Team:ETH Zurich/modeling/int

From 2014.igem.org

(Difference between revisions)
(Characterization)
(Assumptions)
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=== Assumptions ===
=== Assumptions ===
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* The back-reaction from DBxb1 binding to site inactive is considered to be negligible, compared to the flipping rate. That is to say that once a site is active, it can only be flipped. Thus, an active site would only be a transitional state in our whole cell model. As the flipping is not modeled in our integrase subsystem, active sites are not transformed into flipped sites at the end of the information pipeline. Thus, we consider that we can express the switching rate given active site concentration.
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;Assumption A
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:The back-reaction from DBxb1 binding to site inactive is considered to be negligible, compared to the flipping rate. That is to say that once a site is active, it can only be flipped. Thus, an active site would only be a transitional state in our whole cell model. As the flipping is not modeled in our integrase subsystem, active sites are not transformed into flipped sites at the end of the information pipeline. Thus, we consider that we can express the switching rate given active site concentration.
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* As switching needs two active sites to be effective (for more information on flipping, check the [https://2014.igem.org/Team:ETH_Zurich/modeling/xor XOR gate page]), the switching rate is approximated to: $${(\frac{SA_{Bxb1}}{S_{TOT}})}^2$$ This approximation is understated by statistical considerations.
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;Assumption B
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:As switching needs two active sites to be effective (for more information on flipping, check the [https://2014.igem.org/Team:ETH_Zurich/modeling/xor XOR gate page]), the switching rate is approximated to: $${(\frac{SA_{Bxb1}}{S_{TOT}})}^2$$ This approximation is understated by statistical considerations.
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* We assume quasi-steady state for SA<sub>Bxb1</sub> and for DBxb1, as they are both involved in binding reactions.
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;Assumption C
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:We assume quasi-steady state for SA<sub>Bxb1</sub> and for DBxb1, as they are both involved in binding reactions.
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* The degradation rate of Bxb1, d<sub>Bxb1</sub>, is related to the degradation rate of DBxb1, d<sub>DBxb1</sub>, by a factor 2. d<sub>Bxb1</sub> = 2 * d<sub>DBxb1</sub>
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;Assumption D
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:The degradation rate of Bxb1, d<sub>Bxb1</sub>, is related to the degradation rate of DBxb1, d<sub>DBxb1</sub>, by a factor 2. d<sub>Bxb1</sub> = 2 * d<sub>DBxb1</sub>
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* The activation by aTc is assumed to be dominant over degradation of Bxb1 and dimerization of Bxb1. It is supposed to be valid on the range of aTc concentration considered.
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;Assumption E
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:The activation by aTc is assumed to be dominant over degradation of Bxb1 and dimerization of Bxb1. It is supposed to be valid on the range of aTc concentration considered.$$\frac{k_{mRNA_{Bxb1}}*(A_L + B_L * \frac{[aTc]^n}{[aTc]^n+K_L^n})}{d_{Bxb1}K_{DBxb1}} >> 1$$ with $$K_{DBxb1} = \frac{k_{-DBxb1} + d_{DBxb1}}{k_{DBxb1}}$$
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$$\frac{k_{mRNA_{Bxb1}}*(A_L + B_L * \frac{[aTc]^n}{[aTc]^n+K_L^n})}{d_{Bxb1}K_{DBxb1}} >> 1$$
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with $$K_{DBxb1} = \frac{k_{-DBxb1} + d_{DBxb1}}{k_{DBxb1}}$$
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=== Parameter fitting ===
=== Parameter fitting ===

Revision as of 11:31, 12 October 2014

iGEM ETH Zurich 2014