Self-assembly systems play crucial roles in a broad range of critical biological processes. Investigation of such systems is impeded by the innate stochastic noise of the systems and current experimental limitations. Understanding of such systems, especially complex virus capsid self-assembly systems, is essential for us to build predictive models of cellular function, find novel treatments for many human diseases and build novel nano-machines. Quantitative modeling of virus capsid self-assembly kinetics provides a valuable adjunct to experimental work in understanding self-assembly by allowing us to perform model-assisted interpretation of assembly systems too complex for detailed experimental dissection and to extrapolate results from in vitro experimental conditions to the cellular environment. However, many such computational methods have difficulty in achieving high efficiency and accuracy at the same time.
This thesis develops an efficient computational tool using a local rules model, a stochastic queue-based discrete-event simulation algorithm and the Java language to allow the investigation of virus capsid self-assembly kinetics. The simulation program is then used to study (1) the contribution of oligomer/oligomer binding to capsid assembly kinetics, (2) the scaling effects on virus capsid-like self-assembly, and (3) the parameter space of complex self-assembly.
|School:||Carnegie Mellon University|
|School Location:||United States -- Pennsylvania|
|Source:||DAI-B 68/12, Dissertation Abstracts International|
|Subjects:||Bioinformatics, Virology, Computer science|
|Keywords:||Assembly kinetics, Capsid self-assembly, Discrete-event simulation, Gillespie model, Stochastic simulation, Virology|
Copyright in each Dissertation and Thesis is retained by the author. All Rights Reserved
The supplemental file or files you are about to download were provided to ProQuest by the author as part of a
dissertation or thesis. The supplemental files are provided "AS IS" without warranty. ProQuest is not responsible for the
content, format or impact on the supplemental file(s) on our system. in some cases, the file type may be unknown or
may be a .exe file. We recommend caution as you open such files.
Copyright of the original materials contained in the supplemental file is retained by the author and your access to the
supplemental files is subject to the ProQuest Terms and Conditions of use.
Depending on the size of the file(s) you are downloading, the system may take some time to download them. Please be