begin name
essunger2
end name

begin reactions
CD4TproductionV {1.0}$EXTERNAL = {1.0}V
VinfectionCD4T {1.0}Ta + {1.0}V = {1.0}Tastarstar
activationCD4TrestingMemoryInfected {1.0}Tmstarstar = {1.0}Tastarstar
activationCD4TrestingMemoryPlain {1.0}Tm = {1.0}Ta
activationCD4TrestingNaivePlain {1.0}Tv = {1.0}Ta
clearanceV {1.0}V = {1.0}$EXTERNAL
deathCD4TactiveInfected {1.0}Ttot + {1.0}Tastarstar = {1.0}$EXTERNAL
deathCD4TactivePlain {1.0}Ta + {1.0}Ttot = {1.0}$EXTERNAL
deathCD4TrestingMemoryInfected {1.0}Ttot + {1.0}Tmstarstar = {1.0}$EXTERNAL
deathCD4TrestingMemoryPlain {1.0}Tm + {1.0}Ttot = {1.0}$EXTERNAL
deathCD4TrestingNaivePlain {1.0}Tv + {1.0}Ttot = {1.0}$EXTERNAL
fractionVinfectionCD4T {1.0}Tastarstar = {1.0}Tmstarstar
growthCD4T {1.0}Ta = {1.0}Ttot
sourceCD4T {1.0}$EXTERNAL = {1.0}Ttot + {1.0}Tv
v14 {1.0}$EXTERNAL = {1.0}Tm
v16 {1.0}$EXTERNAL = {1.0}Tmstarstar
v9 {1.0}Tastarstar = {1.0}Ttot
end reactions

begin rate equations
CD4TproductionV = muAA*N0*(1 + (gamma*t^2)/(Tc^2 + t^2))*Tastarstar[t]
VinfectionCD4T = kI*Ta[t]*V[t]
activationCD4TrestingMemoryInfected = kB*Tmstarstar[t]
activationCD4TrestingMemoryPlain = kB*Tm[t]
activationCD4TrestingNaivePlain = kA*Tv[t]
clearanceV = muVV*V[t]
deathCD4TactiveInfected = muAA*Tastarstar[t]
deathCD4TactivePlain = muA*Ta[t]
deathCD4TrestingMemoryInfected = muM*Tmstarstar[t]
deathCD4TrestingMemoryPlain = muM*Tm[t]
deathCD4TrestingNaivePlain = muV*Tv[t]
fractionVinfectionCD4T = kI*phi*Ta[t]*V[t]
growthCD4T = r*Ta[t]*(1 - Ttot[t]/Tmax)
sourceCD4T = s
v14 = 2*r*Ta[t]*(1 - Ttot[t]/Tmax)
v16 = 2*rStar*Tastarstar[t]*(1 - Ttot[t]/Tmax)
v9 = rStar*Tastarstar[t]*(1 - Ttot[t]/Tmax)
end rate equations

begin parameters
N0 = 600.0
Tc = 15000.0
Tmax = 1500.0
gamma = 130.0
kA = 0.00495
kB = 0.0055
kI = 0.0007
muA = 0.02
muAA = 0.5
muM = 0.013
muV = 0.013
muVV = 0.75
phi = 1.0
r = 1.5
rStar = 0.0
s = 8.076
default = 1.0
end parameters

begin initial conditions
Ta[0] = Tai
Tastarstar[0] = Tastarstari
Tm[0] = Tmi
Tmstarstar[0] = Tmstarstari
Ttot[0] = Ttoti
Tv[0] = Tvi
V[0] = Vi
end initial conditions

begin initial values
Tai = 10.0
Tastarstari = 0.0
Tmi = 540.0
Tmstarstari = 0.0
Ttoti = 1000.0
Tvi = 450.0
Vi = 5e-05
end initial values

begin assignment rules
end assignment rules

begin function definitions
end function definitions

begin events
end events

begin process annotations
end process annotations

begin species annotations
end species annotations

begin units
end units