# =========================================================================
# ACT photosynthetic exciton transfer
#
# Applied constructor-theory case:
# A photosynthetic antenna must deliver an electronic excitation to a
# reaction center before it is lost.
#
# This example is intentionally careful:
# it does NOT assume that long-lived electronic coherence is required.
# Instead it models a more modest and defensible claim:
#
#   - a tuned complex CAN exploit short-lived excitonic/vibronic assistance
#     to make reaction-center delivery possible;
#   - a detuned, strongly decohered contrast complex CAN'T achieve the
#     same transfer task efficiently in the same regime.
#
# The example is ACT-style because it expresses the application in terms
# of possible and impossible tasks.
# =========================================================================

@prefix : <http://example.org/act/photosynthesis/> .
@prefix arc: <https://example.org/arc#> .
@prefix log: <http://www.w3.org/2000/10/swap/log#> .

:case a arc:Case ;
  arc:question "Can a tuned photosynthetic antenna deliver excitation efficiently to a reaction center by short-lived quantum-assisted transfer, while a detuned contrast complex cannot?" .

# -------------------------
# Shared application target
# -------------------------

:reactionCenter a :ReactionCenter .
:harvestTask a :ExcitationDeliveryTask ;
  :target :reactionCenter ;
  :lossChannel :ExcitonRecombination .

# -------------------------------
# Device A: tuned antenna complex
# -------------------------------

# This complex has the structural ingredients usually invoked in careful,
# modern discussions of quantum-assisted transfer:
# - coupled excitonic states
# - some delocalization
# - a vibronic bridge
# - a downhill energetic route
# - short, not long-lived, coherence
# - moderate rather than overwhelming dephasing
:tunedAntenna a :LightHarvestingComplex ;
  :encodes :ExcitonPathway ;
  :excitonCoupling :Strong ;
  :stateDelocalization :Present ;
  :vibronicBridge :Tuned ;
  :energyLandscape :DownhillToReactionCenter ;
  :electronicCoherenceLifetime :Short ;
  :dephasing :Moderate ;
  :connectedTo :reactionCenter .

# ----------------------------------
# Device B: detuned contrast complex
# ----------------------------------

# This one lacks the helpful alignment:
# - weaker coupling
# - no useful delocalization
# - no vibronic bridge
# - a trapping mismatch
# - strong dephasing
:detunedAntenna a :LightHarvestingComplex ;
  :encodes :ExcitonPathway ;
  :excitonCoupling :Weak ;
  :stateDelocalization :Absent ;
  :vibronicBridge :Absent ;
  :energyLandscape :TrappingMismatch ;
  :electronicCoherenceLifetime :VeryShort ;
  :dephasing :Strong ;
  :connectedTo :reactionCenter .

# ---------------------------------
# CAN rules — what becomes possible
# ---------------------------------

# Strong excitonic coupling plus some delocalization makes
# coherent pathway sampling possible.
{ ?C a :LightHarvestingComplex ;
     :excitonCoupling :Strong ;
     :stateDelocalization :Present . }
=>
{ ?C :can :CoherentPathwaySampling . } .

# A tuned vibronic bridge plus non-overwhelming dephasing
# makes vibronically assisted transfer possible.
{ ?C a :LightHarvestingComplex ;
     :vibronicBridge :Tuned ;
     :dephasing :Moderate . }
=>
{ ?C :can :VibronicallyAssistedTransfer . } .

# This is the careful "science of can" claim:
# short-lived electronic coherence is enough for a useful
# transfer contribution when the bridge and landscape are
# favorable. Long-lived coherence is not required here.
{ ?C a :LightHarvestingComplex ;
     :electronicCoherenceLifetime :Short ;
     :energyLandscape :DownhillToReactionCenter . }
=>
{ ?C :can :ShortLivedQuantumAssistance . } .

# Efficient exciton transfer is possible when coherent
# pathway sampling, vibronic assistance, and a downhill
# energetic route are all available.
{ ?C :can :CoherentPathwaySampling .
  ?C :can :VibronicallyAssistedTransfer .
  ?C :can :ShortLivedQuantumAssistance .
  ?C :energyLandscape :DownhillToReactionCenter . }
=>
{ ?C :can :EfficientExcitonTransfer . } .

# If efficient transfer is possible and the antenna is
# connected to the reaction center, reaction-center delivery
# is possible.
{ ?C :can :EfficientExcitonTransfer ;
     :connectedTo ?RC .
  ?RC a :ReactionCenter . }
=>
{ ?C :can :DeliverExcitationToReactionCenter . } .

# -------------------------------------
# CAN'T rules — what becomes impossible
# -------------------------------------

# Weak coupling and absent delocalization block coherent
# pathway sampling.
{ ?C a :LightHarvestingComplex ;
     :excitonCoupling :Weak ;
     :stateDelocalization :Absent . }
=>
{ ?C :cannot :CoherentPathwaySampling . } .

# No vibronic bridge and strong dephasing block vibronically
# assisted transfer.
{ ?C a :LightHarvestingComplex ;
     :vibronicBridge :Absent ;
     :dephasing :Strong . }
=>
{ ?C :cannot :VibronicallyAssistedTransfer . } .

# A trapping mismatch blocks directed downhill delivery.
{ ?C a :LightHarvestingComplex ;
     :energyLandscape :TrappingMismatch . }
=>
{ ?C :cannot :DirectedReactionCenterTransfer . } .

# If the complex cannot sample pathways coherently and
# cannot use vibronic assistance, efficient transfer is not
# achievable in this operating picture.
{ ?C :cannot :CoherentPathwaySampling .
  ?C :cannot :VibronicallyAssistedTransfer . }
=>
{ ?C :cannot :EfficientExcitonTransfer . } .

# Even if some transfer happens, a trapping mismatch blocks
# efficient delivery to the reaction center in this case.
{ ?C :cannot :DirectedReactionCenterTransfer . }
=>
{ ?C :cannot :DeliverExcitationToReactionCenter . } .

{ ?C :cannot :EfficientExcitonTransfer . }
=>
{ ?C :cannot :DeliverExcitationToReactionCenter . } .

# ------
# Checks
# ------

# Positive checks for the tuned complex.
{ :tunedAntenna :can :CoherentPathwaySampling . }
=> { :case :checkC1 :Passed . } .

{ :tunedAntenna :can :VibronicallyAssistedTransfer . }
=> { :case :checkC2 :Passed . } .

{ :tunedAntenna :can :ShortLivedQuantumAssistance . }
=> { :case :checkC3 :Passed . } .

{ :tunedAntenna :can :EfficientExcitonTransfer . }
=> { :case :checkC4 :Passed . } .

{ :tunedAntenna :can :DeliverExcitationToReactionCenter . }
=> { :case :checkC5 :Passed . } .

# Negative checks for the detuned complex.
{ :detunedAntenna :cannot :CoherentPathwaySampling . }
=> { :case :checkC6 :Passed . } .

{ :detunedAntenna :cannot :VibronicallyAssistedTransfer . }
=> { :case :checkC7 :Passed . } .

{ :detunedAntenna :cannot :DirectedReactionCenterTransfer . }
=> { :case :checkC8 :Passed . } .

{ :detunedAntenna :cannot :EfficientExcitonTransfer . }
=> { :case :checkC9 :Passed . } .

{ :detunedAntenna :cannot :DeliverExcitationToReactionCenter . }
=> { :case :checkC10 :Passed . } .

# ----------------
# ARC-style output
# ----------------

{ :case :checkC1 :Passed .
  :case :checkC2 :Passed .
  :case :checkC3 :Passed .
  :case :checkC4 :Passed .
  :case :checkC5 :Passed .
  :case :checkC6 :Passed .
  :case :checkC7 :Passed .
  :case :checkC8 :Passed .
  :case :checkC9 :Passed .
  :case :checkC10 :Passed . }
=>
{
  :out log:outputString """ACT photosynthetic exciton transfer

Answer
YES for the tuned antenna complex.
NO for the detuned, strongly decohered contrast complex.

Reason Why
The tuned complex can sample exciton pathways coherently, use vibronically assisted transfer, and exploit short-lived quantum assistance along a downhill route to the reaction center. That makes efficient exciton transfer and reaction-center delivery possible in this case. The detuned contrast complex lacks the same alignment: coherent pathway sampling is blocked, vibronic assistance is unavailable, and the energy landscape is mismatched, so efficient reaction-center delivery is not possible in the same operating picture.

Check
C1  OK - the tuned complex can sample exciton pathways coherently
C2  OK - the tuned complex can use vibronically assisted transfer
C3  OK - short-lived quantum assistance is enough in the tuned downhill regime
C4  OK - efficient exciton transfer is possible in the tuned complex
C5  OK - the tuned complex can deliver excitation to the reaction center
C6  OK - the detuned complex cannot sample pathways coherently
C7  OK - the detuned complex cannot use vibronically assisted transfer
C8  OK - the detuned complex cannot achieve directed reaction-center transfer
C9  OK - the detuned complex cannot achieve efficient exciton transfer
C10 OK - the detuned complex cannot deliver excitation efficiently to the reaction center
""" .
} .