Using NEURON for reaction-diffusion modeling of extracellular dynamics (Newton et al 2018)

Development of credible clinically-relevant brain simulations has been slowed due to a focus on electrophysiology in computational neuroscience, neglecting the multiscale whole-tissue modeling approach used for simulation in most other organ systems. We have now begun to extend the NEURON simulation platform in this direction by adding extracellular modeling. NEURON's extracellular reaction-diffusion is supported by an intuitive Python-based where/who/what command sequence, derived from that used for intracellular reaction diffusion, to support coarse-grained macroscopic extracellular models. This simulation specification separates the expression of the conceptual model and parameters from the underlying numerical methods. In the volume-averaging approach used, the macroscopic model of tissue is characterized by free volume fraction—the proportion of space in which species are able to diffuse, and tortuosity—the average increase in path length due to obstacles. These tissue characteristics can be defined within particular spatial regions, enabling the modeler to account for regional differences, due either to intrinsic organization, particularly gray vs. white matter, or to pathology such as edema. We illustrate simulation development using spreading depression, a pathological phenomenon thought to play roles in migraine, epilepsy and stroke.

Model Type: Extracellular

Cell Type(s): Hodgkin-Huxley neuron

Transmitters: Ions

Model Concept(s): Reaction-diffusion

Simulation Environment: NEURON

Implementer(s): Newton, Adam J H [adam.newton at]; McDougal, Robert [robert.mcdougal at]


Newton AJH, McDougal RA, Hines ML, Lytton WW. (2018). Using NEURON for Reaction-Diffusion Modeling of Extracellular Dynamics. Frontiers in neuroinformatics. 12 [PubMed]

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