Biological Basis of the AlphaSynapse Model

The AlphaSynapse class in the provided code models a synaptic connection characterized primarily by its alpha-function conductance profile, a common way to represent synaptic transmission in computational neuroscience. This model is focused on the dynamics of synaptic conductance as mediated by neurotransmitter receptors, specifically those related to excitatory synaptic inputs.

Key Biological Concepts

1. Synaptic Transmission: Synapses are the junctions where neurons communicate via neurotransmitters. The AlphaSynapse focuses on excitatory synaptic transmission mediated by AMPA receptors.

2. AMPAR-Mediated Synapse: AMPAR (AMPA receptor) is a subtype of glutamate receptor that mediates fast excitatory synaptic transmission in the central nervous system. The code specifies properties such as g_syn_m, the maximal AMPAR conductance, indicative of the peak conductance achievable when the receptors are fully activated.

3. Synaptic Conductance: Conductance changes in response to neurotransmitter release are modeled using an alpha-function, originally described by Rall (1967). The alpha-function is a mathematical representation of the transient conductance increase following synaptic activation, characterized by a rapid rise and a slower exponential decay. This is captured in the code using a time constant tau_syn.

4. Reversal Potential (E_syn): The reversal potential is the membrane potential at which the net flow of ions through the AMPAR is zero. For excitatory synapses, this value (E_syn = 0 mV) typically lies between the neural resting and threshold potentials.

5. Conduction Scaling: The conductanceScalingFactor likely serves to normalize or scale the theoretical conductance to a biologically relevant range, matching empirical observations or other model components.

6. Cumulative Synaptic Effects: The convolution operation in produceConductanceByConvolution() models how postsynaptic conductance accumulates over time as action potentials arrive at the synapse, mirroring biological processes where multiple neurotransmitter releases affect ion channel activity continuously over time.

7. Preset Synaptic Input (PSTH): Peristimulus Time Histogram (psth) is used to quantify synaptic input. The model treats presynaptic spike trains traditionally recorded as PSTH, using them as input to simulate synaptic conductance changes.

Overall Model Goal

This AlphaSynapse model is meant to encapsulate the dynamics of excitatory synaptic transmission through AMPARs, simulating how synaptic conductance affects postsynaptic potentials. By doing so, it correlates synaptic inputs with neuronal outputs via conductance changes modeled accurately to biological phenomena observed in neural tissues. This forms a part of larger neural circuit models aimed at understanding complex neural computations underpinning behavior or pathologies.