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; Garcia Dopico, Antonio; Peña Sanchez, Jose Maria; Rucabado, Gabriel y 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.

Descripción

Título: Neurite, a finite difference large scale parallel program for the simulation of the electrical signal propagation in neurites under mechanical loading
Autor/es:
  • Garcia Grajales, Julian Andres
  • Garcia Dopico, Antonio
  • Peña Sanchez, Jose Maria
  • Rucabado, Gabriel
  • Jérusalem, Antoine
Tipo de Documento: Artículo
Título de Revista/Publicación: Neuroinformatics
Fecha: 2014
Materias:
Escuela: Centro de Supercomputación y Visualización de Madrid (CeSViMa) (UPM)
Departamento: Otro
Licencias Creative Commons: Reconocimiento - Sin obra derivada - No comercial

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Resumen

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.

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ID de Registro: 35445
Identificador DC: http://oa.upm.es/35445/
Identificador OAI: oai:oa.upm.es:35445
Depositado por: Memoria Investigacion
Depositado el: 27 Abr 2016 07:24
Ultima Modificación: 27 Abr 2016 07:24
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