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Models that contain the Current : I K

(Activated by strong depolarization; delayed rectifier)

   Models   Description
3D model of the olfactory bulb (Migliore et al. 2014)
This entry contains a link to a full HD version of movie 1 and the NEURON code of the paper: "Distributed organization of a brain microcircuit analysed by three-dimensional modeling: the olfactory bulb" by M Migliore, F Cavarretta, ML Hines, and GM Shepherd.
A dynamic model of the canine ventricular myocyte (Hund, Rudy 2004)
The Hund-Rudy dynamic (HRd) model is based on data from the canine epicardial ventricular myocyte. Rate-dependent phenomena associated with ion channel kinetics, action potential properties and Ca2+ handling are simulated by the model. See paper for more and details.
A Model Circuit of Thalamocortical Convergence (Behuret et al. 2013)
“… Using dynamic-clamp techniques in thalamic slices in vitro, we combined theoretical and experimental approaches to implement a realistic hybrid retino-thalamo-cortical pathway mixing biological cells and simulated circuits. … The study of the impact of the simulated cortical input on the global retinocortical signal transfer efficiency revealed a novel control mechanism resulting from the collective resonance of all thalamic relay neurons. We show here that the transfer efficiency of sensory input transmission depends on three key features: i) the number of thalamocortical cells involved in the many-to-one convergence from thalamus to cortex, ii) the statistics of the corticothalamic synaptic bombardment and iii) the level of correlation imposed between converging thalamic relay cells. In particular, our results demonstrate counterintuitively that the retinocortical signal transfer efficiency increases when the level of correlation across thalamic cells decreases. …”
A model for pituitary GH(3) lactotroph (Wu and Chang 2005)
The ATP-sensitive K(+) (K(ATP)) channels are composed of sulfonylurea receptor and inwardly rectifying K(+) channel (Kir6.2) subunit. These channels are regulated by intracellular ADP/ATP ratio and play a role in cellular metabolism. ... The objective of this study was to determine whether Diethyl pyrocarbonate (DEPC) modifies K(ATP)-channel activity in pituitary GH(3) cells. ... Simulation studies also demonstrated that the increased conductance of K(ATP)-channels used to mimic DEPC actions reduced the frequency of spontaneous action potentials and fluctuation of intracellular Ca(2+). The results indicate that chemical modification with DEPC enhances K(ATP)-channel activity and influences functional activities of pituitary GH(3) cells. See paper for more and details.
A Model of Multiple Spike Initiation Zones in the Leech C-interneuron (Crisp 2009)
The leech C-interneuron and its electrical synapse with the S-interneuron exhibit unusual properties: an asymmetric delay when impulses travel from one soma to the other, and graded C-interneuron impulse amplitudes under elevated divalent cation concentrations. These properties have been simulated using a SNNAP model in which the C-interneuron has multiple, independent spike initiation zones associated with individual electrical junctions with the C-interneuron.
A Moth MGC Model-A HH network with quantitative rate reduction (Buckley & Nowotny 2011)
We provide the model used in Buckley & Nowotny (2011). It consists of a network of Hodgkin Huxley neurons coupled by slow GABA_B synapses which is run alongside a quantitative reduction described in the associated paper.
A multiphysics neuron model for cellular volume dynamics (Lee et al. 2011)
This paper introduces a novel neuron model, where the cell volume is a time-varying variable and multiple physical principles are combined to build governing equations. Using this model, we analyzed neuronal volume responses during excitation, which elucidated the waveforms of fast intrinsic optical signals observed experimentally across the literature. In addition, we analyzed volume responses on a longer time scale with repetitive stimulation to study the characteristics of slow cell swelling.
A network model of tail withdrawal in Aplysia (White et al 1993)
The contributions of monosynaptic and polysynaptic circuitry to the tail-withdrawal reflex in the marine mollusk Aplysia californica were assessed by the use of physiologically based neural network models. Effects of monosynaptic circuitry were examined by the use of a two-layer network model with four sensory neurons in the input layer and one motor neuron in the output layer. Results of these simulations indicated that the monosynaptic circuit could not account fully for long-duration responses of tail motor neurons elicited by tail stimulation. A three-layer network model was constructed by interposing a layer of two excitatory interneurons between the input and output layers of the two-layer network model. The three-layer model could account for long-duration responses in motor neurons. Sensory neurons are a known site of plasticity in Aplysia. Synaptic plasticity at more than one locus modified dramatically the input-output relationship of the three-layer network model. This feature gave the model redundancy in its plastic properties and points to the possibility of distributed memory in the circuitry mediating withdrawal reflexes in Aplysia. Please see paper for more results and details.
A set of reduced models of layer 5 pyramidal neurons (Bahl et al. 2012)
These are the NEURON files for 10 different models of a reduced L5 pyramidal neuron. The parameters were obtained by automatically fitting the models to experimental data using a multi objective evolutionary search strategy. Details on the algorithm can be found at www.g-node.org/emoo and in Bahl et al. (2012).
A simplified cerebellar Purkinje neuron (the PPR model) (Brown et al. 2011)
These models were implemented in NEURON by Sherry-Ann Brown in the laboratory of Leslie M. Loew. The files reproduce Figures 2c-f from Brown et al, 2011 "Virtual NEURON: a Strategy For Merged Biochemical and Electrophysiological Modeling".
A simplified model of NMDA oscillations in lamprey locomotor neurons (Huss et al. 2008)
Using experiments in conjunction with this simplified model, we sought to understand the basic mechanisms behind NMDA-induced oscillations in lamprey locomotor neurons, specifically (a) how the oscillation frequency depends on NMDA concentration and why, and (b) what the minimal number of components for generating NMDA oscillations is (in vitro and in the model).
A simulation method for the firing sequences of motor units (Jiang et al 2006)
" ... a novel model based on the Hodgkin–Huxley (HH) system is proposed, which has the ability to simulate the complex neurodynamics of the firing sequences of motor neurons. The model is presented at the cellular level and network level, and some simulation results from a simple 3-neuron network are presented to demonstrate its applications." See paper for more and details.
A single column thalamocortical network model (Traub et al 2005)
To better understand population phenomena in thalamocortical neuronal ensembles, we have constructed a preliminary network model with 3,560 multicompartment neurons (containing soma, branching dendrites, and a portion of axon). Types of neurons included superficial pyramids (with regular spiking [RS] and fast rhythmic bursting [FRB] firing behaviors); RS spiny stellates; fast spiking (FS) interneurons, with basket-type and axoaxonic types of connectivity, and located in superficial and deep cortical layers; low threshold spiking (LTS) interneurons, that contacted principal cell dendrites; deep pyramids, that could have RS or intrinsic bursting (IB) firing behaviors, and endowed either with non-tufted apical dendrites or with long tufted apical dendrites; thalamocortical relay (TCR) cells; and nucleus reticularis (nRT) cells. To the extent possible, both electrophysiology and synaptic connectivity were based on published data, although many arbitrary choices were necessary.
A threshold equation for action potential initiation (Platkiewicz & Brette 2010)
"We examined in models the influence of Na channel activation, inactivation, slow voltage-gated channels and synaptic conductances on spike threshold. We propose a threshold equation which quantifies the contribution of all these mechanisms. It provides an instantaneous time-varying value of the threshold, which applies to neurons with fluctuating inputs. ... We find that spike threshold depends logarithmically on Na channel density, and that Na channel inactivation and K channels can dynamically modulate it in an adaptive way: the threshold increases with membrane potential and after every action potential. " See paper for more.
A two-stage model of dendritic integration in CA1 pyramidal neurons (Katz et al. 2009)
"... In a two-stage integration model, inputs contribute directly to dendritic spikes, and outputs from multiple branches sum in the axon. ... We used serial-section electron microscopy to reconstruct individual apical oblique dendritic branches of CA1 pyramidal neurons and observe a synapse distribution consistent with the two-stage integration model. Computational modeling suggests that the observed synapse distribution enhances the contribution of each dendritic branch to neuronal output."
Accurate and fast simulation of channel noise in conductance-based model neurons (Linaro et al 2011)
We introduce and operatively present a general method to simulate channel noise in conductance-based model neurons, with modest computational overheads. Our approach may be considered as an accurate generalization of previous proposal methods, to the case of voltage-, ion-, and ligand-gated channels with arbitrary complexity. We focus on the discrete Markov process descriptions, routinely employed in experimental identification of voltage-gated channels and synaptic receptors.
Action Potential initiation and backpropagation in Neocortical L5 Pyramidal Neuron (Hu et al. 2009)
"...Previous computational studies have yielded conflicting conclusions about the role of Na+ channel density and biophysical properties in action potential initiation as a result of inconsistent estimates of channel density. Our modeling studies integrated the immunostaining and electrophysiological results and showed that the lowest threshold for action potential initiation at the distal AIS was largely determined by the density of low-threshold Nav1.6 channels ... Distinct from the function of Nav1.6 channel, the Nav1.2 channel may control action potential backpropagation because of its high density at the proximal AIS and high threshold. ... In conclusion, distal AIS accumulation of Nav1.6 channels determines the low threshold for action potential initiation; whereas proximal AIS accumulation of Nav1.2 channels sets the threshold for the generation of somatodendritic potentials and ensures action potential backpropagation to the soma and dendrites. Thus, Nav1.6 and Nav1.2 channels serve distinct functions in action potential initiation and backpropagation."
Action potential reconstitution from measured current waveforms (Alle et al. 2009)
This NEURON code reconstitutes action potentials in a model of a hippocampal mossy fiber from experimentally measured sodium, potassium and calcium current waveforms as described in Alle et al. (2009).
Action potential-evoked Na+ influx are similar in axon and soma (Fleidervish et al. 2010)
"In cortical pyramidal neurons, the axon initial segment (AIS) is pivotal in synaptic integration. It has been asserted that this is because there is a high density of Na+ channels in the AIS. However, we found that action potential–associated Na+ flux, as measured by high-speed fluorescence Na+ imaging, was about threefold larger in the rat AIS than in the soma. Spike-evoked Na+ flux in the AIS and the first node of Ranvier was similar and was eightfold lower in basal dendrites. ... In computer simulations, these data were consistent with the known features of action potential generation in these neurons."
Active dendrites and spike propagation in a hippocampal interneuron (Saraga et al 2003)
We create multi-compartment models of an Oriens-Lacunosum/Moleculare (O-LM) hippocampal interneuron using passive properties, channel kinetics, densities and distributions specific to this cell type, and explore its signaling characteristics. We find that spike initiation depends on both location and amount of input, as well as the intrinsic properties of the interneuron. Distal synaptic input always produces strong back-propagating spikes whereas proximal input could produce both forward and back-propagating spikes depending on the input strength. Please see paper for more details. Fernanda.Saraga@utoronto.ca
Activity dependent changes in dendritic spine density and spine structure (Crook et al. 2007)
"... In this work, we extend previous modeling studies [27] by combining a model for activity-dependent spine density with one for calcium-mediated spine stem restructuring. ... Additional equations characterize the change in spine density along the dendrite, the current balance equation for an individual spine head, the change in calcium concentration in the spine head, and the dynamics of spine stem resistance. We use computational studies to investigate the changes in spine density and structure for differing synaptic inputs and demonstrate the effects of these changes on the input-output properties of the dendritic branch. ... "
Activity dependent changes in motoneurones (Dai Y et al 2002, Gardiner et al 2002)
These two papers review various experimental papers and examine the effects of activity on motoneurons in a similar 5 compartment model with 10 active conductances. Included are slow (S) and fast (F) type and fast fatigue resistant (FR) and fast fatigable (FF) models corresponding to the types of motoneurons. See papers for more and details.
Activity dependent conductances in a neuron model (Liu et al. 1998)
"... We present a model of a stomatogastric ganglion (STG) neuron in which several Ca2+-dependent pathways are used to regulate the maximal conductances of membrane currents in an activity-dependent manner. Unlike previous models of this type, the regulation and modification of maximal conductances by electrical activity is unconstrained. The model has seven voltage-dependent membrane currents and uses three Ca2+ sensors acting on different time scales. ... The model suggests that neurons may regulate their conductances to maintain fixed patterns of electrical activity, rather than fixed maximal conductances, and that the regulation process requires feedback systems capable of reacting to changes of electrical activity on a number of different time scales."
Amyloid beta (IA block) effects on a model CA1 pyramidal cell (Morse et al. 2010)
The model simulations provide evidence oblique dendrites in CA1 pyramidal neurons are susceptible to hyper-excitability by amyloid beta block of the transient K+ channel, IA. See paper for details.
Amyloid-beta effects on release probability and integration at CA3-CA1 synapses (Romani et al. 2013)
The role of amyloid beta (Aß) in brain function and in the pathogenesis of Alzheimer’s disease remains elusive. Recent publications reported that an increase in Aß concentration perturbs presynaptic release in hippocampal neurons, in particular by increasing release probability of CA3-CA1 synapses. The model predics how this alteration can affect synaptic plasticity and signal integration. The results suggest that the perturbation of release probability induced by increased Aß can significantly alter the spike probability of CA1 pyramidal neurons and thus contribute to abnormal hippocampal function during Alzheimer’s disease.
An allosteric kinetics of NMDARs in STDP (Urakubo et al. 2008)
"... We developed a detailed biophysical model of STDP and found that the model required spike timing-dependent distinct suppression of NMDARs by Ca2+-calmodulin. This led us to predict an allosteric kinetics of NMDARs: a slow and rapid suppression of NMDARs by Ca2+-calmodulin with prespiking -> postspiking and postspiking -> prespiking, respectively. We found that the allosteric kinetics, but not the conventional kinetics, is consistent with specific features of amplitudes and peak time of NMDAR-mediated EPSPs in experiments. ..." See paper for more and details.
AP back-prop. explains threshold variability and rapid rise (McCormick et al. 2007, Yu et al. 2008)
This simple axon-soma model explained how the rapid rising phase in the somatic spike is derived from the propagated axon initiated spike, and how the somatic spike threshold variance is affected by spike propagation.
AP initiation and propagation in type II cochlear ganglion cell (Hossain et al 2005)
The model of type II cochlear ganglion cell was based on the immunostaining of the mouse auditory pathway. Specific antibodies were used to map the distribution of voltage-dependent sodium channels along the two unmyelinated axon-like processes of the bipolar ganglion cells. Three distinct hot spots were detected. A high density of sodium channels was present over the entire trajectory of sensory endings beneath the outer hair cells (the most distal portion of the peripheral axon). THE other two hot spots were localized in the initial segments of both of the axons that flank the unmyelinated bipolar ganglion cell bodies.

A biophysical model indicates that all three hot spots might play important roles in action potential initiation and propagation. For instance, the hot spot in the receptor segment is important for transforming the receptor potentials into a full blown action potential (Supplemental Fig. 1). The hot spots in the two paraganglionic axon initial segments are there to ensure the successful propagation of action potentials from the peripheral to the central axon through the cell body.

The Readme.txt file provides step by step instructions on how to recreate Figures 6 and 7 of Hossain et al., 2005 paper.

Axonal gap junctions produce fast oscillations in cerebellar Purkinje cells (Traub et al. 2008)
Examines how electrical coupling between proximal axons produces fast oscillations in cerebellar Purkinje cells. Traub RD, Middleton SJ, Knopfel T, Whittington MA (2008) Model of very fast (>75 Hz) network oscillations generated by electrical coupling between the proximal axons of cerebellar Purkinje cells. European Journal of Neuroscience in press.
Axonal NaV1.6 Sodium Channels in AP Initiation of CA1 Pyramidal Neurons (Royeck et al. 2008)
"... We show that the Na+ channel NaV1.6 displays a striking aggregation at the AIS of cortical neurons. ... In combination with simulations using a realistic computer model of a CA1 pyramidal cell, our results imply that a hyperpolarized voltage-dependence of activation of AIS NaV1.6 channels is important both in determining spike threshold and localizing spike initiation to the AIS. ... These results suggest that NaV1.6 subunits at the AIS contribute significantly to its role as spike trigger zone and shape repetitive discharge properties of CA1 neurons."
Axonal Projection and Interneuron Types (Helmstaedter et al. 2008)
"Interneurons in layer 2/3 (L2/3) of the somatosensory cortex show 4 types of axonal projection patterns with reference to the laminae and borders of columns in rat barrel cortex (Helmstaedter et al. 2008a). Here, we analyzed the dendritic geometry and electrical excitability of these interneurons. ... We conclude that 1) dendritic polarity is correlated to intrinsic electrical excitability, and 2) the axonal projection pattern represents an independent classifier of interneurons. "
Basal ganglia-thalamic network model for deep brain stimulation (So et al. 2011)
This is a model of the basal ganglia-thalamic network, modified from the Rubin and Terman model (High frequency stimulation of the Subthalamic Nucleus, Rubin and Terman 2004). We subsequently used this model to investigate the effectiveness of STN and GPi DBS as well as lesion when various proportions of local cells and fibers of passage were activated or silenced. The BG network exhibited characteristics consistent with published experimental data, both on the level of single cells and on the network level. Perhaps most notably, and in contrast to the original RT model, the changes in the thalamic error index with changes in the DBS frequency matched well the changes in clinical symptoms with changes in DBS frequency.
Biophysical and phenomenological models of spike-timing dependent plasticity (Badoual et al. 2006)
"Spike-timing dependent plasticity (STDP) is a form of associative synaptic modification which depends on the respective timing of pre- and post-synaptic spikes. The biophysical mechanisms underlying this form of plasticity are currently not known. We present here a biophysical model which captures the characteristics of STDP, such as its frequency dependency, and the effects of spike pair or spike triplet interactions. ... A simplified phenomenological model is also derived..."
Biophysically detailed model of the mouse sino-atrial node cell (Kharche et al. 2011)
This model is developed to study the role of various electrophysiological mechanisms in generating cardiac pacemaking action potentials (APs).The model incorporates membrane ionic currents and intracellular mechanisms contributing to spontaneous mouse SAN APs. The model was validated by testing the functional roles of individual membrane currents in one and multiple parameter analyses.The roles of intracellular Ca2+-handling mechanisms on cardiac pacemaking were also investigated in the model.
Biophysically realistic neural modeling of the MEG mu rhythm (Jones et al. 2009)
"Variations in cortical oscillations in the alpha (7–14 Hz) and beta (15–29 Hz) range have been correlated with attention, working memory, and stimulus detection. The mu rhythm recorded with magnetoencephalography (MEG) is a prominent oscillation generated by Rolandic cortex containing alpha and beta bands. Despite its prominence, the neural mechanisms regulating mu are unknown. We characterized the ongoing MEG mu rhythm from a localized source in the finger representation of primary somatosensory (SI) cortex. Subjects showed variation in the relative expression of mu-alpha or mu-beta, which were nonoverlapping for roughly 50% of their respective durations on single trials. To delineate the origins of this rhythm, a biophysically principled computational neural model of SI was developed, with distinct laminae, inhibitory and excitatory neurons, and feedforward (FF, representative of lemniscal thalamic drive) and feedback (FB, representative of higher-order cortical drive or input from nonlemniscal thalamic nuclei) inputs defined by the laminar location of their postsynaptic effects. ..."
Breakdown of accmmodation in nerve: a possible role for INAp (Hennings et al 2005)
The present modeling study suggests that persistent, low-threshold, rapidly activating sodium currents have a key role in breakdown of accommodation, and that breakdown of accommodation can be used as a tool for studying persistent sodium current under normal and pathological conditions. See paper for more and details.
Burst induced synaptic plasticity in Apysia sensorimotor neurons (Phares et al 2003)
The Aplysia sensorimotor synapse is a key site of plasticity for several simple forms of learning. Intracellular stimulation of sensory neurons to fire a burst of action potentials at 10 Hz for 1 sec led to significant homosynaptic depression of postsynaptic responses. During the burst, the steady-state depressed phase of the postsynaptic response, which was only 20% of the initial EPSP of the burst, still contributed to firing the motor neuron. To explore the functional contribution of transient homosynaptic depression to the response of the motor neuron, computer simulations of the sensorimotor synapse with and without depression were compared. Depression allowed the motor neuron to produce graded responses over a wide range of presynaptic input strength. Thus, synaptic depression increased the dynamic range of the sensorimotor synapse and can, in principle, have a profound effect on information processing. Please see paper for results and details.
Bursting activity of neuron R15 in Aplysia (Canavier et al 1991, Butera et al 1995)
An equivalent circuit model of the R15 bursting neuron in Aplysia has been combined with a fluid compartment model, resulting in a model that incorporates descriptions of most of the membrane ion channels that are known to exist in the somata of R15, as well as providing a Ca2+ balance on the cell. ... (from the second paper) we have implemented proposed mechanisms for the modulation of two ionic currents (IR and ISI) that play key roles in regulating its spontaneous electrical activity. The model was sufficient to simulate a wide range of endogenous activity in the presence of various concentrations of 5-HT or DA. See papers for more and details.
Bursting and resonance in cerebellar granule cells (D`Angelo et al. 2001)
In this study we report theta-frequency (3–12 Hz) bursting and resonance in rat cerebellar granule cells and show that these neurons express a previously unidentified slow repolarizing K1 current (IK-slow ). Our experimental and modeling results indicate that IK-slow was necessary for both bursting and resonance. See paper for more.
CA1 interneuron: K currents (Lien et al 2002)
NEURON mod files for slow and fast K-DR, and K-A potassium currents in inhibitory interneurones of stratum oriens-alveus of the hippocampal CA1 region.
CA1 pyramidal cell: I_NaP and I_M contributions to somatic bursting (Golomb et al 2006)
To study the mechanisms of bursting, we have constructed a conductance-based, one-compartment model of CA1 pyramidal neurons. In this neuron model, reduced [Ca2+]o is simulated by negatively shifting the activation curve of the persistent Na+ current (INaP), as indicated by recent experimental results. The neuron model accounts, with different parameter sets, for the diversity of firing patterns observed experimentally in both zero and normal [Ca2+]o. Increasing INaP in the neuron model induces bursting and increases the number of spikes within a burst, but is neither necessary nor sufficient for bursting. We show, using fast-slow analysis and bifurcation theory, that the M-type K+ current (IM) allows bursting by shifting neuronal behavior between a silent and a tonically-active state, provided the kinetics of the spike generating currents are sufficiently, though not extremely, fast. We suggest that bursting in CA1 pyramidal cells can be explained by a single compartment *square bursting* mechanism with one slow variable, the activation of IM. See paper for more and details.
CA1 pyramidal cell: reconstructed axonal arbor and failures at weak gap junctions (Vladimirov 2011)
Model of pyramidal CA1 cells connected by gap junctions in their axons. Cell geometry is based on anatomical reconstruction of rat CA1 cell (NeuroMorpho.Org ID: NMO_00927) with long axonal arbor. Model init_2cells.hoc shows failures of second spike propagation in a spike doublet, depending on conductance of an axonal gap junction. Model init_ring.hoc shows that spike failure result in reentrant oscillations of a spike in a loop of axons connected by gap junctions, where one gap junction is weak. The paper shows that in random networks of axons connected by gap junctions, oscillations are driven by single pacemaker loop of axons. The shortest loop, around which a spike can travel, is the most likely pacemaker. This principle allows us to predict the frequency of oscillations from network connectivity and visa versa. We propose that this type of oscillations corresponds to so-called fast ripples in epileptic hippocampus.
CA1 pyramidal neuron (Migliore et al 1999)
Hippocampal CA1 pyramidal neuron model from the paper M.Migliore, D.A Hoffman, J.C. Magee and D. Johnston (1999) Role of an A-type K+ conductance in the back-propagation of action potentials in the dendrites of hippocampal pyramidal neurons, J. Comput. Neurosci. 7, 5-15. Instructions are provided in the below README file.Contact michele.migliore@pa.ibf.cnr.it if you have any questions about the implementation of the model.
CA1 pyramidal neuron synaptic integration (Li and Ascoli 2006, 2008)
The model shows how different input patterns (irregular & asynchronous, irregular & synchronous, regular & asynchronous, regular & synchronous) affect the neuron's output rate when 1000 synapses are distributed in the proximal apical dendritic tree of a hippocampus CA1 pyramidal neuron.
CA1 pyramidal neuron: as a 2-layer NN and subthreshold synaptic summation (Poirazi et al 2003)
We developed a CA1 pyramidal cell model calibrated with a broad spectrum of in vitro data. Using simultaneous dendritic and somatic recordings, and combining results for two different response measures (peak vs. mean EPSP), two different stimulus formats (single shock vs. 50 Hz trains), and two different spatial integration conditions (within vs. between-branch summation), we found the cell's subthreshold responses to paired inputs are best described as a sum of nonlinear subunit responses, where the subunits correspond to different dendritic branches. In addition to suggesting a new type of experiment and providing testable predictions, our model shows how conclusions regarding synaptic arithmetic can be influenced by an array of seemingly innocuous experimental design choices.
CA1 pyramidal neuron: calculation of MRI signals (Cassara et al. 2008)
NEURON mod files from the paper: Cassarà AM, Hagberg GE, Bianciardi M, Migliore M, Maraviglia B. Realistic simulations of neuronal activity: A contribution to the debate on direct detection of neuronal currents by MRI. Neuroimage. 39:87-106 (2008). In this paper, we use a detailed calculation of the magnetic field produced by the neuronal currents propagating over a hippocampal CA1 pyramidal neuron placed inside a cubic MR voxel of length 1.2 mm to estimate the Magnetic Resonance signal.
CA1 pyramidal neuron: conditional boosting of dendritic APs (Watanabe et al 2002)
Model files from the paper Watanabe S, Hoffman DA, Migliore M, Johnston D (2002). The experimental and modeling results support the hypothesis that dendritic K-A channels and the boosting of back-propagating action potentials contribute to the induction of LTP in CA1 neurons. See the paper for details. Questions about the model may be addressed to Michele Migliore: michele.migliore@pa.ibf.cnr.it
CA1 pyramidal neuron: dendritic spike initiation (Gasparini et al 2004)
NEURON mod files from the paper: Sonia Gasparini, Michele Migliore, and Jeffrey C. Magee On the initiation and propagation of dendritic spikes in CA1 pyramidal neurons, J. Neurosci., J. Neurosci. 24:11046-11056 (2004).
CA1 pyramidal neuron: depolarization block (Bianchi et al. 2012)
NEURON files from the paper: On the mechanisms underlying the depolarization block in the spiking dynamics of CA1 pyramidal neurons by D.Bianchi, A. Marasco, A.Limongiello, C.Marchetti, H.Marie,B.Tirozzi, M.Migliore (2012). J Comput. Neurosci. In press. DOI: 10.1007/s10827-012-0383-y. Experimental findings shown that under sustained input current of increasing strength neurons eventually stop firing, entering a depolarization block. We analyze the spiking dynamics of CA1 pyramidal neuron models using the same set of ionic currents on both an accurate morphological reconstruction and on its reduction to a single-compartment. The results show the specic ion channel properties and kinetics that are needed to reproduce the experimental findings, and how their interplay can drastically modulate the neuronal dynamics and the input current range leading to depolarization block.
CA1 pyramidal neuron: effects of Ih on distal inputs (Migliore et al 2004)
NEURON mod files from the paper: M. Migliore, L. Messineo, M. Ferrante Dendritic Ih selectively blocks temporal summation of unsynchronized distal inputs in CA1 pyramidal neurons, J.Comput. Neurosci. 16:5-13 (2004). The model demonstrates how the dendritic Ih in pyramidal neurons could selectively suppress AP generation for a volley of excitatory afferents when they are asynchronously and distally activated.
CA1 pyramidal neuron: effects of Lamotrigine on dendritic excitability (Poolos et al 2002)
NEURON mod files from N. Poolos, M. Migliore, and D. Johnston, Nature Neuroscience (2002). The experimental and modeling results in this paper demonstrate for the first time that neuronal excitability can be altered by pharmaceuticals acting selectively on dendrites, and suggest an important role for Ih in controlling dendritic excitability and epileptogenesis.
CA1 pyramidal neuron: effects of R213Q and R312W Kv7.2 mutations (Miceli et al. 2013)
NEURON mod files from the paper: Miceli et al, Genotype–phenotype correlations in neonatal epilepsies caused by mutations in the voltage sensor of Kv7.2 potassium channel subunits, PNAS 2013 Feb 25. [Epub ahead of print] In this paper, functional studies revealed that in homomeric or heteromeric configuration with KV7.2 and/or KV7.3 subunits, R213W and R213Q mutations markedly destabilized the open state, causing a dramatic decrease in channel voltage sensitivity. Modeling these channels in CA1 hippocampal pyramidal cells revealed that both mutations increased cell firing frequency, with the R213Q mutation prompting more dramatic functional changes compared with the R213W mutation.
CA1 pyramidal neuron: functional significance of axonal Kv7 channels (Shah et al. 2008)
The model used in this paper confirmed the experimental findings suggesting that axonal Kv7 channels are critically and uniquely required for determining the inherent spontaneous firing of hippocampal CA1 pyramids, independently of alterations in synaptic activity. The model predicts that the axonal Kv7 density could be 3-5 times that at the soma.
CA1 pyramidal neuron: Ih current (Migliore et al. 2012)
NEURON files from the paper: Migliore M, Migliore R (2012) Know Your Current Ih: Interaction with a Shunting Current Explains the Puzzling Effects of Its Pharmacological or Pathological Modulations. PLoS ONE 7(5): e36867. doi:10.1371/journal.pone.0036867. Experimental findings on the effects of Ih current modulation, which is particularly involved in epilepsy, appear to be inconsistent. In the paper, using a realistic model we show how and why a shunting current, such as that carried by TASK-like channels, dependent on the Ih peak conductance is able to explain virtually all experimental findings on Ih up- or down-regulation by modulators or pathological conditions.
CA1 pyramidal neuron: integration of subthreshold inputs from PP and SC (Migliore 2003)
The model shows how the experimentally observed increase in the dendritic density of Ih and IA could have a major role in constraining the temporal integration window for the main CA1 synaptic inputs.
Ca1 pyramidal neuron: reduction model (Marasco et al. 2012)
"... Here we introduce a new, automatic and fast method to map realistic neurons into equivalent reduced models running up to >40 times faster while maintaining a very high accuracy of the membrane potential dynamics during synaptic inputs, and a direct link with experimental observables. The mapping of arbitrary sets of synaptic inputs, without additional fine tuning, would also allow the convenient and efficient implementation of a new generation of large-scale simulations of brain regions reproducing the biological variability observed in real neurons, with unprecedented advances to understand higher brain functions."
CA1 pyramidal neuron: schizophrenic behavior (Migliore et al. 2011)
NEURON files from the paper: A modeling study suggesting how a reduction in the context-dependent input on CA1 pyramidal neurons could generate schizophrenic behavior. by M. Migliore, I. De Blasi, D. Tegolo, R. Migliore, Neural Networks,(2011), doi:10.1016/j.neunet.2011.01.001. Starting from the experimentally supported assumption on hippocampal neurons we explore an experimentally testable prediction at the single neuron level. The model shows how and to what extent a pathological hypofunction of a contextdependent distal input on a CA1 neuron can generate hallucinations by altering the normal recall of objects on which the neuron has been previously tuned. The results suggest that a change in the context during the recall phase may cause an occasional but very significant change in the set of active dendrites used for features recognition, leading to a distorted perception of objects.
CA1 pyramidal neuron: signal propagation in oblique dendrites (Migliore et al 2005)
NEURON mod files from the paper: M. Migliore, M. Ferrante, GA Ascoli (2005). The model shows how the back- and forward propagation of action potentials in the oblique dendrites of CA1 neurons could be modulated by local properties such as morphology or active conductances.
CA1 Pyramidal Neuron: slow Na+ inactivation (Migliore 1996)
Model files from the paper: M. Migliore, Modeling the attenuation and failure of action potentials in the dendrites of hippocampal neurons, Biophys. J. 71:2394-403 (1996). Please see the below readme file for installation and use instructions. Contact michele.migliore@pa.ibf.cnr.it if you have any questions about the implementation of the model.
CA1 pyramidal neuron: synaptically-induced bAP predicts synapse location (Sterratt et al. 2012)
This is an adaptation of Poirazi et al.'s (2003) CA1 model that is used to measure BAP-induced voltage and calcium signals in spines after simulated Schaffer collateral synapse stimulation. In the model, the peak calcium concentration is highly correlated with soma-synapse distance under a number of physiologically-realistic suprathreshold stimulation regimes and for a range of dendritic morphologies. There are also simulations demonstrating that peak calcium can be used to set up a synaptic democracy in a homeostatic manner, whereby synapses regulate their synaptic strength on the basis of the difference between peak calcium and a uniform target value.
CA1 pyramidal neurons: binding properties and the magical number 7 (Migliore et al. 2008)
NEURON files from the paper: Single neuron binding properties and the magical number 7, by M. Migliore, G. Novara, D. Tegolo, Hippocampus, in press (2008). In an extensive series of simulations with realistic morphologies and active properties, we demonstrate how n radial (oblique) dendrites of these neurons may be used to bind n inputs to generate an output signal. The results suggest a possible neural code as the most effective n-ple of dendrites that can be used for short-term memory recollection of persons, objects, or places. Our analysis predicts a straightforward physiological explanation for the observed puzzling limit of about 7 short-term memory items that can be stored by humans.
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.
CA1 pyramidal neurons: effects of a Kv7.2 mutation (Miceli et al. 2009)
NEURON mod files from the paper: Miceli et al, Neutralization of a unique, negatively-charged residue in the voltage sensor of K(V)7.2 subunits in a sporadic case of benign familial neonatal seizures, Neurobiol Dis., in press (2009). In this paper, the model revealed that the gating changes introduced by a mutation in K(v)7.2 genes encoding for the neuronal KM current in a case of benign familial neonatal seizures, increased cell firing frequency, thereby triggering the neuronal hyperexcitability which underlies the observed neonatal epileptic condition.
CA1 pyramidal neurons: effects of Alzheimer (Culmone and Migliore 2012)
The model predicts possible therapeutic treatments of Alzheimers's Disease in terms of pharmacological manipulations of channels' kinetic and activation properties. The results suggest how and which mechanism can be targeted by a drug to restore the original firing conditions. The simulations reproduce somatic membrane potential in control conditions, when 90% of membrane is affected by AD (Fig.4A of the paper), and after treatment (Fig.4B of the paper).
CA1 pyramidal neurons: effects of Kv7 (M-) channels on synaptic integration (Shah et al. 2011)
NEURON mod files from the paper: Shah et al., 2011. In this study, using a combination of electrophysiology and computational modelling, we show that these channels selectively influence peri-somatic but not dendritic post-synaptic excitatory synaptic potential (EPSP) integration in CA1 pyramidal cells. This may be important for their relative contributions to physiological processes such as synaptic plasticity as well as patho-physiological conditions such as epilepsy.
CA1 stratum radiatum interneuron multicompartmental model (Katona et al. 2011)
The model examines dendritic NMDA-spike generation and propagation in the dendrites of CA1 stratum radiatum interneurons. It contains NMDA-channels in a clustered pattern on a dendrite and K-channels. The simulation shows the whole NMDA spike and the rising phase of the traces in separate windows.
CA3 pyramidal neuron (Lazarewicz et al 2002)
The model shows how using a CA1-like distribution of active dendritic conductances in a CA3 morphology results in dendritic initiation of spikes during a burst.
CA3 Pyramidal Neuron (Migliore et al 1995)
Model files from the paper: M. Migliore, E. Cook, D.B. Jaffe, D.A. Turner and D. Johnston, Computer simulations of morphologically reconstructed CA3 hippocampal neurons, J. Neurophysiol. 73, 1157-1168 (1995). Demonstrates how the same cell could be bursting or non bursting according to the Ca-independent conductance densities. Includes calculation of intracellular Calcium. Instructions are provided in the below README file. Contact michele.migliore@pa.ibf.cnr.it if you have any questions about the implementation of the model.
CA3 pyramidal neuron (Safiulina et al. 2010)
In this review some of the recent work carried out in our laboratory concerning the functional role of GABAergic signalling at immature mossy fibres (MF)-CA3 principal cell synapses has been highlighted. To compare the relative strength of CA3 pyramidal cell output in relation to their MF glutamatergic or GABAergic inputs in postnatal development, a realistic model was constructed taking into account the different biophysical properties of these synapses.
CA3 pyramidal neuron: firing properties (Hemond et al. 2008)
In the paper, this model was used to identify how relative differences in K+ conductances, specifically KC, KM, & KD, between cells contribute to the different characteristics of the three types of firing patterns observed experimentally.
Caffeine-induced electrical oscillations in Aplysia neurons (Komendantov, Kononenko 2000)
It has been found that in cultured Aplysia neurons bath applications of 40 mM cafffeine evokes oscillations of the membrane potential with about a 40 mV amplitude with a frequency of 0.2 to 0.5 Hz. The most probable mechanism of these caffeine-induced oscillations is inhibition of voltage-activated outward potassium current and, as can be seen from our mathematical modeling, slowdown of inactivation of inward sodium current. It seems likely that these oscillations have a purely membrane origin. Please see paper for results and details.
Calcium and potassium currents of olfactory bulb juxtaglomerular cells (Masurkar and Chen 2011)
Inward and outward currents of the olfactory bulb juxtaglomerular cells are characterized in the experiments and modeling in these two Masurkar and Chen 2011 papers.
Calcium influx during striatal upstates (Evans et al. 2013)
"... To investigate the mechanisms that underlie the relationship between calcium and AP timing, we have developed a realistic biophysical model of a medium spiny neuron (MSN). ... Using this model, we found that either the slow inactivation of dendritic sodium channels (NaSI) or the calcium inactivation of voltage-gated calcium channels (CDI) can cause high calcium corresponding to early APs and lower calcium corresponding to later APs. We found that only CDI can account for the experimental observation that sensitivity to AP timing is dependent on NMDA receptors. Additional simulations demonstrated a mechanism by which MSNs can dynamically modulate their sensitivity to AP timing and show that sensitivity to specifically timed pre- and postsynaptic pairings (as in spike timing-dependent plasticity protocols) is altered by the timing of the pairing within the upstate. …"
Calcium response prediction in the striatal spines depending on input timing (Nakano et al. 2013)
We construct an electric compartment model of the striatal medial spiny neuron with a realistic morphology and predict the calcium responses in the synaptic spines with variable timings of the glutamatergic and dopaminergic inputs and the postsynaptic action potentials. The model was validated by reproducing the responses to current inputs and could predict the electric and calcium responses to glutamatergic inputs and back-propagating action potential in the proximal and distal synaptic spines during up and down states.
Calcium waves and mGluR-dependent synaptic plasticity in CA1 pyr. neurons (Ashhad & Narayanan 2013)
A morphologically realistic, conductance-based model equipped with kinetic schemes that govern several calcium signalling modules and pathways in CA1 pyramidal neurons
Cardiac action potentials and pacemaker activity of sinoatrial node (DiFrancesco & Noble 1985)
"Equations have been developed to describe cardiac action potentials and pacemaker activity. The model takes account of extensive developments in experimental work ..."
Cardiac Atrial Cell (Courtemanche et al 1998)
Marc Courtemanche, Rafael J. Ramirez, and Stanley Nattel. Ionic mechanisms underlying human atrial action potential properties insights from a mathematical model Am J Physiol Heart Circ Physiol 1998 275: H301-H321. The implementation of this model in NEURON was contributed by Ingemar Jacobson.
Cardiac Atrial Cell (Courtemanche et al 1998) (C++)
The mechanisms underlying many important properties of the human atrial action potential (AP) are poorly understood. Using specific formulations of the K+, Na+, and Ca2+ currents based on data recorded from human atrial myocytes, along with representations of pump, exchange, and background currents, we developed a mathematical model of the AP. The model AP resembles APs recorded from human atrial samples and responds to rate changes, L-type Ca2+ current blockade, Na+/Ca2+ exchanger inhibition, and variations in transient outward current amplitude in a fashion similar to experimental recordings. Rate-dependent adaptation of AP duration, an important determinant of susceptibility to atrial fibrillation, was attributable to incomplete L-type Ca2+ current recovery from inactivation and incomplete delayed rectifier current deactivation at rapid rates. Experimental observations of variable AP morphology could be accounted for by changes in transient outward current density, as suggested experimentally. We conclude that this mathematical model of the human atrial AP reproduces a variety of observed AP behaviors and provides insights into the mechanisms of clinically important AP properties.
Cerebellar Golgi cell (Solinas et al. 2007a, 2007b)
"... Our results suggest that a complex complement of ionic mechanisms is needed to fine-tune separate aspects of the neuronal response dynamics. Simulations also suggest that the Golgi cell may exploit these mechanisms to obtain a fine regulation of timing of incoming mossy fiber responses and granular layer circuit oscillation and bursting."
Cerebellar purkinje cell (De Schutter and Bower 1994)
Tutorial simulation of a cerebellar Purkinje cell. This tutorial is based upon a GENESIS simulation of a cerebellar Purkinje cell, modeled and fine-tuned by Erik de Schutter. The tutorial assumes that you have a basic knowledge of the Purkinje cell and its synaptic inputs. It gives visual insight in how different properties as concentrations and channel conductances vary and interact within a real Purkinje cell.
Cerebellar purkinje cell: interacting Kv3 and Na currents influence firing (Akemann, Knopfel 2006)
Purkinje neurons spontaneously generate action potentials in the absence of synaptic drive and thereby exert a tonic, yet plastic, input to their target cells in the deep cerebellar nuclei. Purkinje neurons express two ionic currents with biophysical properties that are specialized for high-frequency firing: resurgent sodium currents and potassium currents mediated by Kv3.3. … Numerical simulations indicated that Kv3.3 increases the spontaneous firing rate via cooperation with resurgent sodium currents. We conclude that the rate of spontaneous action potential firing of Purkinje neurons is controlled by the interaction of Kv3.3 potassium currents and resurgent sodium currents. See paper for more and details.
Cerebellar purkinje cell: K and Ca channels regulate APs (Miyasho et al 2001)
We adopted De Schutter and Bower's model as the starting point, then modified the descriptions of several ion channels, such as the P-type Ca channel and the delayed rectifier K channel, and added class-E Ca channels and D-type K channels to the model. Our new model reproduces most of our experimental results and supports the conclusions of our experimental study that class-E Ca channels and D-type K channels are present and functioning in the dendrites of Purkinje neurons.
Cerebellar Purkinje Cell: resurgent Na current and high frequency firing (Khaliq et al 2003)
These mod files supplied by Dr Raman are for the below two references. ... we modeled action potential firing by simulating eight currents directly recorded from Purkinje cells in both wild-type and (mutant) med mice. Regular, high-frequency firing was slowed in med Purkinje neurons. In addition to disrupted sodium currents, med neurons had small but significant changes in potassium and leak currents. Simulations indicated that these modified non-sodium currents could not account for the reduced excitability of med cells but instead slightly facilitated spiking. The loss of NaV1.6-specific kinetics, however, slowed simulated spontaneous activity. Together, the data suggest that across a range of conditions, sodium currents with a resurgent component promote and accelerate firing. See papers for more and details.
CN bushy, stellate neurons (Rothman, Manis 2003)
Using kinetic data from three different K+ currents in acutely isolated neurons, a single electrical compartment model representing the soma of a ventral cochlear nucleus (VCN) neuron was created. The K+ currents include a fast transient current (IA), a slow-inactivating low-threshold current (ILT), and a noninactivating high-threshold current (IHT). The model also includes a fast-inactivating Na+ current, a hyperpolarization-activated cation current (Ih), and 1-50 auditory nerve synapses. With this model, the role IA, ILT, and IHT play in shaping the discharge patterns of VCN cells is explored. Simulation results indicate these currents have specific roles in shaping the firing patterns of stellate and bushy CN cells. (see readme.txt and the papers, esp 2003c, for details). Any questions regarding these implementations should be directed to: pmanis@med.unc.edu 2 April 2004 Paul B Manis, Ph.D.
CN bushy, stellate neurons (Rothman, Manis 2003) (Brian)
Cochlear neuron model of Rothman & Manis (2003). Adapted from the Neuron implementation.
CN pyramidal fusiform cell (Kanold, Manis 2001)
Pyramidal cells in the dorsal cochlear nucleus (DCN) show three characteristic discharge patterns in response tones: pauser, buildup, and regular firing. Experimental evidence suggests that a rapidly inactivating K+ current (I(KIF)) plays a critical role in generating these discharge patterns. To explore the role of I(KIF), we used a computational model based on the biophysical data. The model replicated the dependence of the discharge pattern on the magnitude and duration of hyperpolarizing prepulses, and I(KIF) was necessary to convey this dependence. Experimentally, half-inactivation voltage and kinetics of I(KIF) show wide variability. Varying these parameters in the model ... suggests that pyramidal cells can adjust their sensitivity to different temporal patterns of inhibition and excitation by modulating the kinetics of I(KIF). Overall, I(KIF) is a critical conductance controlling the excitability of DCN pyramidal cells. (See readme.txt and paper for details). Any questions regarding these implementations should be directed to: pmanis@med.unc.edu 2 April 2004 Paul B Manis, Ph.D.
Coincidence detection in avian brainstem (Simon et al 1999)
A detailed biophysical model of coincidence detector neurons in the nucleus laminaris (auditory brainstem) which are purported to detect interaural time differences (ITDs) from Simon et al 1999.
Comparison of DA-based Stochastic Algorithms (Pezo et al. 2014, in press)
" ... Here we review and test a set of the most recently published DA (Langevin-based Diffusion Approximation) implementations (Dangerfield et al., 2012; Linaro et al., 2011; Huang et al., 2013a; Orio and Soudry, 2012; Schmandt and Galán, 2012; Goldwyn et al., 2011; Güler, 2013), comparing all of them in a set of numerical simulations that asses numerical accuracy and computational efficiency on three different models: the original Hodgkin and Huxley model, a model with faster sodium channels, and a multi-compartmental model inspired in granular cells. ..."
Comparison of full and reduced globus pallidus models (Hendrickson 2010)
In this paper, we studied what features of realistic full model activity patterns can and cannot be preserved by morphologically reduced models. To this end, we reduced the morphological complexity of a full globus pallidus neuron model possessing active dendrites and compared its spontaneous and driven responses to those of the reduced models.
Compartmentalization of GABAergic inhibition by dendritic spines (Chiu et al. 2013)
A spiny dendrite model supports the hypothesis that only inhibitory inputs on spine heads, not shafts, compartmentalizes inhibition of calcium signals to spine heads as seen in paired inhibition with back-propagating action potential experiments on prefrontal cortex layer 2/3 pyramidal neurons in mouse (Chiu et al. 2013).
Competing oscillator 5-cell circuit and Parameterscape plotting (Gutierrez et al. 2013)
Our 5-cell model consists of competing fast and slow oscillators connected to a hub neuron with electrical and inhibitory synapses. Motivated by the Stomatogastric Ganglion (STG) circuit in the crab, we explored the patterns of coordination in the network as a function of the electrical coupling and inhibitory synapse strengths with the help of a novel visualization method that we call the "Parameterscape." The code submitted here will allow you to run circuit simulations and to produce a Parameterscape with the results.
Complex CA1-neuron to study AP initiation (Wimmer et al. 2010)
Complex model of a pyramidal CA1-neuron, adapted from Royeck, M., et al. Role of axonal NaV1.6 sodium channels in action potential initiation of CA1 pyramidal neurons. Journal of neurophysiology 100, 2361-2380 (2008). It contains a biophysically realistic morphology comprising 265 compartments (829 segments) and 15 different distributed Ca2+- and/or voltage-dependent conductances.
Computational aspects of feedback in neural circuits (Maass et al 2006)
It had previously been shown that generic cortical microcircuit models can perform complex real-time computations on continuous input streams, provided that these computations can be carried out with a rapidly fading memory. We investigate ... the computational capability of such circuits in the more realistic case where not only readout neurons, but in addition a few neurons within the circuit have been trained for specific tasks. This is essentially equivalent to the case where the output of trained readout neurons is fed back into the circuit. We show that this new model overcomes the limitation of a rapidly fading memory. In fact, we prove that in the idealized case without noise it can carry out any conceiv- able digital or analog computation on time-varying inputs. But even with noise the resulting computational model can perform a large class of biologically relevant real-time computations that require a non-fading memory. ... In particular we show that ... generic cortical microcircuits with feedback provide a new model for working memory that is consistent with a large set of biological constraints. See paper for more and details.
Computational Model of a Central Pattern Generator (Cataldo et al 2006)
The buccal ganglia of Aplysia contain a central pattern generator (CPG) that mediates rhythmic movements of the foregut during feeding. This CPG is a multifunctional circuit and generates at least two types of buccal motor patterns (BMPs), one that mediates ingestion (iBMP) and another that mediates rejection (rBMP). The present study used a computational approach to examine the ways in which an ensemble of identified cells and synaptic connections function as a CPG. Hodgkin-Huxley-type models were developed that mimicked the biophysical properties of these cells and synaptic connections. The results suggest that the currently identified ensemble of cells is inadequate to produce rhythmic neural activity and that several key elements of the CPG remain to be identified.
Computational neuropharmacology of CA1 pyramidal neuron (Ferrante et al. 2008)
In this paper, the model was used to show how neuroactive drugs targeting different neuronal mechanisms affect the signal integration in CA1 pyramidal neuron. Ferrante M, Blackwell KT, Migliore M, Ascoli GA (2008)
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.
Computer simulations of neuron-glia interactions mediated by ion flux (Somjen et al. 2008)
"... To examine the effect of glial K+ uptake, we used a model neuron equipped with Na+, K+, Ca2+ and Cl− conductances, ion pumps and ion exchangers, surrounded by interstitial space and glia. The glial membrane was either “passive”, incorporating only leak channels and an ion exchange pump, or it had rectifying K+ channels. We computed ion fluxes, concentration changes and osmotic volume changes. ... We conclude that voltage gated K+ currents can boost the effectiveness of the glial “potassium buffer” and that this buffer function is important even at moderate or low levels of excitation, but especially so in pathological states."
Conduction in uniform myelinated axons (Moore et al 1978)
Examines the relative sensitivity of the velocity of impulse propagation to changes in nodal and internodal parameters.
Consequences of HERG mutations in the long QT syndrome (Clancy, Rudy 2001)
This study demonstrates which mutations can prolong APD sufficiently to generate early afterdepolarizations (EADs), which may trigger life-threatening arrhythmias. The severity of the phenotype is shown to depend on the specific kinetic changes and how they affect I(Kr) during the time course of the action potential. See paper for more and details.
Contrast invariance by LGN synaptic depression (Banitt et al. 2007)
"Simple cells in layer 4 of the primary visual cortex of the cat show contrast-invariant orientation tuning, in which the amplitude of the peak response is proportional to the stimulus contrast but the width of the tuning curve hardly changes with contrast. This study uses a detailed model of spiny stellate cells (SSCs) from cat area 17 to explain this property. The model integrates our experimental data, including morphological and intrinsic membrane properties and the number and spatial distribution of four major synaptic input sources of the SSC: the dorsal lateral geniculate nucleus (dLGN) and three cortical sources. ... The model response is in close agreement with experimental results, in terms of both output spikes and membrane voltage (amplitude and fluctuations), with reasonable exceptions given that recurrent connections were not incorporated."
Control of vibrissa motoneuron firing (Harish and Golomb 2010)
We construct and analyze a single-compartment, conductance-based model of vibrissa motoneurons. Low firing rates are supported in extended regimes by adaptation currents and the minimal firing rate decreases with the persistent sodium conductance gNaP and increases with M-potassium and h-cation conductances. Suprathreshold resonance results from the locking properties of vMN firing to stimuli and from reduction of firing rates at low frequencies by slow M and afterhyperpolarization potassium conductances. h conductance only slightly affects the suprathreshold resonance. When a vMN is subjected to a small periodic CPG input, serotonergically induced gNaP elevation may transfer the system from quiescence to a firing state that is highly locked to the CPG input.
Correcting space clamp in dendrites (Schaefer et al. 2003 and 2007)
In voltage-clamp experiments, incomplete space clamp distorts the recorded currents, rendering accurate analysis impossible. Here, we present a simple numerical algorithm that corrects such distortions. The method enabled accurate retrieval of the local densities, kinetics, and density gradients of somatic and dendritic channels. The correction method was applied to two-electrode voltage-clamp recordings of K currents from the apical dendrite of layer 5 neocortical pyramidal neurons. The generality and robustness of the algorithm make it a useful tool for voltage-clamp analysis of voltage-gated currents in structures of any morphology that is amenable to the voltage-clamp technique.
Current flow during PAP in squid axon at diameter change (Joyner et al 1980)
From the paper abstract: An impulse ... sees an increased electrical load at regions of increasing diameter or at branch points with certain morphologies. We present here theoretical and experimental studies on the changes in membrane current and axial current associated with diameter changes. The theoretical studies were done with numerical solutions for cable equations that were generalized to include a varying diameter; the Hodgkin-Huxley equations were used to represent the membrane properties. ... As an action potential approaches a region of increased electrical load, the action potential amplitude and rate of rise decrease, but there is a marked increase in the magnitude of the inward sodium current. ... (See paper for more details.)
Currents contributing to decision making in neurons B31-B32 of Aplysia (Hurwitz et al. 2008)
"Biophysical properties of neurons contributing to the ability of an animal to decide whether or not to respond were examined. B31/B32, two pairs of bilaterally symmetrical Aplysia neurons, are major participants in deciding to initiate a buccal motor program, the neural correlate of a consummatory feeding response. B31/B32 respond to an adequate stimulus after a delay, during which time additional stimuli influence the decision to respond. B31/B32 then respond with a ramp depolarization followed by a sustained soma depolarization and axon spiking that is the expression of a commitment to respond to food. Four currents contributing to decision making in B31/B32 were characterized, and their functional effects were determined, in current- and voltage-clamp experiments and with simulations. ... Hodgkin-Huxley kinetic analyses were performed on the outward currents. Simulations using equations from these analyses showed that IK-V and IK-A slow the ramp depolarization preceding the sustained depolarization. The three outward currents contribute to braking the B31/B32 depolarization and keeping the sustained depolarization at a constant voltage. The currents identified are sufficient to explain the properties of B31/B32 that play a role in generating the decision to feed."
D2 dopamine receptor modulation of interneuronal activity (Maurice et al. 2004)
"... Using a combination of electrophysiological, molecular, and computational approaches, the studies reported here show that D2 dopamine receptor modulation of Na+ currents underlying autonomous spiking contributes to a slowing of discharge rate, such as that seen in vivo. Four lines of evidence support this conclusion. ... Fourth, simulation of cholinergic interneuron pacemaking revealed that a modest increase in the entry of Na+ channels into the slow-inactivated state was sufficient to account for the slowing of pacemaker discharge. These studies establish a cellular mechanism linking dopamine and the reduction in striatal cholinergic interneuron activity seen in the initial stages of associative learning." See paper for more and details.
Data-driven, HH-type model of the lateral pyloric (LP) cell in the STG (Nowotny et al. 2008)
This model was developed using voltage clamp data and existing LP models to assemble an initial set of currents which were then adjusted by extensive fitting to a long data set of an isolated LP neuron. The main points of the work are a) automatic fitting is difficult but works when the method is carefully adjusted to the problem (and the initial guess is good enough). b) The resulting model (in this case) made reasonable predictions for manipulations not included in the original data set, e.g., blocking some of the ionic currents. c) The model is reasonably robust against changes in parameters but the different parameters vary a lot in this respect. d) The model is suitable for use in a network and has been used for this purpose (Ivanchenko et al. 2008)
DBS of a multi-compartment model of subthalamic nucleus projection neurons (Miocinovic et al. 2006)
We built a comprehensive computational model of subthalamic nucleus (STN) deep brain stimulation (DBS) in parkinsonian macaques to study the effects of stimulation in a controlled environment. The model consisted of three fundamental components: 1) a three-dimensional (3D) anatomical model of the macaque basal ganglia, 2) a finite element model of the DBS electrode and electric field transmitted to the tissue medium, and 3) multicompartment biophysical models of STN projection neurons, GPi fibers of passage, and internal capsule fibers of passage. Populations of neurons were positioned within the 3D anatomical model. Neurons were stimulated with electrode positions and stimulation parameters defined as clinically effective in two parkinsonian monkeys. The model predicted axonal activation of STN neurons and GPi fibers during STN DBS. Model predictions regarding the degree of GPi fiber activation matched well with experimental recordings in both monkeys.
Demyelinated and remyelinating axon conductances (Hines, Shrager 1991)
Hines, Michael and Peter Shrager (1991). A computational test of the requirements for conduction in demyelinated axons. J. Restorative Neurology and Neuroscience. 3 81--93.
Dendritic Na inactivation drives a decrease in ISI (Fernandez et al 2005)
We use a combination of dynamical analysis and electrophysiological recordings to demonstrate that spike broadening in dendrites is primarily caused by a cumulative inactivation of dendritic Na(+) current. We further show that a reduction in dendritic Na(+) current increases excitability by decreasing the interspike interval (ISI) and promoting burst firing.
Dendritic Na+ spike initiation and backpropagation of APs in active dendrites (Nevian et al. 2007)
NEURON model used to create simulations shown in figure 6 of the paper. The model includes two point processes; one for dendritic spike initiation and the other for somatic action potential generation. The effect of filtering by imperfect recording electrode can be examined in somatic and dendritic locations.
Dendritic processing of excitatory synaptic input in GnRH neurons (Roberts et al. 2006)
"... we used electrophysiological recordings and neuronal reconstructions to generate computer models of (Gonadotopin-Releasing Hormone) GnRH neurons to examine the effects of synaptic inputs at varying distances from the soma along dendrites. ... analysis of reduced morphology models indicated that this population of cells is unlikely to exhibit low-frequency tonic spiking in the absence of synaptic input. ... applying realistic patterns of synaptic input to modeled GnRH neurons indicates that synapses located more than about 30% of the average dendrite length from the soma cannot drive firing at frequencies consistent with neuropeptide release. Thus, processing of synaptic input to dendrites of GnRH neurons is probably more complex than simple summation."
Dendritic signals command firing dynamics in a Cerebellar Purkinje Cell model (Genet et al. 2010)
This model endows the dendrites of a reconstructed Purkinje cells (PC) with the mechanism of Ca-dependent plateau potentials and spikes described in Genet, S., and B. Delord. 2002. A biophysical model of nonlinear dynamics underlying plateau potentials and calcium spikes in Purkinje cell dendrites. J. Neurophysiol. 88:2430–2444). It is a part of a comprehensive mathematical study suggesting that active electric signals in the dendrites of PC command epochs of firing and silencing of the PC soma.
Dendritica (Vetter et al 2001)
Dendritica is a collection of programs for relating dendritic geometry and signal propagation. The programs are based on those used for the simulations described in: Vetter, P., Roth, A. & Hausser, M. (2001) For reprint requests and additional information please contact Dr. M. Hausser, email address: m.hausser@ucl.ac.uk
Dentate Gyrus Feed-forward inhibition (Ferrante et al. 2009)
In this paper, the model was used to show how that FFI can change a steeply sigmoidal input-output (I/O) curve into a double-sigmoid typical of buffer systems.
Dentate gyrus granule cell: calcium and calcium-dependent conductances (Aradi and Holmes 1999)
We have constructed a detailed model of a hippocampal dentate granule (DG) cell that includes nine different channel types. Channel densities and distributions were chosen to reproduce reported physiological responses observed in normal solution and when blockers were applied. The model was used to explore the contribution of each channel type to spiking behavior with particular emphasis on the mechanisms underlying postspike events. ... The model was used to predict changes in channel densities that could lead to epileptogenic burst discharges and to predict the effect of altered buffering capacity on firing behavior. We conclude that the clustered spatial distributions of calcium related channels, the presence of slow delayed rectifier potassium currents in dendrites, and calcium buffering properties, together, might explain the resistance of DG cells to the development of epileptogenic burst discharges.
Dentate gyrus network model (Santhakumar et al 2005)
Mossy cell loss and mossy fiber sprouting are two characteristic consequences of repeated seizures and head trauma. However, their precise contributions to the hyperexcitable state are not well understood. Because it is difficult, and frequently impossible, to independently examine using experimental techniques whether it is the loss of mossy cells or the sprouting of mossy fibers that leads to dentate hyperexcitability, we built a biophysically realistic and anatomically representative computational model of the dentate gyrus to examine this question. The 527-cell model, containing granule, mossy, basket, and hilar cells with axonal projections to the perforant-path termination zone, showed that even weak mossy fiber sprouting (10-15% of the strong sprouting observed in the pilocarpine model of epilepsy) resulted in the spread of seizure-like activity to the adjacent model hippocampal laminae after focal stimulation of the perforant path. See reference for more and details.
Dentate gyrus network model (Tejada et al 2014)
" ... Here we adapted an existing computational model of the dentate gyrus (J Neurophysiol 93: 437-453, 2005) by replacing the reduced granule cell models with morphologically detailed models coming from (3D) reconstructions of mature cells. ... Different fractions of the mature granule cell models were replaced by morphologically reconstructed models of newborn dentate granule cells from animals with PILO-induced Status Epilepticus, which have apical dendritic alterations and spine loss, and control animals, which do not have these alterations. This complex arrangement of cells and processes allowed us to study the combined effect of mossy fiber sprouting, altered apical dendritic tree and dendritic spine loss in newborn granule cells on the excitability of the dentate gyrus model. Our simulations suggest that alterations in the apical dendritic tree and dendritic spine loss in newborn granule cells have opposing effects on the excitability of the dentate gyrus after Status Epilepticus. Apical dendritic alterations potentiate the increase of excitability provoked by mossy fiber sprouting while spine loss curtails this increase. "
Deterministic chaos in a mathematical model of a snail neuron (Komendantov and Kononenko 1996)
"Chaotic regimes in a mathematical model of pacemaker activity in the bursting neurons of a snail Helix pomatia, have been investigated. The model includes a slow-wave generating mechanism, a spike-generating mechanism, an inward Ca current, intracellular Ca ions, [Ca2+]in, their fast buffering and uptake by intracellular Ca stores, and a [Ca2+]in-inhibited Ca current. Chemosensitive voltage-activated conductance, gB*, responsible for termination of the spike burst, and chemosensitive sodium conductance, gNa*, responsible for the depolarization phase of the slow-wave, were used as control parameters. ... Time courses of the membrane potential and [Ca2+]in were employed to analyse different regimes in the model. ..."
Dichotomy of action-potential backpropagation in CA1 pyramidal neuron dendrites (Golding et al 2001)
From reference below and Corrigendum: J Neurophysiol 87:1a, 2002 (better versions of figures 2, 3, 5 and 7 because of poor print quality in the original article; as of 2/2006, these figures are perfectly fine in the PDF of the original article that is currently available from the publisher's WWW site). Examines the anatomical and biophysical factors that account for the fact that retrograde invasion of spikes into the apical dendritic tree past 300 um succeeds in some CA1 pyramidal neurons but fails in others.
Differences between type A and B photoreceptors (Blackwell 2006)
In Hermissenda crassicornis, the memory of light associated with turbulence is stored as changes in intrinsic and synaptic currents in both type A and type B photoreceptors. These photoreceptor types exhibit qualitatively different responses to light and current injection, and these differences shape the spatiotemporal firing patterns that control behavior. Thus the objective of the study was to identify the mechanisms underlying these differences. The approach was to develop a type B model that reproduced characteristics of type B photoreceptors recorded in vitro, and then to create a type A model by modifying a select number of ionic currents. Comparison of type A models with characteristics of type A photoreceptors recorded in vitro revealed that type A and type B photoreceptors have five main differences, three that have been characterized experimentally and two that constitute hypotheses to be tested with experiments in the future. See paper for more and details.
Differential modulation of pattern and rate in a dopamine neuron model (Canavier and Landry 2006)
"A stylized, symmetric, compartmental model of a dopamine neuron in vivo shows how rate and pattern can be modulated either concurrently or differentially. If two or more parameters in the model are varied concurrently, the baseline firing rate and the extent of bursting become decorrelated, which provides an explanation for the lack of a tight correlation in vivo and is consistent with some independence of the mechanisms that generate baseline firing rates versus bursting. ..." See paper for more and details.
Dorsal root ganglion (DRG) neuronal model (Amir, Devor 2003)
The model shows that an electrically excitable soma is not necessary for spike through-conduction in the t-shaped geometry of a dorsal root ganglion neuron axon. Electrical excitability of the soma is required, however, for soma spike invasion. See papers for details and more.
Dorsal root ganglion (DRG) neuronal model (Kovalsky et al. 2009)
This model, diverged from oscillatory parameters seen in live cells and failed to produce characteristic ectopic discharge patterns. Here we show that use of a more complete set of Na+ conductances--which includes several delayed components--enables simulation of the entire repertoire of oscillation-triggered electrogenic phenomena seen in live dorsal root ganglion (DRG) neurons. This includes a physiological window of induction and natural patterns of spike discharge. An INa+ component at 2-20 ms was particularly important, even though it represented only a tiny fraction of overall INa+ amplitude. With the addition of a delayed rectifier IK+ the singlet firing seen in some DRG neurons can also be simulated. The model reveals the key conductances that underlie afferent ectopia, conductances that are potentially attractive targets in the search for more effective treatments of neuropathic pain.
Drosophila 3rd instar larval aCC motoneuron (Gunay et al. 2014, submitted)
Single compartmental, ball-and-stick models implemented in XPP and full morphological model in Neuron. Paper has been submitted and correlates anatomical properties with electrophysiological recordings from these hard-to-access neurons. For instance we make predictions about location of the spike initiation zone, channel distributions, and synaptic input parameters.
DRt neuron model (Sousa et al., 2014)
Despite the importance and significant clinical impact of understanding information processing in the nociceptive system, the functional properties of neurons in many parts of this system are still unknown. In this work we performed whole-cell patch-clamp recording in rat brainstem blocks to characterize the electrophysiological properties of neurons in the dorsal reticular nucleus (DRt), a region known to be involved in pronociceptive modulation. We also compared properties of DRt neurons with those in the adjacent parvicellular reticular nucleus (PCRt) and in neighboring regions outside the reticular formation. We found that neurons in the DRt and PCRt had similar electrophysiological properties and exhibited mostly tonic-like firing patterns, whereas neurons outside the reticular formation showed a larger diversity of firing-patterns. The dominance of tonic neurons in the DRt supports previous conclusions that these neurons encode stimulus intensity through their firing frequency.
Dynamic cortical interlaminar interactions (Carracedo et al. 2013)
"... Here we demonstrate the mechanism underlying a purely neocortical delta rhythm generator and show a remarkable laminar, cell subtype and local subcircuit delineation between delta and nested theta rhythms. We show that spike timing during delta-nested theta rhythms controls an iterative, reciprocal interaction between deep and superficial cortical layers resembling the unsupervised learning processes proposed for laminar neural networks by Hinton and colleagues ... and mimicking the alternating cortical dynamics of sensory and memory processing during wakefulness."
Dynamical model of olfactory bulb mitral cell (Rubin, Cleland 2006)
This four-compartment mitral cell exhibits endogenous subthreshold oscillations, phase resetting, and evoked spike phasing properties as described in electrophysiological studies of mitral cells. It is derived from the prior work of Davison et al (2000) and Bhalla and Bower (1993). See readme.txt for details.
Effect of slowly inactivating IKdr to delayed firing of action potentials (Wu et al. 2008)
"The properties of slowly inactivating delayed-rectifier K+ current (IKdr) were investigated in NG108-15 neuronal cells differentiated with long-term exposure to dibutyryl cyclic AMP. ... The computer model, in which state-dependent inactivation of IKdr was incorporated, was also implemented to predict the firing behavior present in NG108-15 cells. ... Our theoretical work and the experimental results led us to propose a pivotal role of slowly inactivating IKdr in delayed firing of APs in NG108-15 cells. The results also suggest that aconitine modulation of IKdr gating is an important molecular mechanism through which it can contribute to neuronal firing."
Effect of voltage sensitive fluorescent proteins on neuronal excitability (Akemann et al. 2009)
"Fluorescent protein voltage sensors are recombinant proteins that are designed as genetically encoded cellular probes of membrane potential using mechanisms of voltage-dependent modulation of fluorescence. Several such proteins, including VSFP2.3 and VSFP3.1, were recently reported with reliable function in mammalian cells. ... Expression of these proteins in cell membranes is accompanied by additional dynamic membrane capacitance, ... We used recordings of sensing currents and fluorescence responses of VSFP2.3 and of VSFP3.1 to derive kinetic models of the voltage-dependent signaling of these proteins. Using computational neuron simulations, we quantitatively investigated the perturbing effects of sensing capacitance on the input/output relationship in two central neuron models, a cerebellar Purkinje and a layer 5 pyramidal neuron. ... ". The Purkinje cell model is included in ModelDB.
Effects of increasing CREB on storage and recall processes in a CA1 network (Bianchi et al. 2013)
Several recent results suggest that boosting the CREB pathway improves hippocampal-dependent memory in healthy rodents and restores this type of memory in an AD mouse model. However, not much is known about how CREB-dependent neuronal alterations in synaptic strength, excitability and LTP can boost memory formation in the complex architecture of a neuronal network. Using a model of a CA1 microcircuit, we investigate whether hippocampal CA1 pyramidal neuron properties altered by increasing CREB activity may contribute to improve memory storage and recall. With a set of patterns presented to a network, we find that the pattern recall quality under AD-like conditions is significantly better when boosting CREB function with respect to control. The results are robust and consistent upon increasing the synaptic damage expected by AD progression, supporting the idea that the use of CREB-based therapies could provide a new approach to treat AD.
Electrically-coupled Retzius neurons (Vazquez et al. 2009)
"Dendritic electrical coupling increases the number of effective synaptic inputs onto neurons by allowing the direct spread of synaptic potentials from one neuron to another. Here we studied the summation of excitatory postsynaptic potentials (EPSPs) produced locally and arriving from the coupled neuron (transjunctional) in pairs of electrically-coupled Retzius neurons of the leech. We combined paired recordings of EPSPs, the production of artificial EPSPs (APSPs) in neuron pairs with different coupling coefficients and simulations of EPSPs produced in the coupled dendrites. ..."
Endothelin action on pituitary latotrophs (Bertram et al. 2006)
Endothelin (ET-1, -2, and -3 designate three genes which produce different endothelin isopeptides) is a prolactin inhibiting substance of hypothalmic origin. ET-1 binding is part of at least four G protein signaling pathways in lactotrophs. The sequence of events in these pathways following the presentation of nano- and pico-molar concentrations of ET-1 is modeled in the paper.
Engaging distinct oscillatory neocortical circuits (Vierling-Claassen et al. 2010)
"Selective optogenetic drive of fast-spiking (FS) interneurons (INs) leads to enhanced local field potential (LFP) power across the traditional “gamma” frequency band (20–80 Hz; Cardin et al., 2009). In contrast, drive to regular-spiking (RS) pyramidal cells enhances power at lower frequencies, with a peak at 8 Hz. The first result is consistent with previous computational studies emphasizing the role of FS and the time constant of GABAA synaptic inhibition in gamma rhythmicity. However, the same theoretical models do not typically predict low-frequency LFP enhancement with RS drive. To develop hypotheses as to how the same network can support these contrasting behaviors, we constructed a biophysically principled network model of primary somatosensory neocortex containing FS, RS, and low-threshold spiking (LTS) INs. ..."
Enhanced Excitability in Hermissenda: modulation by 5-HT (Cai et al 2003)
Serotonin (5-HT) applied to the exposed but otherwise intact nervous system results in enhanced excitability of Hermissenda type-B photoreceptors. Several ion currents in the type-B photoreceptors are modulated by 5-HT, including the A-type K+ current (IK,A), sustained Ca2+ current (ICa,S), Ca-dependent K+ current (IK,Ca), and a hyperpolarization-activated inward rectifier current (Ih). In this study,we developed a computational model that reproduces physiological characteristics of type B photoreceptors, e.g. resting membrane potential, dark-adapted spike activity, spike width, and the amplitude difference between somatic and axonal spikes. We then used the model to investigate the contribution of different ion currents modulated by 5-HT to the magnitudes of enhanced excitability produced by 5-HT. See paper for results and more details.
Epilepsy may be caused by very small functional changes in ion channels (Thomas et al. 2009)
We used a previously published model of the dentate gyrus with varying degrees of mossy fibre sprouting.We preformed a sensitivity analysis where we systematically varied individual properties of ion channels. The results predict that genetic variations in the properties of sodium channels are likely to have the biggest impact on network excitability. Furthermore, these changes may be as small as 1mV, which is currently undetectable using standard experimental practices.
Estimation and Production of Time Intervals (Migliore et al 2001)
NEURON model files from the paper M. Migliore, L. Messineo, M. Cardaci, G.F. Ayala, Quantitative modeling of perception and production of time intervals, J.Neurophysiol. 86, 2754-2760 (2001). Contact michele.migliore@pa.ibf.cnr.it if you have any questions about the implementation of the model.
Excitability of PFC Basal Dendrites (Acker and Antic 2009)
".. We carried out multi-site voltage-sensitive dye imaging of membrane potential transients from thin basal branches of prefrontal cortical pyramidal neurons before and after application of channel blockers. We found that backpropagating action potentials (bAPs) are predominantly controlled by voltage-gated sodium and A-type potassium channels. In contrast, pharmacologically blocking the delayed rectifier potassium, voltage-gated calcium or Ih, conductance had little effect on dendritic action potential propagation. Optically recorded bAP waveforms were quantified and multicompartmental modeling (NEURON) was used to link the observed behavior with the underlying biophysical properties. The best-fit model included a non-uniform sodium channel distribution with decreasing conductance with distance from the soma, together with a non-uniform (increasing) A-type potassium conductance. AP amplitudes decline with distance in this model, but to a lesser extent than previously thought. We used this model to explore the mechanisms underlying two sets of published data involving high frequency trains of action potentials, and the local generation of sodium spikelets. ..."
Excitability of the soma in central nervous system neurons (Safronov et al 2000)
The ability of the soma of a spinal dorsal horn neuron, a spinal ventral horn neuron, and a hippocampal pyramidal neuron to generate action potentials was studied using experiments and computer simulations. By comparing recordings ... of a dorsal horn neuron with simulated responses, it was shown that computer models can be adequate for the study of somatic excitability. The modeled somata of both spinal neurons were unable to generate action potentials, showing only passive and local responses to current injections. ... In contrast to spinal neurons, the modeled soma of the hippocampal pyramidal neuron generated spikes with an overshoot of +9 mV. It is concluded that the somata of spinal neurons cannot generate action potentials and seem to resist their propagation from the axon to dendrites. ... See paper for more and details.
Failure of Deep Brain Stimulation in a basal ganglia neuronal network model (Dovzhenok et al. 2013)
"… Recently, a lot of interest has been devoted to desynchronizing delayed feedback deep brain stimulation (DBS). ... This study explores the action of delayed feedback stimulation on partially synchronized oscillatory dynamics, similar to what one observes experimentally in parkinsonian patients. …" Implemented by Andrey Dovzhenok, to whom questions should be addressed.
Fast oscillations in inhibitory networks (Maex, De Schutter 2003)
We observed a new phenomenon of resonant synchronization in computer-simulated networks of inhibitory neurons in which the synaptic current has a delayed onset, reflecting finite spike propagation and synaptic transmission times. At the resonant level of network excitation, all neurons fire synchronously and rhythmically with a period approximately four times the mean delay of the onset of the inhibitory synaptic current. ... By varying the axonal delay of the inhibitory connections, networks with a realistic synaptic kinetics can be tuned to frequencies from 40 to >200 Hz. ... We conclude that the delay of the synaptic current is the primary parameter controlling the oscillation frequency of inhibitory networks and propose that delay-induced synchronization is a mechanism for fast brain rhythms that depend on intact inhibitory synaptic transmission.
Fast-spiking cortical interneuron (Golomb et al. 2007)
Cortical fast-spiking (FS) interneurons display highly variable electrophysiological properties. We hypothesize that this variability emerges naturally if one assumes a continuous distribution of properties in a small set of active channels. We construct a minimal, single-compartment conductance-based model of FS cells that includes transient Na+, delayed-rectifier K+, and slowly inactivating d-type K+ conductances. The model may display delay to firing. Stuttering (elliptic bursting) and subthreshold oscillations may be observed for small Na+ window current.
Febrile seizure-induced modifications to Ih (Chen et al 2001)
Modeling and experiments in the paper Chen K,Aradi I, Thom N,Eghbal-Ahmadi M, Baram TZ, and Soltesz I (2001) support the hypothesis that modified Ih currents strongly influence inhibitory inputs in CA1 cells and that the depolarizing shift in Ih activation plays a primary role in this process. Please see the paper for details. Some modeling details are available at http://www.ucihs.uci.edu/anatomy/soltesz/supp.htm Correspondance should be addressed to isoltesz@uci.edu (modeling was done by Ildiko Aradi, iaradi@uci.edu)
Feedforward heteroassociative network with HH dynamics (Lytton 1998)
Using the original McCulloch-Pitts notion of simple on and off spike coding in lieu of rate coding, an Anderson-Kohonen artificial neural network (ANN) associative memory model was ported to a neuronal network with Hodgkin-Huxley dynamics.
Firing patterns in stuttering fast-spiking interneurons (Klaus et al. 2011)
This is a morphologically extended version of the fast-spiking interneuron by Golomb et al. (2007). The model captures the stuttering firing pattern and subthreshold oscillations in response to step current input as observed in many cortical and striatal fast-spiking cells.
Fluctuating synaptic conductances recreate in-vivo-like activity (Destexhe et al 2001)
This model (and experiments) reported in Destexhe, Rudolh, Fellous, and Sejnowski (2001) support the hypothesis that many of the characteristics of cortical neurons in vivo can be explained by fast glutamatergic and GABAergic conductances varying stochastically. Some of these cortical neuron characteristics of fluctuating synaptic origin are a depolarized membrane potential, the presence of high-amplitude membrane potential fluctuations, a low input resistance and irregular spontaneous firing activity. In addition, the point-conductance model could simulate the enhancement of responsiveness due to background activity. For more information please contact Alain Destexhe. email: Destexhe@iaf.cnrs-gif.fr
Fly lobular plate VS cell (Borst and Haag 1996, et al. 1997, et al. 1999)
In a series of papers the authors conducted experiments to develop understanding and models of fly visual system HS, CS, and VS neurons. This model recreates the VS neurons from those papers with enough success to merit approval by Borst although some discrepancies remain (see readme).
FS Striatal interneuron: K currents solve signal-to-noise problems (Kotaleski et al 2006)
... We show that a transient potassium (KA) current allows the Fast Spiking (FS) interneuron to strike a balance between sensitivity to correlated input and robustness to noise, thereby increasing its signal-to-noise ratio (SNR). First, a compartmental FS neuron model was created to match experimental data from striatal FS interneurons in cortex–striatum–substantia nigra organotypic cultures. Densities of sodium, delayed rectifier, and KA channels were optimized to replicate responses to somatic current injection. Spontaneous AMPA and GABA synaptic currents were adjusted to the experimentally measured amplitude, rise time, and interevent interval histograms. Second, two additional adjustments were required to emulate the remaining experimental observations. GABA channels were localized closer to the soma than AMPA channels to match the synaptic population reversal potential. Correlation among inputs was required to produce the observed firing rate during up-states. In this final model, KA channels were essential for suppressing down-state spikes while allowing reliable spike generation during up-states. ... Our results suggest that KA channels allow FS interneurons to operate without a decrease in SNR during conditions of increased dopamine, as occurs in response to reward or anticipated reward. See paper for more and details.
Functional impact of dendritic branch point morphology (Ferrante et al., 2013)
" ... Here, we first quantified the morphological variability of branch points from two-photon images of rat CA1 pyramidal neurons. We then investigated the geometrical features affecting spike initiation, propagation, and timing with a computational model validated by glutamate uncaging experiments. The results suggest that even subtle membrane readjustments at branch point could drastically alter the ability of synaptic input to generate, propagate, and time action potentials."
Functional structure of mitral cell dendritic tuft (Djurisic et al. 2008)
The computational modeling component of Djurisic et al. 2008 addressed two primary questions: whether amplification by active currents is necessary to explain the relatively mild attenuation suffered by tuft EPSPs spreading along the primary dendrite to the soma; what accounts for the relatively uniform peak EPSP amplitude throughout the tuft. These simulations show that passive spread from tuft to soma is sufficient to yield the low attenuation of tuft EPSPs, and that random distribution of a biologically plausible number of excitatory synapses throughout the tuft can produce the experimentally observed uniformity of depolarization.
Gamma and theta rythms in biophysical models of hippocampus circuits (Kopell et al. 2011)
" ... the main rhythms displayed by the hippocampus, the gamma (30–90 Hz) and theta (4–12 Hz) rhythms. We concentrate on modeling in vitro experiments, but with an eye toward possible in vivo implications. ... We use simpler biophysical models; all cells have a single compartment only, and the interneurons are restricted to two types: fast-spiking (FS) basket cells and oriens lacunosum-moleculare (O-LM) cells. ... , we aim not so much at reproducing dynamics in great detail, but at clarifying the essential mechanisms underlying the production of the rhythms and their interactions (Kopell, 2005). ..."
Gamma oscillations in hippocampal interneuron networks (Bartos et al 2002)
To examine whether an interneuron network with fast inhibitory synapses can act as a gamma frequency oscillator, we developed an interneuron network model based on experimentally determined properties. In comparison to previous interneuron network models, our model was able to generate oscillatory activity with higher coherence over a broad range of frequencies (20-110 Hz). In this model, high coherence and flexibility in frequency control emerge from the combination of synaptic properties, network structure, and electrical coupling.
Gamma oscillations in hippocampal interneuron networks (Wang, Buzsaki 1996)
The authors investigated the hypothesis that 20-80Hz neuronal (gamma) oscillations can emerge in sparsely connected network models of GABAergic fast-spiking interneurons. They explore model NN synchronization and compare their results to anatomical and electrophysiological data from hippocampal fast spiking interneurons.
Gap-junction coupled network activity depends on coupled dendrites diameter (Gansert et al. 2007)
"... We have previously shown that the amplitude of electrical signals propagating across gap-junctionally coupled passive cables is maximized at a unique diameter. This suggests that threshold-dependent signals may propagate through gap junctions for a finite range of diameters around this optimal value. Here we examine the diameter dependence of action potential propagation across model networks of dendro-dendritically coupled neurons. The neurons in these models have passive soma and dendrites and an action potential-generating axon. We show that propagation of action potentials across gap junctions occurs only over a finite range of dendritic diameters and that propagation delay depends on this diameter. ...". See paper for more and details.
Gating of steering signals through phasic modulation of reticulospinal neurons (Kozlov et al. 2014)
" ... We use the lamprey as a model for investigating the role of this phasic modulation of the reticulospinal activity, because the brainstem–spinal cord networks are known down to the cellular level in this phylogenetically oldest extant vertebrate. We describe how the phasic modulation of reticulospinal activity from the spinal CPG ensures reliable steering/turning commands without the need for a very precise timing of on- or offset, by using a biophysically detailed large-scale (19,600 model neurons and 646,800 synapses) computational model of the lamprey brainstem–spinal cord network. To verify that the simulated neural network can control body movements, including turning, the spinal activity is fed to a mechanical model of lamprey swimming. ..."
Geometry-induced features of current transfer in neuronal dendrites (Korogod, Kulagina 1998)
The impact of dendritic geometry on somatopetal transfer of the current generated by steady uniform activation of excitatory synaptic conductance distributed over passive, or active (Hodgkin-Huxley type), dendrites was studied in simulated neurons.
Global structure, robustness, and modulation of neuronal models (Goldman et al. 2001)
"The electrical characteristics of many neurons are remarkably robust in the face of changing internal and external conditions. At the same time, neurons can be highly sensitive to neuromodulators. We find correlates of this dual robustness and sensitivity in a global analysis of the structure of a conductance-based model neuron. ..."
Globus pallidus neuron models with differing dendritic Na channel expression (Edgerton et al., 2010)
A set of 9 multi-compartmental rat GP neuron models (585 compartments) differing only in their expression of dendritic fast sodium channels were compared in their synaptic integration properties. Dendritic fast sodium channels were found to increase the importance of distal synapses (both excitatory AND inhibitory), increase spike timing variability with in vivo-like synaptic input, and make the model neurons highly sensitive to clustered synchronous excitation.
Grid cell oscillatory interference with noisy network oscillators (Zilli and Hasselmo 2010)
To examine whether an oscillatory interference model of grid cell activity could work if the oscillators were noisy neurons, we implemented these simulations. Here the oscillators are networks (either synaptically- or gap-junction--coupled) of one or more noisy neurons (either Izhikevich's simple model or a Hodgkin-Huxley--type biophysical model) which drive a postsynaptic cell (which may be integrate-and-fire, resonate-and-fire, or the simple model) which should fire spatially as a grid cell if the simulation is successful.
Half-center oscillator database of leech heart interneuron model (Doloc-Mihu & Calabrese 2011)
We have created a database (HCO-db) of instances of a half-center oscillator computational model [Hill et al., 2001] for analyzing how neuronal parameters influence network activity. We systematically explored the parameter space of about 10.4 million simulated HCO instances and corresponding isolated neuron model simulations obtained by varying a set of selected parameters (maximal conductance of intrinsic and synaptic currents) in all combinations using a brute-force approach. We classified these HCO instances by their activity characteristics into identifiable groups. We built an efficient relational database table (HCO-db) with the resulting instances characteristics.
High frequency oscillations in a hippocampal computational model (Stacey et al. 2009)
"... Using a physiological computer model of hippocampus, we investigate random synaptic activity (noise) as a potential initiator of HFOs (high-frequency oscillations). We explore parameters necessary to produce these oscillations and quantify the response using the tools of stochastic resonance (SR) and coherence resonance (CR). ... Our results show that, under normal coupling conditions, synaptic noise was able to produce gamma (30–100 Hz) frequency oscillations. Synaptic noise generated HFOs in the ripple range (100–200 Hz) when the network had parameters similar to pathological findings in epilepsy: increased gap junctions or recurrent synaptic connections, loss of inhibitory interneurons such as basket cells, and increased synaptic noise. ... We propose that increased synaptic noise and physiological coupling mechanisms are sufficient to generate gamma oscillations and that pathologic changes in noise and coupling similar to those in epilepsy can produce abnormal ripples."
High frequency stimulation of the Subthalamic Nucleus (Rubin and Terman 2004)
" ... Using a computational model, this paper considers the hypothesis that DBS works by replacing pathologically rhythmic basal ganglia output with tonic, high frequency firing. In our simulations of parkinsonian conditions, rhythmic inhibition from GPi to the thalamus compromises the ability of thalamocortical relay (TC) cells to respond to depolarizing inputs, such as sensorimotor signals. High frequency stimulation of STN regularizes GPi firing, and this restores TC responsiveness, despite the increased frequency and amplitude of GPi inhibition to thalamus that result. We provide a mathematical phase plane analysis of the mechanisms that determine TC relay capabilities in normal, parkinsonian, and DBS states in a reduced model. This analysis highlights the differences in deinactivation of the low-threshold calcium T -current that we observe in TC cells in these different conditions. ..."
Hippocampal basket cell gap junction network dynamics (Saraga et al. 2006)
2 cell network of hippocampal basket cells connected by gap junctions. Paper explores how distal gap junctions and active dendrites can tune network dynamics.
Hippocampal CA3 network and circadian regulation (Stanley et al. 2013)
This model produces the hippocampal CA3 neural network model used in the paper below. It has two modes of operation, a default mode and a circadian mode. In the circadian mode, parameters are swept through a range of values. This model can be quite easily adapted to produce theta and gamma oscillations, as certain parameter sweeps will reveal (see Figures). BASH scripts interact with GENESIS 2.3 to implement parameter sweeps. The model contains four cell types derived from prior papers. CA3 pyramidal are derived from Traub et al (1991); Basket, stratum oriens (O-LM), and Medial Septal GABAergic (MSG) interneurons are taken from Hajos et al (2004).
Hippocampus temporo-septal engram shift model (Lytton 1999)
Temporo-septal engram shift model of hippocampal memory. The model posits that memories gradually move along the hippocampus from a temporal encoding site to ever more septal sites from which they are recalled. We propose that the sense of time is encoded by the location of the engram along the temporo-septal axis.
Hodgkin-Huxley model of persistent activity in PFC neurons (Winograd et al. 2008) (NEURON python)
The paper demonstrate a form of graded persistent activity activated by hyperpolarization. This phenomenon is modeled based on a slow calcium regulation of Ih, similar to that introduced earlier for thalamic neurons (see Destexhe et al., J Neurophysiol. 1996). The only difference is that the calcium signal is here provided by the high-threshold calcium current (instead of the low-threshold calcium current in thalamic neurons).
Hodgkin-Huxley model of persistent activity in prefrontal cortex neurons (Winograd et al. 2008)
The paper demonstrate a form of graded persistent activity activated by hyperpolarization. This phenomenon is modeled based on a slow calcium regulation of Ih, similar to that introduced earlier for thalamic neurons (see Destexhe et al., J Neurophysiol. 1996). The only difference is that the calcium signal is here provided by the high-threshold calcium current (instead of the low-threshold calcium current in thalamic neurons).
Hodgkin-Huxley models of different classes of cortical neurons (Pospischil et al. 2008)
"We review here the development of Hodgkin– Huxley (HH) type models of cerebral cortex and thalamic neurons for network simulations. The intrinsic electrophysiological properties of cortical neurons were analyzed from several preparations, and we selected the four most prominent electrophysiological classes of neurons. These four classes are “fast spiking”, “regular spiking”, “intrinsically bursting” and “low-threshold spike” cells. For each class, we fit “minimal” HH type models to experimental data. ..."
Hodgkin-Huxley with dynamic ion concentrations (Hubel and Dahlem, 2014)
The classical Hodgkin--Huxley (HH) model neglects the time-dependence of ion concentrations in spiking dynamics. The dynamics is therefore limited to a time scale of milliseconds, which is determined by the membrane capacitance multiplied by the resistance of the ion channels, and by the gating time constants. This model includes slow dynamics in an extended HH framework that simulates time-dependent ion concentrations, pumps, and buffers. Fluxes across the neuronal membrane change intra- and extracellular ion concentrations, whereby the latter can also change through contact to reservoirs in the surroundings. The dynamics on three distinct slow times scales is determined by the cell volume-to-surface-area ratio and the membrane permeability (seconds), the buffer time constants (tens of seconds), and the slower backward buffering (minutes to hours). The modulatory dynamics and the newly emerging excitable dynamics corresponds to pathological conditions observed in epileptiform burst activity, and spreading depression in migraine aura and stroke, respectively.
Homeostatic synaptic plasticity (Rabinowitch and Segev 2006a,b)
(2006a): "We investigated analytically and numerically the interplay between two opposing forms of synaptic plasticity: positive-feedback, long-term potentiation/depression (LTP/LTD), and negative-feedback, homeostatic synaptic plasticity (HSP). A detailed model of a CA1 pyramidal neuron, with numerous HSP-modifiable dendritic synapses, demonstrates that HSP may have an important role in selecting which spatial patterns of LTP/LTD are to last. ... Despite the negative-feedback nature of HSP, under both local and global HSP, numerous synaptic potentiations/depressions can persist. These experimentally testable results imply that HSP could be significantly involved in shaping the spatial distribution of synaptic weights in the dendrites and not just normalizing it, as is currently believed." (2006b): "Homeostatic synaptic plasticity (HSP) is an important mechanism attributed with the slow regulation of the neuron's activity. Whenever activity is chronically enhanced, HSP weakens the weights of the synapses in the dendrites and vice versa. Because dendritic morphology and its electrical properties partition the dendritic tree into functional compartments, we set out to explore the interplay between HSP and dendritic compartmentalization. ... The spatial distribution of synaptic weights throughout the dendrites will markedly differ under the local versus global HSP mechanisms. We suggest an experimental paradigm to unravel which type of HSP mechanism operates in the dendritic tree. The answer to this question will have important implications to our understanding of the functional organization of the neuron."
Homosynaptic plasticity in the tail withdrawal circuit (TWC) of Aplysia (Baxter and Byrne 2006)
The tail-withdrawal circuit of Aplysia provides a useful model system for investigating synaptic dynamics. Sensory neurons within the circuit manifest several forms of synaptic plasticity. Here, we developed a model of the circuit and investigated the ways in which depression (DEP) and potentiation (POT) contributed to information processing. DEP limited the amount of motor neuron activity that could be elicited by the monosynaptic pathway alone. POT within the monosynaptic pathway did not compensate for DEP. There was, however, a synergistic interaction between POT and the polysynaptic pathway. This synergism extended the dynamic range of the network, and the interplay between DEP and POT made the circuit respond preferentially to long-duration, low-frequency inputs.
Hypocretin and Locus Coeruleus model neurons (Carter et al 2012)
Conductance based model of the hypocretin neurons (HCRT) and another one of the Locus Coeruleus one (LC). The HCRT drive the LCs via the HCRT receptor on the LCs. The LCs lead to the awakening of the mice if the number of spikes raises over 10 spikes in 10 seconds window.
Hysteresis in voltage gating of HCN channels (Elinder et al 2006, Mannikko et al 2005)
We found that HCN2 and HCN4 channels expressed in oocytes from the frog Xenopus laevis do not display the activation kinetic changes that we (previously) observed in spHCN and HCN1. However, HCN2 and HCN4 channels display changes in their tail currents, suggesting that these channels also undergo mode shifts and that the conformational changes underlying the mode shifts are due to conserved aspects of HCN channels. With computer modelling, we show that in channels with relatively slow opening kinetics and fast mode-shift transitions, such as HCN2 and HCN4 channels, the mode shift effects are not readily observable, except in the tail kinetics. Computer simulations of sino-atrial node action potentials suggest that the HCN2 channel, together with the HCN1 channel, are important regulators of the heart firing frequency and that the mode shift is an important property to prevent arrhythmic firing. We conclude that although all HCN channels appear to undergo mode shifts – and thus may serve to prevent arrhythmic firing – it is mainly observable in ionic currents from HCN channels with faster kinetics. See papers for more and details.
I A in Kenyon cells resemble Shaker currents (Pelz et al 1999)
Cultured Kenyon cells from the mushroom body of the honeybee, Apis mellifera, show a voltage-gated, fast transient K1 current that is sensitive to 4-aminopyridine, an A current. The kinetic properties of this A current and its modulation by extracellular K1 ions were investigated in vitro with the whole cell patch-clamp technique. The A current was isolated from other voltage-gated currents either pharmacologically or with suitable voltage-clamp protocols. Hodgkin- and Huxley-style mathematical equations were used for the description of this current and for the simulation of action potentials in a Kenyon cell model. The data of the A current were incorporated into a reduced computational model of the voltage-gated currents of Kenyon cells. In addition, the model contained a delayed rectifier K current, a Na current, and a leakage current. The model reproduces several experimental features and makes predictions. See paper for details and results.
IA and IT interact to set first spike latency (Molineux et al 2005)
Using patch clamp and modeling, we illustrate that spike latency characteristics are the product of an interplay between I(A) and low-threshold calcium current (I(T)) that requires a steady-state difference in the inactivation parameters of the currents. Furthermore, we show that the unique first-spike latency characteristics of stellate cells have important implications for the integration of coincident IPSPs and EPSPs, such that inhibition can shift first-spike latency to differentially modulate the probability of firing.
Ih tunes oscillations in an In Silico CA3 model (Neymotin et al. 2013)
" ... We investigated oscillatory control using a multiscale computer model of hippocampal CA3, where each cell class (pyramidal, basket, and oriens-lacunosum moleculare cells), contained type-appropriate isoforms of Ih. Our model demonstrated that modulation of pyramidal and basket Ih allows tuning theta and gamma oscillation frequency and amplitude. Pyramidal Ih also controlled cross-frequency coupling (CFC) and allowed shifting gamma generation towards particular phases of the theta cycle, effected via Ih’s ability to set pyramidal excitability. ..."
Impact of dendritic atrophy on intrinsic and synaptic excitability (Narayanan & Chattarji, 2010)
These simulations examined the atrophy induced changes in electrophysiological properties of CA3 pyramidal neurons. We found these neurons change from bursting to regular spiking as atrophy increases. Region-specific atrophy induced region-specific increases in synaptic excitability in a passive dendritic tree. All dendritic compartments of an atrophied neuron had greater synaptic excitability and a larger voltage transfer to the soma than the control neuron.
Impact of dendritic size and topology on pyramidal cell burst firing (van Elburg and van Ooyen 2010)
The code provided here was written to systematically investigate which of the physical parameters controlled by dendritic morphology underlies the differences in spiking behaviour observed in different realizations of the 'ping-pong'-model. Structurally varying dendritic topology and length in a simplified model allows us to separate out the physical parameters derived from morphology underlying burst firing.

To perform the parameter scans we created a new NEURON tool the MultipleRunControl which can be used to easily set up a parameter scan and write the simulation results to file.

Using this code we found that not input conductance but the arrival time of the return current, as measured provisionally by the average electrotonic path length, determines whether the pyramidal cell (with ping-pong model dynamics) will burst or fire single spikes.
INa and IKv4.3 heterogeneity in canine LV myocytes (Flaim et al 2006)
"The roles of sustained components of INa and IKv43 in shaping the action potentials (AP) of myocytes isolated from the canine left ventricle (LV) have not been studied in detail. Here we investigate the hypothesis that these two currents can contribute substantially to heterogeneity of early repolarization and arrhythmic risk.... The resulting simulations illustrate ways in which KChIP2- and Ca2+- dependent control of IKv43 can result in a sustained outward current that can neutralize INaL in a rate- and myocyte subtype-dependent manner. Both these currents appear to play significant roles in modulating AP duration and rate dependence in midmyocardial myocytes. ... By design, these models allow upward integration into organ models or may be used as a basis for further investigations into cellular heterogeneities." See paper for more and details.
Increased computational accuracy in multi-compartmental cable models (Lindsay et al. 2005)
Compartmental models of dendrites are the most widely used tool for investigating their electrical behaviour. Traditional models assign a single potential to a compartment. This potential is associated with the membrane potential at the centre of the segment represented by the compartment. All input to that segment, independent of its location on the segment, is assumed to act at the centre of the segment with the potential of the compartment. By contrast, the compartmental model introduced in this article assigns a potential to each end of a segment, and takes into account the location of input to a segment on the model solution by partitioning the effect of this input between the axial currents at the proximal and distal boundaries of segments. For a given neuron, the new and traditional approaches to compartmental modelling use the same number of locations at which the membrane potential is to be determined, and lead to ordinary differential equations that are structurally identical. However, the solution achieved by the new approach gives an order of magnitude better accuracy and precision than that achieved by the latter in the presence of point process input.
Inferring connection proximity in electrically coupled networks (Cali et al. 2007)
In order to explore electrical coupling in the nervous system and its network-level organization, it is imperative to map the electrical synaptic microcircuits, in analogy with in vitro studies on monosynaptic and disynaptic chemical coupling. However, “walking” from cell to cell over large distances with a glass pipette is challenging, and microinjection of (fluorescent) dyes diffusing through gap-junctions remains so far the only method available to decipher such microcircuits even though technical limitations exist. Based on circuit theory, we derived analytical descriptions of the AC electrical coupling in networks of isopotential cells. We then proposed an operative electrophysiological protocol to distinguish between direct electrical connections and connections involving one or more intermediate cells. This method allows inferring the number of intermediate cells, generalizing the conventional coupling coefficient, which provides limited information. We provide here some analysis and simulation scripts that used to test our method through computer simulations, in vitro recordings, theoretical and numerical methods. Key words: Gap-Junctions; Electrical Coupling; Networks; ZAP current; Impedance.
Information-processing in lamina-specific cortical microcircuits (Haeusler and Maass 2006)
A major challenge for computational neuroscience is to understand the computational function of lamina-specific synaptic connection patterns in stereotypical cortical microcircuits.We approach this problem by studying ... the dynamical system defined by more realistic cortical microcircuit models as a whole and by investigating the influence that its laminar structure has on the transmission and fusion of information within this dynamical system. The circuit models that we examine consist of Hodgkin--Huxley neurons with dynamic synapses... We investigate to what extent this cortical microcircuit template supports the accumulation and fusion of information contained in generic spike inputs into layer 4 and layers 2/3 and how well it makes this information accessible to projection neurons in layers 2/3 and layer 5. ... We conclude that computer simulations of detailed lamina-specific cortical microcircuit models provide new insight into computational consequences of anatomical and physiological data. See paper for more and details.
Interacting synaptic conductances during, distorting, voltage clamp (Poleg-Polsky and Diamond 2011)
This simulation examines the accuracy of the voltage clamp technique in detecting the excitatory and the inhibitory components of the synaptic drive.
Intracortical synaptic potential modulation by presynaptic somatic potential (Shu et al. 2006, 2007)
" ... Here we show that the voltage fluctuations associated with dendrosomatic synaptic activity propagate significant distances along the axon, and that modest changes in the somatic membrane potential of the presynaptic neuron modulate the amplitude and duration of axonal action potentials and, through a Ca21- dependent mechanism, the average amplitude of the postsynaptic potential evoked by these spikes. These results indicate that synaptic activity in the dendrite and soma controls not only the pattern of action potentials generated, but also the amplitude of the synaptic potentials that these action potentials initiate in local cortical circuits, resulting in synaptic transmission that is a mixture of triggered and graded (analogue) signals."
Investigation of different targets in deep brain stimulation for Parkinson`s (Pirini et al. 2009)
"We investigated by a computational model of the basal ganglia the different network effects of deep brain stimulation (DBS) for Parkinson’s disease (PD) in different target sites in the subthalamic nucleus (STN), the globus pallidus pars interna (GPi), and the globus pallidus pars externa (GPe). A cellular-based model of the basal ganglia system (BGS), based on the model proposed by Rubin and Terman (J Comput Neurosci 16:211–235, 2004), was developed. ... Our results suggest that DBS in the STN could functionally restore the TC relay activity, while DBS in the GPe and in the GPi could functionally over-activate and inhibit it, respectively. Our results are consistent with the experimental and the clinical evidences on the network effects of DBS."
Ionic mechanisms of bursting in CA3 pyramidal neurons (Xu and Clancy 2008)
"... We present a single-compartment model of a CA3 hippocampal pyramidal neuron based on recent experimental data. We then use the model to determine the roles of primary depolarizing currents in burst generation. The single compartment model incorporates accurate representations of sodium (Na+) channels (NaV1.1) and T-type calcium (Ca2+) channel subtypes (CaV3.1, CaV3.2, and CaV3.3). Our simulations predict the importance of Na+ and T-type Ca2+ channels in hippocampal pyramidal cell bursting and reveal the distinct contribution of each subtype to burst morphology. We also performed fastslow analysis in a reduced comparable model, which shows that our model burst is generated as a result of the interaction of two slow variables, the T-type Ca2+ channel activation gate and the Ca2+-dependent potassium (K+) channel activation gate. The model reproduces a range of experimentally observed phenomena including afterdepolarizing potentials, spike widening at the end of the burst, and rebound. Finally, we use the model to simulate the effects of two epilepsy-linked mutations: R1648H in NaV1.1 and C456S in CaV3.2, both of which result in increased cellular excitability."
Ionic mechanisms of dendritic spikes (Almog and Korngreen 2014)
We used a combined experimental and numerical parameter peeling procedure was implemented to optimize a detailed ionic mechanism for the generation and propagation of dendritic spikes in neocortical L5 pyramidal neurons. Run the cc_run.hoc to get a demo for dendritic calcium spike generated by coincidence of a back-propagating AP and distal synaptic input.
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.
Kenyon cells in the honeybee (Wustenberg et al 2004)
The mushroom body of the insect brain is an important locus for olfactory information processing and associative learning. ... Current- and voltage-clamp analyses were performed on cultured Kenyon cells from honeybees. ... Voltage-clamp analyses characterized a fast transient Na+ current (INa), a delayed rectifier K+ current (IK,V) and a fast transient K+ current (IK,A). Using the neurosimulator SNNAP, a Hodgkin-Huxley type model was developed and used to investigate the roles of the different currents during spiking. The model led to the prediction of a slow transient outward current (IK,ST) that was subsequently identified by reevaluating the voltage-clamp data. Simulations indicated that the primary currents that underlie spiking are INa and IK,V, whereas IK,A and IK,ST primarily determined the responsiveness of the model to stimuli such constant or oscillatory injections of current. See paper for more details.
Ketamine disrupts theta modulation of gamma in a computer model of hippocampus (Neymotin et al 2011)
"Abnormalities in oscillations have been suggested to play a role in schizophrenia. We studied theta-modulated gamma oscillations in a computer model of hippocampal CA3 in vivo with and without simulated application of ketamine, an NMDA receptor antagonist and psychotomimetic. Networks of 1200 multi-compartment neurons (pyramidal, basket and oriens-lacunosum moleculare, OLM, cells) generated theta and gamma oscillations from intrinsic network dynamics: basket cells primarily generated gamma and amplified theta, while OLM cells strongly contributed to theta. ..."
KInNeSS : a modular framework for computational neuroscience (Versace et al. 2008)
The xml files provided here implement a network of excitatory and inhibitory spiking neurons, governed by either Hodgkin-Huxley or quadratic integrate-and-fire dynamical equations. The code is used to demonstrate the capabilities of the KInNeSS software package for simulation of networks of spiking neurons. The simulation protocol used here is meant to facilitate the comparison of KInNeSS with other simulators reviewed in Brette et al. (2007). See the associated paper "Versace et al. (2008) KInNeSS : a modular framework for computational neuroscience." for an extensive description of KInNeSS .
KV1 channel governs cerebellar output to thalamus (Ovsepian et al. 2013)
The output of the cerebellum to the motor axis of the central nervous system is orchestrated mainly by synaptic inputs and intrinsic pacemaker activity of deep cerebellar nuclear (DCN) projection neurons. Herein, we demonstrate that the soma of these cells is enriched with KV1 channels produced by mandatory multi-merization of KV1.1, 1.2 alpha andKV beta2 subunits. Being constitutively active, the K+ current (IKV1) mediated by these channels stabilizes the rate and regulates the temporal precision of self-sustained firing of these neurons. ... Through the use of multi-compartmental modelling and ... the physiological significance of the described functions for processing and communication of information from the lateral DCN to thalamic relay nuclei is established.
Kv4.3, Kv1.4 encoded K channel in heart cells & tachy. (Winslow et al 1999, Greenstein et al 2000)
(1999) We present a model of the canine midmyocardial ventricular action potential and Ca2+ transient. The model is used to estimate the degree of functional upregulation and downregulation of Na/Ca exchanger protein and sarcoplasmic reticulum Ca ATPase in heart failure using data obtained from 2 different experimental protocols. (2000): A model of canine I:(to1) (the Ca(2+)-independent transient outward current) is formulated as the combination of Kv4.3 and Kv1.4 currents and is incorporated into an existing canine ventricular myocyte model. Simulations demonstrate strong coupling between L-type Ca(2+) current and I:(Kv4.3) and predict a bimodal relationship between I:(Kv4.3) density and APD whereby perturbations in I:(Kv4.3) density may produce either prolongation or shortening of APD, depending on baseline I:(to1) current level. See each paper for more and details.
Lamprey spinal CPG neuron (Huss et al. 2007)
This is a model of a generic locomotor network neuron in the lamprey spinal cord. The given version is assumed to correspond to an interneuron; motoneurons can also be modelled by changing the dendritic tree morphology.
Large scale model of the olfactory bulb (Yu et al., 2013)
The readme file currently contains links to the results for all the 72 odors investigated in the paper, and the movie showing the network activity during learning of odor k3-3 (an aliphatic ketone).
Lateral dendrodenditic inhibition in the Olfactory Bulb (David et al. 2008)
Mitral cells, the principal output neurons of the olfactory bulb, receive direct synaptic activation from primary sensory neurons. Shunting inhibitory inputs delivered by granule cell interneurons onto mitral cell lateral dendrites are believed to influence spike timing and underlie coordinated field potential oscillations. Lateral dendritic shunt conductances delayed spiking to a degree dependent on both their electrotonic distance and phase of onset. Recurrent inhibition significantly narrowed the distribution of mitral cell spike times, illustrating a tendency towards coordinated synchronous activity. This result suggests an essential role for early mechanisms of temporal coordination in olfaction. The model was adapted from Davison et al, 2003, but include additional noise mechanisms, long lateral dendrite, and specific synaptic point processes.
Layer V PFC pyramidal neuron used to study persistent activity (Sidiropoulou & Poirazi 2012)
"... Here, we use a compartmental modeling approach to search for discriminatory features in the properties of incoming stimuli to a PFC pyramidal neuron and/or its response that signal which of these stimuli will result in persistent activity emergence. Furthermore, we use our modeling approach to study cell-type specific differences in persistent activity properties, via implementing a regular spiking (RS) and an intrinsic bursting (IB) model neuron. ... Collectively, our results pinpoint to specific features of the neuronal response to a given stimulus that code for its ability to induce persistent activity and predict differential roles of RS and IB neurons in persistent activity expression. "
Learning intrinsic excitability in Medium Spiny Neurons (Scheler 2014)
"We present an unsupervised, local activation-dependent learning rule for intrinsic plasticity (IP) which affects the composition of ion channel conductances for single neurons in a use-dependent way. We use a single-compartment conductance-based model for medium spiny striatal neurons in order to show the effects of parameterization of individual ion channels on the neuronal membrane potential-curent relationship (activation function). We show that parameter changes within the physiological ranges are sufficient to create an ensemble of neurons with significantly different activation functions. ... "
Leech Heart (HE) Motor Neuron conductances contributions to NN activity (Lamb & Calabrese 2013)
"... To explore the relationship between conductances, and in particular how they influence the activity of motor neurons in the well characterized leech heartbeat system, we developed a new multi-compartmental Hodgkin-Huxley style leech heart motor neuron model. To do so, we evolved a population of model instances, which differed in the density of specific conductances, capable of achieving specific output activity targets given an associated input pattern. ... We found that the strengths of many conductances, including those with differing dynamics, had strong partial correlations and that these relationships appeared to be linked by their influence on heart motor neuron activity. Conductances that had positive correlations opposed one another and had the opposite effects on activity metrics when perturbed whereas conductances that had negative correlations could compensate for one another and had similar effects on activity metrics. "
Leech heart interneuron network model (Hill et al 2001, 2002)
We have created a computational model of the timing network that paces the heartbeat of the medicinal leech, Hirudo medicinalis. In the intact nerve cord, segmental oscillators are mutually entrained to the same cycle period. Although experiments have shown that the segmental oscillators are coupled by inhibitory coordinating interneurons, the underlying mechanisms of intersegmental coordination have not yet been elucidated. To help understand this coordination, we have created a simple computational model with two variants: symmetric and asymmetric. See references for more details. Biologically realistic network models with two, six, and eight cells and a tutorial are available at the links to Calabrese's web site below.
Leech Mechanosensory Neurons: Synaptic Facilitation by Reflected APs (Baccus 1998)
This model by Stephen Baccus explores the phenomena of action potential (AP) propagation at branch boints in axons. APs are sometimes transmitted down the efferent processes and sometimes are reflected back to the axon of AP origin or neither. See the paper for details. The model zip file contains a readme.txt which list introductory steps to follow to run the simulation. Stephen Baccus's email address: baccus@fas.harvard.edu
Leech S Cell: Modulation of Excitability by Serotonin (Burrell and Crisp 2007)
Serotonergic modulation of the afterhyperpolarization (AHP) contributes to the regulation of the excitability of the leech S cell, a neuron critical for sensitization of the shortening reflex. Pharmacological and physiological data suggest that three currents contribute to the S cell's afterhyperpolarization: a charybdotoxin-sensitive, fast calcium-dependent potassium current (fAHP); a tubocurare-sensitive, calcium-dependent potassium current (mAHP); and, a saxitoxin-sensitive, afterdepolarization current (ADP). This single-compartment model of the S cell is constructed using fAHP, mAHP and ADP currents, and shows that reduction of the conductances to mimic the effects of serotonin is sufficient to enhance excitability (repetitive firing). Burrell BD, Crisp KM (2007) Serotonergic modulation of afterhyperpolarization in a neuron that contributes to learning in the leech. J Neurophysiol, in press.
LGMD Variability and logarithmic compression in dendrites (Jones and Gabbiani, 2012, 2012B)
A compartmental model of the LGMD with a simplified, rake shaped, excitatory dendrite. It receives spontaneous input and excitatory and inhibitory synaptic inputs triggered by visual stimuli. It generates realistic responses to looming through the velocity dependent scaling and delay of individual excitatory synaptic inputs, with variability. We use the model to show that the key determinants of output variability are spontaneous input and temporal jitter of the excitatory inputs, rather than variability in magnitude of individual inputs (2012B, J Neurophysiol). We also use the model to analyze the transformation of the excitatory signals through the visual pathway; concluding that the representation of stimulus velocity is transformed from an expansive relationship at the level of the LGMD inputs to a logarithmic one at the level of its membrane potential (2012, J Neurosci).
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).
Low dose of dopamine may stimulate prolactin secretion by increasing K currents (Tabak et al. 2006)
".. We considered the fast K+ currents flowing through large-conductance BK channels and through A-type channels. We developed a minimal lactotroph model to investigate the effects of these two currents. Both IBK and IA could transform the electrical pattern of activity from spiking to bursting, but through distinct mechanisms. IBK always increased the intracellular Ca2+ concentration, while IA could either increase or decrease it. Thus, the stimulatory effects of DA could be mediated by a fast K+ conductance which converts tonically spiking cells to bursters. In addition, the study illustrates that a heterogeneous distribution of fast K+ conductances could cause heterogeneous lactotroph firing patterns."
Low Threshold Calcium Currents in TC cells (Destexhe et al 1998)
In Destexhe, Neubig, Ulrich, and Huguenard (1998) experiments and models examine low threshold calcium current's (IT, or T-current) distribution in thalamocortical (TC) cells. Multicompartmental modeling supports the hypothesis that IT currents have a density at least several fold higher in the dendrites than the soma. The IT current contributes significantly to rebound bursts and is thought to have important network behavior consequences. See the paper for details. See also http://cns.iaf.cnrs-gif.fr Correspondance may be addressed to Alain Destexhe: Destexhe@iaf.cnrs-gif.fr
Mammalian Ventricular Cell (Beeler and Reuter 1977)
This classic model of ventricular myocardial fibres was implemented by Francois Gannier. "... Four individual components of ionic current were formulated mathematically in terms of Hodgkin-Huxley type equations. The model incorporates two voltage- and time-dependent inward currents, the excitatory inward sodium current, illa, and a secondary or slow inward current, is, primarily carried by calcium ions. A time-independent outward potassium current, iK1, exhibiting inward-going rectification, and a voltage- and time-dependent outward current, i.1, primarily carried by potassium ions, are further elements of the model...."
Markov Chain-based Stochastic Shielding Hodgkin Huxley Model (Schmandt, Galan 2012)
Markovian model for single-channel recordings of Ik_1 in ventricular cells (Matsuoka et al 2003)
The interaction between many currents in a cardiac ventricular model are examined in this paper. One of the main contributions come from a current called IK_1. An XPP version of this model was supplied by Hsieng-Jung Lai, Jiun-Shian Wu, Sheng-Nan Wu, Ruey J. Sung, Han-Dong Chang. Please see paper and model for more and details.
Mathematical model for windup (Aguiar et al. 2010)
"Windup is characterized as a frequency-dependent increase in the number of evoked action potentials in dorsal horn neurons in response to electrical stimulation of afferent C-fibers. ... The approach presented here relies on mathematical and computational analysis to study the mechanism(s) underlying windup. From experimentally obtained windup profiles, we extract the time scale of the facilitation mechanisms that may support the characteristics of windup. Guided by these values and using simulations of a biologically realistic compartmental model of a wide dynamic range (WDR) neuron, we are able to assess the contribution of each mechanism for the generation of action potentials windup. ..."
MEC layer II stellate cell: Synaptic mechanisms of grid cells (Schmidt-Hieber & Hausser 2013)
This study investigates the cellular mechanisms of grid field generation in Medial Entorhinal Cortex (MEC) layer II stellate cells.
Mechanisms of fast rhythmic bursting in a layer 2/3 cortical neuron (Traub et al 2003)
This simulation is based on the reference paper listed below.

This port was made by Roger D Traub and Maciej T Lazarewicz (mlazarew@seas.upenn.edu) Thanks to Ashlen P Reid for help with porting a morphology of the cell.

Mechanisms of very fast oscillations in axon networks coupled by gap junctions (Munro, Borgers 2010)
Axons connected by gap junctions can produce very fast oscillations (VFOs, > 80 Hz) when stimulated randomly at a low rate. The models here explore the mechanisms of VFOs that can be seen in an axonal plexus, (Munro & Borgers, 2009): a large network model of an axonal plexus, small network models of axons connected by gap junctions, and an implementation of the model underlying figure 12 in Traub et al. (1999) . The large network model consists of 3,072 5-compartment axons connected in a random network. The 5-compartment axons are the 5 axonal compartments from the CA3 pyramidal cell model in Traub et al. (1994) with a fixed somatic voltage. The random network has the same parameters as the random network in Traub et al. (1999), and axons are stimulated randomly via a Poisson process with a rate of 2/s/axon. The small network models simulate waves propagating through small networks of axons connected by gap junctions to study how local connectivity affects the refractory period.
Medial vestibular neuron models (Quadroni and Knopfel 1994)
The structure and the parameters of the model cells were chosen to reproduce the responses of type A and type B MVNns as described in electrophysiological recordings. The emergence of oscillatory firing under these two specific experimental conditions is consistent with electrophysiological recordings not used during construction of the model. We, therefore, suggest that these models have a high predictive value.
MEG of Somatosensory Neocortex (Jones et al. 2007)
"... To make a direct and principled connection between the SI (somatosensory primary neocortex magnetoencephalography) waveform and underlying neural dynamics, we developed a biophysically realistic computational SI model that contained excitatory and inhibitory neurons in supragranular and infragranular layers. ... our model provides a biophysically realistic solution to the MEG signal and can predict the electrophysiological correlates of human perception."
Mixed mode oscillations as a mechanism for pseudo-plateau bursting (Vo et al. 2010)
"We combine bifurcation analysis with the theory of canard-induced mixed mode oscillations to investigate the dynamics of a novel form of bursting. This bursting oscillation, which arises from a model of the electrical activity of a pituitary cell, is characterized by small impulses or spikes riding on top of an elevated voltage plateau. ..."
MNTB Neuron: Kv3.1 currents (Wang et al 1998)
Model of Medial Nucleus of the Trapezoid Body (MNTB) neurons described in Lu-Yang Wang, Li Gan, Ian D. Forsythe and Leonard K. Kaczmarek. Contribution of the Kv3.1 potassium channel to high-frequency firing in mouse auditory neurones. J. Physiol (1998) 509.1 183-194. Created by David Kornfeld, Byram Hills High School, Armonk NY. Please email dbk1@mindspring.com for questions about the model. See Readme.txt below for more info.
Model of arrhythmias in a cardiac cells network (Casaleggio et al. 2014)
" ... Here we explore the possible processes leading to the occasional onset and termination of the (usually) non-fatal arrhythmias widely observed in the heart. Using a computational model of a two-dimensional network of cardiac cells, we tested the hypothesis that an ischemia alters the properties of the gap junctions inside the ischemic area. ... In conclusion, our model strongly supports the hypothesis that non-fatal arrhythmias can develop from post-ischemic alteration of the electrical connectivity in a relatively small area of the cardiac cell network, and suggests experimentally testable predictions on their possible treatments."
Model of long range transmission of gamma oscillation (Murray 2007)
"... A minimal mathematical model was developed for a preliminary study of long-range neural transmission of gamma oscillation from the CA3 to the entorhinal cortex via the CAI region of the hippocampus, a subset within a larger complex set of pathways. A module was created for each local population of neurons with common intrinsic properties and connectivity to simplify the connection process and make the model more flexible. Three modules were created using MATLAB Simulink® and tested to confirm that they transmit gamma through the system. The model also revealed that a portion of the signal from CAI to the entorhinal cortex may be lost in transmission under certain conditions."
Model of repetitive firing in Grueneberg ganglion olfactory neurons (Liu et al., 2012)
This model is constructed based on properties of Na+ and K+ currents observed in whole-cell patch clamp recordings of mouse Grueneberg ganglion neurons in acute slices. Two distinct Na+ conductances representing the TTX-sensitive and TTX-resistant currents and one delayed rectifier K+ currrent are included. By modulating the maximal conductances of Na+ currents, one can reproduce the regular, phasic, and sporadic patterns of repetitive firing found in the patch clamp experiments.
Model of SK current`s influence on precision in Globus Pallidus Neurons (Deister et al. 2009)
" ... In numerical simulations, the availability of both Na+ and A-type K+ channels during autonomous firing were reduced when SK channels were removed, and a nearly equal reduction in Na+ and K+ subthreshold-activated ion channel availability produced a large decrease in the neuron's slope conductance near threshold. This change made the neuron more sensitive to intrinsically generated noise. In vivo, this change would also enhance the sensitivity of GP (Globus Pallidus) neurons to small synaptic inputs."
Modeling conductivity profiles in the deep neocortical pyramidal neuron (Wang K et al. 2013)
"With the rapid increase in the number of technologies aimed at observing electric activity inside the brain, scientists have felt the urge to create proper links between intracellular- and extracellular-based experimental approaches. Biophysical models at both physical scales have been formalized under assumptions that impede the creation of such links. In this work, we address this issue by proposing amulticompartment model that allows the introduction of complex extracellular and intracellular resistivity profiles. This model accounts for the geometrical and electrotonic properties of any type of neuron through the combination of four devices: the integrator, the propagator, the 3D connector, and the collector. ..."
Modeling interactions in Aplysia neuron R15 (Yu et al 2004)
"The biophysical properties of neuron R15 in Aplysia endow it with the ability to express multiple modes of oscillatory electrical activity, such as beating and bursting. Previous modeling studies examined the ways in which membrane conductances contribute to the electrical activity of R15 and the ways in which extrinsic modulatory inputs alter the membrane conductances by biochemical cascades and influence the electrical activity. The goals of the present study were to examine the ways in which electrical activity influences the biochemical cascades and what dynamical properties emerge from the ongoing interactions between electrical activity and these cascades." See paper for more and details.
Modelling reduced excitability in aged CA1 neurons as a Ca-dependent process (Markaki et al. 2005)
"We use a multi-compartmental model of a CA1 pyramidal cell to study changes in hippocampal excitability that result from aging-induced alterations in calcium-dependent membrane mechanisms. The model incorporates N- and L-type calcium channels which are respectively coupled to fast and slow afterhyperpolarization potassium channels. Model parameters are calibrated using physiological data. Computer simulations reproduce the decreased excitability of aged CA1 cells, which results from increased internal calcium accumulation, subsequently larger postburst slow afterhyperpolarization, and enhanced spike frequency adaptation. We find that aging-induced alterations in CA1 excitability can be modelled with simple coupling mechanisms that selectively link specific types of calcium channels to specific calcium-dependent potassium channels."
Models of Na channels from a paper on the PKC control of I Na,P (Baker 2005)
"The tetrodotoxin-resistant (TTX-r) persistent Na(+) current, attributed to Na(V)1.9, was recorded in small (< 25 mum apparent diameter) dorsal root ganglion (DRG) neurones cultured from P21 rats and from adult wild-type and Na(V)1.8 null mice. ... Numerical simulation of the up-regulation qualitatively reproduced changes in sensory neurone firing properties. ..." Note: models of NaV1.8 and NaV1.9 and also persistent and transient Na channels that collectively model Nav 1.1, 1.6, and 1.7 are present in this model.
Modulation of neuronal synchronization by D4 dopamine receptor-mediated phospholipid methylation
"We describe a new molecular mechanism of dopamine-induced membrane protein modulation that can tune neuronal oscillation frequency to attention related gamma rhythm. This mechanism is based on the unique ability of D4 dopamine receptors (D4R) to carry out phospholipid methylation (PLM) that may affect the kinetics of ion channels. We show that by deceasing the inertia of the delayed rectifier potassium channel, a transition to 40 Hz oscillations can be achieved. ..."
Modulation of septo-hippocampal theta activity by GABAA receptors (Hajos et al. 2004)
θ Frequency oscillation of the septo-hippocampal system has been considered as a prominent activity associated with cognitive function and affective processes. ... In the present experiments we applied a combination of computational and physiological techniques to explore the functional role of GABAA receptors in θ oscillation. ... In parallel to these experimental observations, a computational model has been constructed by implementing a septal GABA neuron model with a CA1 hippocampal model containing three types of neurons (including oriens and basket interneurons and pyramidal cells; latter modeled by multicompartmental techniques; for detailed model description with network parameters see online addendum: http://geza.kzoo.edu/theta). This connectivity made the network capable of simulating the responses of the septo-hippocampal circuitry to the modulation of GABAA transmission, and the presently described computational model proved suitable to reveal several aspects of pharmacological modulation of GABAA receptors. In addition, computational findings indicated different roles of distinctively located GABAA receptors in θ generation.
Multiple modes of a conditional neural oscillator (Epstein, Marder 1990)
We present a model for a conditional bursting neuron consisting of five conductances: Hodgkin-Huxley type time- and voltage-dependent Na+ and K+ conductances, a calcium activated voltage-dependent K+ conductance, a calcium-inhibited time- and voltage-dependent Ca++ conductance, and a leakage Cl- conductance. Different bursting and silent modes and transitions between them are analyzed in the model and compared to bursting modes in experiment. See the paper for details.
Multiscale interactions between chemical and electric signaling in LTP (Bhalla 2011)
"Synaptic plasticity leads to long-term changes in excitability, whereas cellular homeostasis maintains excitability. Both these processes involve interactions between molecular events, electrical events, and network activity. Here I explore these intersections with a multilevel model that embeds molecular events following synaptic calcium influx into a multicompartmental electrical model of a CA1 hippocampal neuron. ..."
Multiscale model of olfactory receptor neuron in mouse (Dougherty 2009)
Collection of XPP (.ode) files simulating the signal transduction (slow) and action potential (fast) currents in the olfactory receptor neuron of mouse. Collection contains model configured for dual odorant pulse delivery and model configured for prolonged odorant delivery. For those interested more in transduction processes, each whole cell recording model comes with a counter part file configured to show just the slow transduction current for ease of use and convenience. These transduction-only models typically run faster than the full multi-scale models but do not demonstrate action potentials.
Myelinated axon conduction velocity (Brill et al 1977)
Examines conduction velocity as function of internodal length.
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.
MyFirstNEURON (Houweling, Sejnowski 1997)
MyFirstNEURON is a NEURON demo by Arthur Houweling and Terry Sejnowski. Perform experiments from the book 'Electrophysiology of the Neuron, A Companion to Shepherd's Neurobiology, An Interactive Tutorial' by John Huguenard & David McCormick, Oxford University Press 1997, or design your own one or two cell simulation. For more information see http://www.cnl.salk.edu/Simulations. Salk Institute, Computational Neurobiology Lab, 10010 North Torrey Pines Rd., La Jolla CA 092037. Email: arthur@salk.edu
Na channel mutations in the dentate gyrus (Thomas et al. 2009)
These are source files to generate the data in Figure 6 from "Mossy fiber sprouting interacts with sodium channel mutations to increase dentate gyrus excitability" Thomas EA, Reid CA, Petrou S, Epilepsia (2009)
Na+ channel dependence of AP initiation in cortical pyramidal neuron (Kole et al. 2008)
In this simulation action potential initiation, action potential properties and the role of axon initial segment Na+ channels are investigated in a realistic model of a layer 5 pyramidal neuron axon initial segment. The main Na+ channel properties were constrained by experimental data and the axon initial segment was reconstructed. Model parameters were constrained by direct recordings at the axon initial segment.
Nav1.6 sodium channel model in globus pallidus neurons (Mercer et al. 2007)
Model files for the paper Mercer JN, Chan CS, Tkatch T, Held J, Surmeier DJ. Nav1.6 sodium channels are critical to pacemaking and fast spiking in globus pallidus neurons.,J Neurosci. 2007 Dec 5;27(49):13552-66.
Neocort. pyramidal cells subthreshold somatic voltage controls spike propagation (Munro Kopell 2012)
There is suggestive evidence that pyramidal cell axons in neocortex may be coupled by gap junctions into an ``axonal plexus" capable of generating Very Fast Oscillations (VFOs) with frequencies exceeding 80 Hz. It is not obvious, however, how a pyramidal cell in such a network could control its output when action potentials are free to propagate from the axons of other pyramidal cells into its own axon. We address this problem by means of simulations based on 3D reconstructions of pyramidal cells from rat somatosensory cortex. We show that somatic depolarization enables propagation via gap junctions into the initial segment and main axon, while somatic hyperpolarization disables it. We show further that somatic voltage cannot effectively control action potential propagation through gap junctions on minor collaterals; action potentials may therefore propagate freely from such collaterals regardless of somatic voltage. In previous work, VFOs are all but abolished during the hyperpolarization phase of slow-oscillations induced by anesthesia in vivo. This finding constrains the density of gap junctions on collaterals in our model and suggests that axonal sprouting due to cortical lesions may result in abnormally high gap junction density on collaterals, leading in turn to excessive VFO activity and hence to epilepsy via kindling.
Neocortical Layer I: I-A and I-K (Zhou, Hablitz 1996)
NEURON mod files for the I-A and I-K currents from the paper: Zhou FM, Hablitz JJ. Layer I neurons of the rat neocortex. II. Voltage-dependent outward currents. J Neurophysiol 1996 76:668-82.
Neocortical pyramidal neuron: deep; effects of dopamine (Durstewitz et al 2000)
"... Simulated dopamine strongly enhanced high, delay-type activity but not low, spontaneous activity in the model network. Furthermore the strength of an afferent stimulation needed to disrupt delay-type activity increased with the magnitude of the dopamine-induced shifts in network parameters, making the currently active representation much more stable. Stability could be increased by dopamine-induced enhancements of the persistent Na(+) and N-methyl-D-aspartate (NMDA) conductances. Stability also was enhanced by a reduction in AMPA conductances. The increase in GABA(A) conductances that occurs after stimulation of dopaminergic D1 receptors was necessary in this context to prevent uncontrolled, spontaneous switches into high-activity states (i.e., spontaneous activation of task-irrelevant representations). In conclusion, the dopamine-induced changes in the biophysical properties of intrinsic ionic and synaptic conductances conjointly acted to highly increase stability of activated representations in PFC networks and at the same time retain control over network behavior and thus preserve its ability to adequately respond to task-related stimuli. ..." See paper and references for more and details.
Nerve terminal currents at lizard neuromuscular junction (Lindgren, Moore 1989)
Loose patch clamp measurement of presynaptic ionic currents at lizard neuromuscular junction compared with computer simulations.
Network model of the granular layer of the cerebellar cortex (Maex, De Schutter 1998)
We computed the steady-state activity of a large-scale model of the granular layer of the rat cerebellum. Within a few tens of milliseconds after the start of random mossy fiber input, the populations of Golgi and granule cells became entrained in a single synchronous oscillation, the basic frequency of which ranged from 10 to 40 Hz depending on the average rate of firing in the mossy fiber population. ... The synchronous, rhythmic firing pattern was robust over a broad range of biologically realistic parameter values and to parameter randomization. Three conditions, however, made the oscillations more transient and could desynchronize the entire network in the end: a very low mossy fiber activity, a very dominant excitation of Golgi cells through mossy fiber synapses (rather than through parallel fiber synapses), and a tonic activation of granule cell GABAA receptors (with an almost complete absence of synaptically induced inhibitory postsynaptic currents). The model predicts that, under conditions of strong mossy fiber input to the cerebellum, Golgi cells do not only control the strength of parallel fiber activity but also the timing of the individual spikes. Provided that their parallel fiber synapses constitute an important source of excitation, Golgi cells fire rhythmically and synchronized with granule cells over large distances along the parallel fiber axis. See paper for more and details.
Network model with neocortical architecture (Anderson et al. 2011 plus under review paper)
Architecturally realistic neocortical model using seven classes of excitatory and inhibitory single compartment Hodgkin-Huxley cells. This is an addendum to ModelDB Accession # 98902, Studies of stimulus parameters for seizure disruption (Anderson et al. 2007). Wiring is adapted from the minicolumn hypothesis and incorporates visual and neocortical wiring data. Simulation demonstrates spontaneous bursting onset and cessation. This activity can be induced by random fluctuations in the surrounding background input (Manuscript in preparation).
Network recruitment to coherent oscillations in a hippocampal model (Stacey et al. 2011)
"... Here we demonstrate, via a detailed computational model, a mechanism whereby physiological noise and coupling initiate oscillations and then recruit neighboring tissue, in a manner well described by a combination of Stochastic Resonance and Coherence Resonance. We develop a novel statistical method to quantify recruitment using several measures of network synchrony. This measurement demonstrates that oscillations spread via preexisting network connections such as interneuronal connections, recurrent synapses, and gap junctions, provided that neighboring cells also receive sufficient inputs in the form of random synaptic noise. ..."
Neuronal morphology goes digital ... (Parekh & Ascoli 2013)
An illustration of a NEURON model and why reconstructing morphologies is useful in this regard (i.e. investigating spatial/temporal aspect of how different currents and voltage propagate in dendrites).
Neurophysiological impact of inactivation pathways in A-type K+ channels (Fineberg et al 2012)
These models predict the differential effects of varying pathways of inactivation (closed state inactivation, CSI, or open state inactivation, OSI). Specifically, Markov models of Kv4 potassium channels with CSI or CSI+OSI were inserted into the CA1 pyramidal neuron model from Migliore et al (1999; ModelDB accession #2796) to determine the neurophysiological impact of inactivation pathways. Furthermore, Markov models of Kv4.2 and Kv3.4 channels are used to illustrate a method by which to test what pathway of inactivation a channel uses.
Nigral dopaminergic neurons: effects of ethanol on Ih (Migliore et al. 2008)
We use a realistic computational model of dopaminergic neurons in vivo to suggest that ethanol, through its effects on Ih, modifies the temporal structure of the spiking activity. The model predicts that the dopamine level may increase much more during bursting than pacemaking activity, especially in those brain regions with a slow dopamine clearance rate. The results suggest that a selective pharmacological remedy could thus be devised against the rewarding effects of ethanol that are postulated to mediate alcohol abuse and addiction, targeting the specific HCN genes expressed in dopaminergic neurons.
Nodes of Ranvier with left-shifted Nav channels (Boucher et al. 2012)
The two programs CLSRanvier.f and propagation.f simulate the excitability of a myelinated axon with injured nodes of Ranvier. The injury is simulated as the Coupled Left Shift (CLS) of the activation(V) and inactivation(V) (availability) of a fraction of Nav channels.
Nodose sensory neuron (Schild et al. 1994, Schild and Kunze 1997)
This is a simulink implementation of the model described in Schild et al. 1994, and Schild and Kunze 1997 papers on Nodose sensory neurons. These papers describe the sensitivity these models have to their parameters and the match of the models to experimental data.
Novel Na current with slow de-inactivation (Tsutsui, Oka 2002)
The authors found a novel Na current in teleost thalamic nuclei was well described by the m^3 h Hodgkin-Huxley model. The kinetic parameters derived from their experiments (see the reference for details) revealed that the h gate had a large time constant (~100ms at -80 to -50mV). This explains the thalamic neurons long refractory period and the gradual recovery of AP amplitude as the inter spike interval grows.
O-LM interneuron model (Lawrence et al. 2006)
Exploring the kinetics and distribution of the muscarinic potassium channel, IM, in 2 O-LM interneuron morphologies. Modulation of the ion channel by drugs such as XE991 (antagonist) and retigabine (agonist) are simulated in the models to examine the role of IM in spiking properties.
Olfactory bulb cluster formation (Migliore et al. 2010)
Functional roles of distributed synaptic clusters in the mitral-granule cell network of the olfactory bulb.
Olfactory bulb granule cell: effects of odor deprivation (Saghatelyan et al 2005)
The model supports the experimental findings on the effects of postnatal odor deprivation, and shows that a -10mV shift in the Na activation or a reduction in the dendritic length of newborn GC could independently explain the observed increase in excitability.
Olfactory bulb mitral and granule cell column formation (Migliore et al. 2007)
In the olfactory bulb, the processing units for odor discrimination are believed to involve dendrodendritic synaptic interactions between mitral and granule cells. There is increasing anatomical evidence that these cells are organized in columns, and that the columns processing a given odor are arranged in widely distributed arrays. Experimental evidence is lacking on the underlying learning mechanisms for how these columns and arrays are formed. We have used a simplified realistic circuit model to test the hypothesis that distributed connectivity can self-organize through an activity-dependent dendrodendritic synaptic mechanism. The results point to action potentials propagating in the mitral cell lateral dendrites as playing a critical role in this mechanism, and suggest a novel and robust learning mechanism for the development of distributed processing units in a cortical structure.
Olfactory bulb mitral and granule cell: dendrodendritic microcircuits (Migliore and Shepherd 2008)
This model shows how backpropagating action potentials in the long lateral dendrites of mitral cells, together with granule cell actions on mitral cells within narrow columns forming glomerular units, can provide a mechanism to activate strong local inhibition between arbitrarily distant mitral cells. The simulations predict a new role for the dendrodendritic synapses in the multicolumnar organization of the granule cells.
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.
Olfactory bulb mitral cell: synchronization by gap junctions (Migliore et al 2005)
In a realistic model of two electrically connected mitral cells, the paper shows that the somatically-measured experimental properties of Gap Junctions (GJs) may correspond to a variety of different local coupling strengths and dendritic distributions of GJs in the tuft. The model suggests that the propagation of the GJ-induced local tuft depolarization is a major mechanim for intraglomerular synchronization of mitral cells.
Olfactory Bulb Network (Davison et al 2003)
A biologically-detailed model of the mammalian olfactory bulb, incorporating the mitral and granule cells and the dendrodendritic synapses between them. The results of simulation experiments with electrical stimulation agree closely in most details with published experimental data. The model predicts that the time course of dendrodendritic inhibition is dependent on the network connectivity as well as on the intrinsic parameters of the synapses. In response to simulated odor stimulation, strongly activated mitral cells tend to suppress neighboring cells, the mitral cells readily synchronize their firing, and increasing the stimulus intensity increases the degree of synchronization. For more details, see the reference below.
Olfactory bulb network model of gamma oscillations (Bathellier et al. 2006; Lagier et al. 2007)
This model implements a network of 100 mitral cells connected with asynchronous inhibitory "synapses" that is meant to reproduce the GABAergic transmission of ensembles of connected granule cells. For appropriate parameters of this special synapse the model generates gamma oscillations with properties very similar to what is observed in olfactory bulb slices (See Bathellier et al. 2006, Lagier et al. 2007). Mitral cells are modeled as single compartment neurons with a small number of different voltage gated channels. Parameters were tuned to reproduce the fast subthreshold oscillation of the membrane potential observed experimentally (see Desmaisons et al. 1999).
Olfactory Computations in Mitral-Granule cell circuits (Migliore & McTavish 2013)
Model files for the entry "Olfactory Computations in Mitral-Granule Cell Circuits" of the Springer Encyclopedia of Computational Neuroscience by Michele Migliore and Tom Mctavish. The simulations illustrate two typical Mitral-Granule cell circuits in the olfactory bulb of vertebrates: distance-independent lateral inhibition and gating effects.
Olfactory Mitral Cell (Bhalla, Bower 1993)
This is a conversion to NEURON of the mitral cell model described in Bhalla and Bower (1993). The original model was written in GENESIS and is available by joining BABEL, the GENESIS users' group.
Olfactory Mitral Cell (Davison et al 2000)
A four-compartment model of a mammalian olfactory bulb mitral cell, reduced from the complex 286-compartment model described by Bhalla and Bower (1993). The compartments are soma/axon, secondary dendrites, primary dendrite shaft and primary dendrite tuft. The reduced model runs 75 or more times faster than the full model, making its use in large, realistic network models of the olfactory bulb practical.
Olfactory Mitral Cell (Shen et al 1999)
Mitral cell model with standard parameters for the paper: Shen, G.Y., Chen, W. R., Midtgaard, J., Shepherd, G.M., and Hines, M.L. (1999) Computational Analysis of Action Potential Initiation in Mitral Cell Soma and Dendrites Based on Dual Patch Recordings. Journal of Neurophysiology 82:3006. Contact Michael.Hines@yale.edu if you have any questions about the implementation of the model.
Olfactory Mitral cell: AP initiation modes (Chen et al 2002)
The mitral cell primary dendrite plays an important role in transmitting distal olfactory nerve input from olfactory glomerulus to the soma-axon initial segment. To understand how dendritic active properties are involved in this transmission, we have combined dual soma and dendritic patch recordings with computational modeling to analyze action-potential initiation and propagation in the primary dendrite.
Olfactory Mitral Cell: I-A and I-K currents (Wang et al 1996)
NEURON mod files for the I-A and I-K currents from the paper: X.Y. Wang, J.S. McKenzie and R.E. Kemm, Whole-cell K+ currents in identified olfactory bulb output neurones of rats. J Physiol. 1996 490.1:63-77. Please see the readme.txt included in the model file for more information.
Optical stimulation of a channelrhodopsin-2 positive pyramidal neuron model (Foutz et al 2012)
A computational tool to explore the underlying principles of optogenetic neural stimulation. This "light-neuron" model consists of theoretical representations of the light dynamics generated by a fiber optic in brain tissue, coupled to a multicompartment cable model of a cortical pyramidal neuron (Hu et al. 2009, ModelDB #123897) embedded with channelrhodopsin-2 (ChR2) membrane dynamics. Simulations predict that the activation threshold is sensitive to many of the properties of ChR2 (density, conductivity, and kinetics), tissue medium (scattering and absorbance), and the fiber-optic light source (diameter and numerical aperture). This model system represents a scientific instrument to characterize the effects of optogenetic neuromodulation, as well as an engineering design tool to help guide future development of optogenetic technology.
Paradoxical GABA-mediated excitation (Lewin et al. 2012)
"GABA is the key inhibitory neurotransmitter in the adult central nervous system, but in some circumstances can lead to a paradoxical excitation that has been causally implicated in diverse pathologies from endocrine stress responses to diseases of excitability including neuropathic pain and temporal lobe epilepsy. We undertook a computational modeling approach to determine plausible ionic mechanisms of GABAA-dependent excitation in isolated post-synaptic CA1 hippocampal neurons because it may constitute a trigger for pathological synchronous epileptiform discharge. In particular, the interplay intracellular chloride accumulation via the GABAA receptor and extracellular potassium accumulation via the K/Cl co-transporter KCC2 in promoting GABAA-mediated excitation is complex. ..."
Parameter estimation for Hodgkin-Huxley based models of cortical neurons (Lepora et al. 2011)
Simulation and fitting of two-compartment (active soma, passive dendrite) for different classes of cortical neurons. The fitting technique indirectly matches neuronal currents derived from somatic membrane potential data rather than fitting the voltage traces directly. The method uses an analytic solution for the somatic ion channel maximal conductances given approximate models of the channel kinetics, membrane dynamics and dendrite. This approach is tested on model-derived data for various cortical neurons.
Parametric computation and persistent gamma in a cortical model (Chambers et al. 2012)
Using the Traub et al (2005) model of the cortex we determined how 33 synaptic strength parameters control gamma oscillations. We used fractional factorial design to reduce the number of runs required to 4096. We found an expected multiplicative interaction between parameters.
Periodicity in Na channel properties alters model neuron excitability (Majumdar and Sikdar 2007)
"... We have shown earlier that the duration and amplitude of a prolonged depolarization alter all the steady state and kinetic parameters of rNav1.2a voltage gated Na channel in a pseudo-oscillatory fashion. In the present study, we show that the Hodgkin–Huxley voltage and time dependent rate constants of activation (am and bm) and fast inactivation (ah and bh), obtained from the analyses of Na currents and steady state activation and inactivation plots, following application of prepulses in both slow (1–100 s) and fast (100–1000 ms) ranges, vary with the duration of a prepulse in a pseudo-oscillatory manner. ..."
Persistent synchronized bursting activity in cortical tissues (Golomb et al 2005)
The program simulates a one-dimensional model of a cortical tissue with excitatory and inhibitory populations.
PreBotzinger Complex inspiratory neuron with NaP and CAN currents (Park and Rubin 2013)
We have built on earlier models to develop a single-compartment Hodgkin-Huxley type model incorporating NaP and CAN currents, both of which can play important roles in bursting of inspiratory neurons in the PreBotzinger Complex of the mammalian respiratory brain stem. The model tracks the evolution of membrane potential, related (in)activation variables, calcium concentration, and available fraction of IP3 channels. The model can produce several types of bursting, presented and analyzed from a dynamical systems perspective in our paper.
Prediction for the presence of voltage-gated Ca2+ channels in myelinated central axons (Brown 2003)
"The objective of this current study was to investigate whether voltage gated Ca(2+) channels are present on axons of the adult rat optic nerve (RON). Simulations of axonal excitability using a Hodgkin-Huxley based one-compartment model incorporating I(Na), I(K) and leak currents were used to predict conditions under which the potential contribution of a Ca(2+) current to an evoked action potential could be measured. ... , as predicted by the simulation, reducing the repolarizing effect of I(K) by adding the K(+) channel blocker 4-AP revealed a Ca(2+) component on the repolarizing phase of the action potential that was blocked by the Ca(2+) channel inhibitor nifedipine."
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."
Properties of aconitine-induced block of KDR current in NG108-15 neurons (Lin et al. 2008)
"The effects of aconitine (ACO), a highly toxic alkaloid, on ion currents in differentiated NG108-15 neuronal cells were investigated in this study. ACO (0.3-30 microM) suppressed the amplitude of delayed rectifier K+ current (IK(DR)) in a concentration-dependent manner with an IC50 value of 3.1 microM. The presence of ACO enhanced the rate and extent of IK(DR) inactivation, although it had no effect on the initial activation phase of IK(DR). ... A modeled cell was designed to duplicate its inhibitory effect on spontaneous pacemaking. ... Taken together, the experimental data and simulations show that ACO can block delayed rectifier K+ channels of neurons in a concentration- and state-dependent manner. Changes in action potentials induced by ACO in neurons in vivo can be explained mainly by its blocking actions on IK(DR) and INa."
Pyramidal neuron coincidence detection tuned by dendritic branching pattern (Schaefer et al 2006)
"... We examined the relationship between dendritic arborization and the coupling between somatic and dendritic action potential (AP) initiation sites in layer 5 (L5) neocortical pyramidal neurons. Coupling was defined as the relative reduction in threshold for initiation of a dendritic calcium AP due to a coincident back-propagating AP. Simulations based on reconstructions of biocytin-filled cells showed that addition of oblique branches of the main apical dendrite in close proximity to the soma (d < 140 um) increases the coupling between the apical and axosomatic AP initiation zones, whereas incorporation of distal branches decreases coupling. ... We conclude that variation in dendritic arborization may be a key determinant of variability in coupling (49+-17%; range 19-83%; n = 37) and is likely to outweigh the contribution made by variations in active membrane properties. Thus coincidence detection of inputs arriving from different cortical layers is strongly regulated by differences in dendritic arborization."
Pyramidal Neuron Deep, Superficial; Aspiny, Stellate (Mainen and Sejnowski 1996)
This package contains compartmental models of four reconstructed neocortical neurons (layer 3 Aspiny, layer 4 Stellate, layer 3 and layer 5 Pyramidal neurons) with active dendritic currents using NEURON. Running this simulation demonstrates that an entire spectrum of firing patterns can be reproduced in this set of model neurons which share a common distribution of ion channels and differ only in their dendritic geometry. The reference paper is: Z. F. Mainen and T. J. Sejnowski (1996) Influence of dendritic structure on firing pattern in model neocortical neurons. Nature 382: 363-366. See also http://www.cnl.salk.edu/~zach/methods.html and http://www.cnl.salk.edu/~zach/ More info in readme.txt file below made visible by clicking on the patdemo folder and then on the readme.txt file.
Pyramidal Neuron Deep: Constrained by experiment (Dyhrfjeld-Johnsen et al. 2005)
"... As a practical demonstration of the use of CoCoDat we constructed a detailed computer model of an intrinsically bursting (IB) layer V pyramidal neuron from the rat barrel cortex supplementing experimental data (Schubert et al., 2001) with information extracted from the database. The pyramidal neuron morphology (Fig. 10B) was reconstructed from histological sections of a biocytin-stained IB neuron using the NeuroLucida software package..."
Pyramidal Neuron Deep: K+ kinetics (Korngreen, Sakmann 2000)
NEURON mod files for the slow and fast K+ currents from the paper: Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats: subtypes and gradients A. Korngreen and B. Sakmann, J.Physiol. 525.3, 621-639 (2000).
Pyramidal Neuron: Deep, Thalamic Relay and Reticular, Interneuron (Destexhe et al 1998, 2001)
This package shows single-compartment models of different classes of cortical neurons, such as the "regular-spiking", "fast-spiking" and "bursting" (LTS) neurons. The mechanisms included are the Na+ and K+ currents for generating action potentials (INa, IKd), the T-type calcium current (ICaT), and a slow voltage-dependent K+ current (IM). See http://cns.fmed.ulaval.ca/alain_demos.html
Pyramidal neurons switch from integrators to resonators (Prescott et al. 2008)
During wakefulness, pyramidal neurons in the intact brain are bombarded by synaptic input that causes tonic depolarization, increased membrane conductance (i.e. shunting), and noisy fluctuations in membrane potential; by comparison, pyramidal neurons in acute slices typically experience little background input. Such differences in operating conditions can compromise extrapolation of in vitro data to explain neuronal operation in vivo. ... in slice experiments, we show that CA1 hippocampal pyramidal cells switch from integrators to resonators, i.e. from class 1 to class 2 excitability. The switch is explained by increased outward current contributed by the M-type potassium current IM ... Thus, even so-called “intrinsic” properties may differ qualitatively between in vitro and in vivo conditions.
Pyramidal neurons: IKHT offsets activation of IKLT to increase gain (Fernandez et al 2005)
This matlab model was supplied by Dr Fernandez. It provides the model specification for the below paper. The influence of a high threshold K current on low threshold K and Na currents (especially frequency-current relationships) are studied in the paper with both experiments and modeling. Please see the reference for more and details.
Rapid desynchronization of an electrically coupled Golgi cell network (Vervaeke et al. 2010)
Electrical synapses between interneurons contribute to synchronized firing and network oscillations in the brain. However, little is known about how such networks respond to excitatory synaptic input. In addition to detailed electrophysiological recordings and histological investigations of electrically coupled Golgi cells in the cerebellum, a detailed network model of these cells was created. The cell models are based on reconstructed Golgi cell morphologies and the active conductances are taken from an earlier abstract Golgi cell model (Solinas et al 2007, accession no. 112685). Our results show that gap junction coupling can sometimes be inhibitory and either promote network synchronization or trigger rapid network desynchronization depending on the synaptic input. The model is available as a neuroConstruct project and can executable scripts can be generated for the NEURON simulator.
Rat subthalamic projection neuron (Gillies and Willshaw 2006)
A computational model of the rat subthalamic nucleus projection neuron is constructed using electrophysiological and morphological data and a restricted set of channel specifications. The model cell exhibits a wide range of electrophysiological behaviors characteristic of rat subthalamic neurons. It reveals that a key set of three channels play a primary role in distinguishing behaviors: a high-voltage-activated calcium channel (Cav 1.2.-1.3), a low-voltage-activated calcium channel (Cav 3.-), and a small current calcium-activated potassium channel (KCa 2.1-2.3). See paper for more and details.
Reciprocal regulation of rod and cone synapse by NO (Kourennyi et al 2004)
We constructed models of rod and cone photoreceptors using NEURON software to predict how changes in Ca channels would affect the light response in these cells and in postsynaptic horizontal cells.
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.
Recurrent discharge in a reduced model of cat spinal motoneuron (Balbi et al, 2013)
Following a distal stimulation of a motor fibre, only a fraction of spinal motoneurons are able to produce a re-excitation of the initial segment leading to an orthodromically conducted action potential, known as recurrent discharge. In order to show the reciprocal interplay of the axonal initial segment and the soma leading to recurrent discharge in detail, a reduced model of a cat spinal motoneuron was developed.
Regulation of a slow STG rhythm (Nadim et al 1998)
Frequency regulation of a slow rhythm by a fast periodic input. Nadim, F., Manor, Y., Nusbaum, M. P., Marder, E. (1998) J. Neurosci. 18: 5053-5067
Regulation of firing frequency in a midbrain dopaminergic neuron model (Kuznetsova et al. 2010)
A dopaminergic (DA) neuron model with a morphologicaly realistic dendritic architecture. The model captures several salient features of DA neurons under different pharmacological manipulations and exhibits depolarization block for sufficiently high current pulses applied to the soma.
Regulation of the firing pattern in dopamine neurons (Komendantov et al 2004)
Midbrain dopaminergic (DA) neurons in vivo exhibit two major firing patterns: single-spike firing and burst firing. The firing pattern expressed is dependent on both the intrinsic properties of the neurons and their excitatory and inhibitory synaptic inputs. Experimental data suggest that the activation of NMDA and GABAA receptors is crucial contributor to the initiation and suppression of burst firing, respectively, and that blocking calcium-activated potassium channels can facilitate burst firing. This multi-compartmental model of a DA neuron with a branching structure was developed and calibrated based on in vitro experimental data to explore the effects of different levels of activation of NMDA and GABAA receptors as well as the modulation of the SK current on the firing activity.
Rejuvenation model of dopamine neuron (Chan et al. 2007)
Model files for the paper C. Savio Chan, et al. 'Rejuvenation' protects neurons in mouse models of Parkinson's disease, Nature 447, 1081-1086(28 June 2007).
Reliability of Morris-Lecar neurons with added T, h, and AHP currents (Zeldenrust et al. 2013)
We investigated the reliability of the timing of spikes in a spike train in a Morris-Lecar model with several extensions. A frozen Gaussian noise current, superimposed on a DC current, was injected. The neuron responded with spike trains that showed trial-to-trial variability. The reliability depends on the shape (steepness) of the current input versus spike frequency output curve. The model also allowed to study the contribution of three relevant ionic membrane currents to reliability: a T-type calcium current, a cation selective h-current and a calcium dependent potassium current in order to allow bursting, investigate the consequences of a more complex current-frequency relation and produce realistic firing rates.
Response properties of neocort. neurons to temporally modulated noisy inputs (Koendgen et al. 2008)
Neocortical neurons are classified by current–frequency relationship. This is a static description and it may be inadequate to interpret neuronal responses to time-varying stimuli. Theoretical studies (Brunel et al., 2001; Fourcaud-Trocmé et al. 2003; Fourcaud-Trocmé and Brunel 2005; Naundorf et al. 2005) suggested that single-cell dynamical response properties are necessary to interpret ensemble responses to fast input transients. Further, it was shown that input-noise linearizes and boosts the response bandwidth, and that the interplay between the barrage of noisy synaptic currents and the spike-initiation mechanisms determine the dynamical properties of the firing rate. In order to allow a reader to explore such simulations, we prepared a simple NEURON implementation of the experiments performed in Köndgen et al., 2008 (see also Fourcaud-Trocmé al. 2003; Fourcaud-Trocmé and Brunel 2005). In addition, we provide sample MATLAB routines for exploring the sandwich model proposed in Köndgen et al., 2008, employing a simple frequdency-domain filtering. The simulations and the MATLAB routines are based on the linear response properties of layer 5 pyramidal cells estimated by injecting a superposition of a small-amplitude sinusoidal wave and a background noise, as in Köndgen et al., 2008.
Retinal Ganglion Cell: I-K (Skaliora et al 1995)
NEURON mod files for the K-DR current from the paper: Skaliora I, Robinson DW, Scobey RP, Chalupa LM. Properties of K+ conductances in cat retinal ganglion cells during the period of activity-mediated refinements in retinofugal pathways. Eur J Neurosci 1995 7(7):1558-1568. See the readme.txt file below for more information.
Rhesus Monkey Layer 3 Pyramidal Neurons: V1 vs PFC (Amatrudo, Weaver et al. 2012)
Whole-cell patch-clamp recordings and high-resolution 3D morphometric analyses of layer 3 pyramidal neurons in in vitro slices of monkey primary visual cortex (V1) and dorsolateral granular prefrontal cortex (dlPFC) revealed that neurons in these two brain areas possess highly distinctive structural and functional properties. ... Three-dimensional reconstructions of V1 and dlPFC neurons were incorporated into computational models containing Hodgkin-Huxley and AMPA- and GABAA-receptor gated channels. Morphology alone largely accounted for observed passive physiological properties, but led to AP firing rates that differed more than observed empirically, and to synaptic responses that opposed empirical results. Accordingly, modeling predicts that active channel conductances differ between V1 and dlPFC neurons. The unique features of V1 and dlPFC neurons are likely fundamental determinants of area-specific network behavior. The compact electrotonic arbor and increased excitability of V1 neurons support the rapid signal integration required for early processing of visual information. The greater connectivity and dendritic complexity of dlPFC neurons likely support higher level cognitive functions including working memory and planning.
Role of Ih in firing patterns of cold thermoreceptors (Orio et al., 2012)
" ... Here we investigated the role of Ih in cold-sensitive (CS) nerve endings, where cold sensory transduction actually takes place. Corneal CS nerve endings in mice show a rhythmic spiking activity at neutral skin temperature that switches to bursting mode when the temperature is lowered. ... Mathematical modeling shows that the firing phenotype of CS nerve endings from HCN1−/− mice can be reproduced by replacing HCN1 channels with the slower HCN2 channels rather than by abolishing Ih. We propose that Ih carried by HCN1 channels helps tune the frequency of the oscillation and the length of bursts underlying regular spiking in cold thermoreceptors, having important implications for neural coding of cold sensation. "
Role of KCNQ1 and IKs in cardiac repolarization (Silva, Rudy 2005)
Detailed Markov models of IKs (the slow delayed rectifier K+ current) and its alpha-subunit KCNQ1 were developed. The model is compared to experiment in the paper. The role of IKs in disease and drug treatments is elucidated (the prevention of excessive action potential prolongation and development of arrhythmogenic early afterdepolarizations). See paper for more and details.
Role of KCNQ1 and IKs in cardiac repolarization (Silva, Rudy 2005) (XPP)
Detailed Markov model of IKs (the slow delayed rectifier K+ current) is supplied here in XPP. The model is compared to experiment in the paper. The role of IKs in disease and drug treatments is elucidated (the prevention of excessive action potential prolongation and development of arrhythmogenic early afterdepolarizations). See also paper authors code and reference for more and details. This XPP version of the model reproduces Figure 3C in the paper by default. These model files were submitted by: Dr. Sheng-Nan Wu, Han-Dong Chang, Jiun-Shian Wu Department of Physiology National Cheng Kung University Medical College
Roles of I(A) and morphology in AP prop. in CA1 pyramidal cell dendrites (Acker and White 2007)
" ...Using conductance-based models of CA1 pyramidal cells, we show that underlying “traveling wave attractors” control action potential propagation in the apical dendrites. By computing these attractors, we dissect and quantify the effects of IA channels and dendritic morphology on bAP amplitudes. We find that non-uniform activation properties of IA can lead to backpropagation failure similar to that observed experimentally in these cells. ... "
Salamander retinal ganglian cells: morphology influences firing (Sheasby, Fohlmeister 1999)
Nerve impulse entrainment and other excitation and passive phenomena are analyzed for a morphologically diverse and exhaustive data set (n=57) of realistic (3-dimensional computer traced) soma-dendritic tree structures of ganglion cells in the tiger salamander (Ambystoma tigrinum) retina.
Salamander retinal ganglion cell: ion channels (Fohlmeister, Miller 1997)
A realistic five (5) channel spiking model reproduces the bursting behavior of tiger salamander ganglion cells in the retina. Please see the readme for more information.
Selective control of cortical axonal spikes by a slowly inactivating K+ current (Shu et al. 2007)
We discovered a low-threshold, slowly inactivating K+ current, containing Kv1.2 alpha subunits, in axon initial segment, playing a key role in the modulation of spike threshold and spike duration as well as the spike timing in prefrontal cortex layer V pyramidal cell of ferrets and rats. A kd.mod file implements this D current and put it in the axonal model: Neuron_Dcurrent.hoc. Run the model to see the gradual modulation effect over seconds on spike shape.
Self-organized olfactory pattern recognition (Kaplan & Lansner 2014)
" ... We present a large-scale network model with single and multi-compartmental Hodgkin–Huxley type model neurons representing olfactory receptor neurons (ORNs) in the epithelium, periglomerular cells, mitral/tufted cells and granule cells in the olfactory bulb (OB), and three types of cortical cells in the piriform cortex (PC). Odor patterns are calculated based on affinities between ORNs and odor stimuli derived from physico-chemical descriptors of behaviorally relevant real-world odorants. ... The PC was implemented as a modular attractor network with a recurrent connectivity that was likewise organized through Hebbian–Bayesian learning. We demonstrate the functionality of the model in a one-sniff-learning and recognition task on a set of 50 odorants. Furthermore, we study its robustness against noise on the receptor level and its ability to perform concentration invariant odor recognition. Moreover, we investigate the pattern completion capabilities of the system and rivalry dynamics for odor mixtures."
Serotonergic modulation of Aplysia sensory neurons (Baxter et al 1999)
The present study investigated how the modulation of these currents altered the spike duration and excitability of sensory neurons and examined the relative contributions of PKA- and PKC-mediated effects to the actions of 5-HT. A Hodgkin-Huxley type model was developed that described the ionic conductances in the somata of sensory neurons. The descriptions of these currents and their modulation were based largely on voltageclamp data from sensory neurons. Simulations were preformed with the program SNNAP (Simulator for Neural Networks and Action Potentials). The model was sufficient to replicate empirical data that describes the membrane currents, action potential waveform and excitability as well as their modulation by application of 5-HT, increased levels of adenosine cyclic monophosphate or application of active phorbol esters. The results provide several predictions that warrant additional experimental investigation and illustrate the importance of considering indirect as well as direct effects of modulatory agents on the modulation of membrane currents. See paper for more details.
Short term plasticity of synapses onto V1 layer 2/3 pyramidal neuron (Varela et al 1997)
This archive contains 3 mod files for NEURON that implement the short term synaptic plasticity model described in Varela, J.A., Sen, K., Gibson, J., Fost, J., Abbott, L.R., and Nelson, S.B.. A quantitative description of short-term plasticity at excitatory synapses in layer 2/3 of rat primary visual cortex. Journal of Neuroscience 17:7926-7940, 1997. Contact ted.carnevale@yale.edu if you have questions about this implementation of the model.
Simple and accurate Diffusion Approximation algorithm for stochastic ion channels
" ... We derived the (Stochastic Differential Equations) SDE explicitly for any given ion channel kinetic scheme. The resulting generic equations were surprisingly simple and interpretable – allowing an easy, transparent and efficient (Diffusion Approximation) DA implementation, avoiding unnecessary approximations. The algorithm was tested in a voltage clamp simulation and in two different current clamp simulations, yielding the same results as (Markov Chains) MC modeling. Also, the simulation efficiency of this DA method demonstrated considerable superiority over MC methods, except when short time steps or low channel numbers were used."
Simulated cortical color opponent receptive fields self-organize via STDP (Eguchi et al., 2014)
"... In this work, we address the problem of understanding the cortical processing of color information with a possible mechanism of the development of the patchy distribution of color selectivity via computational modeling. ... Our model of the early visual system consists of multiple topographically-arranged layers of excitatory and inhibitory neurons, with sparse intra-layer connectivity and feed-forward connectivity between layers. Layers are arranged based on anatomy of early visual pathways, and include a retina, lateral geniculate nucleus, and layered neocortex. ... After training with natural images, the neurons display heightened sensitivity to specific colors. ..."
Simulated light response in rod photoreceptors (Liu and Kourennyi 2004)
We developed a complete computer model of the rod, which accurately reproduced the main features of the light response and allowed us to demonstrate that it was suppression of Kx channels that was essential for slowing SLR and increasing excitability of rods. The results reported in this work further establish the importance of Kx channels in rod photoreceptor function.
Simulation study of Andersen-Tawil syndrome (Sung et al 2006)
Patients with Andersen-Tawil syndrome (ATS) mostly have mutations on the KCNJ2 gene producing loss of function or dominant-negative suppression of the inward rectifier K(+) channel Kir2.1. However, clinical manifestations of ATS including dysmorphic features, periodic paralysis (hypo-, hyper-, or normokalemic), long QT, and ventricular arrhythmias (VA) are considerably variable. Using a modified dynamic Luo-Rudy simulation model of cardiac ventricular myocyte, we elucidate the mechanisms of VA in ATS. We adopted a kinetic model of KCNJ2 in which channel block by Mg(+2) and spermine was incorporated. In this study, we attempt to examine the effects of KCNJ2 mutations on the ventricular action potential (AP), single-channel Markovian models were reformulated and incorporated into the dynamic Luo-Rudy model for rapidly and slowly delayed rectifying K(+) currents and KCNJ2 channel. During pacing at 1.0 Hz with [K(+)]o at 5.4 mM, a stepwise 10% reduction of Kir2.1 channel conductance progressively prolonged the terminal repolarization phase of AP along with gradual depolarization of the resting membrane potential (RMP). At 90% reduction, early after- depolarizations (EADs) became inducible and RMP was depolarized to -55.0 mV (control: -90.1 mV) followed by emergence of spontaneous action potentials (SAP). Both EADs and SAP were facilitated by a decrease in [K(+)]o and suppressed by increase in [K(+)]o. beta-adrenergic stimulation enhanced delayed after-depolarizations (DADs) and could also facilitate EADs as well as SAP in the setting of low [K(+)]o and reduced Kir2.1 channel conductance. In conclusion, the spectrum of VA in ATS includes (1) triggered activity mediated by EADs and/or DADs, and (2) abnormal automaticity manifested as SAP. These VA can be aggravated by a decrease in [K(+)]o and beta-adrenergic stimulation, and may potentially induce torsades de pointes and cause sudden death. In patients with ATS, the hypokalemic form of periodic paralysis should have the highest propensity to VA especially during physical activities.
Simulations of oscillations in piriform cortex (Wilson & Bower 1992)
"1. A large-scale computer model of the piriform cortex was constructed on the basis of the known anatomic and physiological organization of this region. 2. The oscillatory field potential and electroencephalographic (EEG) activity generated by the model was compared with actual physiological results. The model was able to produce patterns of activity similar to those recorded physiologically in response to both weak and strong electrical shocks to the afferent input. The model also generated activity patterns similar to EEGs recorded in behaving animals. 3. ..."
Single compartment Dorsal Lateral Medium Spiny Neuron w/ NMDA and AMPA (Biddell and Johnson 2013)
A biophysical single compartment model of the dorsal lateral striatum medium spiny neuron is presented here. The model is an implementation then adaptation of a previously described model (Mahon et al. 2002). The model has been adapted to include NMDA and AMPA receptor models that have been fit to dorsal lateral striatal neurons. The receptor models allow for excitation by other neuron models.
Single E-I oscillating network with amplitude modulation (Avella Gonzalez et al. 2012)
"... Intriguingly, the amplitude of ongoing oscillations, such as measured in EEG recordings, fluctuates irregularly, with episodes of high amplitude (HAE) alternating with episodes of low amplitude (LAE). ... Here, we show that transitions between HAE and LAE in the alpha/beta frequency band occur in a generic neuronal network model consisting of interconnected inhibitory (I) and excitatory (E) cells that are externally driven by sustained depolarizing currents(cholinergic input) and trains of action potentials that activate excitatory synapses. In the model, action potentials onto inhibitory cells represent input from other brain areas and desynchronize network activity, being crucial for the emergence of amplitude fluctuations. ..."
Single neuron with ion concentrations to model anoxic depolarization (Zandt et al. 2011)
A minimal single neuron model, including changing ion concentrations and homeostasis mechanisms. It shows the sudden depolarization that occurs after prolonged anoxia/ischemia.
Site of impulse initiation in a neuron (Moore et al 1983)
Examines the effect of temperature, the taper of the axon hillock, and HH channel density on antidromic spike invasion into the soma and spike initiation under dendritic stimulation.
Small world networks of Type I and Type II Excitable Neurons (Bogaard et al. 2009)
Implemented with NEURON 5.9, four model neurons with varying excitability properties affect the spatiotemporal patterning of small world networks of homogeneous and heterogeneous cell population.
Sodium channel mutations causing generalized epilepsy with febrile seizures + (Barela et al. 2006)
A novel mutation, R859C, in the Nav1.1 sodium channel was identified in a 4-generation, 33-member Caucasian family with a clinical presentation consistent with GEFS+. The mutation neutralizes a positively charged arginine in the domain 2 S4 voltage sensor of the Nav1.1 channel Ą subunit. When the mutation was placed in the rat Nav1.1 channel and expressed in Xenopus oocytes, the mutant channel displayed a positive shift in the voltage-dependence of sodium channel activation, slower recovery from slow inactivation, and lower levels of current compared to the wild-type channel. Computational analysis suggests that neurons expressing the mutant channel have higher thresholds for firing a single action potential and for firing multiple action potentials, along with decreased repetitive firing. Therefore, this mutation should lead to decreased neuronal excitability, in contrast to most previous GEFS+ sodium channel mutations that have changes predicted to increase neuronal firing.
Software for teaching neurophysiology of neuronal circuits (Grisham et al. 2008)
"To circumvent the many problems in teaching neurophysiology as a “wet lab,” we developed SWIMMY, a virtual fish that swims by moving its virtual tail by means of a virtual neural circuit. ... Using SWIMMY, students (1) review the basics of neurophysiology, (2) identify the neurons in the circuit, (3) ascertain the neurons’ synaptic interconnections, (4) discover which cells generate the motor pattern of swimming, (5) discover how the rhythm is generated, and finally (6) use an animation that corresponds to the activity of the motoneurons to discover the behavioral effects produced by various lesions and explain them in terms of their neural underpinnings. ..."
Software for teaching the Hodgkin-Huxley model (Hernandez & Zurek 2013) (SENB written in NEURON hoc)
" ... The SENB software offers several advantages for teaching and learning electrophysiology. First, SENB offers ease and flexibility in determining the number of stimuli. Second, SENB allows immediate and simultaneous visualization, in the same window and time frame, of the evolution of the electrophysiological variables. Third, SENB calculates parameters such as time and space constants, stimuli frequency, cellular area and volume, sodium and potassium equilibrium potentials, and propagation velocity of the action potentials. ..."
Space clamp problems in neurons with voltage-gated conductances (Bar-Yehuda and Korngreen 2008)
" ... using numerical simulations, we show that the distortions of voltage-gated K+ and Ca2+ currents are substantial even in neurons with short dendrites. The simulations also demonstrate that passive cable theory cannot be used to justify voltage-clamping of neurons, due to significant shunting to the reversal potential of the voltage-gated conductance during channel activation. ... "
Spatial summation of excitatory and inhibitory inputs in pyramidal neurons (Hao et al. 2010)
"... Based on realistic modeling and experiments in rat hippocampal slices, we derived a simple arithmetic rule for spatial summation of concurrent excitatory glutamatergic inputs (E) and inhibitory GABAergic inputs (I). The somatic response can be well approximated as the sum of the excitatory postsynaptic potential (EPSP), the inhibitory postsynaptic potential (IPSP), and a nonlinear term proportional to their product (k*EPSP*IPSP), where the coefficient k reflects the strength of shunting effect. ..."
Spike Initiation in Neocortical Pyramidal Neurons (Mainen et al 1995)
This model reproduces figure 3A from the paper Mainen ZF, Joerges J, Huguenard JR, Sejnowski TJ (1995). Please see the paper for detail whose full text is available at http://www.cnl.salk.edu/~zach/methods.html Email Zach Mainen for questions: mainen@cshl.org
Spike propagation and bouton activation in terminal arborizations (Luscher, Shiner 1990)
Action potential propagation in axons with bifurcations involving short collaterals with synaptic boutons has been simulated ... The architecture of the terminal arborizations has a profound effect on the activation pattern of synapses, suggesting that terminal arborizations not only distribute neural information to postsynaptic cells but may also be able to process neural information presynaptically. Please see paper for details.
Spike repolarization in axon collaterals (Foust et al. 2011)
Voltage sensing dye experiments and simulations characterize the location and re-polarizing function of Kv1 channels in cortical neurons. "... (the papers) results indicate that action potential-induced synaptic transmission may operate through a mix of analog–digital transmission owing to the properties of Kv1 channels in axon collaterals and presynaptic boutons."
Spikes,synchrony,and attentive learning by laminar thalamocort. circuits (Grossberg & Versace 2007)
"... The model hereby clarifies, for the first time, how the following levels of brain organization coexist to realize cognitive processing properties that regulate fast learning and stable memory of brain representations: single cell properties, such as spiking dynamics, spike-timing-dependent plasticity (STDP), and acetylcholine modulation; detailed laminar thalamic and cortical circuit designs and their interactions; aggregate cell recordings, such as current-source densities and local field potentials; and single cell and large-scale inter-areal oscillations in the gamma and beta frequency domains. ..."
Spinal Motor Neuron (Dodge, Cooley 1973)
Dodge & Cooley (1973) "Action Potential of the Motorneuron" IBM J. Res. Develop. May 219--229
Spinal Motor Neuron (McIntyre et al 2002)
Simulation of peripheral nervous system (PNS) mylelinated axon. This model is described in detail in: McIntyre CC, Richardson AG, and Grill WM.(2002)
Spinal Motor Neuron: Na, K_A, and K_DR currents (Safronov, Vogel 1995)
NEURON mod files for the Na, K-A, and K-DR currents from the paper: Safronov, B.V. and Vogel,W. Single voltage-activated Na+ and K+ channels in the somata of rat motorneurons. Journal of Physiology 487.1:91-106 (1995). See the readme.txt file for more information.
Spine fusion and branching effects synaptic response (Rusakov et al 1996, 1997)
This compartmental model of a hippocampal granule cell has spinous synapses placed on the second-order dendrites. Changes in shape and connectivity of the spines usually does not effect the synaptic response of the cell unless active conductances are incorporated into the spine membrane (e.g. voltage-dependent Ca2+ channels). With active conductances, spines can generate spike-like events. We showed that changes like fusion and branching, or in fact any increase in the equivalent spine neck resistance, could trigger a dramatic increase in the spine's influence on the dendritic shaft potential.
Spontaneous firing caused by stochastic channel gating (Chow, White 1996)
NEURON implementation of model of stochastic channel gating, resulting in spontaneous firing. Qualitatively reproduces the phenomena described in the reference.
Spreading depression model for FHM3 with Nav1.1 mutation (Dahlem et al. 2014)
Familial hemiplegic migraine (FHM) is a rare subtype of migraine with aura. A mutation causing FHM type 3 (FHM3) has been identified in SCN1A encoding the Nav1.1 Na+ channel. This genetic defect affects the inactivation gate. The code describes an extended Hodgkin-Huxley framework with dynamic ion concentrations in a wilde-type and mutant form.
Squid axon (Hodgkin, Huxley 1952) (LabAXON)
The classic HH model of squid axon membrane implemented in LabAXON. Hodgkin, A.L., Huxley, A.F. (1952)
Squid axon (Hodgkin, Huxley 1952) (NEURON)
The classic HH model of squid axon membrane implemented in NEURON. Hodgkin, A.L., Huxley, A.F. (1952)
Squid axon (Hodgkin, Huxley 1952) (SBML, XPP, other)
An SBML (and related XPP and other formats) implementation of the classic HH paper is available in the BIOMODELS database http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=BIOMD0000000020. Clicking on the XPP link will download an executable version of the HH model.
Squid axon (Hodgkin, Huxley 1952) (SNNAP)
The classic HH model of squid axon membrane implemented in SNNAP. Hodgkin, A.L., Huxley, A.F. (1952)
Squid axon (Hodgkin, Huxley 1952) used in (Chen et al 2010) (R language)
"... Previous work showed that magnetic electrical field-induced antinoceptive action is mediated by activation of capsaicin-sensitive sensory afferents. In this study, a modified Hodgkin-Huxley model, in which TRP-like current (I-TRP) was incorporated, was implemented to predict the firing behavior of action potentials (APs), as the model neuron was exposed to sinusoidal changes in externally-applied voltage. ... Our simulation results suggest that modulation of TRP-like channels functionally expressed in small-diameter peripheral sensory neurons should be an important mechanism through which it can contribute to the firing pattern of APs."
Squid axon: Bifurcation analysis of mode-locking (Lee & Kim 2006) (Gangal et al. under preparation)
The model was built with the purpose of finding mode lockings between the input sinusoidal current frequency and the output frequency. Phase plase plane analysis, spike statistics, mode locking formulation etc. can be done with the help of the model. Any additional functionality can be added as the base code return the correct action potential values.
State and location dependence of action potential metabolic cost (Hallermann et al., 2012)
With this model of a layer 5 pyramidal neuron the state and location dependence of the ATP usage and the metabolic efficiency of action potentials can be analyzed. Model parameters were constrained by direct subcellular recordings at dendritic, somatic and axonal compartments.
STD-dependent and independent encoding of Input irregularity as spike rate (Luthman et al. 2011)
"... We use a conductance-based model of a CN neuron to study the effect of the regularity of Purkinje cell spiking on CN neuron activity. We find that increasing the irregularity of Purkinje cell activity accelerates the CN neuron spike rate and that the mechanism of this recoding of input irregularity as output spike rate depends on the number of Purkinje cells converging onto a CN neuron. ..."
STDP promotes synchrony of inhibitory networks in the presence of heterogeneity (Talathi et al 2008)
"Recently Haas et al. (J Neurophysiol 96: 3305–3313, 2006), observed a novel form of spike timing dependent plasticity (iSTDP) in GABAergic synaptic couplings in layer II of the entorhinal cortex. Depending on the relative timings of the presynaptic input at time tpre and the postsynaptic excitation at time tpost, the synapse is strengthened (delta_t = tpost − tpre > 0) or weakened (delta_t < 0). The temporal dynamic range of the observed STDP rule was found to lie in the higher gamma frequency band (≥40 Hz), a frequency range important for several vital neuronal tasks. In this paper we study the function of this novel form of iSTDP in the synchronization of the inhibitory neuronal network. In particular we consider a network of two unidirectionally coupled interneurons (UCI) and two mutually coupled interneurons (MCI), in the presence of heterogeneity in the intrinsic firing rates of each coupled neuron. ..."
Stochastic 3D model of neonatal rat spinal motoneuron (Ostroumov 2007)
" ... Although existing models of motoneurons have indicated the distributed role of certain conductances in regulating firing, it is unclear how the spatial distribution of certain currents is ultimately shaping motoneuron output. Thus, it would be helpful to build a bridge between histological and electrophysiological data. The present report is based on the construction of a 3D motoneuron model based on available parameters applicable to the neonatal spinal cord. ..."
Stochastic calcium mechanisms cause dendritic calcium spike variability (Anwar et al. 2013)
" ... In single Purkinje cells, spontaneous and synaptically evoked dendritic calcium bursts come in a variety of shapes with a variable number of spikes. The mechanisms causing this variability have never been investigated thoroughly. In this study, a detailed computational model employing novel simulation routines is applied to identify the roles that stochastic ion channels, spatial arrangements of ion channels and stochastic intracellular calcium have towards producing calcium burst variability. … Our findings suggest that stochastic intracellular calcium mechanisms play a crucial role in dendritic calcium spike generation and are, therefore, an essential consideration in studies of neuronal excitability and plasticity."
Stochastic ion channels and neuronal morphology (Cannon et al. 2010)
"... We introduce and validate new computational tools that enable efficient generation and simulation of models containing stochastic ion channels distributed across dendritic and axonal membranes. Comparison of five morphologically distinct neuronal cell types reveals that when all simulated neurons contain identical densities of stochastic ion channels, the amplitude of stochastic membrane potential fluctuations differs between cell types and depends on sub-cellular location. ..." The code is downloadable and more information is available at http://www.psics.org/
Striatal Output Neuron (Mahon, Deniau, Charpier, Delord 2000)
Striatal output neurons (SONs) integrate glutamatergic synaptic inputs originating from the cerebral cortex. In vivo electrophysiological data have shown that a prior depolarization of SONs induced a short-term (1 sec)increase in their membrane excitability, which facilitated the ability of corticostriatal synaptic potentials to induce firing. Here we propose, using a computational model of SONs, that the use-dependent, short-term increase in the responsiveness of SONs mainly results from the slow kinetics of a voltage-dependent, slowly inactivating potassium A-current. This mechanism confers on SONs a form of intrinsic short-term memory that optimizes the synaptic input–output relationship as a function of their past activation.
Structure-dynamics relationships in bursting neuronal networks revealed (Mäki-Marttunen et al. 2013)
This entry includes tools for generating and analyzing network structure, and for running the neuronal network simulations on them.
Studies of stimulus parameters for seizure disruption using NN simulations (Anderson et al. 2007)
Architecturally realistic neocortical model using seven classes of excitatory and inhibitory single compartment Hodgkin-Huxley cells. Wiring is adapted to minicolumn hypothesis and incorporates visual and neocortical data. Simulation demonstrates spontaneous bursting onset and cessation, and activity can be altered with external electric field.
Study of augmented Rubin and Terman 2004 deep brain stim. model in Parkinsons (Pascual et al. 2006)
" ... The model by Rubin and Terman [31] represents one of the most comprehensive and biologically plausible models of DBS published recently. We examined the validity of the model, replicated its simulations and tested its robustness. While our simulations partially reproduced the results presented by Rubin and Terman [31], several issues were raised including the high complexity of the model in its non simplified form, the lack of robustness of the model with respect to small perturbations, the nonrealistic representation of the thalamus and the absence of time delays. Computational models are indeed necessary, but they may not be sufficient in their current forms to explain the effect of chronic electrical stimulation on the activity of the basal ganglia (BG) network in PD."
Submyelin Potassium accumulation in Subthalamic neuron (STN) axons (Bellinger et al. 2008)
"To better understand the direct effects of DBS (Deep brain stimulation) on central neurons, a computational model of a myelinated axon has been constructed which includes the effects of K+ accumulation within the peri-axonal space. Using best estimates of anatomic and electrogenic model parameters for in vivo STN axons, the model predicts a functional block along the axon due to K+ accumulation in the submyelin space. ... These results suggest that therapeutic DBS of the STN likely results in a functional block for many STN axons, although a subset of STN axons may also be activated at the stimulating frequency. "
Subthreshold inact. of K channels modulates APs in bitufted interneurons (Korngreen et al 2005)
... In this study we show that in bitufted interneurones from layer 2/3 of the somatosensory cortex, the height and width of APs recorded at the soma are sensitive to changes in the resting membrane potential, suggesting subthreshold activity of voltage-gated conductances. Attributes of K+ currents examined in nucleated patches revealed a fast subthreshold-inactivating K+ conductance (Kf ) and a slow suprathreshold-inactivating K+ conductance (Ks ). Simulations of these K+ conductances, incorporated into a Hodgkin–Huxley-type model, suggested that during a single AP or during low frequency trains of APs, subthreshold inactivation of Kf was the primary modulator of AP shape, whereas during trains of APs the shape was governed to a larger degree by Ks resulting in the generation of smaller and broader APs. ... Compartmental simulation of the back-propagating AP suggested a mechanism for the modulation of the back-propagating AP height and width by subthreshold activation of Kf . We speculate that this signal may modulate retrograde GABA release and consequently depression of synaptic efficacy of excitatory input from neighbouring pyramidal neurones.
Sympathetic neuron (Wheeler et al 2004)
This study shows how synaptic convergence and plasticity can interact to generate synaptic gain in autonomic ganglia and thereby enhance homeostatic control. Using a conductance-based computational model of an idealized sympathetic neuron, we simulated the postganglionic response to noisy patterns of presynaptic activity and found that a threefold amplification in postsynaptic spike output can arise in ganglia, depending on the number and strength of nicotinic synapses, the presynaptic firing rate, the extent of presynaptic facilitation, and the expression of muscarinic and peptidergic excitation. See references for details.
Sympathetic Preganglionic Neurone (Briant et al. 2014)
A model of a sympathetic preganglionic neurone of muscle vasoconstrictor-type.
Synaptic gating at axonal branches, and sharp-wave ripples with replay (Vladimirov et al. 2013)
The computational model of in vivo sharp-wave ripples with place cell replay. Excitatory post-synaptic potentials at dendrites gate antidromic spikes arriving from the axonal collateral, and thus determine when the soma and the main axon fire. The model allows synchronous replay of pyramidal cells during sharp-wave ripple event, and the replay is possible in both forward and reverse directions.
Synaptic information transfer in computer models of neocortical columns (Neymotin et al. 2010)
"... We sought to measure how the activity of the network alters information flow from inputs to output patterns. Information handling by the network reflected the degree of internal connectivity. ... With greater connectivity strength, the recurrent network translated activity and information due to contribution of activity from intrinsic network dynamics. ... At still higher internal synaptic strength, the network corrupted the external information, producing a state where little external information came through. The association of increased information retrieved from the network with increased gamma power supports the notion of gamma oscillations playing a role in information processing."
Synaptic integration in a model of granule cells (Gabbiani et al 1994)
We have developed a compartmental model of a turtle cerebellar granule cell consisting of 13 compartments that represent the soma and 4 dendrites. We used this model to investigate the synaptic integration of mossy fiber inputs in granule cells. See reference or abstract at PubMed link below for more information.
Synaptic integration of an identified nonspiking interneuron in crayfish (Takashima et al 2006)
This GENESIS simulation shows how a single or compound excitatory synaptic potential evoked by mechanosensory stimulation spreads over the dendrites of the LDS interneuron that is one of the identified nonspiking interneurons in the central nervous system of crayfish Procambarus clarkii. The model is based on physiological experiments carried out by Akira Takashima using single-electrode voltage clamp techniques and also 3-D morphometry of the interneuron carried out by Ryou Hikosaka using confocal laser scanning microscopic techniques. The physiological and morphological studies were coordinated by Masakazu Takahata.
Synchrony by synapse location (McTavish et al. 2012)
This model considers synchrony between mitral cells induced via shared granule cell interneurons while taking into account the spatial constraints of the system. In particular, since inhibitory inputs decay passively along the lateral dendrites, this model demonstrates that an optimal arrangement of the inhibitory synapses will be near the cell bodies of the relevant mitral cells.
Synergistic inhibitory action of oxcarbazepine on INa and IK (Huang et al. 2008)
"Oxcarbazepine (OXC), one of the newer anti-epileptic drugs, has been demonstrating its efficacy on wide-spectrum neuropsychiatric disorders. ... With the aid of patch-clamp technology, we first investigated the effects of OXC on ion currents in NG108-15 neuronal cells differentiated with cyclic AMP. We found OXC ... caused a reversible reduction in the amplitude of voltage-gated Na+ current (INa) ... and produce(d) a significant prolongation in the recovery of INa inactivation. ... Moreover, OXC could suppress the amplitude of delayed rectifier K+ current (IK(DR)), with no effect on M-type K+ current (IK(M)). ... Furthermore, the simulations, based on hippocampal pyramidal neurons (Pinsky-Rinzel model) and a network of the Hodgkin-Huxley model, were analysed to investigate the effect of OXC on action potentials. Taken together, our results suggest that the synergistic blocking effects on INa and IK(DR) may contribute to the underlying mechanisms through which OXC affects neuronal function in vivo."
Temperature-Sensitive conduction at axon branch points (Westerfield et al 1978)
Propagation of impulses through branching regions of squid axons was examined experimentally and with computer simulations. The ratio of postbranch/prebranch diameters at which propagation failed was very sensitive to temperature.
Temporal decorrelation by intrinsic cellular dynamics (Wang et al 2003)
"... Recent investigations in primary visual (V1) cortical neurons have demonstrated that adaptation to prolonged changes in stimulus contrast is mediated in part through intrinsic ionic currents, a Ca2+ activated K+ current (IKCa) and especially a Na+ activated K+ current (IKNa). The present study was designed to test the hypothesis that the activation of adaptation ionic currents may provide a cellular mechanism for temporal decorrelation in V1. A conductance-based neuron model was simulated, which included an IKCa and an IKNa. We show that the model neuron reproduces the adaptive behavior of V1 neurons in response to high contrast inputs. ...". See paper for details and more.
Thalamic neuron: Modeling rhythmic neuronal activity (Meuth et al. 2005)
The authors use an in vitro cell model of a single acutely isolated thalamic neuron in the NEURON simulation environment to address and discuss questions in an undergraduate course. Topics covered include passive electrical properties, composition of action potentials, trains of action potentials, multicompartment modeling, and research topics. The paper includes detailed instructions on how to run the simulations in the appendix.
Thalamic reticular neurons: the role of Ca currents (Destexhe et al 1996)
The experiments and modeling reported in this paper show how intrinsic bursting properties of RE cells may be explained by dendritic calcium currents.
Thalamic transformation of pallidal input (Hadipour-Niktarash 2006)
"In Parkinson’s disease, neurons of the internal segment of the globus pallidus (GPi) display the low-frequency tremor-related oscillations. These oscillatory activities are transmitted to the thalamic relay nuclei. Computer models of the interacting thalamocortical (TC) and thalamic reticular (RE) neurons were used to explore how the TC-RE network processes the low-frequency oscillations of the GPi neurons. ..."
The dynamics underlying pseudo-plateau bursting in a pituitary cell model (Teka et al. 2011)
" ... pseudo-plateau bursts, are unlike bursts studied mathematically in neurons (plateau bursting) and the standard fast-slow analysis used for plateau bursting is of limited use. Using an alternative fast-slow analysis, with one fast and two slow variables, we show that pseudo-plateau bursting is a canard-induced mixed mode oscillation. ..." See paper for other results.
The relationship between two fast/slow analysis techniques for bursting oscill. (Teka et al. 2012)
"Bursting oscillations in excitable systems reflect multi-timescale dynamics. These oscillations have often been studied in mathematical models by splitting the equations into fast and slow subsystems. Typically, one treats the slow variables as parameters of the fast subsystem and studies the bifurcation structure of this subsystem. This has key features such as a z-curve (stationary branch) and a Hopf bifurcation that gives rise to a branch of periodic spiking solutions. In models of bursting in pituitary cells, we have recently used a different approach that focuses on the dynamics of the slow subsystem. Characteristic features of this approach are folded node singularities and a critical manifold. … We find that the z-curve and Hopf bifurcation of the twofast/ one-slow decomposition are closely related to the voltage nullcline and folded node singularity of the one-fast/two-slow decomposition, respectively. They become identical in the double singular limit in which voltage is infinitely fast and calcium is infinitely slow."
The role of ATP-sensitive potassium channels in a hippocampal neuron (Huang et al. 2007)
"Hyperglycemia-related neuronal excitability and epileptic seizures are not uncommon in clinical practice. However, their underlying mechanism remains elusive. ATP-sensitive K(+) (K(ATP)) channels are found in many excitable cells, including cardiac myocytes, pancreatic beta cells, and neurons. These channels provide a link between the electrical activity of cell membranes and cellular metabolism. We investigated the effects of higher extracellular glucose on hippocampal K(ATP) channel activities and neuronal excitability. The cell-attached patch-clamp configuration on cultured hippocampal cells and a novel multielectrode recording system on hippocampal slices were employed. In addition, a simulation modeling hippocampal CA3 pyramidal neurons (Pinsky-Rinzel model) was analyzed to investigate the role of K(ATP) channels in the firing of simulated action potentials. ..."
Tight junction model of CNS myelinated axons (Devaux and Gow 2008)
Two models are included: 1) a myelinated axon is represented by an equivalent circuit with a double cable design but includes a tight junction in parallel with the myelin membrane RC circuit (called double cable model, DCM). 2) a myelinated axon is represented by an equivalent circuit with a double cable design but includes a tight junction in series with the myelin RC circuit (called tight junction model, TJM). These models have been used to simulate data from compound action potentials measured in mouse optic nerve from Claudin 11-null mice in Fig. 6 of: Devaux, J.J. & Gow, A. (2008) Tight Junctions Potentiate The Insulative Properties Of Small CNS Myelinated Axons. J Cell Biol 183, 909-921.
Tonic firing in substantia gelatinosa neurons (Melnick et al 2004)
Ionic conductances underlying excitability in tonically firing neurons (TFNs) from substantia gelatinosa (SG) were studied by the patch-clamp method in rat spinal cord slices. ... Suppression of Ca2+ and KCA currents ... did not abolish the basic pattern of tonic firing, indicating that it was generated by voltage-gated Na+ and K+ currents. ... on the basis of present data, we created a model of TFN and showed that Na+ and KDR currents are sufficient to generate a basic pattern of tonic firing. It is concluded that the balanced contribution of all ionic conductances described here is important for generation and modulation of tonic firing in SG neurons. See paper for more and details.
Transfer properties of Neuronal Dendrites (Korogod et al 1998)
The somatopetal current transfer was studied in mathematical models of a reconstructed brainstem motoneuron with tonically activated excitatory synaptic inputs uniformly distributed over the dendritic arborization. See paper and below readme.txt for more information.
TTX-R Na+ current effect on cell response (Herzog et al 2001)
"Small dorsal root ganglion (DRG) neurons, which include nociceptors, express multiple voltage-gated sodium currents. In addition to a classical fast inactivating tetrodotoxin-sensitive (TTX-S) sodium current, many of these cells express a TTX-resistant (TTX-R) sodium current that activates near -70 mV and is persistent at negative potentials. To investigate the possible contributions of this TTX-R persistent (TTX-RP) current to neuronal excitability, we carried out computer simulations using the Neuron program with TTX-S and -RP currents, fit by the Hodgkin-Huxley model, that closely matched the currents recorded from small DRG neurons. ..." See paper for more and details.
TTX-R Na+ current effect on cell response (Herzog et al 2001) (MATLAB)
"Small dorsal root ganglion (DRG) neurons, which include nociceptors, express multiple voltage-gated sodium currents. In addition to a classical fast inactivating tetrodotoxin-sensitive (TTX-S) sodium current, many of these cells express a TTX-resistant (TTX-R) sodium current that activates near -70 mV and is persistent at negative potentials. To investigate the possible contributions of this TTX-R persistent (TTX-RP) current to neuronal excitability, we carried out computer simulations using the Neuron program with TTX-S and -RP currents, fit by the Hodgkin-Huxley model, that closely matched the currents recorded from small DRG neurons. ..." See paper for more and details.
Turtle visual cortex model (Nenadic et al. 2003, Wang et al. 2005, Wang et al. 2006)
This is a model of the visual cortex of freshwater turtles that is based upon the known anatomy and physiology of individual neurons. The model was published in three papers (Nenadic et al., 2003; Wang et al., 2005; Wang et al., 2006), which should be consulted for full details on its construction. The model has also been used in several papers (Robbins and Senseman, 2004; Du et al., 2005; Du et al., 2006). It is implemented in GENESIS (Bower and Beeman, 1998).
Understanding how fast activating K+ channels promote bursting in pituitary cells (Vo et al 2014)
"... Experimental observations have shown ... that fast-activating voltage- and calcium-dependent potassium (BK) current tends to promote bursting in pituitary cells. This burst promoting effect requires fast activation of the BK current, otherwise it is inhibitory to bursting. In this work, we analyze a pituitary cell model in order to answer the question of why the BK activation must be fast to promote bursting. ..."
Using Strahler’s analysis to reduce realistic models (Marasco et al, 2013)
Building on our previous work (Marasco et al., (2012)), we present a general reduction method based on Strahler's analysis of neuron morphologies. We show that, without any fitting or tuning procedures, it is possible to map any morphologically and biophysically accurate neuron model into an equivalent reduced version. Using this method for Purkinje cells, we demonstrate how run times can be reduced up to 200-fold, while accurately taking into account the effects of arbitrarily located and activated synaptic inputs. Reference: Marasco A, Limongiello A, & Migliore M (2013), Using Strahler’s analysis to reduce up to 200-fold the run time of realistic neuron models, Sci. Rep. 3, 2934; DOI:10.1038/srep02934 in press.
Ventricular cell model (Guinea-pig-type) (Luo, Rudy 1991, +10 other papers!) (C++)
A mathematical model of the membrane action potential of the mammalian ventricular cell is introduced. The model is based, whenever possible, on recent single-cell and single-channel data and incorporates the possibility of changing extracellular potassium concentration [K]o. ... The results are consistent with recent experimental observations, and the model simulations relate these phenomena to the underlying ionic channel kinetics. See paper for more and details.
Visual Cortex Neurons: Dendritic computations (Archie, Mel 2000)
Neuron and C program files from Archie, K.A. and Mel, B.W. A model of intradendritic computation of binocular disparity. Nature Neuroscience 3:54-63, 2000 The original files for this model are located at the web site
Vomeronasal sensory neuron (Shimazaki et al 2006)
NEURON model files from the papers: Shimazaki et al, Chem. Senses, epub ahead of print (2006) Electrophysiological properties and modeling of murine vomeronasal sensory neurons in acute slice preparations. The model reproduces quantitatively the experimentally observed firing rates of these neurons under a wide range of input currents.


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