A Computational Model of the Secondary Hemostasis Pathway in Reaction Systems

Abstract

Reaction Systems (RSs) are a computational framework inspired by biochemical mechanisms. An RS defines a finite set of reactions over a finite set of entities (molecules, proteins, etc). Starting from an initial set of entities (the initial state), a computation is performed by applying all reactions to a state in order to produce the following state, giving rise to a sequence of sets of entities. RSs have shown to be a general computational framework whose application ranges from the modeling of biological phenomena to molecular chemistry and computer science. In this paper, we contribute to research on the application of RSs for modeling biological systems. We consider the problem of modeling hemostasis, for which several models have been defined, starting from the 1960s. Previous models are based on sets of ordinary differential equations, while we develop a discrete model in RSs for pathways of the secondary hemostasis. Then, we implement our model in BioReSolve, a computational framework for RSs that we have previously defined which provides tools for the specification and verification of properties. By using the tools in BioReSolve we derive important observations on the model behaviour for hemostasis, and in particular, we study the role of three important inhibitors, verifying that their presence or absence leads to phenomena such as thrombophilia, or thromboembolism, or excessive coagulation, etc. We can also study computationally the causality relations between the molecules involved in the reactions showing which entities play a fundamental role, thus contributing to the design of more effective and specialized drugs. Our work can hence help to show how to model complex biological systems in RSs and derive computationally and biologically relevant properties of the systems.