ArticleJournal of computational biology : a journal of computational molecular cell biology2012
A computational approach to increase time scales in Brownian dynamics-based reaction-diffusion modeling.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
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- A computational study of co-inhibitory immune complex assembly at the interface between T cells and antigen presenting cells.PLoS computational biology · 2021Article
- A multiscale study on the mechanisms of spatial organization in ligand-receptor interactions on cell surfaces.Computational and structural biotechnology journal · 2021Article
- Multiscale simulation unravel the kinetic mechanisms of inflammasome assembly.Biochimica et biophysica acta. Molecular cell research · 2020Article
- A computational model for understanding the oligomerization mechanisms of TNF receptor superfamily.Computational and structural biotechnology journal · 2020Article
- FISIK: Framework for the Inference of In Situ Interaction Kinetics from Single-Molecule Imaging Data.Biophysical journal · 2019Article
- Why microbes secrete molecules to modify their environment: the case of iron-chelating siderophores.Journal of the Royal Society, Interface · 2019Article
- Integrating Structural Information to Study the Dynamics of Protein-Protein Interactions in Cells.Structure (London, England : 1993) · 2018Article
- A Multiscale Computational Model for Simulating the Kinetics of Protein Complex Assembly.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Understanding the Functional Roles of Multiple Extracellular Domains in Cell Adhesion Molecules with a Coarse-Grained Model.Journal of molecular biology · 2017Article
- A Computational Model for Kinetic Studies of Cadherin Binding and Clustering.Biophysical journal · 2016Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- Revisiting Plant Plasma Membrane Lipids in Tobacco: A Focus on Sphingolipids.Plant physiology · 2016Article
- Reaching new levels of realism in modeling biological macromolecules in cellular environments.Journal of molecular graphics & modelling · 2013Review
- Dynamics simulations for engineering macromolecular interactions.Chaos (Woodbury, N.Y.) · 2013Article
- Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems.Physical review. XArticle
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2 authors.
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Abstract
Particle-based Brownian dynamics simulations offer the opportunity to not only simulate diffusion of particles but also the reactions between them. They therefore provide an opportunity to integrate varied biological data into spatially explicit models of biological processes, such as signal transduction or mitosis. However, particle based reaction-diffusion methods often are hampered by the relatively small time step needed for accurate description of the reaction-diffusion framework. Such small time steps often prevent simulation times that are relevant for biological processes. It is therefore of great importance to develop reaction-diffusion methods that tolerate larger time steps while maintaining relatively high accuracy. Here, we provide an algorithm, which detects potential particle collisions prior to a BD-based particle displacement and at the same time rigorously obeys the detailed balance rule of equilibrium reactions. We can show that for reaction-diffusion processes of particles mimicking proteins, the method can increase the typical BD time step by an order of magnitude while maintaining similar accuracy in the reaction diffusion modelling.
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