This document describes how a number of spatially homogeneous chemical systems can be modeled in the stochastic pi-calculus and simulated using the Stochastic Pi Machine. Each of the systems presented here was previously defined as a set of reaction equations, which were simulated using the Gillespie algorithm. For further details on the models and the references to the original literature, see...

Biochemical dynamics are often determined by series of single molecule events such as gene expression and reactions involving protein concentrations at nanomolar concentrations. Molecular fluctuations, consequently, may be of biological significance. For example, heterogeneity in clonal populations is believed to arise from molecular fluctuations in gene expression. A realistic description, the...

There is great potential to be explored regarding the use of agent-based modelling and simulation as an alternative paradigm to investigate early-stage cancer interactions with the immune system. It does not suffer from some limitations of ordinary differential equation models, such as the lack of stochasticity, representation of individual behaviours rather than aggregates and individual memor...

The stochastic simulation algorithm commonly known as Gillespie's algorithm (originally derived for modelling well-mixed systems of chemical reactions) is now used ubiquitously in the modelling of biological processes in which stochastic effects play an important role. In well-mixed scenarios at the sub-cellular level it is often reasonable to assume that times between successive reaction/inter...

In various biochemical systems, discrete and stochastic approaches are more appropriate than continuous and deterministic approaches when the system has small numbers of molecules. Before the emergence of the stochastic simulation algorithm (SSA) by Gillespie, chemical master equations were used to stochastically model. Solving the master equations is often mathematically intractable. Therefore...

The Gillespie stochastic simulation algorithm represents one of the main physical abstractions exploited for the simulation of biological systems modeled by means of concurrent calculi. While the faithful modelling of bio-systems often requires multi-compartment semantics, the original Gillespie algorithm considers only one fixed-size volume. In this paper we introduce an extended formalisation...

Higher education in general (Bogue, 1998) and study abroad programming in particular (Gillespie, Braskamp & Braskamp, 1999) are hardly strangers to stringent demands for accountability. What is new to higher education and to study abroad is the demand for accountability in terms of measurable student learning outcomes. This article is a first report from a system-wide initiative to document lea...

Stochastic simulations are one of the cornerstones of the analysis of dynamical processes on complex networks, and are often the only accessible way to explore their behavior. The development of fast algorithms is paramount to allow large-scale simulations. The Gillespie algorithm can be used for fast simulation of stochastic processes, and variants of it have been applied to simulate dynamical...