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.

Electromechanical coupling of waves in nerve fibres

“…This model provides a framework for damage mechanisms in neurons. For this purpose a special simulation package Neurite has been developed (García-Grajales et al, 2015).…”

Tuning the Cell and Biological Tissue Environment through Magneto-Active Materials

“…Other pioneering work is due to Babbs and Shi [59] and focused on mild retraction of myelin due to stretch and crush injuries. These ideas were then taken by Jerusalem and co-authors and incorporated into 1D [60,61] and 3D [62] finite element frameworks to explore the effects of mechanical deformation and strain rate on axonal electrophysiology. In addition, alternative 3D non-axisymmetric mechano-electrophysiological models have been proposed [63][64][65].…”

The Primary Role of the Electric Near-Field in Brain Function

“…(2) the coupling model reflects the disease model into the nerve fiber model as a set of altered parameters. (3) the nerve fiber model for both the Internodal regions (IR) and the nodes of Ranvier (NR) [38].…”