diff --git a/elements/neuron/README.md b/elements/neuron/README.md index 2187d84..c62f8f4 100644 --- a/elements/neuron/README.md +++ b/elements/neuron/README.md @@ -329,6 +329,55 @@ 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**: + +— ms: + +- Resting at -70 mV: Leak channels + pumps (keep at resting) +- VDB Depolarization : ~1-2 ms: Na⁺ enters (some VGSCs open) +- Opened VGSC and then remain closed for a refractory period +- Spike if depolarized above threshold: to -50 mV +- Ca2+ enter +- Repolarization to -70 mV: ~1-2 ms: K⁺ exits (VG K⁺ channels open) ← NOT pumps! +- After-hyperpolarization: ~5-20 ms: K⁺ channels still open + +— secs: + +- Return to exact -70 mV: ~100-1000 ms: Na⁺/K⁺ pumps restore gradients +- Ca2+ accumulation + +— mins: + +- VGSC modulation + +--- + +**G expression**: + +— ms: + +- based on VDB, VGSC open and let Na+ in. VGSG then go into refractory +- if Na fullness then ApCtx. Here the threshold is based only on the integration of Na+ +- increase SpikeTrainTraces (fast at spike) +- increase Ca2+ traces +- decrease Na: fast pump which decreases Na+, we do not model K+ +-- there is a tug of war between Na entering and exiting. Na can reach fullness only if VDB increases fast (derivative) +- there are 2 context: ApCtx and SomaRefractory imlemented with timers and tunable +- decrease SpikeTraintraces slow, only if away from spiketrain this is empty + +- Tune: +-- The threshold is tuned during the spiketrain. Low threshold at rest, to increase sensitivity, threshold increase during spike to increase discrimination + +— secs: + +- SpikeTrainTraces + +— mins: + +- 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. @@ -371,6 +420,20 @@ In this model we decide to simplify: - We do not model bAP distance attenuation — all spines receive the bAP at full amplitude regardless of their position - We do not model structural plasticity — spine neck widening and retraction are not implemented +— ms: + +- Each active spine contributes VPost (EPSP) to VDB +- VDB decays passively each ms + +— secs: + +- nothing in the simplified model + +— mins: + +- nothing in the simplified model + (structural remodelling of spine neck geometry under LTP/LTD would live here if added later) + The simplifications imply that: - Removing spine neck resistance means all spines contribute equally to V_dend regardless of their geometry or location. The physical basis of synaptic weighting by dendritic position is lost. All EPSPs are treated as equivalent inputs to the shared pool. diff --git a/elements/neuron/axon.md b/elements/neuron/axon.md index 0f9d597..d252f82 100644 --- a/elements/neuron/axon.md +++ b/elements/neuron/axon.md @@ -6,15 +6,15 @@ include_toc: true ## AXON: Container +Expansions and modulations: +- is expanded by: [NEURON](neuron.md) +- expands: [PRESYNAPSE](presynapse.md) + The axon does not contain specific behavior. - We might add balancing of ATP within PRE later. Here we comprehend it as a “cable” transporting the AP from SOMA to Presynapse. It expands PRESYNAPSE which: - l'equivalente del tuning della PRESYNAPSE, come espansione dell'AXON, e' fatta da excitation/inhibition in winnertakeall. Per equivalente si intende che e' uno spostare PRESYNAPSE da actual, come se fosse un tuning. - the associations between PRESYNAPSE, POSTSYNAPSE e SYNAPSE is performed by the "bind" in excitation/inhibition in winnertakeall. Because we have to make sure that the correct binding is performed when intricating actuals. -Expansions and modulations: -- is expanded by: [NEURON](neuron.md) -- expands: [PRESYNAPSE](presynapse.md) - ```Gen AXON diff --git a/elements/neuron/d-branch.md b/elements/neuron/d-branch.md index 08c11d9..07fe9a2 100644 --- a/elements/neuron/d-branch.md +++ b/elements/neuron/d-branch.md @@ -4,30 +4,9 @@ include_toc: true # d-branch.md -Qui comprendiamo: - -- D-BRANCH: Dendritic Branch - ## D-BRANCH -**Simplified behaviors**: - -— ms: - -- Each active spine contributes VPost (EPSP) to VDB -- VDB decays passively each ms - -— secs: - -- nothing in the simplified model - -— mins: - -- nothing in the simplified model - (structural remodelling of spine neck geometry under LTP/LTD would live here if added later) - ---- -Intro: +Expansions and modulations: - is expanded by: [NEURON](neuron.md) - expands: [POSTSYNAPSE](posynapse.md) diff --git a/elements/neuron/neuron.md b/elements/neuron/neuron.md index 308b9ad..f32bf3f 100644 --- a/elements/neuron/neuron.md +++ b/elements/neuron/neuron.md @@ -6,12 +6,12 @@ include_toc: true ## NEURON -Nel folder Appunti ci sono i comportamenti osservabili, dai quali siamo partiti, riducendone il numero per semplificare in questa prima fase. La forza della comprensione G. e' che possiamo aggiungere man mano nuovi comportamenti, senza gettare via nulla per ripartire da zero, come saremmo costretti a fare in una comprensione tradizionale.In questa prima comprensione, cerchiamo di fare un'espressione la piu' semplice possibile per valutare la sintassi e la grammatica e l'enliving dell'espressione. - Expansions and modulations: - is expanded by: modules - expands: [AXON](axon.md), [SOMA](soma.md), [D_BRANCH](d-branch.md) +Nel folder Appunti ci sono i comportamenti osservabili, dai quali siamo partiti, riducendone il numero per semplificare in questa prima fase. La forza della comprensione G. e' che possiamo aggiungere man mano nuovi comportamenti, senza gettare via nulla per ripartire da zero, come saremmo costretti a fare in una comprensione tradizionale.In questa prima comprensione, cerchiamo di fare un'espressione la piu' semplice possibile per valutare la sintassi e la grammatica e l'enliving dell'espressione. + ```Gen include: diff --git a/elements/neuron/soma.md b/elements/neuron/soma.md index 80c164c..9578ee9 100644 --- a/elements/neuron/soma.md +++ b/elements/neuron/soma.md @@ -4,64 +4,28 @@ include_toc: true # soma.md -Qui comprendiamo: +## SOMA: Comprehension -- SOMA: il soma -- VGSC-SOMA-H: Na ion channels. Open only when VDB high -- VGSC-SOMA-M: Na ion channels. Open only when VDB medium -- VGSC-SOMA-L: Na ion channels. Open only when VDB low +Expansions and modulations: +- is expanded by: [NEURON](neuron.md) +- expands: SOMA_VGSC ---- +```Gen +SOMA + type: comprehension -**Simplified verifiable behaviors**: + expand_comprehension: + &SOMA_VGSC-H: SOMA_VGSC (full: 50x, active: 20x, empty: 10x) + &SOMA_VGSC-M: SOMA_VGSC (full: 50x, active: 20x, empty: 10x) + &SOMA_VGSC_L: SOMA_VGSC (full: 50x, active: 20x, empty: 10x) -— ms: - -- Resting at -70 mV: Leak channels + pumps (keep at resting) -- VDB Depolarization : ~1-2 ms: Na⁺ enters (some VGSCs open) -- Opened VGSC and then remain closed for a refractory period -- Spike if depolarized above threshold: to -50 mV -- Ca2+ enter -- Repolarization to -70 mV: ~1-2 ms: K⁺ exits (VG K⁺ channels open) ← NOT pumps! -- After-hyperpolarization: ~5-20 ms: K⁺ channels still open - -— secs: - -- Return to exact -70 mV: ~100-1000 ms: Na⁺/K⁺ pumps restore gradients -- Ca2+ accumulation - -— mins: - -- VGSC modulation - ---- - -**G expression**: - -— ms: - -- based on VDB, VGSC open and let Na+ in. VGSG then go into refractory -- if Na fullness then ApCtx. Here the threshold is based only on the integration of Na+ -- increase SpikeTrainTraces (fast at spike) -- increase Ca2+ traces -- decrease Na: fast pump which decreases Na+, we do not model K+ --- there is a tug of war between Na entering and exiting. Na can reach fullness only if VDB increases fast (derivative) -- there are 2 context: ApCtx and SomaRefractory imlemented with timers and tunable -- decrease SpikeTraintraces slow, only if away from spiketrain this is empty - -- Tune: --- The threshold is tuned during the spiketrain. Low threshold at rest, to increase sensitivity, threshold increase during spike to increase discrimination - -— secs: - -- SpikeTrainTraces - -— mins: - -- Tune: --- refractory lenght - ---- + instantiate_container: + MAIN-SOMA [] + SOMA_VGSC_H_TUN [pass: &SOMA_VGSC_H] + SOMA_VGSC_M_TUN [pass: &SOMA_VGSC_M] + SOMA_VGSC_L_TUN [pass: &SOMA_VGSC_L] + +``` **Tubs:** @@ -75,31 +39,10 @@ Qui comprendiamo: - **SomaRefractory**: tracce di refractory ---- - -## SOMA: Comprehension +### MAIN-SOMA: Container ```Gen -SOMA - type: comprehension - - expand_comprehension: - &VGSC-SOMA-H: VGSC-SOMA (full: 50x, active: 20x, empty: 10x) - &VGSC-SOMA-M: VGSC-SOMA (full: 50x, active: 20x, empty: 10x) - &VGSC-SOMA-L: VGSC-SOMA (full: 50x, active: 20x, empty: 10x) - - instantiate_container: - SOMA-BEH [] - VGSC-SOMA-H-TUN [pass: &VGSC-SOMA-H] - VGSC-SOMA-M-TUN [pass: &VGSC-SOMA-M] - VGSC-SOMA-L-TUN [pass: &VGSC-SOMA-L] - -``` - -### SOMA-BEH: Container - -```Gen -SOMA-BEH +MAIN-SOMA type: container activity_scope: !DAY @@ -116,14 +59,14 @@ SOMA-BEH ##### SOMA-Status: ( active: 60x ) contextor -As dendrites deliver current (VDB​), the soma acts like a capacitor. It "stores" this charge in the form of membrane potential. This contextualizes VGSC-SOMA to open ion channels that let Na+ ions in. +As dendrites deliver current (VDB​), the soma acts like a capacitor. It "stores" this charge in the form of membrane potential. This contextualizes SOMA_VGSC to open ion channels that let Na+ ions in. This only applies if not ApCtx, or in other words, SOMA is not in refractory period. ```Gen SOMA-Status: ( active: 60x ) type: contextor - contained_by: SOMA-BEH + contained_by: MAIN-SOMA in_context: any condition: ( VDB fullness ) AND NOT AP_ctx @@ -147,7 +90,7 @@ La fullness di Na rappresenta il threshold e puo' essere modificato. La fullness ```Gen SomaSpike: ( active: 30x ) type: contextor - contained_by: SOMA-BEH + contained_by: MAIN-SOMA in_context: any condition: ( Na fullness ) AND ( SomaRefractory emptiness ) @@ -162,7 +105,7 @@ Lo spill deve essere piu' lento dell'increase che avviene in ActiveAP ```Gen SomaRefractorySpill: ( active: 16x ) type: accumulator - contained_by: SOMA-BEH + contained_by: MAIN-SOMA in_context: any hypothesis: NOT ( SomaRefractory empty ) @@ -183,7 +126,7 @@ Durante la fase effettiva di spike: ```Gen ActiveAP: ( active: 8x ) type: accumulator - contained_by: SOMA-BEH + contained_by: MAIN-SOMA in_context: Ap_ctx hypothesis: NOT Na empty @@ -208,7 +151,7 @@ Questo potrebbe non servire se eliminiamo tutti Na durante ActiveAP. ```Gen NaSpill: ( active: 8x ) type: accumulator - contained_by: SOMA-BEH + contained_by: MAIN-SOMA in_context: NaSpill_ctx hypothesis: NOT ( Na emptiness ) @@ -216,12 +159,12 @@ NaSpill: ( active: 8x ) trace: ``` -## VGSC-SOMA: Comprehension +## SOMA_VGSC: Comprehension Voltage Gated Sodium Channel: difficult to open (High) ```Gen -container: VGSC-SOMA-H +container: SOMA_VGSC-H tub_local: VGSCRefractoryH ( full: 60x, active: 30x, empty: 0x ) @@ -233,7 +176,7 @@ container: VGSC-SOMA-H VDBMaxCtx ( contained_by: SOMA ) ``` -### sec: VGSC-SOMA-H +### sec: SOMA_VGSC-H #### VGSC-H_Status: ( active: 60x ) contextor @@ -242,7 +185,7 @@ Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di ```Gen VGSC-H_Status: ( active: 60x ) type: contextor - contained_by: VGSC-SOMA-H + contained_by: SOMA_VGSC-H in_context: any condition: VDBMaxCtx AND ( VGSCRefractoryH emptiness ) @@ -260,7 +203,7 @@ Questo sopra è il commmento della versione precedente, ora la quantità di NA i ```Gen NaEnterH: ( active: 1x ) type: accumulator - contained_by: VGSC-SOMA-H + contained_by: SOMA_VGSC-H in_context: NaEnterH_ctx hypothesis: ( NOT Na full ) @@ -279,7 +222,7 @@ Lo Spill deve avere un rf maggiore dell'interacting che incrementa VGSCRefractor ```Gen VGSCRefractoryHSpill: ( active: 1x ) type: accumulator - contained_by: VGSC-SOMA-H + contained_by: SOMA_VGSC-H in_context: VGSCRefractoryHSpill_ctx hypothesis: NOT ( VGSCRefractoryH empty ) @@ -287,12 +230,12 @@ VGSCRefractoryHSpill: ( active: 1x ) trace: None ``` -## VGSC-SOMA-M: container +## SOMA_VGSC-M: container Voltage Gated Sodium Channel: less difficult to open (Medium) ```Gen -container: VGSC-SOMA-M +container: SOMA_VGSC-M tub_local: VGSCRefractoryM ( full: 60x, active: 30x, empty: 0x ) @@ -304,7 +247,7 @@ container: VGSC-SOMA-M VDBMedCtx ( contained_by: SOMA ) ``` -### sec: VGSC-SOMA-M +### sec: SOMA_VGSC-M #### VGSC-M_TPC: ( active: 60x ) contextor @@ -313,7 +256,7 @@ Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di ```Gen VGSC-M_Status: ( active: 60x ) type: contextor - contained_by: VGSC-SOMA-M + contained_by: SOMA_VGSC-M in_context: VDBMediumCtx OR VDBMaxCtx condition: ( VGSCRefractoryH emptiness ) @@ -328,7 +271,7 @@ Questo sopra è il commmento della versione precedente, ora la quantità di NA i ```Gen NaEnterM: ( active: 1x ) type: accumulator - contained_by: VGSC-SOMA-M + contained_by: SOMA_VGSC-M in_context: NaEnterM_ctx hypothesis: ( NOT Na full ) @@ -347,7 +290,7 @@ Lo Spill deve avere un rf maggiore dell'interacting che incrementa VGSCRefractor ```Gen VGSCRefractoryMSpill: ( active: 1x ) type: accumulator - contained_by: VGSC-SOMA-M + contained_by: SOMA_VGSC-M in_context: any hypothesis: NOT ( VGSCRefractoryM empty ) @@ -355,12 +298,12 @@ VGSCRefractoryMSpill: ( active: 1x ) trace: None ``` -## VGSC-SOMA-L: container +## SOMA_VGSC_L: container Voltage Gated Sodium Channel: easy to open (Low) ```Gen -container: VGSC-SOMA-L +container: SOMA_VGSC_L tub_local: VGSCRefractoryL ( full: 60x, active: 30x, empty: 0x ) @@ -372,7 +315,7 @@ container: VGSC-SOMA-L VDBLowCtx ( contained_by: SOMA ) ``` -### sec: VGSC-SOMA-L +### sec: SOMA_VGSC_L #### VGSC-L_TPC: ( active: 60x ) contextor @@ -381,7 +324,7 @@ Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di ```Gen VGSC-L_Status: ( active: 60x ) type: contextor - contained_by: VGSC-SOMA-L + contained_by: SOMA_VGSC_L in_context: VDBLowCtx OR VDBMediumCtx OR VDBMaxCtx condition: ( VGSCRefractoryH emptiness ) @@ -396,7 +339,7 @@ Questo sopra è il commmento della versione precedente, ora la quantità di NA i ```Gen NaEnterL: ( active: 1x ) type: accumulator - contained_by: VGSC-SOMA-L + contained_by: SOMA_VGSC_L in_context: NaEnterL_ctx hypothesis: ( NOT Na full ) @@ -415,6 +358,7 @@ Lo Spill deve avere un rf maggiore dell'interacting che incrementa VGSCRefractor ```Gen VGSCRefractoryLSpill: ( active: 1x ) type: accumulator + contained_by: VGSC-L-SOMA in_context: any @@ -424,14 +368,14 @@ VGSCRefractoryLSpill: ( active: 1x ) ``` -## VGSC-SOMA-TUN: Tuner +## SOMA_VGSC_TUN: Tuner ```Gen -VGSC-SOMA-TUN +SOMA_VGSC_TUN type: tuner contained_by: SOMA - tunes: SOMA/expansion/VGSC-SOMA + tunes: SOMA/expansion/SOMA_VGSC context_intricated: - TunPossible ( contained_by: DAY-N ) @@ -446,7 +390,7 @@ VGSC-SOMA-TUN ```Gen check_tpc: ( active: 60x ) type: contextor - contained_by: VGSC-SOMA-TUN + contained_by: SOMA_VGSC-TUN in_context: TunPossible condition: ?? diff --git a/organs/tectum/tectum.md b/organs/tectum/tectum.md index 734a93e..59ef808 100644 --- a/organs/tectum/tectum.md +++ b/organs/tectum/tectum.md @@ -6,13 +6,13 @@ include_toc: true ## TECTUM -Qui comprendiamo il collegamento fra moduli tipo winnertakeall che mettono a disposizione delle interfacce che devono essere collegate fra moduli. I neuroni sono gia' dichiarati nei moduli, quello che manca sono gli ASTROCYTE. Consideriamo che gli ASTROCYTE sono interni ad un organo. - Expansions and modulations: - is expanded by: [ORGANISM](../../organism.md) - expands: [WINNERTAKEALL](../../modules/winnertakeall/winnertakeall.md), [ASTROCYTE](../../elements/astrocyte/astrocyte.md) - tunes: [PRESYNAPSE](../../elements/neuron/presynapse.md), [POSTSYNAPSE](../../elements/neuron/postsynapse.md), [ASTROSYNAPSE](../../elements/astrocyte/astrosynapse.md) +Qui comprendiamo il collegamento fra moduli tipo winnertakeall che mettono a disposizione delle interfacce che devono essere collegate fra moduli. I neuroni sono gia' dichiarati nei moduli, quello che manca sono gli ASTROCYTE. Consideriamo che gli ASTROCYTE sono interni ad un organo. + ```Gen include: