ArticleMolecular biology of the cell2021
Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry.
Article in Molecular biology of the cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 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
18 citing papers in PubMed.
- Continuum and discrete modeling of binding-site distribution-mediated reactions on lipid surfaces.Biophysical journal · 2026Article
- Predicting Cardiovascular Events with Time-Lagged Inflammatory Dynamics: Stochastic Delay Modeling.Computational and structural biotechnology journal · 2026Article
- A membrane-driven biochemical oscillator tunable by the volume to surface area ratio.bioRxiv : the preprint server for biology · 2025Article
- Parallelization of Particle-Based Reaction-Diffusion Simulations Using MPI.Journal of computational chemistry · 2025Article
- From homogeneity to heterogeneity: Refining stochastic simulations of gene regulation.Computational and structural biotechnology journal · 2025Article
- Role of intercellular interactions on single cell and population level responses: considerations for multicellular bioreporter design.Frontiers in molecular biosciences · 2025Article
- Molecular Crowding by Computational Approaches.Sub-cellular biochemistry · 2025Review
- MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface.PLoS computational biology · 2024Article
- Incorporating temporal information during feature engineering bolsters emulation of spatio-temporal emergence.Bioinformatics (Oxford, England) · 2024Article
- Temporal control by cofactors prevents kinetic trapping in retroviral Gag lattice assembly.Biophysical journal · 2023Article
- Implications of different membrane compartmentalization models in particle-basedRoyal Society open science · 2023Article
- Self-assembly coupled to liquid-liquid phase separation.PLoS computational biology · 2023Article
- Modeling membrane reshaping driven by dynamic protein assemblies.Current opinion in structural biology · 2023Review
- Particle-based model of mechanosensory contractility kit assembly.Biophysical journal · 2022Article
- A Review of Mechanics-Based Mesoscopic Membrane Remodeling Methods: Capturing Both the Physics and the Chemical Diversity.The Journal of membrane biology · 2022Review
- Simulation of receptor triggering by kinetic segregation shows role of oligomers and close contacts.Biophysical journal · 2022Article
- WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications.Journal of chemical theory and computation · 2022Article
- Speed limits of protein assembly with reversible membrane localization.The Journal of chemical physics · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
Most of the fascinating phenomena studied in cell biology emerge from interactions among highly organized multimolecular structures embedded into complex and frequently dynamic cellular morphologies. For the exploration of such systems, computer simulation has proved to be an invaluable tool, and many researchers in this field have developed sophisticated computational models for application to specific cell biological questions. However, it is often difficult to reconcile conflicting computational results that use different approaches to describe the same phenomenon. To address this issue systematically, we have defined a series of computational test cases ranging from very simple to moderately complex, varying key features of dimensionality, reaction type, reaction speed, crowding, and cell size. We then quantified how explicit spatial and/or stochastic implementations alter outcomes, even when all methods use the same reaction network, rates, and concentrations. For simple cases, we generally find minor differences in solutions of the same problem. However, we observe increasing discordance as the effects of localization, dimensionality reduction, and irreversible enzymatic reactions are combined. We discuss the strengths and limitations of commonly used computational approaches for exploring cell biological questions and provide a framework for decision making by researchers developing new models. As computational power and speed continue to increase at a remarkable rate, the dream of a fully comprehensive computational model of a living cell may be drawing closer to reality, but our analysis demonstrates that it will be crucial to evaluate the accuracy of such models critically and systematically.
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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.