From c8ed45c0c9c04fb9c8f78c6bfacf826ec2c5f434 Mon Sep 17 00:00:00 2001 From: Sergio Marchetti Date: Sat, 30 May 2026 11:44:26 +0200 Subject: [PATCH 1/4] Update elements/neuron/presynapse.md --- elements/neuron/presynapse.md | 128 +++++++++++++++++----------------- 1 file changed, 64 insertions(+), 64 deletions(-) diff --git a/elements/neuron/presynapse.md b/elements/neuron/presynapse.md index 438bc53..865b15e 100644 --- a/elements/neuron/presynapse.md +++ b/elements/neuron/presynapse.md @@ -24,16 +24,16 @@ PRESYNAPSE intrication: # Scope - !DAY: SCOPE [ ref: &ORGANISM.!DAY] - !NIGHT: SCOPE [ ref: &ORGANISM.!NIGHT] + !DAY: INTRICATION [ ref: &ORGANISM.!DAY] + !NIGHT: INTRICATION [ ref: &ORGANISM.!NIGHT] # Context - *AP: CONTEXT [&SOMA.*AP] + *AP: INTRICATION [ ref: &SOMA.*AP] # Tub - _NT: TUB [ ref: &ASTROSYNAPSE._NT] - _ATP: TUB [ ref: &ASTROCYTE._ATP] - _eCB: TUB [ ref: &POSTSYNAPSE._eCB] + _NT: INTRICATION [ ref: &ASTROSYNAPSE._NT] + _ATP: INTRICATION [ ref: &ASTROCYTE._ATP] + _eCB: INTRICATION [ ref: &POSTSYNAPSE._eCB] instantiation: @@ -41,12 +41,12 @@ PRESYNAPSE *TunePossible: CONTEXT [ref: &...] # Tub - _Ca2+: TUB [ full: 60x, active: 30x, empty: 0x ] + _Ca2: TUB [ full: 60x, active: 30x, empty: 0x ] _Rrp: TUB [ full: 30x, active: 15x, empty: 0x ] _Rp: TUB [ full: 30x, active: 15x, empty: 0x ] _CaTraces: TUB [ full: 50x, active: 0x, empty: 0x ] - _Ca2+FullDev: TUB [ full: 100x, active: _Ca2+.full, empty: 40x ] + _Ca2FullDev: TUB [ full: 100x, active: _Ca2.full, empty: 40x ] # serve al dev # Behaviour @@ -88,11 +88,11 @@ MAIN_PRE **Tubs:** -- **_Ca2+**: Calcium Ion entering the Presynapse when VCGG open that influence NT release. Normally returns to ~0 between spikes; stays elevated when pumps fail. They are key to check the concentration, release NT and modulation +- **_Ca2**: Calcium Ion entering the Presynapse when VCGG open that influence NT release. Normally returns to ~0 between spikes; stays elevated when pumps fail. They are key to check the concentration, release NT and modulation - **_Rrp**: Readily Releasable Pool: The Readily Releasable Pool consists of the vesicles that are "docked" and "primed" at the active zone of the synapse. This pool is very small (usually only about 0.5% to 5% of total vesicles) and can be exhausted quickly during high-frequency firing, leading to "short-term depression" of the signal. Here we consider them as NT ready to be released. - **_Rp**: Reserve Pool: The bulk of the vesicles held further back in the terminal, often tethered by a protein called synapsin. These are only mobilized during intense, prolonged stimulation. This makes up the vast majority of the vesicles (up to 80% or 90%). Here we consider them NT in reserve that can be transfered to RRP and created using Glutamine from Astorcyte. - **_NT**: Neuro Transmitter, released in the synapse by the vescicles. The release increses NT and decreases RRP -- **_CaTraces**: sono le tracce di permanenza della concentrazione di Ca2+. Servono alla modulazione (TUN) +- **_CaTraces**: sono le tracce di permanenza della concentrazione di Ca2. Servono alla modulazione (TUN) - **_eCB**: retrograde signal updates from postsynapsis (postsynaptic input) #### *AP @@ -105,11 +105,11 @@ RF di interacting deve essere MOLTO piu' basso di un RF di AP. In maniera da ess Non consideriamo le vesicles come liberate, ma direttamente gli NT. Questo permette di gestire la quantita' rilasciata di NT, invece di gestire un numero di vescicles. Nella realta' ciascuna vesicle contiene migliaia di NT. Qui mettiamo un floor a questo tipo di comprensione. -Ci sono 4 casi che dipendono da RRP, Ca2+ e indirettamente da concentrazione di NT nella SYN che diventa mGLur che limita in VGCC l'entrata di Ca2+. L'idea e' che la quantita' di RRP sia il driver principale. Gli NT liberati sono di piu' al crescere di RRP e Ca2+ e di meno (indirettamente) al crescere della concentrazione di NT gia' liberati nella SYN. Gli NT nella sinapsi fanno da moderazione alla ulteriore liberazione di NT, ma non bloccano mai totalmente. NT suppression only matters when everything else is already at maximum, which is exactly the biological purpose: it prevents runaway release during peak activity, not during moderate activity. +Ci sono 4 casi che dipendono da RRP, Ca2 e indirettamente da concentrazione di NT nella SYN che diventa mGLur che limita in VGCC l'entrata di Ca2. L'idea e' che la quantita' di RRP sia il driver principale. Gli NT liberati sono di piu' al crescere di RRP e Ca2 e di meno (indirettamente) al crescere della concentrazione di NT gia' liberati nella SYN. Gli NT nella sinapsi fanno da moderazione alla ulteriore liberazione di NT, ma non bloccano mai totalmente. NT suppression only matters when everything else is already at maximum, which is exactly the biological purpose: it prevents runaway release during peak activity, not during moderate activity. --- -NT empty. Qui siamo contestualizzati se Ca2+ full, il che dovrebbe significare indirettamente che non ci sono NT nella SYN. +NT empty. Qui siamo contestualizzati se Ca2 full, il che dovrebbe significare indirettamente che non ci sono NT nella SYN. In tutti i casi di NT @@ -120,7 +120,7 @@ NTreleaseLow in_context: *AP - hypothesis: ( _Ca2+ mediumness ) AND ( _Rrp mediumness ) AND NOT( _ATP empty ) + hypothesis: ( _Ca2 mediumness ) AND ( _Rrp mediumness ) AND NOT( _ATP empty ) action: [_Rrp decrease, _Nt increase, _ATP decrease] trace: None ``` @@ -132,8 +132,8 @@ NTreleaseMedium in_context: *AP - hypothesis: (( _Ca2+ fullness ) AND ( _Rrp mediumness ) OR - ( _Ca2+ mediumness ) AND ( _Rrp fullness )) AND + hypothesis: (( _Ca2 fullness ) AND ( _Rrp mediumness ) OR + ( _Ca2 mediumness ) AND ( _Rrp fullness )) AND NOT( _ATP empty ) action: [_Rrp decrease, Nt increase, _ATP decrease] trace: None @@ -146,13 +146,13 @@ NTreleaseHigh in_context: *AP - hypothesis: ( _Ca2+ fullness ) AND ( _Rrp fullness ) AND + hypothesis: ( _Ca2 fullness ) AND ( _Rrp fullness ) AND NOT( _ATP empty ) action: [_Rrp decrease, NT increase, _ATP decrease] trace: None ``` -##### Ca2+TracesAccLow +##### Ca2TracesAccLow Serve a: @@ -162,38 +162,38 @@ Serve a: - Abbiamo 3 tracce, high, medium and low. Andiamo a verificare una combinazione di queste per fare la modulazione - RF e' a 10, questo dovrebbe essere un RF di campionamento durante *AP context che dovremmo assicurarci sia tipo 100. Il che implicherebbe 10 campionamenti. - The biological meaning is that a synapse that has just been through a burst is primed for fast recovery — the molecular machinery for vesicle docking is already engaged, calcium-dependent priming factors are still elevated, and the system is in a ready state. A synapse that has been silent for several seconds has cooled down and replenishes slowly. -- So after one second of silence CaTrace has fallen to ~37% of its peak value, after two seconds to ~14%, after three seconds to ~5%. It asymptotes toward zero but never exactly reaches it. Between spikes, Ca2+ falls toward zero as the pumps clear it. The result is that CaTrace encodes not the instantaneous calcium level but the recent history of calcium activity — a smoothed, time-averaged measure of how active the synapse has been over the past one to two seconds. +- So after one second of silence CaTrace has fallen to ~37% of its peak value, after two seconds to ~14%, after three seconds to ~5%. It asymptotes toward zero but never exactly reaches it. Between spikes, Ca2 falls toward zero as the pumps clear it. The result is that CaTrace encodes not the instantaneous calcium level but the recent history of calcium activity — a smoothed, time-averaged measure of how active the synapse has been over the past one to two seconds. ```Gen -Ca2+TracesAccuLow +Ca2TracesAccuLow in_context: *AP - hypothesis: (_Ca2+ emptiness) + hypothesis: (_Ca2 emptiness) action: [CaTraceLow increase] trace: None ``` -##### Ca2+TracesAccMedium +##### Ca2TracesAccMedium ```Gen -Ca2+TracesAccMedium +Ca2TracesAccMedium in_context: *AP - hypothesis: (_Ca2+ mediumness) + hypothesis: (_Ca2 mediumness) action: [CaTraceMed increase] trace: None ``` -##### Ca2+TracesAccHigh +##### Ca2TracesAccHigh ```Gen -Ca2+TracesAccumulationHigh +Ca2TracesAccumulationHigh in_context: *AP - hypothesis: (_Ca2+ fullness) + hypothesis: (_Ca2 fullness) action: [CaTraceHigh increase] trace: None ``` @@ -202,7 +202,7 @@ Ca2+TracesAccumulationHigh ##### eCBClearance -eCB dipende da POST. Tende a modulare l'entrata di Ca2+ degli VGCC. +eCB dipende da POST. Tende a modulare l'entrata di Ca2 degli VGCC. Qui non facciamo un flush di eCB, riduciamo ogni mezzo secondo (context) di un RF di questo episodio. @@ -291,7 +291,7 @@ The glutamine crosses into the presynapse, where glutaminase converts it back in The chain reveals why sustained high-frequency firing eventually depletes the synapse even with all replenishment mechanisms running. -The RRP holds at most `Max_RRP = 20` vesicles. At 20 Hz with strong Ca²⁺, release can draw 2-4 vesicles per spike — potentially exhausting the RRP in under a second. The seconds loop can move vesicles from RP to RRP at a maximum rate of `k_rec_fast = 5 /s`, meaning at most 5 vesicles per second under ideal conditions. Release outpaces recruitment by roughly an order of magnitude during a burst. +The RRP holds at most `Max_RRP = 20` vesicles. At 20 Hz with strong Ca2, release can draw 2-4 vesicles per spike — potentially exhausting the RRP in under a second. The seconds loop can move vesicles from RP to RRP at a maximum rate of `k_rec_fast = 5 /s`, meaning at most 5 vesicles per second under ideal conditions. Release outpaces recruitment by roughly an order of magnitude during a burst. The RP holds up to `Max_RP = 200` vesicles — ten times the RRP. At sustained 20 Hz the RP can sustain firing for tens of seconds even after the RRP is repeatedly emptied, as long as recruitment keeps pace. But the minutes loop only refills N_RP once per minute at a rate limited by `Glutamine_pool * conversion_efficiency`. If glucose is low or the astrocyte wave has not fired, this replenishment may add only a fraction of what was consumed. @@ -303,12 +303,12 @@ Gln — depletes over bursts, refilled by glucose (slowest, astrocyte-depend Each tier buys time for the one below it to respond. When all three are depleted simultaneously — which only happens under prolonged high-frequency firing with insufficient glucose — the synapse has no remaining buffer and goes silent until the minutes loop restores the Glutamine_pool. -##### Ca2+TracesClearance +##### Ca2TracesClearance Qui facciamo un flush di CaTraceX. Deve essere fatto a valle del tuning. ```Gen -Ca2+TracesClearance +Ca2TracesClearance in_context: NOT *TunePossible @@ -423,7 +423,7 @@ BEHAVIOR_VGCC_PRE type: behaviour tub_intricated: - - _Ca2+ ( contained_by: PRESYNAPSE-BHE ) + - _Ca2 ( contained_by: PRESYNAPSE-BHE ) - NT ( contained_by: SYN ) context_intricated: @@ -431,12 +431,12 @@ BEHAVIOR_VGCC_PRE snippets: - Ca2+enterLow: ACCUMULATOR [RF: active 12x] - Ca2+enterMedium: ACCUMULATOR [RF: active 6x] - Ca2+enterHigh: ACCUMULATOR [RF: active 3x] + Ca2enterLow: ACCUMULATOR [RF: active 12x] + Ca2enterMedium: ACCUMULATOR [RF: active 6x] + Ca2enterHigh: ACCUMULATOR [RF: active 3x] - Ca2+ClearanceLow: ACCUMULATOR [RF: active 24x] - Ca2+ClearanceHigh: ACCUMULATOR [RF: active 4x] + Ca2ClearanceLow: ACCUMULATOR [RF: active 24x] + Ca2ClearanceHigh: ACCUMULATOR [RF: active 4x] ``` @@ -450,60 +450,60 @@ Here we comprehend the breaking activity on VGCC by: CDI, eCB and mGluR: Qui semplifichiamo: -- Approssimiamo CDI con concentrazione di Ca2+. --- CDI is calcium-dependent inactivation of VGCCs. The inactivation happens because Ca²⁺ enters through the channel and binds to a calmodulin tethered to the channel's intracellular face, physically blocking it from reopening. This is a local, channel-specific event — it requires Ca²⁺ to be flowing through that channel right now, not residual Ca²⁺ drifting in the cytosol between spikes. --- The recovery, by contrast, should run every millisecond unconditionally — CDI de-inactivation is a continuous process that proceeds whenever Ca²⁺ dissociates from calmodulin, which depends on the ambient Ca_micro level at all times. +- Approssimiamo CDI con concentrazione di Ca2. +-- CDI is calcium-dependent inactivation of VGCCs. The inactivation happens because Ca2 enters through the channel and binds to a calmodulin tethered to the channel's intracellular face, physically blocking it from reopening. This is a local, channel-specific event — it requires Ca2 to be flowing through that channel right now, not residual Ca2 drifting in the cytosol between spikes. +-- The recovery, by contrast, should run every millisecond unconditionally — CDI de-inactivation is a continuous process that proceeds whenever Ca2 dissociates from calmodulin, which depends on the ambient Ca_micro level at all times. - Approssimiamo mGluR con concentrazione NT - **Open** — zero active brakes. mGluR alone never escapes this group because its ceiling is alpha_mGluR = 0.4, meaning even at full it only removes 40% of conductance, leaving 60% — still above the 85% threshold. So mGluR is irrelevant to the open/not-open boundary. Only CDI and eCB decide. - **Reduced/partial** — exactly one meaningful brake active. Either CDI has started building (mediumness), or eCB has risen from sustained postsynaptic activity, but not both simultaneously. The system is aware something is happening but has not compounded yet. This is the normal operating range during moderate sustained firing. -- **Suppressed** — two brakes multiplying. The compounding is what defines this zone — no single variable alone produces it (except CDI approaching full). 0.5 × 0.5 = 0.25 remaining is where the synapse starts losing significant transmission efficacy. Biologically this is the pre-silence warning zone: CDI is building from residual Ca²⁺ while eCB is already engaged from postsynaptic activity. +- **Suppressed** — two brakes multiplying. The compounding is what defines this zone — no single variable alone produces it (except CDI approaching full). 0.5 × 0.5 = 0.25 remaining is where the synapse starts losing significant transmission efficacy. Biologically this is the pre-silence warning zone: CDI is building from residual Ca2 while eCB is already engaged from postsynaptic activity. - **Closed — CDI** = full is the only reliable hard rule. Because CDI can reach 1.0 and appears as (1 - CDI_factor) in the formula, it alone drives conductance to zero regardless of eCB and mGluR state. The three-brake overlap corner case (eCB=full + CDI=mediumness + mGluR=full) also reaches here, but in practice CDI reaching full is the primary biological mechanism. Devo controllare che le condizioni sotto siano esaustive. Qui ho confuso high con low, e inoltre ho messo NT per mGluR che devo controllare che abbia senso. -##### Ca2+enterLow +##### Ca2enterLow ```Gen -Ca2+enterLow +Ca2enterLow in_context: *AP - hypothesis: (_Ca2+ empty) AND (eCB empty) - action: [_Ca2+ increase, _ATP decrease] + hypothesis: (_Ca2 empty) AND (eCB empty) + action: [_Ca2 increase, _ATP decrease] trace: None ``` -##### Ca2+enterMedium +##### Ca2enterMedium ```Gen -Ca2+enterMedium +Ca2enterMedium in_context: *AP - hypothesis: (_Ca2+ mediumness) OR - ((eCB mediumness) AND (_Ca2+ empty)) OR - ((eCB full) AND (_Ca2+ empty) AND (NT empty)) - action: [_Ca2+ increase, _ATP decrease] + hypothesis: (_Ca2 mediumness) OR + ((eCB mediumness) AND (_Ca2 empty)) OR + ((eCB full) AND (_Ca2 empty) AND (NT empty)) + action: [_Ca2 increase, _ATP decrease] trace: None ``` -##### Ca2+enterHigh +##### Ca2enterHigh ```Gen -Ca2+enterHigh +Ca2enterHigh in_context: *AP - hypothesis: (_Ca2+ mediumness) AND (eCB full) OR + hypothesis: (_Ca2 mediumness) AND (eCB full) OR (eCB mediumness) - action: [_Ca2+ increase, _ATP decrease] + action: [_Ca2 increase, _ATP decrease] trace: None ``` #### NOT *AP -Qui eliminiamo Ca2+. Il tempo che ci mette ad eliminare il Ca2+ dovrebbe essere minoe dell'inervallo fra un *AP e un'altra. Siccome non comprendiamo per ora _ATP, non c'e' accumulo di Ca2+ per mancanza di _ATP (stanchezza). +Qui eliminiamo Ca2. Il tempo che ci mette ad eliminare il Ca2 dovrebbe essere minoe dell'inervallo fra un *AP e un'altra. Siccome non comprendiamo per ora _ATP, non c'e' accumulo di Ca2 per mancanza di _ATP (stanchezza). Non non comprendiamo anche il ristabilimento del Voltage, con altri Ioni entranti e uscenti, per ora tutto dipende da AP del SOMA. Non comprendiamo per ora: @@ -514,29 +514,29 @@ Non non comprendiamo anche il ristabilimento del Voltage, con altri Ioni entrant Qui disinguiamo: - Ca+2 fullness che si puo' verificare alla fine di un AP -- NOT ca2+ fullness che svuota piu' lentamente +- NOT Ca2 fullness che svuota piu' lentamente - da capire se serve veramente questa distinzione per il tempo di svuotamento. -##### Ca2+ClearanceLow +##### Ca2ClearanceLow ```Gen -Ca2+ClearanceLow +Ca2ClearanceLow in_context: NOT *AP - hypothesis: (NOT _Ca2+ fullness) AND (NOT _Ca2+ empty) - action: [_Ca2+ decrease] + hypothesis: (NOT _Ca2 fullness) AND (NOT _Ca2 empty) + action: [_Ca2 decrease] trace: None ``` -##### Ca2+ClearanceHigh +##### Ca2ClearanceHigh ```Gen -Ca2+ClearanceHigh +Ca2ClearanceHigh in_context: NOT *AP - hypothesis: NOT (Ca2+ empty) - action: [Ca2+ decrease] + hypothesis: NOT (Ca2 empty) + action: [Ca2 decrease] trace: None ``` From a89de909d9fc39df5116fd7c35d2982ced03b524 Mon Sep 17 00:00:00 2001 From: Sergio Marchetti Date: Sat, 30 May 2026 12:04:55 +0200 Subject: [PATCH 2/4] Update elements/neuron/presynapse.md --- elements/neuron/presynapse.md | 79 ++++++++++++++++++----------------- 1 file changed, 41 insertions(+), 38 deletions(-) diff --git a/elements/neuron/presynapse.md b/elements/neuron/presynapse.md index 865b15e..1c4d528 100644 --- a/elements/neuron/presynapse.md +++ b/elements/neuron/presynapse.md @@ -29,6 +29,7 @@ PRESYNAPSE # Context *AP: INTRICATION [ ref: &SOMA.*AP] + *TunePossible: INTRICATION [ref: &...] # To be defined... # Tub _NT: INTRICATION [ ref: &ASTROSYNAPSE._NT] @@ -38,13 +39,14 @@ PRESYNAPSE instantiation: # Context - *TunePossible: CONTEXT [ref: &...] # Tub _Ca2: TUB [ full: 60x, active: 30x, empty: 0x ] _Rrp: TUB [ full: 30x, active: 15x, empty: 0x ] _Rp: TUB [ full: 30x, active: 15x, empty: 0x ] - _CaTraces: TUB [ full: 50x, active: 0x, empty: 0x ] + _CaTracesHigh: TUB [ full: 50x, active: 0x, empty: 0x ] + _CaTracesMedium: TUB [ full: 50x, active: 0x, empty: 0x ] + _CaTracesLow: TUB [ full: 50x, active: 0x, empty: 0x ] _Ca2FullDev: TUB [ full: 100x, active: _Ca2.full, empty: 40x ] # serve al dev @@ -92,7 +94,7 @@ MAIN_PRE - **_Rrp**: Readily Releasable Pool: The Readily Releasable Pool consists of the vesicles that are "docked" and "primed" at the active zone of the synapse. This pool is very small (usually only about 0.5% to 5% of total vesicles) and can be exhausted quickly during high-frequency firing, leading to "short-term depression" of the signal. Here we consider them as NT ready to be released. - **_Rp**: Reserve Pool: The bulk of the vesicles held further back in the terminal, often tethered by a protein called synapsin. These are only mobilized during intense, prolonged stimulation. This makes up the vast majority of the vesicles (up to 80% or 90%). Here we consider them NT in reserve that can be transfered to RRP and created using Glutamine from Astorcyte. - **_NT**: Neuro Transmitter, released in the synapse by the vescicles. The release increses NT and decreases RRP -- **_CaTraces**: sono le tracce di permanenza della concentrazione di Ca2. Servono alla modulazione (TUN) +- **_CaTracesXXX**: sono le tracce di permanenza della concentrazione di Ca2. Servono alla modulazione (TUN) - **_eCB**: retrograde signal updates from postsynapsis (postsynaptic input) #### *AP @@ -120,8 +122,8 @@ NTreleaseLow in_context: *AP - hypothesis: ( _Ca2 mediumness ) AND ( _Rrp mediumness ) AND NOT( _ATP empty ) - action: [_Rrp decrease, _Nt increase, _ATP decrease] + hypothesis: _Ca2 mediumness AND _Rrp mediumness AND NOT _ATP empty + action: [_Rrp decrease, _NT increase, _ATP decrease] trace: None ``` @@ -132,10 +134,10 @@ NTreleaseMedium in_context: *AP - hypothesis: (( _Ca2 fullness ) AND ( _Rrp mediumness ) OR - ( _Ca2 mediumness ) AND ( _Rrp fullness )) AND - NOT( _ATP empty ) - action: [_Rrp decrease, Nt increase, _ATP decrease] + hypothesis: ( _Ca2 fullness AND _Rrp mediumness ) OR + ( _Ca2 mediumness AND _Rrp fullness ) AND + NOT _ATP empty + action: [_Rrp decrease, _NT increase, _ATP decrease] trace: None ``` @@ -146,8 +148,8 @@ NTreleaseHigh in_context: *AP - hypothesis: ( _Ca2 fullness ) AND ( _Rrp fullness ) AND - NOT( _ATP empty ) + hypothesis: ( _Ca2 fullness AND _Rrp fullness ) AND + NOT _ATP empty action: [_Rrp decrease, NT increase, _ATP decrease] trace: None ``` @@ -169,8 +171,8 @@ Ca2TracesAccuLow in_context: *AP - hypothesis: (_Ca2 emptiness) - action: [CaTraceLow increase] + hypothesis: _Ca2 emptiness + action: [ _CaTraceLow increase ] trace: None ``` @@ -181,8 +183,8 @@ Ca2TracesAccMedium in_context: *AP - hypothesis: (_Ca2 mediumness) - action: [CaTraceMed increase] + hypothesis: _Ca2 mediumness + action: [ _CaTraceMed increase ] trace: None ``` @@ -193,8 +195,8 @@ Ca2TracesAccumulationHigh in_context: *AP - hypothesis: (_Ca2 fullness) - action: [CaTraceHigh increase] + hypothesis: _Ca2 fullness + action: [ _CaTraceHigh increase ] trace: None ``` @@ -211,8 +213,8 @@ eCBClearance: ( active: 24x ) # Slow in_context: NOT *AP - hypothesis: NOT (eCB empty) - action: [eCB decrease] + hypothesis: NOT _eCB empty + action: [ _eCB decrease ] trace: None ``` @@ -229,9 +231,9 @@ RPShuttleLow in_context: NOT *AP - hypothesis: (CaTraceLow fullness) OR - (RP emptiness) OR - (_Rrp fullness) + hypothesis: _CaTraceLow fullness OR + _RP emptiness OR + _Rrp fullness action: [RP decrease, _Rrp increase] trace: None ``` @@ -247,10 +249,10 @@ RPShuttleMedium in_context: *AP - hypothesis: (CaTraceMedium fullness) AND (RP mediumness) AND (_Rrp mediumness) OR - (CaTraceHigh fullness) AND (RP mediumness) AND (_Rrp mediumness) OR # signal boost - (CaTraceMedium fullness) AND (RP fullness) AND (_Rrp mediumness) OR # supply boost - (CaTraceMedium fullness) AND (RP mediumness) AND (_Rrp emptiness) # vacancy boost + hypothesis: ( _CaTraceMedium fullness AND _RP mediumness AND _Rrp mediumness ) OR + ( _CaTraceHigh fullness AND _RP mediumness AND _Rrp mediumness ) OR # signal boost + ( _CaTraceMedium fullness AND _RP fullness AND _Rrp mediumness ) OR # supply boost + ( _CaTraceMedium fullness AND _RP mediumness AND _Rrp emptiness ) # vacancy boost action: [RP decrease, _Rrp increase] trace: None ``` @@ -266,10 +268,10 @@ RPShuttleHigh in_context: *AP - hypothesis: (CaTraceHigh fullness) AND (RP fullness) AND (_Rrp mediumness) OR # signal + supply - (CaTraceHigh fullness) AND (RP mediumness) AND (_Rrp emptiness) OR # signal + vacancy - (CaTraceMedium fullness) AND (RP fullness) AND (_Rrp emptiness) # supply + vacancy - action: [RP decrease, _Rrp increase] + hypothesis: ( _CaTraceHigh fullness AND _RP fullness AND _Rrp mediumness ) OR # signal + supply + ( _CaTraceHigh fullness AND _RP mediumness AND _Rrp emptiness ) OR # signal + vacancy + ( _CaTraceMedium fullness AND _RP fullness AND _Rrp emptiness ) # supply + vacancy + action: [ _RP decrease, _Rrp increase] trace: None ``` @@ -312,16 +314,16 @@ Ca2TracesClearance in_context: NOT *TunePossible - hypothesis: NOT (CaTraceHigh empty) - action: [CaTRaceHigh decrease] + hypothesis: NOT _CaTraceHigh empty + action: [ _CaTRaceHigh decrease ] trace: None - hypothesis: NOT (CaTraceMedium empty) - action: [CaTRaceMedium decrease] + hypothesis: NOT _CaTraceMedium empty + action: [ _CaTRaceMedium decrease ] trace: None - hypothesis: NOT (CaTraceLow empty) - action: [CaTRaceLow decrease] + hypothesis: NOT _CaTraceLow empty + action: [ _CaTRaceLow decrease ] trace: None ``` @@ -330,11 +332,12 @@ Ca2TracesClearance ```Gen TUNE_VGCC_PRE - # qui stiamo aggiungendo o eliminando {VGCC_PRE}. Fra un massimo full e minimo empty (empty puo' non essere 0) + type: behaviour + + # qui stiamo aggiungendo o eliminando VGCC_PRE. Fra un massimo full e minimo empty (empty puo' non essere 0) # contained_by: PRESYNAPSE non e' contenuto, si attacca. activity_scope: !DAY - type: behaviour context_intricated: - *TunePossible ( contained_by: DAY-N ) From f55ed02efdec00c28959e55f4373e6b1bda939ae Mon Sep 17 00:00:00 2001 From: Sergio Marchetti Date: Sat, 30 May 2026 12:58:39 +0200 Subject: [PATCH 3/4] Update elements/neuron/presynapse.md --- elements/neuron/presynapse.md | 210 ++++++++++++++++++---------------- 1 file changed, 112 insertions(+), 98 deletions(-) diff --git a/elements/neuron/presynapse.md b/elements/neuron/presynapse.md index 1c4d528..bc3ad7a 100644 --- a/elements/neuron/presynapse.md +++ b/elements/neuron/presynapse.md @@ -13,7 +13,6 @@ Qui comprendiamo: ```Gen PRESYNAPSE - type: comprehension expansion: @@ -24,21 +23,23 @@ PRESYNAPSE intrication: # Scope - !DAY: INTRICATION [ ref: &ORGANISM.!DAY] - !NIGHT: INTRICATION [ ref: &ORGANISM.!NIGHT] + !DAY: INTRICATION [ ref: &ORGANISM.!DAY ] + !NIGHT: INTRICATION [ ref: &ORGANISM.!NIGHT ] # Context - *AP: INTRICATION [ ref: &SOMA.*AP] - *TunePossible: INTRICATION [ref: &...] # To be defined... + *AP: INTRICATION [ ref: &SOMA.*AP ] + *TunePossible: INTRICATION [ ref: &... ] # To be defined... # Tub - _NT: INTRICATION [ ref: &ASTROSYNAPSE._NT] - _ATP: INTRICATION [ ref: &ASTROCYTE._ATP] - _eCB: INTRICATION [ ref: &POSTSYNAPSE._eCB] + _NT: INTRICATION [ ref: &ASTROSYNAPSE._NT ] + _ATP: INTRICATION [ ref: &ASTROCYTE._ATP ] + _eCB: INTRICATION [ ref: &POSTSYNAPSE._eCB ] instantiation: # Context + *TryTunUpPreVcgg: CONTEXT [] + *TryTunDownPreVcgg: CONTEXT [] # Tub _Ca2: TUB [ full: 60x, active: 30x, empty: 0x ] @@ -68,24 +69,24 @@ MAIN_PRE snippet: # *AP - @: ACCUMULATOR [snippet: NTreleaseLow, RF: active 12x] - @: ACCUMULATOR [snippet: NTreleaseMedium, RF: active 9x] - @: ACCUMULATOR [snippet: NTreleaseHigh, RF: active 6x] + @: ACCUMULATOR [ snippet: NTreleaseLow, rf: active 12x ] + @: ACCUMULATOR [ snippet: NTreleaseMedium, rf: active 9x ] + @: ACCUMULATOR [ snippet: NTreleaseHigh, rf: active 6x ] - @: ACCUMULATOR [snippet: TracesAccLow, RF: active 3x] - @: ACCUMULATOR [snippet: TracesAccMedium, RF: active 6x] - @: ACCUMULATOR [snippet: TracesAccHigh, RF: active 10x] + @: ACCUMULATOR [ snippet: TracesAccLow, rf: active 3x ] + @: ACCUMULATOR [ snippet: TracesAccMedium, rf: active 6x ] + @: ACCUMULATOR [ snippet: TracesAccHigh, rf: active 10x ] # NOT *AP - @: ACCUMULATOR [snippet: eCBClearenceMedium, RF: active 24x] - @: ACCUMULATOR [snippet: eCBClearenceLow, RF: active 48x] + @: ACCUMULATOR [ snippet: eCBClearenceMedium, rf: active 24x ] + @: ACCUMULATOR [ snippet: eCBClearenceLow, rf: active 48x ] - @: ACCUMULATOR [snippet: RPShuttleLow, RF: active 24x] - @: ACCUMULATOR [snippet: RPShuttleMedium, RF: active 48x] + @: ACCUMULATOR [ snippet: RPShuttleLow, rf: active 24x ] + @: ACCUMULATOR [ snippet: RPShuttleMedium, rf: active 48x ] - @: ACCUMULATOR [snippet: RefillGlutamine, RF: active 24x] + @: ACCUMULATOR [ snippet: RefillGlutamine, rf: active 24x ] - @: ACCUMULATOR [snippet: TracesClearance, RF: active 30x] + @: ACCUMULATOR [ snippet: TracesClearance, rf: active 30x ] ``` **Tubs:** @@ -119,11 +120,12 @@ In tutti i casi di NT ```Gen NTreleaseLow + type: accumulator - in_context: *AP + in_context: *AP - hypothesis: _Ca2 mediumness AND _Rrp mediumness AND NOT _ATP empty - action: [_Rrp decrease, _NT increase, _ATP decrease] + hypothesis: _Ca2 mediumness AND _Rrp mediumness AND NOT _ATP empty + action: [ _Rrp decrease, _NT increase, _ATP decrease ] trace: None ``` @@ -131,13 +133,14 @@ NTreleaseLow ```Gen NTreleaseMedium + type: accumulator - in_context: *AP + in_context: *AP hypothesis: ( _Ca2 fullness AND _Rrp mediumness ) OR ( _Ca2 mediumness AND _Rrp fullness ) AND NOT _ATP empty - action: [_Rrp decrease, _NT increase, _ATP decrease] + action: [ _Rrp decrease, _NT increase, _ATP decrease ] trace: None ``` @@ -145,12 +148,13 @@ NTreleaseMedium ```Gen NTreleaseHigh + type: accumulator - in_context: *AP + in_context: *AP - hypothesis: ( _Ca2 fullness AND _Rrp fullness ) AND - NOT _ATP empty - action: [_Rrp decrease, NT increase, _ATP decrease] + hypothesis: _Ca2 fullness AND _Rrp fullness AND + NOT _ATP empty + action: [ _Rrp decrease, NT increase, _ATP decrease ] trace: None ``` @@ -168,8 +172,9 @@ Serve a: ```Gen Ca2TracesAccuLow + type: accumulator - in_context: *AP + in_context: *AP hypothesis: _Ca2 emptiness action: [ _CaTraceLow increase ] @@ -180,8 +185,9 @@ Ca2TracesAccuLow ```Gen Ca2TracesAccMedium + type: accumulator - in_context: *AP + in_context: *AP hypothesis: _Ca2 mediumness action: [ _CaTraceMed increase ] @@ -192,8 +198,9 @@ Ca2TracesAccMedium ```Gen Ca2TracesAccumulationHigh + type: accumulator - in_context: *AP + in_context: *AP hypothesis: _Ca2 fullness action: [ _CaTraceHigh increase ] @@ -210,8 +217,9 @@ Qui non facciamo un flush di eCB, riduciamo ogni mezzo secondo (context) di un R ```Gen eCBClearance: ( active: 24x ) # Slow + type: accumulator - in_context: NOT *AP + in_context: NOT *AP hypothesis: NOT _eCB empty action: [ _eCB decrease ] @@ -228,13 +236,14 @@ Rate: 0.00 – 0.25 ```Gen RPShuttleLow + type: accumulator - in_context: NOT *AP + in_context: NOT *AP hypothesis: _CaTraceLow fullness OR _RP emptiness OR _Rrp fullness - action: [RP decrease, _Rrp increase] + action: [ _RP decrease, _Rrp increase ] trace: None ``` @@ -246,14 +255,15 @@ Rate: 0.50 – 0.97 ```Gen RPShuttleMedium + type: accumulator - in_context: *AP + in_context: *AP hypothesis: ( _CaTraceMedium fullness AND _RP mediumness AND _Rrp mediumness ) OR ( _CaTraceHigh fullness AND _RP mediumness AND _Rrp mediumness ) OR # signal boost ( _CaTraceMedium fullness AND _RP fullness AND _Rrp mediumness ) OR # supply boost ( _CaTraceMedium fullness AND _RP mediumness AND _Rrp emptiness ) # vacancy boost - action: [RP decrease, _Rrp increase] + action: [ _RP decrease, _Rrp increase ] trace: None ``` @@ -265,13 +275,14 @@ Rate: 1.25 – 1.94 ```Gen RPShuttleHigh + type: accumulator - in_context: *AP + in_context: *AP hypothesis: ( _CaTraceHigh fullness AND _RP fullness AND _Rrp mediumness ) OR # signal + supply ( _CaTraceHigh fullness AND _RP mediumness AND _Rrp emptiness ) OR # signal + vacancy ( _CaTraceMedium fullness AND _RP fullness AND _Rrp emptiness ) # supply + vacancy - action: [ _RP decrease, _Rrp increase] + action: [ _RP decrease, _Rrp increase ] trace: None ``` @@ -311,8 +322,9 @@ Qui facciamo un flush di CaTraceX. Deve essere fatto a valle del tuning. ```Gen Ca2TracesClearance + type: accumulator - in_context: NOT *TunePossible + in_context: NOT *TunePossible hypothesis: NOT _CaTraceHigh empty action: [ _CaTRaceHigh decrease ] @@ -333,32 +345,21 @@ Ca2TracesClearance TUNE_VGCC_PRE type: behaviour - # qui stiamo aggiungendo o eliminando VGCC_PRE. Fra un massimo full e minimo empty (empty puo' non essere 0) # contained_by: PRESYNAPSE non e' contenuto, si attacca. activity_scope: !DAY - context_intricated: - - *TunePossible ( contained_by: DAY-N ) - - tub_passed: - _VgccPre: TUB [pass.@VGCC_PRE] - - tub_local: - - tub_intricated: - snippet: # *TunePossible - CheckVgccPreTun: CONTEXTOR [RF: active 60x] + @: CONTEXTOR [ snippet: CheckVgccPreTun, rf: active 60x ] - *TryTunUpPreVcgg - PossibleUpPreVgccTun: ACCUMULATOR [RF:active 10x] + # *TryTunUpPreVcgg + @: ACCUMULATOR [ snippet: PossibleUpPreVgccTun, rf:active 10x ] - *TryTunDownPreVcgg - PossibleDownPreVgccTun: ACCUMULATOR [RF:active 10x] + # *TryTunDownPreVcgg + @: ACCUMULATOR [ snippet: PossibleDownPreVgccTun, rf:active 10x ] ``` #### *TunePossible @@ -369,13 +370,14 @@ Qui controlliamo che ci siano le condizioni per aumentare o diminuire la quantit ```Gen CheckVgccPreTun + type contextor + + in_context: *TunePossible - in_context: *TunePossible - - condition: ( CaTraceHigh fullness ) + condition: _CaTraceHigh fullness out_context: *TryTunUpPreVcgg - condition: ( CaTraceLow fullness ) + condition: _CaTraceLow fullness out_context: *TryTunDownPreVcgg ``` @@ -383,8 +385,9 @@ CheckVgccPreTun ```Gen PossibleUpPreVgccTun + type: accumulator - in_context: TryTunUpPreVcgg_ctx + in_context: *TryTunUpPreVcgg hypothesis: action: @@ -395,8 +398,9 @@ PossibleUpPreVgccTun ```Gen PossibleDownPreVgccTun + type: accumulator - in_context: TryTunDownPreVcgg_ctx + in_context: *TryTunDownPreVcgg hypothesis: action: @@ -409,10 +413,21 @@ Voltage-Controlled Gated Channels: Qui per ora non gestiamo l'evoluzione della d ```Gen VGCC-PRE - type: comprehension + type: comprehension -instantiate_behaviour: - BEHAVIOR_VGCC_PRE: behaviour [] + # Scope + !DAY: INTRICATION [ ref: &ORGANISM.!DAY ] + !NIGHT: INTRICATION [ ref: &ORGANISM.!NIGHT ] + + # Context + *AP: INTRICATION [ ref: &SOMA.*AP ] + + # Tub + _NT: INTRICATION [ ref: &ASTROSYNAPSE._NT ] + _Ca2: INTRICATION [ ref: &PRESYNAPSE._Ca2 ] + + # Behaviour + @: BEHAVIOUR [ behaviour: VGCC_PRE_BEH ] ``` ### BEHAVIOR_VGCC_PRE @@ -420,26 +435,20 @@ instantiate_behaviour: Voltage-Controlled Gated Channels: Qui per ora non gestiamo l'evoluzione della depolarizzazione. Alla scomparsa dell'AP, i VGCC smettono di funzionare. ```Gen -BEHAVIOR_VGCC_PRE - - activity_scope: !DAY +VGCC_PRE_BEH type: behaviour - tub_intricated: - - _Ca2 ( contained_by: PRESYNAPSE-BHE ) - - NT ( contained_by: SYN ) - - context_intricated: - - AP ( contained_by: SOMA ) - + within_scope: !DAY + snippets: + # *AP + @: ACCUMULATOR [ snippet: Ca2enterLow, rf: active 12x ] + @: ACCUMULATOR [ snippet: Ca2enterMedium, rf: active 6x ] + @: ACCUMULATOR [ snippet: Ca2enterHigh, rf: active 3x ] - Ca2enterLow: ACCUMULATOR [RF: active 12x] - Ca2enterMedium: ACCUMULATOR [RF: active 6x] - Ca2enterHigh: ACCUMULATOR [RF: active 3x] - - Ca2ClearanceLow: ACCUMULATOR [RF: active 24x] - Ca2ClearanceHigh: ACCUMULATOR [RF: active 4x] + # NOT *AP + @: ACCUMULATOR [ snippet: Ca2ClearanceLow, rf: active 24x ] + @: ACCUMULATOR [ snippet: Ca2ClearanceHigh, rf: active 4x ] ``` @@ -469,11 +478,12 @@ Devo controllare che le condizioni sotto siano esaustive. Qui ho confuso high co ```Gen Ca2enterLow + type: accumulator - in_context: *AP + in_context: *AP - hypothesis: (_Ca2 empty) AND (eCB empty) - action: [_Ca2 increase, _ATP decrease] + hypothesis: _Ca2 empty AND _eCB empty + action: [ _Ca2 increase, _ATP decrease ] trace: None ``` @@ -481,13 +491,14 @@ Ca2enterLow ```Gen Ca2enterMedium + type: accumulator - in_context: *AP + in_context: *AP - hypothesis: (_Ca2 mediumness) OR - ((eCB mediumness) AND (_Ca2 empty)) OR - ((eCB full) AND (_Ca2 empty) AND (NT empty)) - action: [_Ca2 increase, _ATP decrease] + hypothesis: _Ca2 mediumness OR + ( _eCB mediumness AND _Ca2 empty ) OR + ( _eCB full AND _Ca2 empty AND _NT empty ) + action: [ _Ca2 increase, _ATP decrease ] trace: None ``` @@ -495,12 +506,13 @@ Ca2enterMedium ```Gen Ca2enterHigh + type: accumulator - in_context: *AP + in_context: *AP - hypothesis: (_Ca2 mediumness) AND (eCB full) OR - (eCB mediumness) - action: [_Ca2 increase, _ATP decrease] + hypothesis: ( _Ca2 mediumness AND _eCB full ) OR + _eCB mediumness + action: [ _Ca2 increase, _ATP decrease ] trace: None ``` @@ -524,11 +536,12 @@ Qui disinguiamo: ```Gen Ca2ClearanceLow + type: accumulator - in_context: NOT *AP + in_context: NOT *AP - hypothesis: (NOT _Ca2 fullness) AND (NOT _Ca2 empty) - action: [_Ca2 decrease] + hypothesis: NOT _Ca2 fullness AND NOT _Ca2 empty + action: [ _Ca2 decrease ] trace: None ``` @@ -536,10 +549,11 @@ Ca2ClearanceLow ```Gen Ca2ClearanceHigh + type: accumulator - in_context: NOT *AP + in_context: NOT *AP - hypothesis: NOT (Ca2 empty) + hypothesis: NOT _Ca2 empty action: [Ca2 decrease] trace: None ``` From 1dd5bac01f25ad23350c43790fe1d8120478bacd Mon Sep 17 00:00:00 2001 From: Sergio Marchetti Date: Sat, 30 May 2026 13:13:17 +0200 Subject: [PATCH 4/4] Update elements/neuron/presynapse.md --- elements/neuron/presynapse.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/elements/neuron/presynapse.md b/elements/neuron/presynapse.md index bc3ad7a..a5dbf09 100644 --- a/elements/neuron/presynapse.md +++ b/elements/neuron/presynapse.md @@ -381,6 +381,8 @@ CheckVgccPreTun out_context: *TryTunDownPreVcgg ``` +#### *TryTunUpPreVcgg + ##### PossibleUpPreVgccTun ```Gen @@ -394,6 +396,8 @@ PossibleUpPreVgccTun trace: ``` +#### *TryTunDownPreVcgg + ##### PossibleDownPreVgccTun: ( active: 10x ) accumulator ```Gen