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Publication - Professor Claire Grierson

    BSim 2.0

    An Advanced Agent-Based Cell Simulator

    Citation

    Matyjaszkiewicz, A, Fiore, G, Annunziata, F, Grierson, CS, Savery, NJ, Marucci, L & Bernardo, Md, 2017, ‘BSim 2.0: An Advanced Agent-Based Cell Simulator’. ACS Synthetic Biology.

    Abstract

    Agent-based models (ABMs) provide a number of advantages relative to traditional continuum modeling approaches, permitting incorporation of great detail and realism into simulations, allowing in silico tracking of single-cell behaviors and correlation of these with emergent effects at the macroscopic level. In this study we present BSim 2.0, a radically new version of BSim, a computational ABM framework for modeling dynamics of bacteria in typical experimental environments including microfluidic chemostats. This is facilitated through the implementation of new methods including cells with capsular geometry that are able to physically and chemically interact with one another, a realistic model of cellular growth, a delay differential equation solver, and realistic environmental geometries.

    Full details in the University publications repository