Modeling
Contents
Introduction
Overview
This report is trying to give a qualitative description of our team’s desalination tool. Before we enter the modelling part of this report, I want to give some basic ideas of our team’s project and some mathematical tools I will use during the modelling. Our team’s project focuses on the worldwide problem-shortage of fresh water. We try to modify the cyanobacterium via the methods and tools of biosynthesis. We want to im-plant the Natronomonas pharaonis halorhodopsin(pHR), which is an archaeal rhodopsin functioning as an inward-directed, lightdriven Cl − pump, into the cyanobacterium. We want to use this protein carried by cyanobacterium and driven by light energy to desalinate the sea water. That’s the very general idea of our project. At the meantime, we modify the corresponding promoter of pHR which makes the expression of pHR inhibited in dark environment. Such a promoter is just like a switch which could control the expression of pHR by the environment. Then, the whole working landscape of our modified cyanobacterium could be divided as following steps:
- Natural Growth
- Dark Expression
- Starving Working
I will explain each process in detail in the following sections.
Natural Growth Process
This process is just as straight forward as its name. In this process, we need our modified cyanobacterium grows naturally to a appropriate population number. The process is mainly determined by the target volume of sea water. It is plain in experiment sense. However, in modelling sense, we need a growth model to describe this process or have a method to measure the density in the end of this process. The reason I will explain later.
Dark Expression Process
In dark expression process, we put our modified cyanobacterium in dark environment. The duration of this process will directly affect the expression level of pHR. The expression level of pHR is critical for the next stage and modelling. In this process, we also need a dark expression model or a method to measure the average expression level of pHR in the end of this process because of the same reason as natural growth process.
Starving Working Process
Starving working process is the most important one. In this process, we need our modified cyanobacterium been in starving status. Then, provided with specific wavelength 3light, the pHR could tranport the Cl − against the gradient of Cl − concentration and reach the purpose of desalination.
Modeling Intro.
As you can see, our team’s project involves a seris of processes. A complete modelling of our bio-system should at least consist of three model: growth model, dark expression model and starving working model. However, it is not necessary and also not wise to model all process one by one. Our focus should put on the last process-starving working process but it is obvious that the result of previous process could affect the fianl process significantly. Thus some parameters in the model of last process, we need obtain by experiment methods. Here I list some parameters reserved for previous process or outside environment:
- The density of cyanobacterium
- The expression level of pHR
- The intensity of light
- The initial concentration of Cl −
Modeling
Assumptions
Variables
Details
Simulation
Conclusion
References
[1] Heterologous Expression of Pharaonis Halorhodopsin in Xenopus laevis Oocytes and Electrophysiological Characterization of Its Light-Driven Cl − Pump Activity Akiteru Seki et al. Biophysical Journal Volume 92 April 2007 2559–2569 2559
[2] Mathematical Physiology James Keener James Sneyd ISBN 978-0-387-75846-6
