A Computational Model of the Secondary Hemostasis Pathway in Reaction Systems

Asma Bendjeddou, Linda Brodo, Moreno Falaschi () and Elisa B. P. Tiezzi
Additional contact information
Asma Bendjeddou: Dipartimento di Ingegneria Dell’Informazione e Scienze Matematiche, Università di Siena, 53100 Siena, Italy
Linda Brodo: Dipartimento di Scienze Economiche e Aziendali, Università di Sassari, 07100 Sassari, Italy
Moreno Falaschi: Dipartimento di Ingegneria Dell’Informazione e Scienze Matematiche, Università di Siena, 53100 Siena, Italy
Elisa B. P. Tiezzi: Dipartimento di Ingegneria Dell’Informazione e Scienze Matematiche, Università di Siena, 53100 Siena, Italy

Mathematics, 2024, vol. 12, issue 15, 1-23

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.

Keywords: reaction systems; SOS semantics; hemostasis; systems biology (search for similar items in EconPapers)
JEL-codes: C (search for similar items in EconPapers)
Date: 2024
References: View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.mdpi.com/2227-7390/12/15/2422/pdf (application/pdf)
https://www.mdpi.com/2227-7390/12/15/2422/ (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:gam:jmathe:v:12:y:2024:i:15:p:2422-:d:1449691

Access Statistics for this article

Mathematics is currently edited by Ms. Emma He

More articles in Mathematics from MDPI
Bibliographic data for series maintained by MDPI Indexing Manager ().