A Calculus of Located Entities

Colloquium: Departmental | April 23 | 1-2:30 p.m. | 320 Soda Hall

 Adriana Compagnoni, Stevens Institute of Technology

 Electrical Engineering and Computer Sciences (EECS)

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-Gardner’s 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

 necula@cs.berkeley.edu, 510-643-1481