# Biological Basis of the Code The provided code models a pulse synapse, referred to as `PulseSyn`, which is part of a computational neuroscience simulation. The primary focus of this model is to simulate ectopic current injection into the axons of neural cells. Ectopic current injection involves directly injecting an electrical current into a neuron at a location that is not a synaptic site. This can be used to artificially simulate synaptic-like inputs or perturbations in neural activity. ## Key Biological Aspects ### Ectopic Current Injection - **Purpose**: This model is used to introduce an "infrequent background stimulus" to a neuron. It simulates the direction and effect of current that does not necessarily occur at the synaptic terminals and often reflects artificial stimulation conditions used in experimental neuroscience. - **Biological analogous**: It mimics scenarios where neurons might receive unexpected depolarizations due to external factors, which can shape neuronal behavior. Experimentally, such injections can help in understanding neuron excitability, synaptic integration, and network dynamics. ### Current Amplitude - **Amplitude (amp)**: The parameter `amp` represents the current amplitude in nanoamperes. Positive values have a depolarizing effect, which means they can make the neuron more likely to fire an action potential. - **Instantaneous Amplitude**: The variable `instantaneous_amp` reflects the current's instantaneous effect on the membrane potential during simulation. This depolarizes the axon to simulate the impact of current injection, effectively mimicking excitatory input. ### Pulse Duration - **Time Interval (time_interval)**: This parameter determines the duration (in milliseconds) that the injected current remains active. This mimics the biological scenario where electrical signals can impact cells for a specific duration, akin to burst firing or prolonged synaptic input. ### On/Off State - **Pulse "On" Mechanism**: The boolean state ‘on’ indicates whether the current pulse is actively stimulating the neuron. This mirrors biological conditions where certain synaptic currents can be transient, dictated by the stochastic properties of neurotransmitter release or modulated signal input. ### Non-specific Current - **NONSPECIFIC_CURRENT i**: This denotes that the current is not specific to any ion channel. Unlike typical synaptic currents that result from specific ion channels (e.g., sodium or potassium currents through voltage-gated or ligand-gated channels), this pulse synapse represents a generalized perturbation of the membrane potential. ### Modelling Framework - **Point Process**: The code uses a point process to handle the timing and magnitude of the current injections, analogous to mimicking discrete events such as synaptic input triggered by neurotransmitter release at synapses. ## Conclusion The code models a simplified neurotransmitter-like effect in axonal compartments by simulating the application of an external current. This is a useful approach in computational studies of neuronal dynamics where one seeks to probe the influence of depolarizing currents on neurons within complex networks, such as those featured in the Traub et al. (2005) model.