title: Neurite, a finite difference large scale parallel program for the simulation of electrical signal propagation in neurites under mechanical loading.
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, functions 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, Neurite, has only very recently been proposed. In this paper, we present the implementation details of this model: a finite difference parallel program for simulating electrical signal propagation along neurites under mechanical loading. 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 electrophysiology and mechanics. 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.
authors: IMDEA Materials Institute, Getafe, Madrid, Spain; DATSI Computer Science, Universidad Politécnica de Madrid, Madrid, Spain; Mathematical Institute, University of Oxford, Oxford, UK.
authors: Julián A
authors: JA
authors: García-Grajales
authors: Madrid Supercomputing and Visualization Center.
authors: Gabriel
authors: G
authors: Rucabado
authors: DATSI Computer Science, Universidad Politécnica de Madrid, Madrid, Spain.
authors: Antonio
authors: A
authors: García-Dopico
authors: DATSI Computer Science, Universidad Politécnica de Madrid, Madrid, Spain.
authors: José-María
authors: JM
authors: Peña
authors: Department of Engineering Science, University of Oxford, Oxford, UK; Mathematical Institute, University of Oxford, Oxford, UK.
authors: Antoine
authors: A
authors: Jérusalem
mesh_terms: D001369:Axons / Q000502:physiology; D001696:Biomechanical Phenomena; D003196:Computer Graphics; D055724:Electrophysiological Phenomena; D008959:Models, Neurological; D009186:Myelin Sheath / Q000502:physiology; D016501:Neurites / Q000502:physiology*; D013997:Time Factors; D016474:Weight-Bearing