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Systems Biology Conceptual Modeling by Means of Discrete-event Simulation (DNA-RNA-Protein)

J.W. Yeol, I. Barjis, J. Barjis, S. Berri and Y. Ryu
Polytechnic University, US

Keywords:
discrete-event, simulation, glycolytic

Abstract:
In this paper discrete-event simulation modeling technique is used to model and simulate biological processes. In particular, we study application of discrete-event simulation to model processes taking place in Glycolosis and capture dynamic behavior of reactions that occur in it. Glycolosis is the beginning of generation of metabolic energy from Carbohydrates metabolism, where in this process one molecule of Glucose is converted into two molecules of Pyrovate, with concomitant generation of two molecules of ATP. During this process some of the potential energy stored in the hexose structure is released and used to derive the synthesis of ATP from ADP. There will be give an overview of the carbohydrate metabolism and a Petri net model would be constructed for the carbohydrate metabolism, which will show all the involved pathways in carbohydrate metabolism. However the paper would concentrate on Glycolosis, which is the initial pathway in the catabolism of carbohydrates. The main purpose of this paper was to develop a modeling methodology for the process of glycolosis using discrete-event simulation. Why should we bother to model a biological process at the first place? Well, the answer is that: first to develop an abstract description of dynamic system (in this case the process of glycolosis); second simulation and modeling allows decisions to be pre-tested before implementation; and third real-life laboratory experimentation or standard analysis of a system or process is often too complex or/and expensive. So it would allow researchers to be in control of the experiment. They would be able to pre-test their laboratory experiment by touch of few buttons, without spending time and material in laboratory. Educational institutions would be able to use this modeling techniques and simulation to replace the dry text. Students would better digest the subject if the observe the biological process of glycolosis visually rather then reading dry text what would happen to glucose once in the body. This could be a very useful tool for educational institutions in teaching the biological processes, as it would allow them to simulate the process and students would visually observe what happens in each step of reaction and what are the involved substrates or cofactors. They would see how the reaction could not be completed if not all the necessary substrates and cofactors present (in case of sychronization process, e.g. glycolosis).

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