The Bond-Calculus: A Process Algebra for Complex Biological Interaction Dynamics (1804.07603v2)

Abstract: We present the bond-calculus, a process algebra for modelling biological and chemical systems featuring nonlinear dynamics, multiway interactions, and dynamic bonding of agents. Mathematical models based on differential equations have been instrumental in modelling and understanding the dynamics of biological systems. Quantitative process algebras aim to build higher level descriptions of biological systems, capturing the agents and interactions underlying their behaviour, and can be compiled down to a range of lower level mathematical models. The bond-calculus builds upon the work of Kwiatkowski, Banks, and Stark's continuous pi-calculus by adding a flexible multiway communication operation based on affinity patterns and general kinetic laws. We develop a compositional semantics based on vector fields and linear operators, which we use to define the time evolution of this system. This enables simulation and analysis via differential equation generation or stochastic simulation. Finally, we apply our framework to an existing biological model: Kuznetsov's classic model of tumour immune interactions.