PyPNS: multiscale simulation of a peripheral nerve in Python
File(s)Lubba2018_Article_PyPNSMultiscaleSimulationOfAPe.pdf (1.97 MB)
Published version
Author(s)
Type
Journal Article
Abstract
Bioelectronic Medicines that modulate the activity patterns on peripheral nerves have promise as a new way of treating diverse medical conditions from epilepsy to rheumatism. Progress in the field builds upon time consuming and expensive experiments in living organisms. To reduce experimentation load and allow for a faster, more detailed analysis of peripheral nerve stimulation and recording, computational models incorporating experimental insights will be of great help.We present a peripheral nerve simulator that combines biophysical axon models and numerically solved and idealised extracellular space models in one environment. We modeled the extracellular space as a three-dimensional resistive continuum governed by the electro-quasistatic approximation of the Maxwell equations. Potential distributions were precomputed in finite element models for different media (homogeneous, nerve in saline, nerve in cuff) and imported into our simulator. Axons, on the other hand, were modeled more abstractly as one-dimensional chains of compartments. Unmyelinated fibres were based on the Hodgkin- Huxley model; for myelinated fibres, we adapted the model proposed by McIntyre et al. in 2002 to smaller diameters. To obtain realistic axon shapes, an iterative algorithm positioned fibres along the nerve with a variable tortuosity fit to imaged trajectories. We validated our model with data from the stimulated rat vagus nerve. Simulation results predicted that tortuosity alters recorded signal shapes and increases stimulation thresholds. The model we developed can easily be adapted to different nerves, and may be of use for Bioelectronic Medicine research in the future.
Date Issued
2019-01-01
Date Acceptance
2018-05-21
Citation
Neuroinformatics, 2019, 17 (1), pp.63-81
ISSN
1539-2791
Publisher
Springer
Start Page
63
End Page
81
Journal / Book Title
Neuroinformatics
Volume
17
Issue
1
Copyright Statement
© The Author(s) 2018.
This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
Sponsor
GlaxoSmithKline Services Unlimited
Engineering & Physical Science Research Council (EPSRC)
GlaxoSmithKline Services Unlimited
Engineering & Physical Science Research Council (EPSRC)
Grant Number
3000551036
EP/N014529/1
4124843
EP/J021199/1
Subjects
imulation
peripheral nerve
finite element model
biophysics
Bioelectronic Medicines
Publication Status
Published
Date Publish Online
2018-06-15