title: A modeling environment with three-dimensional morphology, A-Cell-3D, and Ca2+ dynamics in a spine.
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.
authors.affiliation: Human Information Systems Laboratories, Kanazawa Institute of Technology, Advanced Research Institute for Science and Engineering, Waseda University, 3-1 Yatsukaho Hakusan Kanazawa, 924-0838 Japan. ichikawa@his.kanazawa-it.ac.jp
authors.forename: Kazuhisa
authors.initials: K
authors.lastname: Ichikawa
mesh_terms: D002118:Calcium / Q000378:metabolism; D003198:Computer Simulation; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008959:Models, Neurological; D009474:Neurons / Q000166:cytology* / Q000378:metabolism; D012984:Software; D014584:User-Computer Interface
chemical_list: D002118:Calcium