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1D-3D Hybrid Modelling: From Multi-Compartment Models to Full Resolution Models in Space and Time

Stephan Grein1, Martin Stepniewski1, Sebastian Reiter1, Markus M Knodel1 and Gillian Queisser1*
  • 1 Goethe Center for Scientific Computing, Germany

The sub-cellular architecture of neurons is composed of numerous organelles that fill the intracellular space and play an active role in signal translation and signal transfer in neurons, from the electrical to the biochemical scale. Organelles like mitochondria and the endoplasmic reticulum form a complex and filigreed three-dimensional neuronal subarchitecture, that strongly influences how signals in the cell are encoded and transported long distances through the neuron. The inhomogeneous occupation of cytosolic space also affects how fast ions can travel through the cytosol. In order to make use of established 1D simulation methods for electrical signaling in neurons [1], [2], [3] such as multi-compartment modeling with NEURON [4] or GENESIS [5], and to integrate the three-dimensional neuronal sub-architecture, that needs to be included in a model to fully understand the detailed dynamics of important signaling events, we developed a 1D-3D hybrid modeling framework, that allows us to couple established multi-compartment models, e.g. [6], and full three-dimensional models for subcellular signaling. These can include the detailed morphology of the cell and its organelles. By reconstructing the three-dimensional morphology from, e.g. .hoc geometry files and a mapping algorithm to map the membrane potential data from a multi-compartment model simulation onto the detailed three-dimensional cell, we are able to use established and published models within this novel framework [7], [8], [9]. We demonstrate how this framework can be used and how the neuronal sub-architecture strongly influences sub-cellular signaling events. In particular we show a proof-of-concept which highlights the benefits of our approach, i. e. we shed light on the effect of differently sized intracellular obstacles, voltage gated calcium channel densities (Borg-Graham [10]) as well as a variable diffusion tensor on the intracellular calcium dynamics [9].

References

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9. Grein S, Stepniewski M, Reiter S, Knodel M, Queisser G:1D-3D Hybrid Modelling: From Multi-Compartment Models to Full Resolution Models in Space and Time 2013 (in preparation).
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Keywords: detailed modeling, 3D models, compartmental models, hybrid modeling, network simulation, biophysical model

Conference: Neuroinformatics 2013, Stockholm, Sweden, 27 Aug - 29 Aug, 2013.

Presentation Type: Poster

Topic: Computational neuroscience

Citation: Grein S, Stepniewski M, Reiter S, Knodel M and Queisser G (2013). 1D-3D Hybrid Modelling: From Multi-Compartment Models to Full Resolution Models in Space and Time. Front. Neuroinform. Conference Abstract: Neuroinformatics 2013. doi: 10.3389/conf.fninf.2013.09.00038

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Received: 29 Apr 2013; Published Online: 11 Jul 2013.

* Correspondence: Prof. Gillian Queisser, Goethe Center for Scientific Computing, Frankfurt am Main, 60325, Germany, gillian.queisser@gcsc.uni-frankfurt.de