Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.
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Transcript of Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.
![Page 1: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/1.jpg)
Simulating A Gene Regulatory Network (GRN)
A Delay Flip-Flop Implementation
![Page 2: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/2.jpg)
2
Outline Simulation Hill Equation Michaelis-Menten BioD Results
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Outline Simulation Hill Equation Michaelis-Menten BioD Results
![Page 4: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/4.jpg)
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Simulation
Why do we simulate ?
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Simulation Cost effective Fast Proven method
An “analytic” model is appropriate when mathematics can be used to find the exact (deterministic) or probable (stochastic) values of the measures of performance.
We cannot test
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Outline Simulation Hill Equation Michaelis-Menten BioD Results
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Outline Simulation Hill Equation Michaelis-Menten BioD Results
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Hill Equation
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Hill Equation
ndegradatio
R from inhibition
tion transcripmax.
][][
1
1.
][mX
KRdt
mXdmXn
R
Q R
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Hill Equation
ndegradatio
R from inhibition
leakagetion transcripmax.
][][
1
1.1.
][mX
KR
aadt
mXdmXn
R
Q R
![Page 11: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/11.jpg)
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Hill Equation
ndegradatio
R2 from inhibition
2
R1 from inhibition
1
leakagetion transcripmax.
][]2[
1
1.
]1[1
1.1.
][21
mX
KR
KR
aadt
mXdmXn
R
n
R
Q RR
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Hill Equation
ndegradatio
A from activationR from inhibition
leakagetion transcripmax.
][][
1
][
.][
1
1.1.
][mX
KA
KA
KR
aadt
mXdmXn
A
n
An
R
Q A
A
R
![Page 13: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/13.jpg)
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Outline Simulation Hill Equation Michaelis-Menten BioD Results
![Page 14: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/14.jpg)
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Outline Simulation Hill Equation Michaelis-Menten BioD Results
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Michaelis-Menten
http://en.wikipedia.org/wiki/Enzyme_kinetics
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Outline Simulation Hill Equation Michaelis-Menten BioD Results
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Outline Simulation Hill Equation Michaelis-Menten BioD Results
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BioD
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BioD
][]4[
1
][4
4
1 mCIcr
KGaldt
mCIcrdmCIcrn
Gal
Gal
![Page 20: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/20.jpg)
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BioD
][][
1
][
.][
1
1.
][1
][mCI
KOmpR
KOmpR
KOmpRP
KCIIdt
mCIdmCIn
OmpR
n
OmpR
n
OmpRP
n
CII
ompf
OmpR
OmpR
OmpRPCII
![Page 21: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/21.jpg)
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BioD
OmpR
OmpR
OmpRPCI n
OmpR
n
OmpR
n
OmpRP
n
CI
ompf
KOmpR
KOmpR
KOmpRP
KCIdt
mCIId
][1
][
.][
1
1.
][1
][
![Page 22: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/22.jpg)
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BioD
][][
1
][ 2 mCII
KCIdt
mCIIdmCIIn
CI
CI
![Page 23: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/23.jpg)
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BioD
][][
3 mOmpRdt
mOmpRdmOmpR
![Page 24: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/24.jpg)
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BioD
]4[][
1
][
.][
1
1.
][1
]4[4 mGal
KOmpR
KOmpR
KOmpRP
KCIdt
mGaldmGaln
OmpR
n
OmpR
n
OmpRP
n
CI
ompf
OmpR
OmpR
OmpRPCI
![Page 25: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/25.jpg)
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BioD
OmpR
OmpR
OmpRPCI n
OmpR
n
OmpR
n
OmpRP
n
CI
ompf
KOmpR
KOmpR
KOmpRP
KCIdt
mTetRd
][1
][
.][
1
1.
][1
][
![Page 26: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/26.jpg)
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BioD
][][
1
][ 6 mTetR
KLacIdt
mTetRdmTetRn
LacI
LacI
![Page 27: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/27.jpg)
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BioD
OmpR
OmpR
OmpRPCII n
OmpR
n
OmpR
n
OmpRP
n
CII
ompf
KOmpR
KOmpR
KOmpRP
KCIIdt
mLacId
][1
][
.][
1
1.
][1
][
![Page 28: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/28.jpg)
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BioD
][][
1
][ 7 mLacI
KTetRdt
mLacIdmLacIn
TetR
TetR
![Page 29: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/29.jpg)
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BioD
].[].[][
CIImCIIdt
CIIdCIICII
![Page 30: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/30.jpg)
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BioD
].[].[][
CImCIdt
CIdCICI
![Page 31: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/31.jpg)
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].[].[]].[12[
.][
12
CImCIK
mCIcrtaR
dt
CIdCICI
taRCI
BioD
![Page 32: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/32.jpg)
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Law of Mass Action
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].[].[]].[12[
.][
12
CImCIK
mCIcrtaR
dt
CIdCICI
taRCI
BioD
![Page 34: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/34.jpg)
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BioD
].[].[][
OmpRmOmpRdt
OmpRdOmpROmpR
![Page 35: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/35.jpg)
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BioD
][
]).[1.(].[
][
OmpRk
OmpRLVOmpRPV
dt
OmpRd
phos
phosdePhos
![Page 36: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/36.jpg)
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BioD
].[].[][
]).[1.(][OmpRPOmpRPV
OmpRk
OmpRLV
dt
OmpRPdOmpRPdePhos
phos
phos
![Page 37: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/37.jpg)
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BioD
]4.[]4.[]4[
44 GalmGaldt
GaldGalGal
![Page 38: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/38.jpg)
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BioD
].[].[][
TetRmTetRdt
TetRdTetRTetR
![Page 39: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/39.jpg)
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BioD
].[].[][
LacImLacIdt
LacIdLacILacI
![Page 40: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/40.jpg)
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Outline Simulation Hill Equation Michaelis-Menten BioD Results
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Outline Simulation Hill Equation Michaelis-Menten BioD Results
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Results
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BioD
![Page 44: Simulating A Gene Regulatory Network (GRN) A Delay Flip-Flop Implementation.](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da75503460f94a9348d/html5/thumbnails/44.jpg)
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Results
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Results
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Results
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Results
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Results
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BioD
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Results
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Results
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Results
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Results
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Questions…