First Steps Towards a Scaling Analysis of a Fully Resolved Electrical Neuron Model

Myra Huymayer (), Michael Lampe (), Arne Nägel () and Gabriel Wittum ()
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Myra Huymayer: G-CSC, Goethe-Universität Frankfurt
Michael Lampe: G-CSC, Goethe-Universität Frankfurt
Arne Nägel: G-CSC, Goethe-Universität Frankfurt
Gabriel Wittum: G-CSC, Goethe-Universität Frankfurt

A chapter in High Performance Computing in Science and Engineering '19, 2021, pp 583-588 from Springer

Abstract: Abstract In computational neuroscience the transmission of electrical signals of neurons is normally simulated by means of point process neurons, which mainly reflect the scale in time, or the classical cable equation which additionally introduces one space dimension. Here we present a fully resolved electrical model based on Gauss’ law and the conservation of charges which considers all space dimensions and is capable to simulate the extracellular and intracellular potential. For these simulations three dimensional volume meshes are required and due to the inherent complexity of the neuronal structure, these 3D-reconstructions yield large data-sets and need efficient solving strategies. The UG4-simulation framework is a powerful software for the solution of partial differential equations on unstructured grids in one, two and three space dimensions and with its efficient, parallel solvers is well suited for this task. Computations of the 3D-cable equation on a simple geometry and on a three-dimensionally reconstructed neuron were performed on the Hazel Hen supercomputer, testing for weak scalability.

Keywords: Multigrid; Parallelization; Three dimensional cable equation; Meshing; Unstructured grids (search for similar items in EconPapers)
Date: 2021
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Persistent link: https://EconPapers.repec.org/RePEc:spr:sprchp:978-3-030-66792-4_39

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DOI: 10.1007/978-3-030-66792-4_39

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