Structural Startability of Reaction Pathways with Petri Net Analysis

Abstract

The systematic exploration of candidate reaction pathways has theoretical and practical significance to understand the mechanism of a complex chemical and biochemical reaction and potentially improve its yield. Therefore, many works deal with issues related to the synthesis of reaction pathways for a given mechanism. One of the most effective method for reaction pathway synthesis is the P-graph algorithm, which is applicable to generate the feasible solution structures for complex reactions, including the catalytic and enzyme-catalytic reactions. As this method produce the possible structures based on dynamic equilibrium state, it is very important to investigate whether these states can be reached from the initial state of the system, i.e., whether the reaction pathway is structurally startable. The present work suggests Petri net analysis methods for the structural startability examinations.

The systematic exploration of candidate reaction pathways has theoretical and practical significance to understand the mechanism of a complex chemical and biochemical reaction and potentially improve its yield. Therefore, many works deal with issues related to the synthesis of reaction pathways for a given mechanism. One of the most effective method for reaction pathway synthesis is the P-graph algorithm, which is applicable to generate the feasible solution structures for complex reactions, including the catalytic and enzyme-catalytic reactions. As this method produce the possible structures based on dynamic equilibrium state, it is very important to investigate whether these states can be reached from the initial state of the system, i.e., whether the reaction pathway is structurally startable. The present work suggests Petri net analysis methods for the structural startability examinations.