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Modeling

Introduction

We have also modeled the improved flip-flop. This models is an extension of the Basic Flip-Flop model. The main reactions at that model were:.

TRANSCRIPTION: RNAp + Promoter → RNAp + Promoter + mRNA

The mRNA production is described using Michaelis-Menten kinetics.

TRANSLATION: mRNA + Ribosomes → mRNA + Ribosomes + Repressor

The Repressor production is also modeled using Michaelis-Menten kinetics.

REPRESSION: Promoter + n · Repressor → Promoter_Repressor_n

Finally we use a Hill kinetics model for the transcription inhibition, which offers an approximation to the cooperative action.

In the new model, we have to include the new reactions involved in the Improved Flip-Flop. These are:

PROTEOLYSIS: Protease + Repressor 1 → Protease

We will consider a mass action rate law, where the protein will be digested according to the protease concentration.

INHIBITION of TRANSLATION: asRNA + mRNA → RNA complex

We assume a mass action rate law again.

Diagram

These two new effects may enhance the robustness of the toggle switch. We will analyze their effects by implementing the model in Simbiology. The following diagram shows all the species and reactions of the model:

Here we can see all the species involved in the new model for the bistable.

The model can be downloaded here:

In the next section, we describe in detail the equations of the model