ReviewJournal of neuroscience methods2013
Approaches and tools for modeling signaling pathways and calcium dynamics in neurons.
Review in Journal of neuroscience methods, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 48 citations in OpenAlex.
- Differential behaviors of calcium-induced calcium release in one dimensional dendrite by Nernst-Planck equation, cable model and pure diffusion model.Cognitive neurodynamics · 2024Article
- Close agreement between deterministic versus stochastic modeling of first-passage time to vesicle fusion.Biophysical journal · 2022Article
- Reinforcing Interdisciplinary Collaborations to Unravel the Astrocyte "Calcium Code".Journal of molecular neuroscience : MN · 2022Review
- Stochastic reaction-diffusion modeling of calcium dynamics in 3D dendritic spines of Purkinje cells.Biophysical journal · 2021Article
- A multi-state model of the CaMKII dodecamer suggests a role for calmodulin in maintenance of autophosphorylation.PLoS computational biology · 2019Article
- What can computational modeling offer for studying the CaNeural regeneration research · 2018Review
- Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures.Frontiers in neuroinformatics · 2018Article
- Pleiotropic effects of schizophrenia-associated genetic variants in neuron firing and cardiac pacemaking revealed by computational modeling.Translational psychiatry · 2017Article
- Load balancing for multi-threaded PDES of stochastic reaction-diffusion in neurons.Journal of simulation : JOS · 2017Article
- Multithreaded Stochastic PDES for Reactions and Diffusions in Neurons.ACM transactions on modeling and computer simulation : a publication of the Association for Computing Machinery · 2017Article
- Neuronal calcium wave propagation varies with changes in endoplasmic reticulum parameters: a computer model.Neural computation · 2015Article
- Calcium: amplitude, duration, or location?The Biological bulletin · 2015Review
- Multiscale model of dynamic neuromodulation integrating neuropeptide-induced signaling pathway activity with membrane electrophysiology.Biophysical journal · 2015Article
- Article
- Parallel Stochastic Discrete Event Simulation of Calcium Dynamics in Neuron.IEEE/ACM transactions on computational biology and bioinformaticsArticle
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Authors and funding
1 author at 1 institution in 1 country.
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Abstract
Signaling pathways are cascades of intracellular biochemical reactions that are activated by transmembrane receptors, and ultimately lead to transcription in the nucleus. In neurons, both calcium permeable synaptic and ionic channels as well as G protein coupled receptors initiate activation of signaling pathway molecules that interact with electrical activity at multiple spatial and time scales. At small temporal and spatial scales, calcium modifies the properties of ionic channels, whereas at larger temporal and spatial scales, various kinases and phosphatases modify the properties of ionic channels, producing phenomena such as synaptic plasticity and homeostatic plasticity. The elongated structure of neuronal dendrites and the organization of multi-protein complexes by anchoring proteins imply that the spatial dimension must be explicit. Therefore, modeling signaling pathways in neurons utilizes algorithms for both diffusion and reactions. The small size of spines coupled with small concentrations of some molecules implies that some reactions occur stochastically. The need for stochastic simulation of many reaction and diffusion events coupled with the multiple temporal and spatial scales makes modeling of signaling pathways a difficult problem. Several different software programs have achieved different aspects of these capabilities. This review explains some of the mathematical formulas used for modeling reactions and diffusion. In addition, it briefly presents the simulators used for modeling reaction-diffusion systems in neurons, together with scientific problems addressed.
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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.