{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["8(9)"],"submitter":["Schoneberg J"],"pubmed_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."],"journal":["PloS one"],"pagination":["e74261"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC3770580"],"repository":["biostudies-literature"],"pubmed_title":["ReaDDy--a software for particle-based reaction-diffusion dynamics in crowded cellular environments."],"pmcid":["PMC3770580"],"pubmed_authors":["Schoneberg J","Noe F"],"additional_accession":[]},"is_claimable":false,"name":"ReaDDy--a software for particle-based reaction-diffusion dynamics in crowded cellular environments.","description":"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.","dates":{"release":"2013-01-01T00:00:00Z","publication":"2013","modification":"2024-11-19T19:38:16.021Z","creation":"2019-03-26T23:21:04Z"},"accession":"S-EPMC3770580","cross_references":{"pubmed":["24040218"],"doi":["10.1371/journal.pone.0074261"]}}