Circuits that contain the Model Concept : Calcium dynamics

(Models that include accumulation (and dissipation) of calcium.) Re-display model names without descriptions

	Models	Description
1.	Ca+/HCN channel-dependent persistent activity in multiscale model of neocortex (Neymotin et al 2016)
		"Neuronal persistent activity has been primarily assessed in terms of electrical mechanisms, without attention to the complex array of molecular events that also control cell excitability. We developed a multiscale neocortical model proceeding from the molecular to the network level to assess the contributions of calcium regulation of hyperpolarization-activated cyclic nucleotide-gated (HCN) channels in providing additional and complementary support of continuing activation in the network. ..."
2.	Computer model of clonazepam's effect in thalamic slice (Lytton 1997)
		Demonstration of the effect of a minor pharmacological synaptic change at the network level. Clonazepam, a benzodiazepine, enhances inhibition but is paradoxically useful for certain types of seizures. This simulation shows how inhibition of inhibitory cells (the RE cells) produces this counter-intuitive effect.
3.	Irregular spiking in NMDA-driven prefrontal cortex neurons (Durstewitz and Gabriel 2006)
		Slow N-Methyl-D-aspartic acid (NMDA) synaptic currents are assumed to strongly contribute to the persistently elevated firing rates observed in prefrontal cortex (PFC) during working memory. During persistent activity, spiking of many neurons is highly irregular. ... The highest interspike-interval (ISI) variability occurred in a transition regime where the subthreshold membrane potential distribution shifts from mono- to bimodality, ... Predictability within irregular ISI series was significantly higher than expected from a noise-driven linear process, indicating that it might best be described through complex (potentially chaotic) nonlinear deterministic processes. Accordingly, the phenomena observed in vitro could be reproduced in purely deterministic biophysical model neurons. High spiking irregularity in these models emerged within a chaotic, close-to-bifurcation regime characterized by a shift of the membrane potential distribution from mono- to bimodality and by similar ISI return maps as observed in vitro. ... NMDA-induced irregular dynamics may have important implications for computational processes during working memory and neural coding.
4.	Lobster STG pyloric network model with calcium sensor (Gunay & Prinz 2010) (Prinz et al. 2004)
		This pyloric network model simulator is a C/C++ program that saves 384 different calcium sensor values that are candidates for activity sensors (Gunay and Prinz, 2010). The simulator was used to scan all of the 20 million pyloric network models that were previously collected in a database (Prinz et al, 2004).
5.	Model of eupnea and sigh generation in respiratory network (Toporikova et al 2015)
		Based on recent in vitro data obtained in the mouse embryo, we have built a computational model consisting of two compartments, interconnected through appropriate synapses. One compartment generates sighs and the other produces eupneic bursts. The model reproduces basic features of simultaneous sigh and eupnea generation (two types of bursts differing in terms of shape, amplitude, and frequency of occurrence) and mimics the effect of blocking glycinergic synapses
6.	Modelling platform of the cochlear nucleus and other auditory circuits (Manis & Compagnola 2018)
		"Models of the auditory brainstem have been an invaluable tool for testing hypotheses about auditory information processing and for highlighting the most important gaps in the experimental literature. Due to the complexity of the auditory brainstem, and indeed most brain circuits, the dynamic behavior of the system may be difficult to predict without a detailed, biologically realistic computational model. Despite the sensitivity of models to their exact construction and parameters, most prior models of the cochlear nucleus have incorporated only a small subset of the known biological properties. This confounds the interpretation of modelling results and also limits the potential future uses of these models, which require a large effort to develop. To address these issues, we have developed a general purpose, bio-physically detailed model of the cochlear nucleus for use both in testing hypotheses about cochlear nucleus function and also as an input to models of downstream auditory nuclei. The model implements conductance-based Hodgkin-Huxley representations of cells using a Python-based interface to the NEURON simulator. ..."
7.	Multiscale model of excitotoxicity in PD (Muddapu and Chakravarthy 2020)
		Parkinson's disease (PD) is a neurodegenerative disorder caused by loss of dopaminergic neurons in Substantia Nigra pars compacta (SNc). Although the exact cause of cell death is not clear, the hypothesis that metabolic deficiency is a key factor has been gaining attention in recent years. In the present study, we investigate this hypothesis using a multi-scale computational model of the subsystem of the basal ganglia comprising Subthalamic Nucleus (STN), Globus Pallidus externa (GPe) and SNc. The proposed model is a multiscale model in that interactions among the three nuclei are simulated using more abstract Izhikevich neuron models, while the molecular pathways involved in cell death of SNc neurons are simulated in terms of detailed chemical kinetics. Simulation results obtained from the proposed model showed that energy deficiencies occurring at cellular and network levels could precipitate the excitotoxic loss of SNc neurons in PD. At the subcellular level, the models show how calcium elevation leads to apoptosis of SNc neurons. The therapeutic effects of several neuroprotective interventions are also simulated in the model. From neuroprotective studies, it was clear that glutamate inhibition and apoptotic signal blocker therapies were able to halt the progression of SNc cell loss when compared to other therapeutic interventions, which only slows down the progression of SNc cell loss.
8.	Multitarget pharmacology for Dystonia in M1 (Neymotin et al 2016)
		" ... We developed a multiscale model of primary motor cortex, ranging from molecular, up to cellular, and network levels, containing 1715 compartmental model neurons with multiple ion channels and intracellular molecular dynamics. We wired the model based on electrophysiological data obtained from mouse motor cortex circuit mapping experiments. We used the model to reproduce patterns of heightened activity seen in dystonia by applying independent random variations in parameters to identify pathological parameter sets. ..."
9.	Nonlinear dendritic processing in barrel cortex spiny stellate neurons (Lavzin et al. 2012)
		This is a multi-compartmental simulation of a spiny stellate neuron which is stimulated by a thalamocortical (TC) and cortico-cortical (CC) inputs. No other cells are explicitly modeled; the presynaptic network activation is represented by the number of active synapses. Preferred and non –preferred thalamic directions thus correspond to larder/smaller number of TC synapses. This simulation revealed that randomly activated synapses can cooperatively trigger global NMDA spikes, which involve participation of most of the dendritic tree. Surprisingly, we found that although the voltage profile of the cell was uniform, the calcium influx was restricted to ‘hot spots’ which correspond to synaptic clusters or large conductance synapses
10.	Olfactory bulb mitral cell gap junction NN model: burst firing and synchrony (O`Connor et al. 2012)
		In a network of 6 mitral cells connected by gap junction in the apical dendrite tuft, continuous current injections of 0.06 nA are injected into 20 locations in the apical tufts of two of the mitral cells. The current injections into one of the cells starts 10 ms after the other to generate asynchronous firing in the cells (Migliore et al. 2005 protocol). Firing of the cells is asynchronous for the first 120 ms. However after the burst firing phase is completed the firing in all cells becomes synchronous.
11.	Olfactory Bulb mitral-granule network generates beta oscillations (Osinski & Kay 2016)
		This model of the dendrodendritic mitral-granule synaptic network generates gamma and beta oscillations as a function of the granule cell excitability, which is represented by the granule cell resting membrane potential.
12.	Principles of Computational Modelling in Neuroscience (Book) (Sterratt et al. 2011)
		"... This book provides a step-by-step account of how to model the neuron and neural circuitry to understand the nervous system at all levels, from ion channels to networks. Starting with a simple model of the neuron as an electrical circuit, gradually more details are added to include the effects of neuronal morphology, synapses, ion channels and intracellular signaling. The principle of abstraction is explained through chapters on simplifying models, and how simplified models can be used in networks. This theme is continued in a final chapter on modeling the development of the nervous system. Requiring an elementary background in neuroscience and some high school mathematics, this textbook is an ideal basis for a course on computational neuroscience."
13.	Realistic barrel cortical column - Matlab (Huang et al., 2022)
		Reconstructed rodent barrel cortical column (thalamic filter-and-fire input, L4 and L2/3 spiking neurons) based on measured distributions, so each run will create a different connectivity). Includes 13 types of inhibitory and excitatory neurons, implemented as Izhikevich neurons. Includes both a Matlab and a Python (NetPyNe) implementation.
14.	Realistic barrel cortical column - NetPyNE (Huang et al., 2022)
		Reconstructed rodent barrel cortical column (thalamic filter-and-fire input, L4 and L2/3 spiking neurons) based on measured distributions, so each run will create a different connectivity). Includes 13 types of inhibitory and excitatory neurons, implemented as Izhikevich neurons. Includes both a Matlab and a Python (NetPyNe) implementation.
15.	State dependent drug binding to sodium channels in the dentate gyrus (Thomas & Petrou 2013)
		A Markov model of sodium channels was developed that includes drug binding to fast inactivated states. This was incorporated into a model of the dentate gyrus to investigate the effects of anti-epileptic drugs on neuron and network properties.
16.	Syn Plasticity Regulation + Information Processing in Neuron-Astrocyte Networks (Vuillaume et al 21)
		"... we consider a model of astrocyte-regulated synapses to investigate this hypothesis at the level of layered networks of interacting neurons and astrocytes. Our simulations hint that gliotransmission sustains the transfer function across layers, although it decorrelates the neuronal activity from the signal pattern..."
17.	Thalamic quiescence of spike and wave seizures (Lytton et al 1997)
		A phase plane analysis of a two cell interaction between a thalamocortical neuron (TC) and a thalamic reticularis neuron (RE).
18.	Thalamic Reticular Network (Destexhe et al 1994)
		Demo for simulating networks of thalamic reticular neurons (reproduces figures from Destexhe A et al 1994)
19.	Thalamocortical and Thalamic Reticular Network (Destexhe et al 1996)
		NEURON model of oscillations in networks of thalamocortical and thalamic reticular neurons in the ferret. (more applications for a model quantitatively identical to previous DLGN model; updated for NEURON v4 and above)

Re-display model names without descriptions