P systems have clear structural analogies with the cell. In practice, difficulties arise when one attempts to represent a biomolecular process using these systems. This chapter suggests some research guidelines as promising ways to gain insight on P systems, and to provide them with further functionalities aimed at increasing their versatility in the modeling of biomolecular processes. Concepts from state transition dynamics are taken to put P systems in a general analysis framework for dynamical discrete systems. An explicit notion of environment is proposed to provide P systems with a regulatory and constraining agent, as real biomolecular processes must deal with. The chapter focuses on a new rewriting strategy inspired by biochemistry, in which reactivities play a central role in driving the rules as it happens during biochemical reactions. Tests on an algorithm implementing rewriting with reactivities, realized on a simulator called Psim, show the capability of this algorithm to express several processes with precision, particularly those presenting oscillatory phenomena. Finally, an analysis of the phenomenon of leukocyte recruitment is also performed using Psim.

P systems for biological dynamics

FRANCO, Giuditta;MANCA, Vincenzo
2006-01-01

Abstract

P systems have clear structural analogies with the cell. In practice, difficulties arise when one attempts to represent a biomolecular process using these systems. This chapter suggests some research guidelines as promising ways to gain insight on P systems, and to provide them with further functionalities aimed at increasing their versatility in the modeling of biomolecular processes. Concepts from state transition dynamics are taken to put P systems in a general analysis framework for dynamical discrete systems. An explicit notion of environment is proposed to provide P systems with a regulatory and constraining agent, as real biomolecular processes must deal with. The chapter focuses on a new rewriting strategy inspired by biochemistry, in which reactivities play a central role in driving the rules as it happens during biochemical reactions. Tests on an algorithm implementing rewriting with reactivities, realized on a simulator called Psim, show the capability of this algorithm to express several processes with precision, particularly those presenting oscillatory phenomena. Finally, an analysis of the phenomenon of leukocyte recruitment is also performed using Psim.
2006
9783540250173
computational modeling of biological dynamics
File in questo prodotto:
Non ci sono file associati a questo prodotto.

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11562/300516
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus ND
  • ???jsp.display-item.citation.isi??? ND
social impact