ArticlePLoS computational biology2016
Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed.
- Process bigraphs and the architecture of compositional systems biology.PLoS computational biology · 2026Article
- From homogeneity to heterogeneity: Refining stochastic simulations of gene regulation.Computational and structural biotechnology journal · 2025Article
- Foundations of a Compositional Systems Biology.ArXiv · 2024Article
- MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface.PLoS computational biology · 2024Article
- Close agreement between deterministic versus stochastic modeling of first-passage time to vesicle fusion.Biophysical journal · 2022Article
- Hybrid modelling of biological systems: current progress and future prospects.Briefings in bioinformatics · 2022Review
- Tools for computational analysis of moving boundary problems in cellular mechanobiology.Wiley interdisciplinary reviews. Systems biology and medicine · 2020Review
- Potential based, spatial simulation of dynamically nested particles.BMC bioinformatics · 2019Article
- Multiscale Stochastic Reaction-Diffusion Algorithms Combining Markov Chain Models with Stochastic Partial Differential Equations.Bulletin of mathematical biology · 2019Article
- Particle-based simulations of polarity establishment reveal stochastic promotion of Turing pattern formation.PLoS computational biology · 2018Article
- Compartmental and Spatial Rule-Based Modeling with Virtual Cell.Biophysical journal · 2017Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Hybrid deterministic-stochastic methods provide an efficient alternative to a fully stochastic treatment of models which include components with disparate levels of stochasticity. However, general-purpose hybrid solvers for spatially resolved simulations of reaction-diffusion systems are not widely available. Here we describe fundamentals of a general-purpose spatial hybrid method. The method generates realizations of a spatially inhomogeneous hybrid system by appropriately integrating capabilities of a deterministic partial differential equation solver with a popular particle-based stochastic simulator, Smoldyn. Rigorous validation of the algorithm is detailed, using a simple model of calcium 'sparks' as a testbed. The solver is then applied to a deterministic-stochastic model of spontaneous emergence of cell polarity. The approach is general enough to be implemented within biologist-friendly software frameworks such as Virtual Cell.
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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.