Schematic representation of the simulation process.

<p>The <b>upper panel</b> of the figure represents the error structure of the model as discussed under ‘evaluation of the sources of variation’. Arrows represent deterministic relations whereas represents the introduction of random variation (represented as an additive process for the sake of simplicity). The <b>middle panel</b> of the figure illustrates how the number of primers in cycle n () is calculated from the initial number of primers () using the cycle efficiencies () and the loss due to side processes (). The <b>lower panel</b> of the figure represents the sequential application of the mathematical model. Within each phase the simulation repeats the same three steps: (<b>1</b>) the number of template copies accumulated during the previous cycles () is converted to fluorescence () by multiplication with . (<b>2</b>) the fluorescence level yields the efficiency by which the template will by duplicated during the current cycle () by using either <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047112#pone.0047112.e259" target="_blank">equation 5</a> or 1 depending on the phase. In step (<b>3</b>) the actual amplification takes place: is multiplied by yielding . This marks the end of the ()th cycle.