ArticleBiophysical journal2006
Reaction diffusion modeling of calcium dynamics with realistic ER geometry.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 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
54 citing papers in PubMed, 115 citations in OpenAlex.
- Calmodulin controls spatial and temporal specificity of calcium-induced calcium release.PLoS computational biology · 2026Article
- Dendritic heterosynaptic plasticity arises from calcium-based input learning.Communications biology · 2026Article
- Plastic Arbor: A modern simulation framework for synaptic plasticity-From single synapses to networks of morphological neurons.PLoS computational biology · 2026Article
- Biophysical modeling identifies an optimal hybrid amoeboid-mesenchymal mechanism for maximal T cell migration speeds.Cell reports · 2026Article
- Biophysical modeling identifies an optimal hybrid amoeboid-mesenchymal mechanism for maximal T cell migration speeds.bioRxiv : the preprint server for biology · 2025Article
- Spatial modeling algorithms for reactions and transport in biological cells.Nature computational science · 2025Article
- Luminal transport through intact endoplasmic reticulum limits the magnitude of localized CaProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Efficient Estimates of Surface Diffusion Parameters for Spatio-Temporally Resolved Virus Replication Dynamics.International journal of molecular sciences · 2024Article
- Dancing with the Stars: Using Image Analysis to Study the Choreography of the Endoplasmic Reticulum and Its Partners and of Movement Within Its Tubules.Methods in molecular biology (Clifton, N.J.) · 2024Article
- The bioelectric mechanisms of local calcium dynamics in cancer cell proliferation: an extension of the A549Frontiers in molecular biosciences · 2024Article
- Kinetics of the thapsigargin-induced CaFrontiers in physiology · 2023Article
- T cell CaFrontiers in immunology · 2023Review
- Close agreement between deterministic versus stochastic modeling of first-passage time to vesicle fusion.Biophysical journal · 2022Article
- Cytosolic Ca2+-dependent Ca2+ release activity primarily determines the ER Ca2+ level in cells expressing the CPVT-linked mutant RYR2.The Journal of general physiology · 2022Article
- Modeling calcium dynamics in neurons with endoplasmic reticulum: existence, uniqueness and an implicit-explicit finite element scheme.Communications in nonlinear science & numerical simulation · 2022Article
- Mathematical Modeling of Calcium Oscillatory Patterns in a Neuron.Interdisciplinary sciences, computational life sciences · 2021Article
- Three-Dimensional Model of Sub-Plasmalemmal CaFrontiers in immunology · 2021Article
- Reaction diffusion system prediction based on convolutional neural network.Scientific reports · 2020Article
- Mechano-Electric Coupling and Arrhythmogenic Current Generation in a Computational Model of Coupled Myocytes.Frontiers in physiology · 2020Article
- Arrhythmogenic Current Generation by Myofilament-Triggered CaBiophysical journal · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 4 institutions in 1 country.
Funding
Abstract
We describe a finite-element model of mast cell calcium dynamics that incorporates the endoplasmic reticulum's complex geometry. The model is built upon a three-dimensional reconstruction of the endoplasmic reticulum (ER) from an electron tomographic tilt series. Tetrahedral meshes provide volumetric representations of the ER lumen, ER membrane, cytoplasm, and plasma membrane. The reaction-diffusion model simultaneously tracks changes in cytoplasmic and ER intraluminal calcium concentrations and includes luminal and cytoplasmic protein buffers. Transport fluxes via PMCA, SERCA, ER leakage, and Type II IP3 receptors are also represented. Unique features of the model include stochastic behavior of IP3 receptor calcium channels and comparisons of channel open times when diffusely distributed or aggregated in clusters on the ER surface. Simulations show that IP3R channels in close proximity modulate activity of their neighbors through local Ca2+ feedback effects. Cytoplasmic calcium levels rise higher, and ER luminal calcium concentrations drop lower, after IP3-mediated release from receptors in the diffuse configuration. Simulation results also suggest that the buffering capacity of the ER, and not restricted diffusion, is the predominant factor influencing average luminal calcium concentrations.
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.