ArticleBioinformatics (Oxford, England)2015
Multiscale reaction-diffusion simulations with Smoldyn.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- From homogeneity to heterogeneity: Refining stochastic simulations of gene regulation.Computational and structural biotechnology journal · 2025Article
- Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience.Briefings in bioinformatics · 2023Article
- A novel stochastic simulation approach enables exploration of mechanisms for regulating polarity site movement.PLoS computational biology · 2021Article
- Coarse-graining molecular dynamics: stochastic models with non-Gaussian force distributions.Journal of mathematical biology · 2020Article
- Stochastic self-tuning hybrid algorithm for reaction-diffusion systems.The Journal of chemical physics · 2019Article
- Multiscale Stochastic Reaction-Diffusion Algorithms Combining Markov Chain Models with Stochastic Partial Differential Equations.Bulletin of mathematical biology · 2019Article
- Multi-resolution dimer models in heat baths with short-range and long-range interactions.Interface focus · 2019Article
- CellOrganizer: Learning and Using Cell Geometries for Spatial Cell Simulations.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning.The Journal of chemical physics · 2017Article
- Reaction rates for reaction-diffusion kinetics on unstructured meshes.The Journal of chemical physics · 2017Article
- Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology.PLoS computational biology · 2016Article
- SpringSaLaD: A Spatial, Particle-Based Biochemical Simulation Platform with Excluded Volume.Biophysical journal · 2016Article
- Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics.Proceedings. Mathematical, physical, and engineering sciences · 2016Article
- Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations.Journal of computational physics · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
unlabelledSmoldyn is a software package for stochastic modelling of spatial biochemical networks and intracellular systems. It was originally developed with an accurate off-lattice particle-based model at its core. This has recently been enhanced with the addition of a computationally efficient on-lattice model, which can be run stand-alone or coupled together for multiscale simulations using both models in regions where they are most required, increasing the applicability of Smoldyn to larger molecule numbers and spatial domains. Simulations can switch between models with only small additions to their configuration file, enabling users with existing Smoldyn configuration files to run the new on-lattice model with any reaction, species or surface descriptions they might already have. AVAILABILITY AND IMPLEMENTATION: Source code and binaries freely available for download at www.smoldyn.org, implemented in C/C++ and supported on Linux, Mac OSX and MS Windows.
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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.