Analog-Cell: Gene Expression Simulation System Based On Concurrent Constraint

From the beginning of the 21st century, information, instead of material, has been becoming a brand new trend of view of science. After a long time study of the composition of material, researchers began to focus on the characteristic of information of the target system. Complex Adaptive Systems, or CAS for short, is a dynamic system which consist many interconnected components. As a new cross subject, CAS is a basic idea of artificial life.Artificial Life is the name given to a new discipline that studies "natural" life by attempting to recreate biological phenomena from scratch within computers and other "artificial" media. Artificial life sees natural life as complex system made up of many organic molecules each of which follows the laws of biochemistry. Artificial life aims at exploring unknown life patterns through what have already understood and constructing new forms of life.Electronic cell, also known as virtual cell, simulates natural cell contracture and kinetics of dynamic behavior of life on computers. Electronic cells often have friendly user interfaces so that they are more convenient for researchers to observe the cell and its environment. Most of the recent research is at the first phase of the development of electronic cell which had been divided into three stages as follow: construction, implementation and application.The precise modeling of biological systems is the footstone of electronic cell. Bertalanffy was the first scientist who uses calculus theory in modeling biological systems. Along with the development of mathematical science, engineering technology and life sciences, high-throughput experimental technique is now the main tool to obtain biological information with enormous data. Based on these data, many different kinds of models of biological systems have been built to quantitatively explain physical laws underlying natural life. Biological systems tend to be very complex. That makes implementation of the mathematical models using advanced programming language, such as C++, a painful task to accomplish. Concurrent constraint programming opened a door to a higher level of abstraction. It makes the model easier to understand. At the mean time, the efficiency of simulation of biological system has been improved. Concurrent constraint programming is a multi-agent concurrent computational model based on constraint system. Expansions of concurrent constraint programming include stochastic concurrent constraint programming, non-deterministic temporal concurrent constraint, hybrid concurrent constraint, stochastic non-deterministic temporal concurrent constraint.Analog-Cell represents gene expression at the molecule level. It provides abundant image information. We built computational reaction models for transcription and translation in Analog-Cell. The principle of Analog-Cell is that all biochemistry reactions in this cell are considered to be a processing of information. We see the environment of our cell as an open system, inside of which plenty of changes are taking places all the time. All the reaction will change the environment likewise. We built this environment in computer; describe biochemistry reactions as functions. When the environment meet the condition of any reaction, this reaction would be triggered so is the relevant function in our system. All reactions communicate through the environment. We carried out investigations on concurrent semantic analysis of Analog-Cell in this paper. We introduced concurrent constraint theory into Analog-Cell and presented a framework of concurrent electronic cell model. We designed a quantitative stochastic control mechanism, which was based on the study of stochastic concurrent constraint programming. It is capable of avoiding the random system mistakes and improving the performance efficiency of Analog-Cell. Based on non-deterministic temporal concurrent constraint theory, we presented an algorithm model to simulate the initiation of transcription. Last but not least, we proposed an algorithm to simulate whole transcription process.Although the study of artificial life in our country is still in its infancy, how to simulate the biological process on computer is not thoroughly learned. We can reproduce the gene expression on the screen with some key figures captured. We hope the more precise simulation can shed some light on life science. Analog-Cell shows the following features: 1. it is an application of CAS. The evolution of the whole system emerges from the simple changes of each particle. 2. The underlying concurrent constraint semantic lowers the workload of Analog-Cell simulation. 3. Analog-Cell shows the dynamic changes in every time step by active images and data reports. On the other hand, Analog-Cell has its flaws, such as: lack of quantitative data to support our simulation; the speed of computers is a restriction of our system; parallel is not an option when we are using single CPU computers. If all these problems were solved, Analog-Cell will be able to precisely and efficiently simulate the biochemistry reactions, reproduce the gene expression network, and finally make a greater contribution to the development of electronic cell.