Last data update: 2014.03.03

R: Analytic model solutions for fluorescence intensity
 analyticSolutions R Documentation

## Analytic model solutions for fluorescence intensity

### Description

Time-dependent and steady-state analytic solution to one-step model for number of mature fluorophores. Where `f` is given as a parameter the returned value is transformed from a molecular population into a fluorescence intensity. For the function names, 0 refers to the dark population of non-mature fluorophores, and 1 to the mature, fluorescent population. 'ss' indicates steady-state solutions. `tss` is the time required to reach steady-state.

### Usage

```tss(m, k)
x0ss(p, m, k)
x1(p, m, k, t, f=1)
x1ss(p, m, k, f=1)
x1fretFP1(p, m1, m2, k, t, E=0, f=1)
x1fretFP1ss(p, m1, m2, k, E=0, f=1)
```

### Arguments

 `p` Protein production rate (molecules produced per unit time). `m` Maturation rate of fluorophore, which can be for either FP1 or FP2 (convert to maturation time with log(2)/m). `m1` Maturation rate of FP1. `m2` Maturation rate of FP2. `k` Protein degradation rate (convert to half-life with log(2)/k). `t` Time (must be non-negative). `E` FRET coefficient representing energy transfer from FP1 to FP2. `f` Proportionality factor relating intensity to the number of molecules. When equal to one then the readout is number of molecules directly.

### Value

A numeric specifying the model solution for the given parameters.

Joseph D. Barry

### Examples

```t0 <- seq(0.001, 1000, by=0.1)
plot(t0, x1(p=10, m=log(2)/5, k=log(2)/100, t=t0), type="l", col="darkgreen",
lwd=2, xlab="Time (min)", ylab="Number of mature fluorophores", cex.lab=1.4)
```

### Results

```
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(TimerQuant)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/TimerQuant/x1.Rd_%03d_medium.png", width=480, height=480)
> ### Name: analyticSolutions
> ### Title: Analytic model solutions for fluorescence intensity
> ### Aliases: tss x0ss x1 x1ss x1fretFP1 x1fretFP1ss
> ### Keywords: x1
>
> ### ** Examples
>
> t0 <- seq(0.001, 1000, by=0.1)
> plot(t0, x1(p=10, m=log(2)/5, k=log(2)/100, t=t0), type="l", col="darkgreen",
+     lwd=2, xlab="Time (min)", ylab="Number of mature fluorophores", cex.lab=1.4)
>
>
>
>
>
> dev.off()
null device
1
>

```