ArticleNeuroinformatics2005
A modeling environment with three-dimensional morphology, A-Cell-3D, and Ca2+ dynamics in a spine.
Article in Neuroinformatics, 2005. 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.
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Who cites it
11 citing papers in PubMed.
- Spatio-temporal Dynamics and Mechanisms of Stress Granule Assembly.PLoS computational biology · 2015Article
- Regulation of signal transduction by spatial parameters: a case in NF-κB oscillation.IET systems biology · 2015Article
- Regulation of NF-κB Oscillation by Nuclear Transport: Mechanisms Determining the Persistency and Frequency of Oscillation.PloS one · 2015Article
- Regulation of nuclear NF-κB oscillation by a diffusion coefficient and its biological implications.PloS one · 2014Article
- Critical role of transient activity of MT1-MMP for ECM degradation in invadopodia.PLoS computational biology · 2013Article
- Roles of spatial parameters on the oscillation of nuclear NF-κB: computer simulations of a 3D spherical cell.PloS one · 2012Article
- Establishment and validation of computational model for MT1-MMP dependent ECM degradation and intervention strategies.PLoS computational biology · 2012Article
- Postsynaptic signal transduction models for long-term potentiation and depression.Frontiers in computational neuroscience · 2010Article
- Review of papers describing neuroinformatics software.Neuroinformatics · 2009Article
- Structural plasticity can produce metaplasticity.PloS one · 2009Article
- Molecular properties of rhodopsin and rod function.The Journal of biological chemistry · 2007Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A-Cell-3D was developed to model and simulate a neuron with three-dimensional (3D) morphology utilizing graphic user interface (GUI)-based operations. A-Cell-3D generates and compartmentalizes 3D morphologies of a whole cell or a part of a cell based on a small number of parameters. A-Cell-3D has functions for embedding biochemical reactions and electrical equivalent circuits in the generated 3D morphology, automatically generating a simulation program for spatiotemporal numerical integration, and for visualizing the simulation results. A-Cell-3D is a free software and will be a powerful tool for both experimental and theoretical researchers in modeling and simulating neurons. The Ca2+ dynamics in a dendritic spine and its parent dendrite were modeled and simulated to demonstrate the capabilities of A-Cell-3D. The constructed reaction-diffusion model comprised Ca2+ entry at the spine head, Ca2+ buffering by endogenous buffers, Ca2+ extrusion, and Ca2+ diffusion with or without exogenous Ca2+ indicator dyes. A simulation program was generated by A-Cell-3D, and differential equations were numerically integrated by the fourth-order Runge-Kutta method.
Indexed as
Identifiers
15897616What 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.