Neuroinformatics

, Volume 3, Issue 1, pp 49–63 | Cite as

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

Original Article

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.

Index Entries

Modeling simulation morphology reaction diffusion Hodgkin-Huxley equation neuron Ca2+ dynamics spine 

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Copyright information

© The Humana Press Inc 2005

Authors and Affiliations

  1. 1.Human Information Systems Laboratories, Kanazawa Institute of Technology, Advanced Research Institute for Science and EngineeringWaseda UniversityKanazawaJapan

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