A Calculus of Located Entities

Adriana Compagnoni
(Stevens Institute of Technology)
Paola Giannini
(Università del Piemonte Orientale)
Catherine Kim
(Stevens Institute of Technology)
Matthew Milideo
(Stevens Institute of Technology)
Vishakha Sharma
(Stevens Institute of Technology)

We define BioScapeL, a stochastic pi-calculus in 3D-space. A novel aspect of BioScapeL is that entities have programmable locations. The programmer can specify a particular location where to place an entity, or a location relative to the current location of the entity. The motivation for the extension comes from the need to describe the evolution of populations of biochemical species in space, while keeping a sufficiently high level description, so that phenomena like diffusion, collision, and confinement can remain part of the semantics of the calculus. Combined with the random diffusion movement inherited from BioScape, programmable locations allow us to capture the assemblies of configurations of polymers, oligomers, and complexes such as microtubules or actin filaments.

Further new aspects of BioScapeL include random translation and scaling. Random translation is instrumental in describing the location of new entities relative to the old ones. For example, when a cell secretes a hydronium ion, the ion should be placed at a given distance from the originating cell, but in a random direction. Additionally, scaling allows us to capture at a high level events such as division and growth; for example, daughter cells after mitosis have half the size of the mother cell.

In Mauricio Ayala-Rincón, Eduardo Bonelli and Ian Mackie: Proceedings 9th International Workshop on Developments in Computational Models (DCM 2013), Buenos Aires, Argentina, 26 August 2013, Electronic Proceedings in Theoretical Computer Science 144, pp. 41–56.
Published: 30th March 2014.

ArXived at: http://dx.doi.org/10.4204/EPTCS.144.4 bibtex PDF
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