Neuron Time Warp

Detailed simulation of chemical reactions and the diffusion of ions through a neuronal membrane presents challenges due to the multiple scales at which this occurs, scales that require development and consolidation of a number of different simulation methodologies. In this paper, we describe Neuron Time Warp (NTW), a part of the NEURON project for development of multi-scale tools for simulations of brain parts and brains. NTW relies upon the Next Subvolume Method, a stochastic Monte Carlo algorithm used to simulate chemical reactions within the membrane of a neuron. We make use of a model of a dendrite branch on which to evaluate NTW's performance using MPI and shared memory on a multi-core machine. This work is a first step towards the development of multi-scale simulation models which are capable of portraying the behavior of a neuron with greater fidelity then is possible with differential equation based models alone.