Team:ETH Zurich/Modeling

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Contents

Overview

To support our colleagues in the lab, we outlined different models for different parts of our project.

Photoinduction

Figure 1: Photoconversion cross sections calculated for various receptors. "-a/d" indicate activation and deactivation of a receptor.

To calculate the activity of light receptors, we devised a model that takes emission spectra of different light sources and absorption spectra, quantum yield and extinction coefficients of the receptors from literature as an input and returns the activation and deactivation constants for the given light conditions.

This model can be used to calculate the activity of a light receptor in a light condition. Together with an mechanistical model of the receptor, it gives an estimate of the transcriptional activation due to light input.

See all the details in Team:ETH_Zurich/Modeling/Photoinduction.


Reaction Network ODE model

Figure 2: Overall circuit design for our decoder

To decode our light receptor input, we created a full deterministic ODE model with the software Ru2ren. As an input to the decoder, we used the constants from our photoconversion model and a mechanistical model of the receptor mode of action.

For this, we have envisioned two circuits:

  1. UVR8-based protection system
  2. Dual LovTAP-Cph1 system

These are described in further detail on the individual pages.



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