Team:Kyoto/GSDD/Modelling

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Modelling

Modelling

Recently, many biologists try to grasp biological systems behavior with computational and mathematical approach. But, when we make a model, in its process, we are apt to lose our sight about what kind things we want to grasp with those approach. So this time firstly we set our position to be clear.

In our simulation, we want to make our intuitive anticipation in our project to be more likely. By making some simple equations and numerically calculating it, we can confirm whether it is theoretically certain or not.

This time we check timer vector’s behavior after we transform yeast with it, for the simplization, we assume each number of base pairs cut off by the end replication problem to be 100 bps. Actually in each replication, by the fluctuation of the length of RNA primers, which are used in the DNA replication at the part of 5’ directing side from replication origin, and by the randomness of the length cut off by the end replication problem, the number of base pairs lost in the process distributes from 0 to about 200 bps.

And we assume the number of cell changes only by the effect of the behavior of timer vector and each cell has no interaction with other cells. In addition, we assume the life duration does not exist and cells die only because of the behavior of timer vector.

Lastly we set the length of LacI binding site repeated sequence to be 10,000 bps. Then we express following equations about cell population and numerically analyze its time development.

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 ==Modelling==
-In recent biology, many biologists try to grasp biological phenomenon with computational, mathematical approach. The purpose of biological simulation is divided into two types; to predict system’s future behavior and to grasp and simplize system’s essential behavior. So when we make some models, we should always consider our own position, on where point we are standing. Otherwise we might lose sight of why we are making it and the result will not show any biological importance.
+Recently, many biologists try to grasp biological systems behavior with computational and mathematical approach. But, when we make a model, in its process, we are apt to lose our sight about what kind things we want to grasp with those approach. So this time firstly we set our position to be clear.
-This time we simulated the behavior of our designed parts with very simple mathematics.
+In our simulation, we want to make our intuitive anticipation in our project to be more likely. By making some simple equations and numerically calculating it, we can confirm whether it is theoretically certain or not.
-===Assumption===
+This time we check timer vector’s behavior after we transform yeast with it, for the simplization, we assume each number of base pairs cut off by the end replication problem to be 100 bps. Actually in each replication, by the fluctuation of the length of RNA primers, which are used in the DNA replication at the part of 5’ directing side from replication origin, and by the randomness of the length cut off by the end replication problem, the number of base pairs lost in the process distributes from 0 to about 200 bps.
-===Condition===
+And we assume the number of cell changes only by the effect of the behavior of timer vector and each cell has no interaction with other cells. In addition, we assume the life duration does not exist and cells die only because of the behavior of timer vector.
-In this modeling we assumed following conditions.
-#
-#
-#
-#
-===Expression===
-===Result of Numerical Calculation===
-===Discussion===
+Lastly we set the length of LacI binding site repeated sequence to be 10,000 bps. Then we express following equations about cell population and numerically analyze its time development.
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