
  Filename       Size       Approximate Download Time (Hours:Minutes:Seconds) 
 
 28.8 Modem   56K Modem   ISDN (64 Kb)   ISDN (128 Kb)   Higher-speed Access 
  etd.pdf 846.14 Kb 00:03:55 00:02:00 00:01:45 00:00:52 00:00:04

Browse All Available ETDs by ( Author | Department )

dla home
etds imagebase journals news ereserve special collections
virgnia tech home contact dla university libraries

If you have questions or technical problems, please Contact DLA.