ArticlePloS one2013
ReaDDy--a software for particle-based reaction-diffusion dynamics in crowded cellular environments.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- AI-driven virtual cell models in preclinical research: technical pathways, validation mechanisms, and clinical translation potential.NPJ digital medicine · 2025Review
- The Brownian dynamics simulator PyRID for reacting and interacting particles written in Python.Cell reports methods · 2025Article
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- Parallelization of Particle-Based Reaction-Diffusion Simulations Using MPI.Journal of computational chemistry · 2025Article
- Comparing simulations of actin filament compression reveals tradeoff between computational cost and capturing supertwist.microPublication biology · 2025Article
- Recent Progress in Modeling and Simulation of Biomolecular Crowding and Condensation Inside Cells.Journal of chemical information and modeling · 2024Review
- Disentanglement of Surface and Confinement Effects for Diene Metathesis in Mesoporous Confinement.ACS omega · 2024Article
- Postsynaptic protein assembly in three and two dimensions studied by mesoscopic simulations.Biophysical journal · 2023Article
- Implications of different membrane compartmentalization models in particle-basedRoyal Society open science · 2023Article
- MitoTNT: Mitochondrial Temporal Network Tracking for 4D live-cell fluorescence microscopy data.PLoS computational biology · 2023Article
- GeomBD3: Brownian Dynamics Simulation Software for Biological and Engineered Systems.Journal of chemical information and modeling · 2022Article
- STEPS 4.0: Fast and memory-efficient molecular simulations of neurons at the nanoscale.Frontiers in neuroinformatics · 2022Article
- Determination of the molecular reach of the protein tyrosine phosphatase SHP-1.Biophysical journal · 2021Article
- Neural network aided approximation and parameter inference of non-Markovian models of gene expression.Nature communications · 2021Article
- Concentration sensing in crowded environments.Biophysical journal · 2021Article
- Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry.Molecular biology of the cell · 2021Article
- Molecular Mechanics Study of Flow and Surface Influence in Ligand-Protein Association.Frontiers in molecular biosciences · 2021Article
- NERDSS: A Nonequilibrium Simulator for Multibody Self-Assembly at the Cellular Scale.Biophysical journal · 2020Article
- Programming and simulating chemical reaction networks on a surface.Journal of the Royal Society, Interface · 2020Article
- pSpatiocyte: a high-performance simulator for intracellular reaction-diffusion systems.BMC bioinformatics · 2020Article
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Authors and funding
2 authors.
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Abstract
We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform-specific implementations or dynamical models that are different from Brownian dynamics.
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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.