Research On The Bio-system Simulations Based On P System Framework

Systems Biology is a kind of new method for biology research,this method emphasis to study biology in a system level.The former molecular biology is working on the microview level,on the other hand,Systems Biology treat the biology items as a whole system. Systems Biology has became the mainstream of research method.Modeling and simulation is one of the key problems in the Systems Biology research,also,it is one of the important and effective tools.A capable modeling and simulation tool could not only describe the biology system clearly and efficiently,but also simulate the system precisely and quickly. So it is quite important in Systems Biology research.The main works of this dissertation are as follow:(1) Presented an optimized algorithm to get step time parameter T.Using the T,the simulation could process at the highest speed without error.The step time parameter T plays an essential role in the precise control of Tau Leaping simulation method.This dissertation discussed T calculation method under the control of changes in reactor content,presented a optimized algorithm to get step time parameter T. Compared with the former way,the optimized method increased the computation complexity, meanwhile,improved the simulation accuracy.If the contents of reactors are vary from others,the improvement of the algorithm is more extraordinary.(2) Combined the P systems modeling framework and stochastic simulation algorithm, proposed the multi-apartment stochastic simulation algorithm.Added the Tau Leaping control rules in the algorithm process,making the algorithm more precise.For the real biology system,chemical reactions happen in multi-apartment.The former simulation method could not simulated the non-uniformity system.The new method,which Combined the P systems modeling framework and stochastic simulation algorithm,could simulated the multi-apartment systems.The new algorithm provided a serial process to solve the two main problems,which are the control of algorithm process and the communication among simulations of multi-apartment.More than that,the algorithm added the Tau Leaping control rule,improved the precision of the simulation.Using the example of Quorum Sensing in Vibrio Fascheri simulation,the dissertation showed that P systems based Tau Leaping method is capable for multi-apartment system simulation.