Including gap junctions into distributed neuronal network simulations

Abstract

Contemporary simulation technology for neuronal networks enables the simulation of brain-scale networks using neuron models with a single or a few compartments. However, distributed simulations at full cell density are still lacking the electrical coupling between cells via so called gap junctions. This is due to the absence of efficient algorithms to simulate gap junctions on large parallel computers. The difficulty is that gap junctions require an instantaneous interaction between the coupled neurons, whereas the efficiency of simulation codes for spiking neurons relies on delayed communication. In a recent paper [15] we describe a technology to overcome this obstacle. Here, we give an overview of the challenges to include gap junctions into a distributed simulation scheme for neuronal networks and present an implementation of the new technology available in the NEural Simulation Tool (NEST 2.10.0). Subsequently we introduce the usage of gap junctions in model scripts as well as benchmarks assessing the performance and overhead of the technology on the supercomputers JUQUEEN and K computer.