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Team:SCUT/Model/Overview
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The design and redesign is one of the hallmarks of synthesis biology. In order to test the consistence of the pathway we designed and the function of scaffold we used, modeling is the most powerful tool to be used before doing experiments. | The design and redesign is one of the hallmarks of synthesis biology. In order to test the consistence of the pathway we designed and the function of scaffold we used, modeling is the most powerful tool to be used before doing experiments. | ||
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For the carbon dioxide fixed part, we use<span> ODEs (ordinary differential equations)</span> to <span>simulate the pathway</span> and proof <span>the function of RuBisCo</span>. With the help of <span>parameter sweep</span>, we find out the <span>optimal reaction rate ratio</span> of the reactions involved in the scaffold. By the way ,we also use <span>the“bottom-up” strategy</span>, the most famous principle of Computer Science, to guide our work. | For the carbon dioxide fixed part, we use<span> ODEs (ordinary differential equations)</span> to <span>simulate the pathway</span> and proof <span>the function of RuBisCo</span>. With the help of <span>parameter sweep</span>, we find out the <span>optimal reaction rate ratio</span> of the reactions involved in the scaffold. By the way ,we also use <span>the“bottom-up” strategy</span>, the most famous principle of Computer Science, to guide our work. | ||
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Revision as of 04:59, 16 October 2014
Background
The design and redesign is one of the hallmarks of synthesis biology. In order to test the consistence of the pathway we designed and the function of scaffold we used, modeling is the most powerful tool to be used before doing experiments.
Carbon dioxide fixed part
For the carbon dioxide fixed part, we use ODEs (ordinary differential equations) to simulate the pathway and proof the function of RuBisCo. With the help of parameter sweep, we find out the optimal reaction rate ratio of the reactions involved in the scaffold. By the way ,we also use the“bottom-up” strategy, the most famous principle of Computer Science, to guide our work.
n-butanol part
For the n-butanol part, in order to simulate the n-butanol biosynthetic pathway in Saccharomyces cerevisiae mitochondria, we construct a model by using Michealis-Menton kinetics and ODEs (ordinary differential equations). The model shows that, with high concentrations of NADH and NADPH in mitochondria, the production of n-butanol will be greatly improved.
Besides, all of our programs run on the MATLAB.
