CoBiC: Context-dependent Bioambient Calculus

Authors:
Luca Bortolussi;Maria G. Vigliotti
Affiliations:
Dipartimento di Matematica ed Informatica, University of Trieste, Trieste, Italy;Department of Computing, Imperial College, 180 Queen's Gate, London SW7 2BZ, UK
Venue:
Electronic Notes in Theoretical Computer Science (ENTCS)
Year:
2009

Citing 5
Cited 3

The chemical abstract machine

POPL '90 Proceedings of the 17th ACM SIGPLAN-SIGACT symposium on Principles of programming languages
BioAmbients: an abstraction for biological compartments

Theoretical Computer Science - Special issue: Computational systems biology
Cell Cycle Control in Eukaryotes: A BioSpi model

Electronic Notes in Theoretical Computer Science (ENTCS)
Modeling Biological Systems in Stochastic Concurrent Constraint Programming

Constraints
A compositional approach to the stochastic dynamics of gene networks

Transactions on Computational Systems Biology IV

Simulation techniques for the calculus of wrapped compartments

Theoretical Computer Science
Measurable stochastics for Brane Calculus

Theoretical Computer Science
Typed stochastic semantics for the calculus of looping sequences

Theoretical Computer Science

Quantified Score

Hi-index	0.00

Visualization

Abstract

In biological phenomena like osmosis, the rate of flow of water molecules in or out of biological compartments depends on the solute concentration and on other forces, like hydrostatic pressure. A similar example is the passive transport of ions in and out the cell membrane. In this paper, we address the problem of faithfully modelling these kind of phenomena with an adequate process calculus. We enhance the ambient calculus stochastic semantics with functional rates, which are calculated by taking into account the volume of ambients and the surrounding environment. A model of osmosis in plant cells will be used as an example to show the new features of our calculus.