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A modeling environment with three-dimensional morphology, A-Cell-3D, and Ca2+ dynamics in a spine

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Abstract

A-Cell-3D was developed to model and simulate a neuron with three-dimensional (3D) morphology utilizing graphic user interface (GUI)-based operations. A-Cell-3D generates and compartmentalizes 3D morphologies of a whole cell or a part of a cell based on a small number of parameters. A-Cell-3D has functions for embedding biochemical reactions and electrical equivalent circuits in the generated 3D morphology, automatically generating a simulation program for spatiotemporal numerical integration, and for visualizing the simulation results. A-Cell-3D is a free software and will be a powerful tool for both experimental and theoretical researchers in modeling and simulating neurons.

The Ca2+ dynamics in a dendritic spine and its parent dendrite were modeled and simulated to demonstrate the capabilities of A-Cell-3D. The constructed reaction-diffusion model comprised Ca2+ entry at the spine head, Ca2+ buffering by endogenous buffers, Ca2+ extrusion, and Ca2+ diffusion with or without exogenous Ca2+ indicator dyes. A simulation program was generated by A-Cell-3D, and differential equations were numerically integrated by the fourth-order Runge-Kutta method.

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Authors and Affiliations

  1. Human Information Systems Laboratories, Kanazawa Institute of Technology, Advanced Research Institute for Science and Engineering, Waseda University, 3-I Yatsukaho Hakusan, 924-0838, Kanazawa, Japan

    Kazuhisa Ichikawa

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  1. Kazuhisa Ichikawa
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Correspondence to Kazuhisa Ichikawa.

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Ichikawa, K. A modeling environment with three-dimensional morphology, A-Cell-3D, and Ca2+ dynamics in a spine. Neuroinform 3, 49–63 (2005). https://doi.org/10.1385/NI:3:1:049

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