BSim 2.0: An Advanced Agent-Based Cell Simulator.
Antoni MatyjaszkiewiczGianfranco FioreFabio AnnunziataClaire S GriersonNigel J SaveryLucia MarucciMario di BernardoPublished in: ACS synthetic biology (2017)
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.
Keyphrases
- single cell
- rna seq
- induced apoptosis
- high throughput
- healthcare
- primary care
- cell cycle arrest
- molecular docking
- oxidative stress
- quality improvement
- circulating tumor cells
- endoplasmic reticulum stress
- signaling pathway
- mesenchymal stem cells
- cell death
- climate change
- virtual reality
- cell proliferation
- human health
- molecular dynamics simulations