A Calculus of Located Entities
Colloquium: Departmental | April 23 | 1-2:30 p.m. | 320 Soda Hall
Adriana Compagnoni, Stevens Institute of Technology
In this paper we define BioScapeL, a stochastic Pi-calculus in 3D-space with abstract locations. It builds on BioScape by associating with each entity a position in space, which is the barycentre of its associated shape. The position of an entity instance is programmable. This is similar to the origin of the affine transformation in Cardelli-Gardners 3π. The motivation for such an extension comes from the need to describe the assembly of configurations such as polymers, oligomers, and complexes in space, while keeping a high level description where diffusion and confinement remain part of the semantics of the calculus. In addition to this programmable deterministic translation, we can specify random translation and scaling.
Random translation is not present in 3π, and scaling is more complex.
Joint work with Paola Giannini, Catherine Kim, Matthew Milideo and Vishakha Sharma