From f88c08636e767674d38b35489d6f179f2b73c6c2 Mon Sep 17 00:00:00 2001 From: ocrampal Date: Mon, 1 Jun 2026 16:13:48 +0200 Subject: [PATCH] varie --- elements/astrocyte/README.md | 8 ++++++-- elements/neuron/README.md | 25 +++++++++++-------------- 2 files changed, 17 insertions(+), 16 deletions(-) diff --git a/elements/astrocyte/README.md b/elements/astrocyte/README.md index fdae898..e2a87da 100644 --- a/elements/astrocyte/README.md +++ b/elements/astrocyte/README.md @@ -1,6 +1,10 @@ +--- +include_toc: true +--- + # README.md -**The astrocyte is not globally uniform — it is locally selective**: +## Calcium wave The calcium wave does not behave like a uniform broadcast. It has two distinct modes: @@ -8,7 +12,7 @@ The first is a **local microdomain response**. When a single synapse fires heavi The second is a **propagating wave**. When activity is sustained and intense enough, the calcium signal spreads from process to process across the astrocyte body and even into neighbouring astrocytes via gap junctions. This is the threshold event that IP3 models. Once the wave propagates, the response is no longer selective — it affects multiple synapses under that astrocyte's territory. -**What this means for your model**: +### Implication for the model Your current model simulates a single tripartite synapse — one presynapse, one postsynapse, one astrocyte process. In that context the selectivity question does not arise because there is only one synapse to serve. diff --git a/elements/neuron/README.md b/elements/neuron/README.md index c62f8f4..74c78ff 100644 --- a/elements/neuron/README.md +++ b/elements/neuron/README.md @@ -329,7 +329,7 @@ In this model we decide to simplify: - We do not model subthreshold oscillations — VSOMA is a simple leaky integrator - We do not model somatic ATP -**Simplified verifiable behaviors**: +#### Simplified verifiable behaviors — ms: @@ -350,9 +350,17 @@ In this model we decide to simplify: - VGSC modulation ---- +The simplifications imply that: -**G expression**: +Removing the axon hillock as a separate compartment means the threshold comparison is applied directly to VSOMA rather than to a spatially distinct zone with its own channel density. In biology the hillock has a lower threshold than the soma body because of its higher Na⁺ channel density — this gradient is absent here. A single fixed threshold applied to VSOMA is a reasonable approximation for a single-compartment model, but it means the model cannot capture phenomena that depend on the hillock's spatial separation from the dendritic integration zone, such as the ability of strong distal dendritic inputs to bypass somatic inhibition. + +Removing neuromodulatory inputs means the threshold and gain of the soma are fixed across the entire simulation. In biology dopamine, serotonin, and acetylcholine continuously adjust VSOMA_threshold and the shape of the f-I curve in response to behavioural state. A neuron in an attentive animal fires more readily to the same input than the same neuron in a drowsy animal. This state-dependence is entirely absent — the soma responds identically to a given VDB at all times. + +Removing subthreshold oscillations means VSOMA behaves as a simple leaky integrator between APs. In some neuron types, voltage-gated channels produce rhythmic subthreshold fluctuations that bias the timing of AP generation toward specific phases of network oscillations. These are not modelled — VSOMA decays smoothly toward rest between threshold crossings. + +ATP is a simplification of convenience — at this stage we do not comprehend the total metabolic load. + +#### G expression — ms: @@ -377,17 +385,6 @@ In this model we decide to simplify: - Tune: -- refractory lenght - -The simplifications imply that: - -Removing the axon hillock as a separate compartment means the threshold comparison is applied directly to VSOMA rather than to a spatially distinct zone with its own channel density. In biology the hillock has a lower threshold than the soma body because of its higher Na⁺ channel density — this gradient is absent here. A single fixed threshold applied to VSOMA is a reasonable approximation for a single-compartment model, but it means the model cannot capture phenomena that depend on the hillock's spatial separation from the dendritic integration zone, such as the ability of strong distal dendritic inputs to bypass somatic inhibition. - -Removing neuromodulatory inputs means the threshold and gain of the soma are fixed across the entire simulation. In biology dopamine, serotonin, and acetylcholine continuously adjust VSOMA_threshold and the shape of the f-I curve in response to behavioural state. A neuron in an attentive animal fires more readily to the same input than the same neuron in a drowsy animal. This state-dependence is entirely absent — the soma responds identically to a given VDB at all times. - -Removing subthreshold oscillations means VSOMA behaves as a simple leaky integrator between APs. In some neuron types, voltage-gated channels produce rhythmic subthreshold fluctuations that bias the timing of AP generation toward specific phases of network oscillations. These are not modelled — VSOMA decays smoothly toward rest between threshold crossings. - -ATP is a simplification of convenience — at this stage we do not comprehend the total metabolic load. - ### Dendritic-branch #### Discursive description