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Models that contain the Modeling Application : NEURON (web link to model) (Home Page)

(NEURON is a simulation environment for developing and exercising models of neurons and networks of neurons. It is particularly well-suited to problems where cable properties of cells play an important role, possibly including extracellular potential close to the membrane), and where cell membrane properties are complex, involving many ion-specific channels, ion accumulation, and second messengers. It evolved from a long collaboration between Michael Hines and John W. Moore at the Department of Neurobiology, Duke University. Their express goal was to create a tool designed specifically for solving the equations that describe nerve cells.)

   Models   Description
A model for how correlation depends on the neuronal excitability type (Hong et al. 2012)
“ … Using simulations and experiments in rat hippocampal neurons, we show here that pairs of neurons receiving correlated input also exhibit correlations arising from precise spike-time synchronization. Contrary to rate comodulation, spike-time synchronization is unaffected by firing rate, thus enabling synchrony- and rate-based coding to operate independently. The type of output correlation depends on whether intrinsic neuron properties promote integration or coincidence detection: “ideal” integrators (with spike generation sensitive to stimulus mean) exhibit rate comodulation, whereas ideal coincidence detectors (with spike generation sensitive to stimulus variance) exhibit precise spike-time synchronization. … Our results explain how different types of correlations arise based on how individual neurons generate spikes, and why spike-time synchronization and rate comodulation can encode different stimulus properties. Our results also highlight the importance of neuronal properties for population-level coding insofar as neural networks can employ different coding schemes depending on the dominant operating mode of their constituent neurons. “
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."
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. "
CA1 pyramidal neuron synaptic integration (Jarsky et al. 2005)
"The perforant-path projection to the hippocampus forms synapses in the apical tuft of CA1 pyramidal neurons. We used computer modeling to examine the function of these distal synaptic inputs, which led to three predictions that we confirmed in experiments using rat hippocampal slices. ... This 'gating' of dendritic spike propagation may be an important activation mode of CA1 pyramidal neurons, and its modulation by neurotransmitters or long-term, activity-dependent plasticity may be an important feature of dendritic integration during mnemonic processing in the hippocampus."
CA1 Pyramidal Neuron: Synaptic Scaling (London, Segev 2001)
London and Segev (2001) discuss location dependent and location independent synaptic scaling in a model CA1 neuron with passive dendrites. The freely available text is followed by a critique by Maggee and Cook who comment that the London and Segev model is accurate and informative and however needs to be augmented by active channels in dendrites. Note: the zip files for this model are stored at the nature neuroscience website - Click above Supplementary Source Code in the readme.html in the model files
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
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.
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.
High-Res. Recordings Using a Real-Time Computational Model of the Electrode (Brette et al. 2008)
"Intracellular recordings of neuronal membrane potential are a central tool in neurophysiology. ... We introduce a computer-aided technique, Active Electrode Compensation (AEC), based on a digital model of the electrode interfaced in real time with the electrophysiological setup. ... AEC should be particularly useful to characterize fast neuronal phenomena intracellularly in vivo."
Ion channel modeling with whole cell and a genetic algorithm (Gurkiewicz and Korngreen 2007)
"... Here we show that a genetic search algorithm in combination with a gradient descent algorithm can be used to fit whole-cell voltage-clamp data to kinetic models with a high degree of accuracy. Previously, ion channel stimulation traces were analyzed one at a time, the results of these analyses being combined to produce a picture of channel kinetics. Here the entire set of traces from all stimulation protocols are analysed simultaneously. The algorithm was initially tested on simulated current traces produced by several Hodgkin-Huxley–like and Markov chain models of voltage-gated potassium and sodium channels. ... Finally, the algorithm was used for finding the kinetic parameters of several voltage-gated sodium and potassium channels models by matching its results to data recorded from layer 5 pyramidal neurons of the rat cortex in the nucleated outside-out patch configuration. The minimization scheme gives electrophysiologists a tool for reproducing and simulating voltage-gated ion channel kinetics at the cellular level."
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. ..."
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."
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."
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. ..."
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. ..."
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.
Voltage attenuation in CA1 pyramidal neuron dendrites (Golding et al 2005)
Voltage attenuation in the apical dendritic field of CA1 pyramidal neurons is particularly strong for epsps spreading toward the soma. High cytoplasmic resistivity and high membrane (leak) conductance appear to be the major determinants of voltage attenuation over most of the apical field, but H current may be responsible for as much as half of the attenuation of distal apical epsps.


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