Cortical Layer 5b pyr. cell with [Na+]i mechanisms, from Hay et al 2011 (Zylbertal et al 2017)

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" ... Based on a large body of experimental recordings from both the soma and dendrites of L5b pyramidal cells in adult rats, we characterized key features of the somatic and dendritic firing and quantified their statistics. We used these features to constrain the density of a set of ion channels over the soma and dendritic surface via multi-objective optimization with an evolutionary algorithm, thus generating a set of detailed conductance-based models that faithfully replicate the back-propagating action potential activated Ca(2+) spike firing and the perisomatic firing response to current steps, as well as the experimental variability of the properties. Furthermore, we show a useful way to analyze model parameters with our sets of models, which enabled us to identify some of the mechanisms responsible for the dynamic properties of L5b pyramidal cells as well as mechanisms that are sensitive to morphological changes. ..."
1 . Hay E, Hill S, Schurmann F, Markram H, Segev I (2011) Models of neocortical layer 5b pyramidal cells capturing a wide range of dendritic and perisomatic active properties. PLoS Comput Biol 7:e1002107 [PubMed]
2 . Zylbertal A, Yarom Y, Wagner S (2017) The Slow Dynamics of Intracellular Sodium Concentration Increase the Time Window of Neuronal Integration: A Simulation Study Front. Comput. Neurosci. 11(85):1-16
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Neocortex;
Cell Type(s):
Channel(s): Na/Ca exchanger; Na/K pump; I Sodium;
Gap Junctions:
Simulation Environment: NEURON;
Model Concept(s): Dendritic Action Potentials; Detailed Neuronal Models; Action Potentials; Reaction-diffusion; Synaptic Plasticity; Active Dendrites;
Implementer(s): Zylbertal, Asaph [asaph.zylbertal at];
Search NeuronDB for information about:  I Sodium; Na/Ca exchanger; Na/K pump;
Model files from the paper:

Zylbertal et al., "The Slow Dynamics of Intracellular Sodium Concentration Increase the Time Window of Neuronal Integration: A Simulation Study", XXXXXXX (2017)
The file reproduces the protocol used in Fig. 5E of the article
by calling the module
The model is adapted from Hay, E., Hill, S., Schürmann, F., Markram, H., and Segev, I. (2011). Models of Neocortical Layer 5b Pyramidal
Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties. PLoS Comput. Biol. 7, e1002107. doi:10.1371/journal.pcbi.1002107.

Questions on how to use this model should be directed to


Changes in intracellular Na+ concentration ([Na+]i) are rarely taken into account when neuronal activity is examined. As opposed to Ca2+, [Na+]i dynamics are strongly affected by longitudinal diffusion, and therefore they are governed by the morphological structure of the neurons, in addition to the localization of influx and efflux mechanisms. Here we examined [Na+]i dynamics and their effects on neuronal computation in three multi-compartmental neuronal models, representing three distinct cell types: accessory olfactory bulb (AOB) mitral cells, cortical layer V pyramidal cells, and cerebellar Purkinje cells. We added [Na+]i as a state variable to these models, and allowed it to modulate the Na+ Nernst potential, the Na+-K+ pump current, and the Na+-Ca2+ exchanger rate. Our results indicate that in most cases [Na+]i dynamics are significantly slower than [Ca2+]i dynamics, and thus may exert a prolonged influence on neuronal computation in a neuronal type specific manner. We show that [Na+]i dynamics affect neuronal activity via three main processes: reduction of EPSP amplitude in repeatedly active synapses due to reduction of the Na+ Nernst potential; activity-dependent hyperpolarization due to increased activity of the Na+-K+ pump; specific tagging of active synapses by extended Ca2+ elevation, intensified by concurrent back-propagating action potentials or complex spikes. Thus, we conclude that [Na+]i dynamics should be considered whenever synaptic plasticity, extensive synaptic input, or bursting activity are examined.

The example protocol simulates the modified pyramidal cell with a train of synaptic inputs in the dendritic hot zone, concurent with evoked calcium spikes (see article figure 5E).

Example use:

Extract the archive, run nrnivmodl in the channels directory
(linux/unix) or mknrndll (mswin or mac os x) (see for more
help) to compile the channels, and run the file After a
while, it will plot the membrane potential (top), the dendritic sodium concentration (middle) and the dendritic calcium concentration (bottom).

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