Simulation and Implementation of Gene Expression Regulation in E-Cell Model Analog-Cell

As one of the most important research fields of artificial life (ALife), electronic cell (E-cell) model is to explore new biological phenomena and rules in silico. The analog-cell, which is the first pattern E-cell model in China, could be used to graphically simulate the processes of gene expression of eukaryote cell in molecule level, including transcription, translation and gene mutation. In order to simulate gene expression more lively and more accurately, plenty of important regulation factors and enzymes for gene expression regulation are added into the extended analog-cell. Algorithms of the reaction mechanisms and the processes in the phases of transcription, mRNA processing and translation are also designed and implemented with the state controlling mechanism, such as DNA unwinding, mRNA capping, aminoacylation, translation initiation and translation termination. Under the mechanism of state controlling, each reactant in the analog-cell has different state values in different states, and the state control of the reaction is performed by the shift of the state value of relevant reactants. The mechanism can keep the materials and energy metabolism highly strict and orderly. Simulated results are shown in some instances graphically, and indicate that the designed algorithms are consistent with the rules of biology and the analog-cell is able to simulate gene expression regulation graphically and effectively. The advantages on the analog-cell and the outlooks are also discussed.