Models that contain the Model Type : Extracellular

(Extracellular voltages or chemical concentrations. Models in the context of the extracellular space.)
Re-display model names without descriptions
    Models   Description
1.  5-neuron-model of neocortex for producing realistic extracellular AP shapes (Van Dijck et al. 2012)
This is a 5-neuron model of neocortex, containing one tufted layer-5 pyramidal cell, two non-tufted pyramidal cells, and two inhibitory interneurons. It was used to reproduce extracellular spike shapes in a study comparing algorithms for spike sorting and electrode selection. The neuron models are adapted from Dyhrfjeld-Johnsen et al. (2005).
2.  A detailed and fast model of extracellular recordings (Camunas-Mesa & Qurioga 2013)
"We present a novel method to generate realistic simulations of extracellular recordings. The simulations were obtained by superimposing the activity of neurons placed randomly in a cube of brain tissue. Detailed models of individual neurons were used to reproduce the extracellular action potentials of close-by neurons. ..."
3.  A model for recurrent spreading depolarizations (Conte et al. 2017)
A detailed biophysical model for a neuron/astrocyte network is developed in order to explore mechanisms responsible for cortical spreading depolarizations. This includes a model for the Na+-glutamate transporter, which allows for a detailed description of reverse glutamate uptake. In particular, we consider the specific roles of elevated extracellular glutamate and K+ in the initiation, propagation and recurrence of spreading depolarizations.
4.  Biophysical model for field potentials of networks of I&F neurons (beim Graben & Serafim 2013)
"... Starting from a reduced three-compartment model of a single pyramidal neuron, we derive an observation model for dendritic dipole currents in extracellular space and thereby for the dendritic field potential (DFP) that contributes to the local field potential (LFP) of a neural population. ... Our reduced three-compartment scheme allows to derive networks of leaky integrate-and-fire (LIF) models, which facilitates comparison with existing neural network and observation models. ..."
5.  CA1 pyramidal neurons: effect of external electric field from power lines (Cavarretta et al. 2014)
The paper discusses the effects induced by an electric field at power lines frequency.
6.  Ca2+ Oscillations in Sympathetic neurons (Friel 1995)
" ... This study focuses on caffeine-induced [Ca2+]i oscillations in sympathetic neurons. ... The aim of the study was to understand the mechanism responsible for the oscillations. As a starting point, [Ca2+]i relaxations were examined after membrane depolarization and exposure to caffeine. For both stimuli, post-stimulus relaxations could be described by the sum of two decaying exponential functions, consistent with a one-pool system in which Ca2+ transport between compartments is regulated by linear Ca2+ pumps and leaks. After modifying the store to include a [Ca2+]i-sensitive leak, the model also exhibits oscillations such as those observed experimentally. ... Thus, a one-pool model with a single [Ca2+]i-sensitive Ca2+ permeability is adequate to account for many of the quantitative properties of steady-state [Ca2+]i oscillations in sympathetic neurons. ..."
7.  CA3 Network Model of Epileptic Activity (Sanjay et. al, 2015)
This computational study investigates how a CA3 neuronal network consisting of pyramidal cells, basket cells and OLM interneurons becomes epileptic when dendritic inhibition to pyramidal cells is impaired due to the dysfunction of OLM interneurons. After standardizing the baseline activity (theta-modulated gamma oscillations), systematic changes are made in the connectivities between the neurons, as a result of step-wise impairment of dendritic inhibition.
8.  Changes of ionic concentrations during seizure transitions (Gentiletti et al. 2016)
"... In order to investigate the respective roles of synaptic interactions and nonsynaptic mechanisms in seizure transitions, we developed a computational model of hippocampal cells, involving the extracellular space, realistic dynamics of Na+, K+, Ca2+ and Cl - ions, glial uptake and extracellular diffusion mechanisms. We show that the network behavior with fixed ionic concentrations may be quite different from the neurons’ behavior when more detailed modeling of ionic dynamics is included. In particular, we show that in the extended model strong discharge of inhibitory interneurons may result in long lasting accumulation of extracellular K+, which sustains the depolarization of the principal cells and causes their pathological discharges. ..."
9.  Contribution of the axon initial segment to APs recorded extracellularly (Telenczuk et al 2018)
"... It was recently proposed that at onset of an (Action Potential) AP the soma and the (Axon Initial Segment) AIS form a dipole. We study the extracellular signature (the extracellular action potential, EAP) generated by such a dipole. First, we demonstrate the formation of the dipole and its extracellular signature in detailed morphological models of a reconstructed pyramidal neuron. Then, we study the EAP waveform and its spatial dependence in models with axonal AP initiation and contrast it with the EAP obtained in models with somatic AP initiation. We show that in the models with axonal AP initiation the dipole forms between somatodendritic compartments and the AIS, and not between soma and dendrites as in the classical models. ..."
10.  Dependence of neuronal firing on astroglial membrane transport mechanisms (Oyehaug et al 2012)
"Exposed to a sufficiently high extracellular potassium concentration ([K?+?]o), the neuron can fire spontaneous discharges or even become inactivated due to membrane depolarisation (‘depolarisation block’). Since these phenomena likely are related to the maintenance and propagation of seizure discharges, it is of considerable importance to understand the conditions under which excess [K?+?]o causes them. To address the putative effect of glial buffering on neuronal activity under elevated [K?+?]o conditions, we combined a recently developed dynamical model of glial membrane ion and water transport with a Hodgkin–Huxley type neuron model. In this interconnected glia-neuron model we investigated the effects of natural heterogeneity or pathological changes in glial membrane transporter density by considering a large set of models with different, yet empirically plausible, sets of model parameters. ..."
11.  Determinants of the intracellular and extracellular waveforms in DA neurons (Lopez-Jury et al 2018)
To systematically address the contribution of AIS, dendritic and somatic compartments to shaping the two-component action potentials (APs), we modeled APs of male mouse and rat dopaminergic neurons. A parsimonious two-domain model, with high (AIS) and lower (dendro-somatic) Na+ conductance, reproduced the notch in the temporal derivatives, but not in the extracellular APs, regardless of morphology. The notch was only revealed when somatic active currents were reduced, constraining the model to three domains. Thus, an initial AIS spike is followed by an actively generated spike by the axon-bearing dendrite (ABD), in turn followed mostly passively by the soma. Larger AISs and thinner ABD (but not soma-to-AIS distance) accentuate the AIS component.
12.  Dipolar extracellular potentials generated by axonal projections (McColgan et al 2017)
" ... Here, we established experimentally and theoretically that contributions of axons to EFPs can be significant. Modeling action potentials propagating along axons, we showed that EFPs were prominent in the presence of terminal zones where axons branch and terminate in close succession, as found in many brain regions. Our models predicted a dipolar far field and a polarity reversal at the center of the terminal zone. ..."
13.  Dipole Localization Kit (Mechler & Victor, 2012)
We localize a single neuron from the spatial sample of its EAP amplitudes recorded with a multisite probe (with 6 or more independent measurement sites or channels, e.g., a silicon polytrode, a stepped tetrode, etc.) This is an inverse problem and we solve it by fitting a model to the EAPs that consists of a volume conductor model of the neural tissue (known), a realistic model of the probe (known), and a single dipole current source of the model neuron (unknown). The dipole is free to change position, size, and orientation (a total of 6 parameters) at each moment during the action potential.
14.  Double cable myelinated axon (Layer 5 pyramidal neuron; Cohen et al 2020)
The periaxonal space in myelinated axons is conductive (~50 ohm cm). Together with a rapidly charging myelin sheath and relatively sealed paranodes, periaxonal conduction shapes the saltating voltage profiles of transaxonal (Vm), transmyelin (Vmy) and transfibre (Vmym) potentials. This model exemplifies double cable saltatory conduction across both time and space, and is the same cell (#6) as seen in Movie S4 of Cohen et al. 2020. This model version allows one to visualize and manipulate the controlling parameters of a propagating action potential. Further notes: The corresponding potentials in NEURON to those named above are v, vext (or vext[0]) and v+vext, respectively. The loaded biophysical parameters were those optimized for this cell (Cohen et al. 2020).
15.  Effect of ionic diffusion on extracellular potentials (Halnes et al 2016)
"Recorded potentials in the extracellular space (ECS) of the brain is a standard measure of population activity in neural tissue. Computational models that simulate the relationship between the ECS potential and its underlying neurophysiological processes are commonly used in the interpretation of such measurements. Standard methods, such as volume-conductor theory and current-source density theory, assume that diffusion has a negligible effect on the ECS potential, at least in the range of frequencies picked up by most recording systems. This assumption remains to be verified. We here present a hybrid simulation framework that accounts for diffusive effects on the ECS potential. ..."
16.  Effects of Chloride accumulation and diffusion on GABAergic transmission (Jedlicka et al 2011)
"In the CNS, prolonged activation of GABA(A) receptors (GABA(A)Rs) has been shown to evoke biphasic postsynaptic responses, consisting of an initial hyperpolarization followed by a depolarization. A potential mechanism underlying the depolarization is an acute chloride (Cl(-)) accumulation resulting in a shift of the GABA(A) reversal potential (E(GABA)). The amount of GABA-evoked Cl(-) accumulation and accompanying depolarization depends on presynaptic and postsynaptic properties of GABAergic transmission, as well as on cellular morphology and regulation of Cl(-) intracellular concentration ([Cl(-)](i)). To analyze the influence of these factors on the Cl(-) and voltage behavior, we studied spatiotemporal dynamics of activity-dependent [Cl(-)](i) changes in multicompartmental models of hippocampal cells based on realistic morphological data. ..."
17.  Electrodiffusive astrocytic and extracellular ion concentration dynamics model (Halnes et al. 2013)
An electrodiffusive formalism was developed for computing the dynamics of the membrane potential and ion concentrations in the intra- and extracellular space in a one-dimensional geometry (cable). This (general) formalism was implemented in a model of astrocytes exchanging K+, Na+ and Cl- ions with the extracellular space (ECS). A limited region (0< x<l/10 where l is the astrocyte length) of the ECS was exposed to an increase in the local K+ concentration. The model is used to explore how astrocytes contribute in transporting K+ out from high-concentration regions via a mechanism known as spatial buffering, which involves local uptake from high concentration regions, intracellular transport, and release of K+ in regions with lower ECS concentrations.
18.  Ephaptic coupling in passive cable and MSO neuron models (Goldwyn & Rinzel 2016)
Simulation code to explore how the synchronous activity of a bundle of neurons generates extracellular voltage, and how this extracellular voltage influences the membrane potential of "nearby" neurons. A non-synaptic mechanism known as ephaptic coupling. A model of a passive cable population (including user-friendly matlab GUI) and a model of medial superior olive neurons are included.
19.  Ephaptic interactions in olfactory nerve (Bokil et al 2001)
Bokil, H., Laaris, N., Blinder, K., Ennis, M., and Keller, A. (2001) Ephaptic interactions in the mammalian olfactory system. J. Neurosci. 21:RC173(1-5)
20.  Extracellular Action Potential Simulations (Gold et al 2007)
This package recreates the the principal experiments described in (Gold, Henze and Koch, 2007) and includes the core code necessary to create your own Extracellular Action Potential Simulations.
21.  Extracellular fields for a three-dimensional network of cells using NEURON (Appukuttan et al 2017)
" ... In the present work, we demonstrate a technique to couple the extracellular fields of individual cells within the NEURON simulation environment. The existing features of the simulator are extended by explicitly defining current balance equations, resulting in the coupling of the extracellular fields of adjacent cells. ..."
22.  Gamma genesis in the basolateral amygdala (Feng et al 2019)
Using in vitro and in vivo data we develop the first large-scale biophysically and anatomically realistic model of the basolateral amygdala nucleus (BL), which reproduces the dynamics of the in vivo local field potential (LFP). Significantly, it predicts that BL intrinsically generates the transient gamma oscillations observed in vivo. The model permitted exploration of the poorly understood synaptic mechanisms underlying gamma genesis in BL, and the model's ability to compute LFPs at arbitrary numbers of recording sites provided insights into the characteristics of the spatial properties of gamma bursts. Furthermore, we show how gamma synchronizes principal cells to overcome their low firing rates while simultaneously promoting competition, potentially impacting their afferent selectivity and efferent drive, and thus emotional behavior.
23.  Glutamate diffusion and AMPA receptor activation in the cerebellar glomerulus (Saftenku 2005)
Synaptic conductances are influenced markedly by the geometry of the space surrounding the synapse since the transient glutamate concentration in the synaptic cleft is determined by this geometry. Our paper is an attempt to understand the reasons for slow glutamate diffusion in the cerebellar glomerulus, a structure situated around the enlarged mossy fiber terminal in the cerebellum and surrounded by a glial sheath. ... Our results suggest at least a 7- to 10-fold lower apparent diffusion coefficient of glutamate in the porous medium of the glomerulus than in water. ... See paper for details and more.
24.  Impedance spectrum in cortical tissue: implications for LFP signal propagation (Miceli et al. 2017)
" ... Here, we performed a detailed investigation of the frequency dependence of the conductivity within cortical tissue at microscopic distances using small current amplitudes within the typical (neuro)physiological micrometer and sub-nanoampere range. We investigated the propagation of LFPs, induced by extracellular electrical current injections via patch-pipettes, in acute rat brain slice preparations containing the somatosensory cortex in vitro using multielectrode arrays. Based on our data, we determined the cortical tissue conductivity over a 100-fold increase in signal frequency (5-500 Hz). Our results imply at most very weak frequency-dependent effects within the frequency range of physiological LFPs. Using biophysical modeling, we estimated the impact of different putative impedance spectra. Our results indicate that frequency dependencies of the order measured here and in most other studies have negligible impact on the typical analysis and modeling of LFP signals from extracellular brain recordings."
25.  Large-scale model of neocortical slice in vitro exhibiting persistent gamma (Tomsett et al. 2014)
This model contains 15 neuron populations (8 excitatory, 7 inhibitory) arranged into 4 cortical layers (layer 1 empty, layers 2/3 combined). It produces a persistent gamma oscillation driven by layer 2/3. It runs using the VERTEX simulator, which is written in Matlab and is available from http://www.vertexsimulator.org
26.  LFP in striatum (Tanaka & Nakamura 2019)
The numerical simulations of LFP generation by cortical pyramidal neuron and medium-sized spiny neurons.
27.  Mechanisms of extraneuronal space shrinkage (Ostby et al 2009)
"Neuronal stimulation causes ~30% shrinkage of the extracellular space (ECS) between neurons and surrounding astrocytes in grey and white matter under experimental conditions. Despite its possible implications for a proper understanding of basic aspects of potassium clearance and astrocyte function, the phenomenon remains unexplained. Here we present a dynamic model that accounts for current experimental data related to the shrinkage phenomenon in wild-type as well as in gene knockout individuals. ... Considering the current state of knowledge, the model framework appears sufficiently detailed and constrained to guide future key experiments and pave the way for more comprehensive astroglia–neuron interaction models for normal as well as pathophysiological situations. "
28.  Modeling extracellular electrical stimulation (Tahayori et al. 2012)
"The validity of approximate equations describing the membrane potential under extracellular electrical stimulation (Meffin et al 2012 J. Neural Eng. 9 065005) is investigated through finite element analysis in this paper. To this end, the finite element method is used to simulate a cylindrical neurite under extracellular stimulation. Laplace's equations with appropriate boundary conditions are solved numerically in three dimensions and the results are compared to the approximate analytic solutions. ..."
29.  Modeling local field potentials (Bedard et al. 2004)
This demo simulates a model of local field potentials (LFP) with variable resistivity. This model reproduces the low-pass frequency filtering properties of extracellular potentials. The model considers inhomogeneous spatial profiles of conductivity and permittivity, which result from the multiple media (fluids, membranes, vessels, ...) composing the extracellular space around neurons. Including non-constant profiles of conductivity enables the model to display frequency filtering properties, ie slow events such as EPSPs/IPSPs are less attenuated than fast events such as action potentials. The demo simulates Fig 6 of the paper.
30.  Modeling single neuron LFPs and extracellular potentials with LFPsim (Parasuram et al. 2016)
LFPsim - Simulation scripts to compute Local Field Potentials (LFP) from cable compartmental models of neurons and networks implemented in the NEURON simulation environment.
31.  Modelling large scale electrodiffusion near morphologically detailed neurons (Solbra et al 2018)
" ... Here, we present the 3-D Kirchhoff-Nernst-Planck (KNP) framework, tailored to explore electrodiffusive effects on large spatiotemporal scales. By assuming electroneutrality, the KNP-framework circumvents charge-relaxation processes on the spatiotemporal scales of nanometers and nanoseconds, and makes it feasible to run simulations on the spatiotemporal scales of millimeters and seconds on a standard desktop computer. In the present work, we use the 3-D KNP framework to simulate the dynamics of ion concentrations and the electrical potential surrounding a morphologically detailed pyramidal cell. ..."
32.  Modulation of hippocampal rhythms by electric fields and network topology (Berzhanskaya et al. 2013)
“… Here we present experimental and computational evidence of the interplay among hippocampal synaptic circuitry, neuronal morphology, external electric fields, and network activity. Electrophysiological data are used to constrain and validate an anatomically and biophysically realistic model of area CA1 containing pyramidal cells and two interneuron types: dendritic- and perisomatic-targeting. We report two lines of results: addressing the network structure capable of generating theta-modulated gamma rhythms, and demonstrating electric field effects on those rhythms. First, theta-modulated gamma rhythms require specific inhibitory connectivity. … The second major finding is that subthreshold electric fields robustly alter the balance between different rhythms. …”
33.  Myelinated nerve fibre myelin resistance dependent on extracellular K+ level (Brazhe et al. 2010)
Excitation leads to rise in paranodal [K]e under the myelin. This causes structural changes in myelin structure and resistance. Current model aims to simulate this aspect. This is a space-clamped model of a double-cable nerve fibre.
34.  Network model with dynamic ion concentrations (Ullah et al. 2009)
This is a network model composed of 100 excitatory and 100 inhibitory neurons with dynamic ion concentrations as described in "The Influence of Sodium and Potassium Dynamics on Excitability, Seizures, and the Stability of Persistent States: II. Network and Glia Dynamics (2009) Journal of Computational Neuroscience, 26:171-183".
35.  Neuromuscular network model of gut motility (Barth et al 2017)
Here we develop an integrated neuromechanical model of the ENS and assess neurostimulation strategies for enhancing gut motility. The model includes a network of enteric neurons, smooth muscle fibers, and interstitial cells of Cajal, which regulate propulsion of a virtual pellet in a model of gut motility.
36.  Perceptual judgments via sensory-motor interaction assisted by cortical GABA (Hoshino et al 2018)
"Recurrent input to sensory cortex, via long-range reciprocal projections between motor and sensory cortices, is essential for accurate perceptual judgments. GABA levels in sensory cortices correlate with perceptual performance. We simulated a neuron-astrocyte network model to investigate how top-down, feedback signaling from a motor network (Nmot) to a sensory network (Nsen) affects perceptual judgments in association with ambient (extracellular) GABA levels. In the Nsen, astrocytic transporters modulated ambient GABA levels around pyramidal cells. A simple perceptual task was implemented: detection of a feature stimulus presented to the Nsen. ..."
37.  PyPNS: Multiscale Simulation of a Peripheral Nerve in Python (Lubba et al 2018)
" ... To reduce experimentation load and allow for a faster, more detailed analysis of peripheral nerve stimulation and recording, computational models incorporating experimental insights will be of great help. We present a peripheral nerve simulator that combines biophysical axon models and numerically solved and idealised extracellular space models in one environment. We modelled the extracellular space as a three-dimensional resistive continuum governed by the electro-quasistatic approximation of the Maxwell equations. ..."
38.  Reconstructing cerebellar granule layer evoked LFP using convolution (ReConv) (Diwakar et al. 2011)
The model allows reconstruction of evoked local field potentials as seen in the cerebellar granular layer. The approach uses a detailed model of cerebellar granule neuron to generate data traces and then uses a "ReConv" or jittered repetitive convolution technique to reproduce post-synaptic local field potentials in the granular layer. The algorithm was used to generate both in vitro and in vivo evoked LFP and reflected the changes seen during LTP and LTD, when such changes were induced in the underlying neurons by modulating release probability of synapses and sodium channel regulated intrinsic excitability of the cells.
39.  Subiculum network model with dynamic chloride/potassium homeostasis (Buchin et al 2016)
This is the code implementing the single neuron and spiking neural network dynamics. The network has the dynamic ion concentrations of extracellular potassium and intracellular chloride. The code contains multiple parameter variations to study various mechanisms of the neural excitability in the context of chloride homeostasis.
40.  The neuro-electronic junction (planar and engulfed electrodes) (Massobrio et al 2018)
Models of the neuron, planar (GPµE) and mushroom-shaped (GMµE) microelectrodes, neuro-electronic junction (microelectrode-electrolyte interface, cleft effect, and protein-glycocalyx electric double layer) are presented. Then, neuronal electrical activity is simulated by HSPICE software, and analyzed as a function of the most sensitive biophysical models parameters such as the neuron-microelectrode cleft width, spreading and seal resistances, ion-channel densities, double-layer properties, and microelectrode geometries.
41.  The virtual slice setup (Lytton et al. 2008)
"In an effort to design a simulation environment that is more similar to that of neurophysiology, we introduce a virtual slice setup in the NEURON simulator. The virtual slice setup runs continuously and permits parameter changes, including changes to synaptic weights and time course and to intrinsic cell properties. The virtual slice setup permits shocks to be applied at chosen locations and activity to be sampled intra- or extracellularly from chosen locations. ..."
42.  Theoretical reconstrucion of field potentials and dendrodendritic synaptic...(Rall & Shepherd 1968)
This was the first application of compartmental modeling using the Rall approach to brain neurons. It combined multicompartmental representation of a mitral cell and a granule cell with the first Hodgkin-Huxley-like action potential to model antidromic activation of the mitral cell, followed by synaptic excitation of the granule cell and synaptic inhibition of the mitral cell. Combined with reconstruction of the field potentials generated around these neurons, and detailed comparisons with single cell recordings, it led to prediction of dendrodendritic interactions mediating self and lateral inhibition of the mitral cells by the granule cells. It has been regarded as the first computational model of a brain microcircuit (see also Shepherd and Brayton, 1979). Recreation of the model is pending.
43.  Using NEURON for reaction-diffusion modeling of extracellular dynamics (Newton et al 2018)
Development of credible clinically-relevant brain simulations has been slowed due to a focus on electrophysiology in computational neuroscience, neglecting the multiscale whole-tissue modeling approach used for simulation in most other organ systems. We have now begun to extend the NEURON simulation platform in this direction by adding extracellular modeling. NEURON's extracellular reaction-diffusion is supported by an intuitive Python-based where/who/what command sequence, derived from that used for intracellular reaction diffusion, to support coarse-grained macroscopic extracellular models. This simulation specification separates the expression of the conceptual model and parameters from the underlying numerical methods. In the volume-averaging approach used, the macroscopic model of tissue is characterized by free volume fraction—the proportion of space in which species are able to diffuse, and tortuosity—the average increase in path length due to obstacles. These tissue characteristics can be defined within particular spatial regions, enabling the modeler to account for regional differences, due either to intrinsic organization, particularly gray vs. white matter, or to pathology such as edema. We illustrate simulation development using spreading depression, a pathological phenomenon thought to play roles in migraine, epilepsy and stroke.

Re-display model names without descriptions