QuantumY <- function (r, J){
##With r being distance and J the spectral overlap
Qo <- 0.60
##Qo is the quantum yield of the donor in the absence of acceptor, this case GFP
K2 <- 2/3
##Dipole orientation factor, for free-flowing 2/3 is a valid assesment
n <- 1.3355
##Refractive index of 5% agarose gel
Nav <- 6.02214179 *10^23
Ro6 <- (9*Qo*log(10, exp(1))*K2*J)/(128*pi^5*n^4*Nav)
E <- 1/(1+(r^6/Ro6))
return(E)
}

r <- vector()
r <- seq(0,1,0.1)

J <- vector()
J <- seq(0,30,1)

QY <- matrix(nrow=length(r), ncol=length(J))
for (dist in 1:length(r)){
for (ovlp in 1:length(J)){
QY[dist,ovlp] <- QuantumY(r[dist], 10^J[ovlp])
}
}

persp(r, J, log(QY), col="lightgreen", theta=45, phi=30, ticktype="detail", 
main="Quantum Yield as a function of r and J", 
ylab="J=10^x", shade=0.5, 
sub="With r distance, and J overlap")