Figure 3

Parameter sweeping. Parameter sweeping. Here, we compare two versions of the gene expression model, one incorporating the host cell genome and one excluding it. The RNA polymerase on-rate constant for binding to the promoter that produces the reporter mRNA is varied until the percentage difference between these models exceeds 5% (the value we have selected as our threshold for a significant difference between the two models, marked by a horizontal dashed line on each plot). The on-rate is first varied by a factor of 10 to determine the general location of the desired value (plot A, left), followed by a sweep on a finer scale to narrow in on an approximately linear region near the threshold crossing (plot B, right). The solid vertical line in Graph B shows the interpolated on-rate constant when the percent difference in transcript production between models crosses the 5% threshold. The parameters for this example are: doubling time = 24 min; plasmid copy number = 10; gene length = 10 bp; and mRNA half-life = 6 min.