Models that contain the Modeling Application : NeuroRD (Home Page)

("Computationally efficient, neuronal reaction-diffusion stochastic simulator (pronounced NeurRDS). Java program which runs on any platform. The algorithm is based on Gillespie's tau-leap reaction algorithm, and the stochastic diffusion algorithm of Blackwell. It uses XML-based model specifications.")
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    Models   Description
1.  Dopamine activation of signaling pathways in a medium spiny projection neuron (Oliveira et al. 2012)
Large scale stochastic reaction-diffusion model of signaling pathways in a medium spiny projection neuron dendrite with spines to investigate whether the critical function of anchoring is to locate PKA near the cAMP that activates it or near its targets, such as AMPA receptors located in the post-synaptic density. Simulations, implemented in NeuroRD, show that PKA colocalization with adenylate cyclase, either in the spine head or in the dendrite, leads to greater phosphorylation of DARPP-32 Thr34 and AMPA receptor GluA1 Ser845 than when PKA is anchored away from adenylate cyclase.
2.  Gq coupled signaling pathways involved in striatal synaptic plasticity (Kim et al. 2013)
Model of Gq coupled signaling pathways underlying synaptic plasticity in striatal medium spiny projection neurons. Reactions and diffusion are implemented stochastically in a dendrite with one or more diffusionally coupled spines. Simulations demonstrate that theta burst stimulation, which produces LTP, increases the ratio of PKC:2AG as compared to 20 Hz stimulation, which produces LTD.
3.  Hippocampus CA1: Simulations of LTP signaling pathways (Kim M et al. 2011)
This is a multi-compartmental, stochastic version of the Kim et al. 2010 paper. There are a few additional reactions, and some of the rate constants have been updated. It addresses the role of molecule anchoring in PKA dependent hippocampal LTP.
4.  Signaling pathways In D1R containing striatal spiny projection neurons (Blackwell et al 2018)
We implemented a mechanistic model of signaling pathways activated by dopamine D1 receptors, acetylcholine receptors, and glutamate. We use our novel, computationally efficient simulator, NeuroRD, to simulate stochastic interactions both within and between dendritic spines. Results show that the combined activity of several key plasticity molecules correctly predicts the occurrence of either LTP, LTD or no plasticity for numerous experimental protocols.
5.  Signaling pathways underlying LTP in hippocampal CA1 pyramidal cells (Jedrzejewska-Szmek et al 2017)
" ...We investigated whether the diverse experimental evidence can be unified by creating a spatial, mechanistic model of multiple signaling pathways in hippocampal CA1 neurons. Our results show that the combination of activity of several key kinases can predict the occurrence of long-lasting forms of LTP for multiple experimental protocols. ..."

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