Foundations of logic programming; (2nd extended ed.)
Foundations of logic programming; (2nd extended ed.)
Term rewriting and all that
On the Computational Power of Biochemistry
AB '08 Proceedings of the 3rd international conference on Algebraic Biology
Electronic Notes in Theoretical Computer Science (ENTCS)
Bio-PEPA: A framework for the modelling and analysis of biological systems
Theoretical Computer Science
A stochastic pi calculus for concurrent objects
AB'07 Proceedings of the 2nd international conference on Algebraic biology
Modelization and simulation of nano devices in nanok calculus
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Efficient, correct simulation of biological processes in the stochastic pi-calculus
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Scalable simulation of cellular signaling networks
APLAS'07 Proceedings of the 5th Asian conference on Programming languages and systems
The biochemical abstract machine BIOCHAM
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
A language for biochemical systems: design and formal specification
Transactions on Computational Systems Biology XII
Rule-based modelling of cellular signalling
CONCUR'07 Proceedings of the 18th international conference on Concurrency Theory
Biochemical reaction rules with constraints
ESOP'11/ETAPS'11 Proceedings of the 20th European conference on Programming languages and systems: part of the joint European conferences on theory and practice of software
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Transcriptional attenuation at E.coli's tryptophan operon is a prime example of RNA-mediated gene regulation. In this paper, we present a discrete stochastic model of the fine-grained control of attenuation, based on chemical reactions. Stochastic simulation of our model confirms results that were previously obtained by master or differential equations. Our approach is easier to understand than master equations, although mathematically well founded. It is compact due to rule schemas that define finite sets of chemical reactions. Object-centered languages based on the π-calculus would yield less intelligible models. Such languages are confined to binary interactions, whereas our model heavily relies on reaction rules with more than two reactants, in order to concisely capture the control of attenuation.