Implementing a global approach for efficiently simulating molecular dynamics in agent-based models of biological tissue

Daniel Bergman; Trachette L Jackson

doi:10.1016/j.xpro.2022.101777

Implementing a global approach for efficiently simulating molecular dynamics in agent-based models of biological tissue

STAR Protoc. 2022 Oct 25;3(4):101777. doi: 10.1016/j.xpro.2022.101777. eCollection 2022 Dec 16.

Authors

Daniel Bergman¹, Trachette L Jackson²

Affiliations

¹ Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address: bergmand@umich.edu.
² Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address: tjacks@umich.edu.

Abstract

This protocol explains how to take an agent-based model (ABM) with molecular dynamics and set it up to solve the molecular dynamics with a global approach. It can be used to speed up simulations significantly while retaining high levels of accuracy with the original ABM. Two options are presented for implementing this global approach, depending on the desired spatial variability in molecular concentrations. Both options coarse-grain the molecular dynamics in space by dividing the microenvironment into regions with uniform concentrations. For complete details on the use and execution of this protocol, please refer to Bergman et al. (2022).

Keywords: Computer sciences; Systems biology.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Algorithms*
Molecular Dynamics Simulation*

Grants and funding

U01 CA243075/CA/NCI NIH HHS/United States