Synapses as stochastic concurrent systems

Authors:
Andrea Bracciali;Marcello Brunelli;Enrico Cataldo;Pierpaolo Degano
Affiliations:
Dipartimento di Informatica, Università di Pisa, Italy;Dipartimento di Biologia, Università di Pisa, Italy;Dipartimento di Biologia, Università di Pisa, Italy;Dipartimento di Informatica, Università di Pisa, Italy
Venue:
Theoretical Computer Science
Year:
2008

Citing 15
Cited 0

Methods in Neuronal Modeling: From synapses to networks

Methods in Neuronal Modeling: From synapses to networks
A compositional approach to performance modelling

A compositional approach to performance modelling
Communicating and mobile systems: the &pgr;-calculus

Communicating and mobile systems: the &pgr;-calculus
Application of a stochastic name-passing calculus to representation and simulation of molecular processes

Information Processing Letters
Simulating, Analyzing, and Animating Dynamical Systems: A Guide Toi Xppaut for Researchers and Students

Simulating, Analyzing, and Animating Dynamical Systems: A Guide Toi Xppaut for Researchers and Students
BioAmbients: an abstraction for biological compartments

Theoretical Computer Science - Special issue: Computational systems biology
Theoretical Neuroscience: Computational and Mathematical Modeling of Neural Systems

Theoretical Neuroscience: Computational and Mathematical Modeling of Neural Systems
On process rate semantics

Theoretical Computer Science
Expressive models for synaptic plasticity

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
Modal logics for brane calculus

CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
Stronger computational modelling of signalling pathways using both continuous and discrete-state methods

CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
VICE: a VIrtual CEll

CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Brane calculi

CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA

Transactions on Computational Systems Biology VII

Quantified Score

Hi-index	5.23

Visualization

Abstract

We present a stochastic model of the presynaptic terminal in the calyx of Held synapse. This model exploits process calculi as a representation language and has a direct computational implementation that supports quantitative simulation trials of the behaviour of the synapse. To our knowledge, it represents the first model of synaptic activity based on process calculi. The model builds upon available data, the fitting of some parameters and developed working hypotheses. Experiments about plasticity have been carried out regarding synaptic facilitation and potentiation. Also, synaptic depression has been considered in a model exhibiting dynamical equilibrium. Overall, the simulation results are coherent with the experimental findings appearing in the literature about the modeled reality. These results represent a quite detailed description of the presynaptic activity. This multidisciplinary work validates some aspects of the approach based on process calculi with respect to the new application domain, such as abstraction, expressiveness and compositionality.