Book Chapter

Accurate Particle-Based Reaction Algorithms for Fixed Timestep Simulators

Stuart T Johnston, Christopher N Angstmann, Satya NV Arjunan, Casper HL Beentjes, Adrien Coulier, Samuel A Isaacson, Ash A Khan, Karen Lipkow, Steven S Andrews

2018 MATRIX Annals | Springer International Publishing | Published : 2020

Abstract

Particle-based simulators are widely used to study biochemical systems involving spatial transport and chemical reactions on sub-cellular length scales. Fixed time step methods can often offer good performance even when simulat ing complex many-particle systems. However, current reaction algorithms approxi mate more detailed molecular dynamics models either inaccurately or slowly. Here, we present new reaction algorithms that better approximate microscopic molecular dynamics models while maintaining good computational efficiency. A “Brownian bridge” algorithm samples reactions using reactant positions both before and after each diffusive step; its simulated dynamics exactly match those of ap..

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