Tcell

breed [tcells tcell]  ; The T cells
breed [DCs DC]  ; The dendritic cells (DCs)

globals [ dt ds tcell-step nDCmeet ]  ; Global variables

links-own [ tDCfree ]  ; Each link tracks how long a T cell is bound to a DC

to setup
  clear-all
  reset-ticks  ; Ensures the tick counter starts at 0

  set-default-shape turtles "circle"  ; All turtles will be circles (spheres)

  set dt 0.5  ; Each time step = 0.5 minutes
  set ds 8    ; 1 patch = 8 µm
  set tcell-step 16 / ds * dt  ; Convert T cell speed to NetLogo units
  set nDCmeet 0  ; Initialize counter for DC-T cell encounters

  create-tcells 100 [
    set color green  ; Make T cells green
    setxyz random-xcor random-ycor random-zcor  ; Place randomly in 3D space
  ]

  create-DCs 2 [
    set size 2  ; Make DCs twice the size of T cells
    set color red  ; Make DCs red
    setxyz random-xcor random-ycor random-zcor  ; Place randomly in 3D space
  ]
end 

to go
  move-tcells  ; Move T cells
  identify-DCbound-tcells  ; Identify which T cells should be bound to DCs
  update-link-status  ; Update bound T cells and free them after 3 min
  tick-advance dt  ; Advances time in real minutes
  plotxy ticks nDCmeet  ; Add data to the plot
end 

to move-tcells
  ask tcells [
    if not any? my-links [  ; Move only if not bound to a DC
      right random-normal 0 90  ; Pick a random turn angle
      roll-right random-normal 0 90  ; Pick a random roll angle
      forward tcell-step  ; Move forward by computed step size
    ]
  ]
end 

to identify-DCbound-tcells
  ask DCs [
    create-links-to tcells with [ color != blue and not any? my-links ] in-radius 2 [  ; Find unlinked T cells in range
      set color red  ; Make the link red to show connection
      set tDCfree 3  ; Bind the T cell for 3 minutes
      ask end2 [
        set color blue  ; Change the T cell's color to blue while bound
        set nDCmeet nDCmeet + 1  ; Increase encounter count
      ]
    ]
  ]
end 

to update-link-status
  ask links [
    set tDCfree tDCfree - dt  ; Reduce timer each time step
    if tDCfree <= 0 [  ; If 3 minutes have passed
      ask end2 [ set color green ]  ; Turn the T cell back to green
      die  ; Remove the link
    ]
  ]
end