[ACS Synth. Biol.] BSim 2.0: an advanced agent-based cell simulator
Agent-based models (ABMs) provide a number of advantages relative to traditional continuum modelling approaches, permitting incorporation of great detail and realism into simulations, allowing in-silico tracking of single-cell behaviours 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 modelling 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.
Antoni Matyjaszkiewicz, Gianfranco Fiore, Fabio Annunziata, Claire Grierson, Nigel Savery, Lucia Marucci, and Mario di Bernardo
ACS Synth. Biol., Just Accepted Manuscript
Publication Date (Web): June 6, 2017
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