BSim 2.0: An Advanced Agent-Based Cell Simulator

作者：Matyjaszkiewicz Antoni; Fiore Gianfranco; Annunziata Fabio; Grierson Claire S; Savery Nigel J; Marucci Lucia^*; di Bernardo Mario^*

来源：ACS Synthetic Biology, 2017, 6(10): 1969-1972.

DOI：10.1021/acssynbio.7b00121

• agent-based simulation
• synthetic biology
• cell populations
• microbial consortia
• gene regulatory network

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 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.

• 出版日期2017-10