Coupled Chemical Reactions in Stochastic Pi-calculus
نویسنده
چکیده
This document describes how a number of spatially homogeneous chemical systems can be modeled in the stochastic pi-calculus and simulated using the Stochastic Pi Machine. Each of the systems presented here was previously defined as a set of reaction equations, which were simulated using the Gillespie algorithm. For further details on the models and the references to the original literature, see: Gillespie, D. (1977) Exact stochastic simulation of coupled chemical reactions. J. Chem. Phys. 81 2340-2361.
منابع مشابه
Computational Modeling for the Activation Cycle of G-proteins by G-protein-coupled Receptors
In this paper, we survey five different computational modeling methods. For comparison, we use the activation cycle of G-proteins that regulate cellular signaling events downstream of G-proteincoupled receptors (GPCRs) as a driving example. Starting from an existing Ordinary Differential Equations (ODEs) model, we implement the G-protein cycle in the stochastic Pi-calculus using SPiM, as Petri-...
متن کاملA Logic for Constrained Process Calculi with Applications to Molecular Biology
Linear implication can represent state transitions, but real transition systems operate under temporal, stochastic or probabilistic constraints that are not directly representable in ordinary linear logic. We propose a general modal extension of intuitionistic linear logic where logical truth is indexed by constraints and hybrid connectives combine constraint reasoning with logical reasoning. T...
متن کاملEPTCS Proceedings of the Fourth Workshop on Membrane Computing and Biologically Inspired Process Calculi 2010
Biological systems typically involve large numbers of components with complex, highly parallel interactions and intrinsic stochasticity. Numerous programming languages have been developed for modelling such systems, many of which are based on process calculi. Most of these calculi, particularly those involving membrane interactions, are expressive enough to generate potentially unbounded number...
متن کاملStochastic modelling of cellular growth and division by means of the pi@ calculus
The application of Concurrency Theory to Systems Biology is in its earliest stage of progress. The metaphor of cells as computing systems by Regev and Shapiro [14] opened the employment of concurrent languages for the modelling of biological systems. Their peculiar characteristics led to the design of many bio-inspired formalisms which achieve higher faithfulness and specificity. In this paper ...
متن کاملTranslating SBML Models into the Stochastic pi-Calculus for Stochastic Simulation
This paper addresses the translation of Systems Biology MarkUp Language (SBML) Level 2 models of network of biochemical reactions to the Biochemical Stochastic π-calculus (SPI). SBML is XML-based formalism for systems biology, while SPI can describe the concurrency of the different interactions occurring in a network of biochemical stochastic reactions. SPI models can be used for simulation by ...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
دوره شماره
صفحات -
تاریخ انتشار 2007