ArticlePLoS computational biology2024
MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface.
Article in PLoS computational biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
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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.
The trial behind it
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Who cites it
15 citing papers in PubMed.
- Distinct nanoscale architectures of GABAergic inhibitory synapses predict diverse synaptic output.bioRxiv : the preprint server for biology · 2026Article
- 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
- AI-driven virtual cell models in preclinical research: technical pathways, validation mechanisms, and clinical translation potential.NPJ digital medicine · 2025Review
- 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 architecture of invaginating rod synapses slows glutamate diffusion and shapes synaptic responses.The Journal of general physiology · 2025Article
- Synaptic cleft geometry modulates NMDAR opening probability by tuning neurotransmitter residence time.Biophysical journal · 2025Article
- Data Hazards as An Ethical Toolkit for Neuroscience.Neuroethics · 2025Article
- Visualizing mechanistic models by integrating site-specific molecular details into reaction networks.Frontiers in molecular biosciences · 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
- 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
- Computer simulations predict the impact of neuronal atrophy on the calcium dynamics in Huntington's disease.PNAS nexus · 2024Article
- Mitochondrial morphology governs ATP production rate.The Journal of general physiology · 2023Article
- Weighted Ensemble Simulation: Advances in methods, software, and applications.Wiley interdisciplinary reviews. Computational molecular scienceArticle
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Biochemical signaling pathways in living cells are often highly organized into spatially segregated volumes, membranes, scaffolds, subcellular compartments, and organelles comprising small numbers of interacting molecules. At this level of granularity stochastic behavior dominates, well-mixed continuum approximations based on concentrations break down and a particle-based approach is more accurate and more efficient. We describe and validate a new version of the open-source MCell simulation program (MCell4), which supports generalized 3D Monte Carlo modeling of diffusion and chemical reaction of discrete molecules and macromolecular complexes in solution, on surfaces representing membranes, and combinations thereof. The main improvements in MCell4 compared to the previous versions, MCell3 and MCell3-R, include a Python interface and native BioNetGen reaction language (BNGL) support. MCell4's Python interface opens up completely new possibilities for interfacing with external simulators to allow creation of sophisticated event-driven multiscale/multiphysics simulations. The native BNGL support, implemented through a new open-source library libBNG (also introduced in this paper), provides the capability to run a given BNGL model spatially resolved in MCell4 and, with appropriate simplifying assumptions, also in the BioNetGen simulation environment, greatly accelerating and simplifying model validation and comparison.
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What Socratic holds
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 Socratic graph.