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

In: High Performance Computing in Science and Engineering '19

Author

Listed:
  • 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)

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.

Suggested Citation

  • Myra Huymayer & Michael Lampe & Arne Nägel & Gabriel Wittum, 2021. "First Steps Towards a Scaling Analysis of a Fully Resolved Electrical Neuron Model," Springer Books, in: Wolfgang E. Nagel & Dietmar H. Kröner & Michael M. Resch (ed.), High Performance Computing in Science and Engineering '19, pages 583-588, Springer.
    • Handle: RePEc:spr:sprchp:978-3-030-66792-4_39
    DOI: 10.1007/978-3-030-66792-4_39
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