ArticleSIAM journal on scientific computing : a publication of the Society for Industrial and Applied Mathematics2008
FAST MONTE CARLO SIMULATION METHODS FOR BIOLOGICAL REACTION-DIFFUSION SYSTEMS IN SOLUTION AND ON SURFACES.
Article in SIAM journal on scientific computing : a publication of the Society for Industrial and Applied Mathematics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 183 papers.
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Who cites it
183 citing papers in PubMed.
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- Presynaptic Trafficking of Glutamate Decarboxylase Isoforms Is Dispensable for Basal GABAergic Neurotransmission.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2026Article
- Charting the nanotopography of inner hair cell synapses using MINFLUX nanoscopy.Science advances · 2025Article
- Coupling Molecular and Cellular Dynamics in a Large-Scale Monte Carlo Simulation.International journal of molecular sciences · 2025Article
- Calcium dynamics in small spaces: Lessons learned from modeling in dendritic spines.Biophysical journal · 2025Review
- The Brownian dynamics simulator PyRID for reacting and interacting particles written in Python.Cell reports methods · 2025Article
- Trans-synaptic molecular context of NMDA receptor nanodomains.Nature communications · 2025Article
- PyReconstruct: A fully open-source, collaborative successor to Reconstruct.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Glycine receptor and release site organization impacts the kinetics of glycinergic synapse currents.Biophysical journal · 2025Article
- Interactions of Therapeutic Antibodies With Presynaptically-Released Misfolded Proteins in Neurodegenerative Diseases. A Spatial Monte-Carlo Simulation Study.CPT: pharmacometrics & systems pharmacology · 2025Article
- Parallelization of Particle-Based Reaction-Diffusion Simulations Using MPI.Journal of computational chemistry · 2025Article
- The architecture of invaginating rod synapses slows glutamate diffusion and shapes synaptic responses.The Journal of general physiology · 2025Article
- A spatial model of autophosphorylation of CaMKII predicts that the lifetime of phospho-CaMKII after induction of synaptic plasticity is greatly prolonged by CaM-trapping.Frontiers in synaptic neuroscience · 2025Article
- In Silico identification and modelling of FDA-approved drugs targeting T-type calcium channels.PloS one · 2025Article
- Data Hazards as An Ethical Toolkit for Neuroscience.Neuroethics · 2025Article
- Spatial modeling algorithms for reactions and transport in biological cells.Nature computational science · 2025Article
- A spatial model of autophosphorylation of CabioRxiv : the preprint server for biology · 2024Article
- Electrophysical cardiac remodeling at the molecular level: Insights into ryanodine receptor activation and calcium-induced calcium release from a stochastic explicit-particle model.Biophysical journal · 2024Article
123 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
Many important physiological processes operate at time and space scales far beyond those accessible to atom-realistic simulations, and yet discrete stochastic rather than continuum methods may best represent finite numbers of molecules interacting in complex cellular spaces. We describe and validate new tools and algorithms developed for a new version of the MCell simulation program (MCell3), which supports generalized Monte Carlo modeling of diffusion and chemical reaction in solution, on surfaces representing membranes, and combinations thereof. A new syntax for describing the spatial directionality of surface reactions is introduced, along with optimizations and algorithms that can substantially reduce computational costs (e.g., event scheduling, variable time and space steps). Examples for simple reactions in simple spaces are validated by comparison to analytic solutions. Thus we show how spatially realistic Monte Carlo simulations of biological systems can be far more cost-effective than often is assumed, and provide a level of accuracy and insight beyond that of continuum methods.
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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.