Team:KULeuven/Modeling

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Modeling Overview

1. Description of the whole system

To make predictions for are plasmid transformed E.coli, a structured segregated model is designed in Simbiology. A graphical representation of the model was build in the block diagram editor . Afterwards reaction equations and parameters were added. We designed one model for the whole system and 3 models for 3 subsystems. The 3 subsystems are antifreeze, freeze and cell death. For more information about these 3 subsystems, we refer to the extended project description and the 3 modelling pages: freeze, antifreeze and cell death.

2. Full Model

There are in total 5 different kinetic equations we used in the model Transcription equation For most promoters, hill kinetics is used, it is a way of quantitatively describing cooperative binding processes, it was developed for hemoglobin in 1913. A Hill coefficient (n) is a measure for the cooperativity. Translation equation RNA degradation Protein degration Assimiliation

3. Simulation tests

In the table below the parameters for our full model are displayed. However it was hard to find accurate parameters, because databases for kinetic parameters are limiting.

The parameters used in this model are:

Parameter	Description	Value	Reference
	Active LacI concentration (LacI which is not inactivated by IPTG)	NA	Notation convention
	IPTG concentration	NA	Notation convention
	Delay due to mRNA production	30	BioNumbers with an approximation: all our contructs are around 1-2kb