Research On Stochastic Diffusion Method And Design Of Cellmatlab Simulation System

Bioinformatics has been developed fast nowadays. Researchers focus on dealing and analyzing of local data from the experiments previously. As the increase of the local data, people transfer focus to a higher level. They want to research and analyze the biology in a systematic view. This leads to the necessary of the software with the functions to model and simulate biology processes in a system view.Firstly, to represent the complex and hard-analyzed biology processes intuitively and conveniently in silicon, and to provide right models to different simulation methods; both are the research topics in this paper. In most biology processes, there are many repeated simple reaction mechanics and multi-timescale reactions. According to these features, this paper promotes using the encapsulation and independence of object to modify Hybrid Functional Petri Net, promotes and defines Orient Object Hybrid Functional Petri Net in representation of biology process. This paper also defines the relative rules of OOHFPN.Secondly, to simulate and analyze the biology process thoroughly and effectively is another topic this paper discusses. After analysis, we find stochasticity generally exists in biology processes. On the other hand, to diffusion-influenced system, the spatial information about the substance is also important. So this paper adds the stochastic diffusion simulation method to our CellMatlab software. The method is based on Smoluchowski model, to view the change in a molecular level, and transforms the reaction rate into binding radius; it leads to the focus on molecular diffusion. The method in paper is the modification to Smoldyn; it uses the time step selection to control the molecular diffusion and the reaction accuracy, and avoids the problems in Smoldyn.OOHFPN with the function of modeling kinds of biology process intuitively, cooperates with the multi methods perfectly , including determinate method, stochastic method and stochastic diffusion method. The two parts make of our software CellMatlab. This paper uses the Model-View -Control pattern to design and realize the graphic editor for user, and we use XML (Extensible Markup Language) to save the model and let it readable .For communication with other software, we provide the conversion between OOHFPN and SBML. At last, we use the stochastic diffusion method simulating the ligand and receptors binding process in the cell membranes of Escherichia coli, to analyze the influence of diffusion and location of molecules in biology process. It argues the importance of the diffusion in simulating methods.