ReviewInternational journal of molecular sciences2012
Spatial simulations in systems biology: from molecules to cells.
Review in International journal of molecular sciences, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed.
- Continuum and discrete modeling of binding-site distribution-mediated reactions on lipid surfaces.Biophysical journal · 2026Article
- Extrapolation of lung pharmacokinetics of bedaquiline across species using physiologically-based pharmacokinetic modelling.British journal of clinical pharmacology · 2025Article
- Implications of different membrane compartmentalization models in particle-basedRoyal Society open science · 2023Article
- A multiscale model of the regulation of aquaporin 2 recycling.NPJ systems biology and applications · 2022Article
- Review
- A Review of Using Mathematical Modeling to Improve Our Understanding of Bacteriophage, Bacteria, and Eukaryotic Interactions.Frontiers in microbiology · 2021Review
- Revealing hidden information in osteoblast's mechanotransduction through analysis of time patterns of critical events.BMC bioinformatics · 2020Article
- pSpatiocyte: a high-performance simulator for intracellular reaction-diffusion systems.BMC bioinformatics · 2020Article
- Article
- Potential based, spatial simulation of dynamically nested particles.BMC bioinformatics · 2019Article
- Generalizing Gillespie's Direct Method to Enable Network-Free Simulations.Bulletin of mathematical biology · 2019Article
- Spatial Stochastic Intracellular Kinetics: A Review of Modelling Approaches.Bulletin of mathematical biology · 2019Review
- Dimensionality of Motion and Binding Valency Govern Receptor-Ligand Kinetics As Revealed by Agent-Based Modeling.Frontiers in immunology · 2017Article
- Simulating the origins of life: The dual role of RNA replicases as an obstacle to evolution.PloS one · 2017Article
- Close to the Edge: Growth Restrained by the NAD(P)H/ATP Formation Flux Ratio.Frontiers in microbiology · 2017Article
- Computational support for a scaffolding mechanism of centriole assembly.Scientific reports · 2016Article
- Membrane related dynamics and the formation of actin in cells growing on micro-topographies: a spatial computational model.BMC systems biology · 2014Article
- Article
- Towards the Physics of Calcium Signalling in Plants.Plants (Basel, Switzerland) · 2013Review
- Reaching new levels of realism in modeling biological macromolecules in cellular environments.Journal of molecular graphics & modelling · 2013Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cells are highly organized objects containing millions of molecules. Each biomolecule has a specific shape in order to interact with others in the complex machinery. Spatial dynamics emerge in this system on length and time scales which can not yet be modeled with full atomic detail. This review gives an overview of methods which can be used to simulate the complete cell at least with molecular detail, especially Brownian dynamics simulations. Such simulations require correct implementation of the diffusion-controlled reaction scheme occurring on this level. Implementations and applications of spatial simulations are presented, and finally it is discussed how the atomic level can be included for instance in multi-scale simulation methods.
Indexed as
Identifiers
What OpenQuestion 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 OpenQuestion graph.