Difference between revisions of "Team:ZJUT-China/Model"
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| − | Our ODE model of the light-controlled arg cutting system ver1.0 . We assumed that the expression rate is proportional to the copy number of the vectors, and vm means the mixture rate of one vector express the cas9, [light signal] we use is a dimensionless parameter here, and the cut off rate of cas9 conform Michaelis-Menten equation. | + | Our ODE model of the light-controlled arg cutting system ver1.0 . We assumed that the expression rate is proportional to the copy number of the vectors, and vm means the mixture rate of one vector express the cas9, [light signal] we use is a dimensionless parameter here, and the cut-off rate of cas9 conform the Michaelis-Menten equation. |
</div> | </div> | ||
<h1>Result</h1> | <h1>Result</h1> | ||
<p> | <p> | ||
| − | This is the result we | + | This is the result we got by the ODE model of the light-controlled arg cutting system ver1.0 |
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<div class="modelingimg"> | <div class="modelingimg"> | ||
<img src="https://static.igem.org/mediawiki/2018/6/6c/T--ZJUT-China--modeling1.png" alt=""> | <img src="https://static.igem.org/mediawiki/2018/6/6c/T--ZJUT-China--modeling1.png" alt=""> | ||
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| − | <h1>System modeling | + | <h1>System modeling Ver3.0</h1> |
<p> | <p> | ||
| − | This presents an issue for researchers and factors who wish to make use of our system of the arg killing parts in a more complex environment. In order to address this issue, we decided to develop a mathematical model of how light signal effects influence the time of | + | This presents an issue for researchers and factors who wish to make use of our system of the arg killing parts in a more complex environment. In order to address this issue, we decided to develop a mathematical model of how light signal effects influence the time of cutting off all args and bacteria's suicide induced by our arg killing system. |
| − | In the light | + | In the light-controlled arg cutting system ver3.0 we want to add 3 repressors, one more sgRNA, and a lysin gene to make our cells can cut off all the args and then suicide in chronological order which is designed. |
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| − | Our ODE model of the light | + | Our ODE model of the light-controlled arg cutting system ver3.0. In this model we considered the expression and degrading rate of the repressor and the effect of the copy numbers of two vectors. |
</div> | </div> | ||
<p> | <p> | ||
| − | Through | + | Through changing the copy numbers of two vectors in our system model, we could get a ratio of the copy numbers letting our system do nothing before we give the light signal, while having a higher reacting rate when we want it to work. |
</p> | </p> | ||
<h1>Result</h1> | <h1>Result</h1> | ||
Revision as of 14:36, 13 October 2018
Team:ZJUT-China
Abstract
In order to make sure that our system could be common used by the researchers who want to clean the arg after experiments, we developed a model to Calculate the point when all arg are cleaned and the bacteria suicide. We got test data of our parts and then built rate equations. And next we used those rate equations to simulate how our system work and tried to find a better ratio of the vector’s copy number.
System modeling Var1.0
d[cut off]/dt=kf*[sg]*[cas9]*[arg]/(km+[arg])
Result
This is the result we got by the ODE model of the light-controlled arg cutting system ver1.0
System modeling Ver3.0
This presents an issue for researchers and factors who wish to make use of our system of the arg killing parts in a more complex environment. In order to address this issue, we decided to develop a mathematical model of how light signal effects influence the time of cutting off all args and bacteria's suicide induced by our arg killing system.
In the light-controlled arg cutting system ver3.0 we want to add 3 repressors, one more sgRNA, and a lysin gene to make our cells can cut off all the args and then suicide in chronological order which is designed.
d[degrade_r1]/t=vm*[repressor_1]/([repressor_1]+km)
d[express_r2]/t=kf*[vector_2]
d[degrade_r2]/t=vm*[repressor_2]/([repressor_2]+km)
d[express_r3]/t=kf*[vector_1]
d[degrade_r3]/t=vm*[repressor_3]/([repressor_3]+km)
d[express_cas]/t=kf*[vector_1]*(vm-[repressor_1])
d[express_sg1]/t=0
d[express_sg2]/t=kf*[vector_2]*(vm-[repressor_2])
d[express_ly]/t=kf*[chromosome]*(vm-[repressor_3])
d[cut off_1]/t=kf*[arg_1]*[sg_1]*[cas9]/(km+[arg_1])
d[cut off_2]/t=kf*[arg_2]*[sg_2]*[cas9]/(km+[arg_2])
Through changing the copy numbers of two vectors in our system model, we could get a ratio of the copy numbers letting our system do nothing before we give the light signal, while having a higher reacting rate when we want it to work.
Result
Discussion
Our modeling and analysis was focused to achieve a better theoretical grounding of forecasting how our system work after we give the light signal. From the test of our ODE model of the light control arg cutting system var3.0, we find give a short pulse light signal can make almost same effect as we constant light signal, so we can find a plan to just give a short pulse light signal but make our system till response as fast as it, and save energy used to give the light signal.
