Aims of the model

Our strategy was based on an input with a quorum sensing molecule production, a molecular communication between two organisms, and an output with the antimicrobial peptides effect. We needed to use a model to simulate this biological system and analyze if this communication was feasible:

Would the quorum sensing molecule (CAI-1) induce a sufficient answer to activate the sensor (Vibrio harveyi)? Would the receptor be able to produce enough molecular message (diacetyl) to communicate with the effector Pichia pastoris? Would the effector produce enough antimicrobial peptides to deliver the guessed output, which is the lysis of V. cholerae to reach a non-toxic concentration?

A model was also crucial regarding the entrepreneurship and the integrated human practices parts of our project: we needed to show to clients and investors, but also to citizens, how our system would work, how we will dimensionate our device, and how long do you have to wait before drinking a non-contaminated water.

To sum up, the goals of our model could be sum up into four objectives:

• Demonstrate the feasibility
• Confirm our wet lab strategy
• Dimensionate
• Estimate the waiting time

Approaches

Two complementary approaches have been used to represent our model. Working with a complex biological system involving three microorganisms and several molecules, the Systemic Biology Graphical Notation (SBGN) was a perfect way to ordinate the system and represent the interactions between organisms and the molecules involved.

The SBGN representation was convenient to elaborate the Ordinary Differential Equations (ODEs) system, which is our second approach. Starting with a complex system, choices have been made to simplify some molecular cascades or some interactions to reduce it to a system of 12 differential equations.