Team:Freiburg/Model

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Modeling

Modeling in synthetic biology and iGEM Freiburg 2017

In synthetic biology, modeling can be applied to a wide range of topics, for example modeling of genetic circuits to predict their outcome and to support, if enough data is available, further development such as optimizing genetic circuits for a desired outcome.

In this subfield of mathematical and computational biology, ordinary differential equations (ODEs) are used to describe the transcriptional and translational process (Chen et al., 1999). ODEs consist of a set of parameters and a system of functions and their derivatives. How they can be set up in their simplest form is shown below.

$f^{\text{'}}\left(t\right)=y\left(z\right)-k1*f\left(t\right)$

(1)

$z\text{'}\left(x\right)=k2*f\left(t\right)-k3*z\left(t\right)$

(2)

The variables are functions of time t where $f\left(t\right)$ describes the mRNA concentration, $y\left(z\right)$ the transcription function and $z\left(t\right)$ the protein concentration. Rate constants are enlisted in the following table.

Rate constant	Description
$k1$	mRNA degradation rate
$k2$	Translation rate
$k3$	Protein degradation rate