Simulating the Interactions of Genes, Proteins, and Metabolities in Cell-Like Entities

摘要

The goal of this project was to create software to model Cell-Like Entities, and to perform initial simulations. A software package was written in Matlab that performs stochastic simulations using a Gillespie-based algorithm of biomolecular networks. Biochemical processes that can be modeled include binding, unbinding, transcription, translation, Michaelis-Menten, and n-th order processes. Models and parameters are defined using several text files. The software package was designed to enable simple porting to high-performance computing platforms. A model to simulate a prototype CLE that responds to an external chemical with production of a particular protein was developed. This detection CLE was further analyzed to quantify the level of stochastic fluctuations over multiple runs, and to determine a combination of input parameters that optimized the detection task.