SpringSaLaD: A Spatial, Particle-Based Biochemical Simulation Platform with Excluded Volume

Overview

Journal Biophys J

Publisher Cell Press

Specialty Biophysics

Date 2016 Feb 4

PMID 26840718

Citations 35

Authors

Paul J Michalski

Leslie M Loew

Affiliations

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Abstract

We introduce Springs, Sites, and Langevin Dynamics (SpringSaLaD), a comprehensive software platform for spatial, stochastic, particle-based modeling of biochemical systems. SpringSaLaD models biomolecules in a coarse-grained manner as a group of linked spherical sites with excluded volume. This mesoscopic approach bridges the gap between highly detailed molecular dynamics simulations and the various methods used to study network kinetics and diffusion at the cellular level. SpringSaLaD is a standalone tool that supports model building, simulation, visualization, and data analysis, all through a user-friendly graphical user interface that should make it more accessible than tools built into more comprehensive molecular dynamics infrastructures. Importantly, for bimolecular reactions we derive an exact expression relating the macroscopic on-rate to the various microscopic parameters with the inclusion of excluded volume; this makes SpringSaLaD more accurate than other tools, which rely on approximate relationships between these parameters.

Citing Articles

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