Neurite, a finite difference large scale parallel program for the simulation of the electrical signal propagation in neurites under mechanical loading

Garcia Grajales, Julian Andres and Garcia Dopico, Antonio and Peña Sanchez, Jose Maria and Rucabado, Gabriel and Jérusalem, Antoine (2014). Neurite, a finite difference large scale parallel program for the simulation of the electrical signal propagation in neurites under mechanical loading. "Neuroinformatics" ; pp.. ISSN 1539-2791.

Description

Title: Neurite, a finite difference large scale parallel program for the simulation of the electrical signal propagation in neurites under mechanical loading
Author/s:
  • Garcia Grajales, Julian Andres
  • Garcia Dopico, Antonio
  • Peña Sanchez, Jose Maria
  • Rucabado, Gabriel
  • Jérusalem, Antoine
Item Type: Article
Título de Revista/Publicación: Neuroinformatics
Date: 2014
ISSN: 1539-2791
Subjects:
Faculty: Centro de Supercomputación y Visualización de Madrid (CeSViMa) (UPM)
Department: Otro
Creative Commons Licenses: Recognition - No derivative works - Non commercial

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Abstract

With the growing body of research on traumatic brain injury and spinal cord injury, computational neuroscience has recently focused its modeling efforts on neuronal functional deficits following mechanical loading. However, in most of these efforts, cell damage is generally only characterized by purely mechanistic criteria, function of quantities such as stress, strain or their corresponding rates. The modeling of functional deficits in neurites as a consequence of macroscopic mechanical insults has been rarely explored. In particular, a quantitative mechanically based model of electrophysiological impairment in neuronal cells has only very recently been proposed (Jerusalem et al., 2013). In this paper, we present the implementation details of Neurite: the finite difference parallel program used in this reference. Following the application of a macroscopic strain at a given strain rate produced by a mechanical insult, Neurite is able to simulate the resulting neuronal electrical signal propagation, and thus the corresponding functional deficits. The simulation of the coupled mechanical and electrophysiological behaviors requires computational expensive calculations that increase in complexity as the network of the simulated cells grows. The solvers implemented in Neurite-explicit and implicit-were therefore parallelized using graphics processing units in order to reduce the burden of the simulation costs of large scale scenarios. Cable Theory and Hodgkin-Huxley models were implemented to account for the electrophysiological passive and active regions of a neurite, respectively, whereas a coupled mechanical model accounting for the neurite mechanical behavior within its surrounding medium was adopted as a link between lectrophysiology and mechanics (Jerusalem et al., 2013). This paper provides the details of the parallel implementation of Neurite, along with three different application examples: a long myelinated axon, a segmented dendritic tree, and a damaged axon. The capabilities of the program to deal with large scale scenarios, segmented neuronal structures, and functional deficits under mechanical loading are specifically highlighted.

Funding Projects

TypeCodeAcronymLeaderTitle
Government of SpainTEC2012-38453-C04-02UnspecifiedUnspecifiedUnspecified
FP7604102HBPEcole Polytechnique Federale de LausanneThe Human Brain Project
FP7306587COMUNEMThe Chancellor, Masters and Scholars of the University of OxfordComputational Multiscale Neuron Mechanics

More information

Item ID: 35445
DC Identifier: http://oa.upm.es/35445/
OAI Identifier: oai:oa.upm.es:35445
Deposited by: Memoria Investigacion
Deposited on: 27 Apr 2016 07:24
Last Modified: 14 May 2019 11:12
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