CalciumSim: Simulator for calcium dynamics on neuron graphs using dimensionally reduced model

Abstract

Calcium signaling has been identified with triggering of gene transcriptions associated with learning and neuroprotection in neurons. Studies indicate that dysregulation of calcium signaling is correlated with severe Alzheimer Disease pathologies. A stable calcium wave or signal arising from triggers in dendritic synapses needs to reach soma with constant amplitude for proper functioning of neurons. In this study, we introduce "CalciumSim", a calcium dynamics simulator which works on dimensionally reduced model. Numerical analysis is conducted to obtain the best configuration of neuron geometry to make the code efficient and fast. Alongside, biologically important insights are derived by modulating and changing parameters of the simulation. The ability of "CalciumSim" to work with real neuron geometries allows user to study calcium signalling in a realistic model.