ArticleBiophysical journal2015
ReaDDyMM: Fast interacting particle reaction-diffusion simulations using graphical processing units.
Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
12 citing papers in PubMed.
- Parallelization of Particle-Based Reaction-Diffusion Simulations Using MPI.Journal of computational chemistry · 2025Article
- Concentration sensing in crowded environments.Biophysical journal · 2021Article
- pSpatiocyte: a high-performance simulator for intracellular reaction-diffusion systems.BMC bioinformatics · 2020Article
- ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics.PLoS computational biology · 2019Article
- Multiscale Methods in Drug Design Bridge Chemical and Biological Complexity in the Search for Cures.Nature reviews. Chemistry · 2018Article
- Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission.Nature communications · 2017Article
- Reaction-diffusion basis of retroviral infectivity.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2016Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- SpringSaLaD: A Spatial, Particle-Based Biochemical Simulation Platform with Excluded Volume.Biophysical journal · 2016Article
- Dynamical Organization of Syntaxin-1A at the Presynaptic Active Zone.PLoS computational biology · 2015Article
- Divide and conquer, faster: speeding up molecular simulations.Biophysical journal · 2015Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
ReaDDy is a modular particle simulation package combining off-lattice reaction kinetics with arbitrary particle interaction forces. Here we present a graphical processing unit implementation of ReaDDy that employs the fast multiplatform molecular dynamics package OpenMM. A speedup of up to two orders of magnitude is demonstrated, giving us access to timescales of multiple seconds on single graphical processing units. This opens up the possibility of simulating cellular signal transduction events while resolving all protein copies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.