Application of a stochastic name-­passing calculus to representation and simulation of molecular processes

Priami, Corrado and Regev, Aviv and Shapiro, Ehud and Silverman, William (2001) Application of a stochastic name-­passing calculus to representation and simulation of molecular processes. UNSPECIFIED.

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    Abstract

    We describe a novel application of a stochastic name passing calculus for the study of biomolecular systems. We specify the structure and dynamics of biochemical networks in a variant of the stochastic P-­calculus, yielding a model which is mathematically well­defined and biologically faithful. We adapt the operational semantics of the calculus to account for both the time and probability of biochemical reactions, and present a computer implementation of the calculus for biochemical simulations.

    Item Type: Departmental Technical Report
    Department or Research center: Information Engineering and Computer Science
    Subjects: UNSPECIFIED
    Uncontrolled Keywords: stochastic P-calculus, bioinformatics, stochastic simulation
    Additional Information: Appeared in Information Processing Letters 80 (2001) 25-31
    Report Number: DIT-02-018
    Repository staff approval on: 21 Jan 2003

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