4,781 research outputs found
Process algebra modelling styles for biomolecular processes
We investigate how biomolecular processes are modelled in process algebras, focussing on chemical reactions. We consider various modelling styles and how design decisions made in the definition of the process algebra have an impact on how a modelling style can be applied. Our goal is to highlight the often implicit choices that modellers make in choosing a formalism, and illustrate, through the use of examples, how this can affect expressability as well as the type and complexity of the analysis that can be performed
A flexible architecture for modeling and simulation of diffusional association
Up to now, it is not possible to obtain analytical solutions for complex
molecular association processes (e.g. Molecule recognition in Signaling or
catalysis). Instead Brownian Dynamics (BD) simulations are commonly used to
estimate the rate of diffusional association, e.g. to be later used in
mesoscopic simulations. Meanwhile a portfolio of diffusional association (DA)
methods have been developed that exploit BD.
However, DA methods do not clearly distinguish between modeling, simulation,
and experiment settings. This hampers to classify and compare the existing
methods with respect to, for instance model assumptions, simulation
approximations or specific optimization strategies for steering the computation
of trajectories.
To address this deficiency we propose FADA (Flexible Architecture for
Diffusional Association) - an architecture that allows the flexible definition
of the experiment comprising a formal description of the model in SpacePi,
different simulators, as well as validation and analysis methods. Based on the
NAM (Northrup-Allison-McCammon) method, which forms the basis of many existing
DA methods, we illustrate the structure and functioning of FADA. A discussion
of future validation experiments illuminates how the FADA can be exploited in
order to estimate reaction rates and how validation techniques may be applied
to validate additional features of the model
Model checking probabilistic and stochastic extensions of the pi-calculus
We present an implementation of model checking for probabilistic and stochastic extensions of the pi-calculus, a process algebra which supports modelling of concurrency and mobility. Formal verification techniques for such extensions have clear applications in several domains, including mobile ad-hoc network protocols, probabilistic security protocols and biological pathways. Despite this, no implementation of automated verification exists. Building upon the pi-calculus model checker MMC, we first show an automated procedure for constructing the underlying semantic model of a probabilistic or stochastic pi-calculus process. This can then be verified using existing probabilistic model checkers such as PRISM. Secondly, we demonstrate how for processes of a specific structure a more efficient, compositional approach is applicable, which uses our extension of MMC on each parallel component of the system and then translates the results into a high-level modular description for the PRISM tool. The feasibility of our techniques is demonstrated through a number of case studies from the pi-calculus literature
A Process Algebra Software Engineering Environment
In previous work we described how the process algebra based language PSF can
be used in software engineering, using the ToolBus, a coordination architecture
also based on process algebra, as implementation model. In this article we
summarize that work and describe the software development process more formally
by presenting the tools we use in this process in a CASE setting, leading to
the PSF-ToolBus software engineering environment. We generalize the refine step
in this environment towards a process algebra based software engineering
workbench of which several instances can be combined to form an environment
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