EdinburghModeling

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|3 ||ArsD degradation ||ArsD->null|| Mass Action||K3=0.05
|3 ||ArsD degradation ||ArsD->null|| Mass Action||K3=0.05
|-
|-
-
|4 ||ArsD production ||promoter1->promoter1+ArsD||Michaelis-Menton ||V4m=0.5, K4m=75
+
|4 ||ArsD production ||promoter1->promoter1+ArsD||Michaelis-Menten ||V4m=0.5, K4m=75
|-
|-
|5 ||ArsR binding to Arsenic (III) ||ArsR+2As(III)=ArsR-2As(III) ||Mass Action ||K5=1000, K-5=0.65
|5 ||ArsR binding to Arsenic (III) ||ArsR+2As(III)=ArsR-2As(III) ||Mass Action ||K5=1000, K-5=0.65
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|7 ||ArsR degradation ||ArsR->null  ||Mass Action ||K7=0.05
|7 ||ArsR degradation ||ArsR->null  ||Mass Action ||K7=0.05
|-
|-
-
|8 ||ArsR production ||promoter2->promoter2+ArsR ||Michaelis-Menton ||V8m=10, K8m=25
+
|8 ||ArsR production ||promoter2->promoter2+ArsR ||Michaelis-Menten ||V8m=10, K8m=25
|-
|-
|9 ||LacI binding to allolactose ||LacI+allolactose=LacI-allolactose ||Mass Action ||K9=10000, K-9=0.1
|9 ||LacI binding to allolactose ||LacI+allolactose=LacI-allolactose ||Mass Action ||K9=10000, K-9=0.1
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|11 ||LacI degradation ||LacI->null  ||Mass Action ||K11=0.1
|11 ||LacI degradation ||LacI->null  ||Mass Action ||K11=0.1
|-
|-
-
|12 ||LacI production ||promoter3->promoter3+LacI ||Michaelis-Menton ||V12m=0.5, K12m=40
+
|12 ||LacI production ||promoter3->promoter3+LacI ||Michaelis-Menten ||V12m=0.5, K12m=40
|-
|-
|13 ||lacZ degradation ||lacZ->null  ||Mass Action ||K13=0.1
|13 ||lacZ degradation ||lacZ->null  ||Mass Action ||K13=0.1
|-
|-
-
|14 ||lacZ production ||promoter1->promoter1+lacZ ||Michaelis-Menton ||V14m=25, K14m=10
+
|14 ||lacZ production ||promoter1->promoter1+lacZ ||Michaelis-Menten ||V14m=25, K14m=10
|-
|-
|15 ||LCI binding to promoter 4 ||LCI+promoter4=LCI-promoter4 ||Mass Action ||K15=10000, K-15=0.5
|15 ||LCI binding to promoter 4 ||LCI+promoter4=LCI-promoter4 ||Mass Action ||K15=10000, K-15=0.5
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|16 ||LCI degradation ||LCI->null  ||Mass Action ||K16=0.1
|16 ||LCI degradation ||LCI->null  ||Mass Action ||K16=0.1
|-
|-
-
|17 ||LCI production ||promoter2->promoter2+LCI ||Michaelis-Menton ||V17m=10, K17m=25
+
|17 ||LCI production ||promoter2->promoter2+LCI ||Michaelis-Menten ||V17m=10, K17m=25
|-
|-
|18 ||Urease degradation ||Urease->null  ||Mass Action ||K18=0.1
|18 ||Urease degradation ||Urease->null  ||Mass Action ||K18=0.1
|-
|-
-
|19 ||Urease production ||promoter4->promoter4+Urease ||Michaelis-Menton ||V19m=10, K19m=40
+
|19 ||Urease production ||promoter4->promoter4+Urease ||Michaelis-Menten ||V19m=10, K19m=40
|}
|}
Note: The units for first, second and third order rate constants are expressed in units of second^-1, nMol^-1*second^-1 and L^2*nMol^-2*second^-1 respectively.
Note: The units for first, second and third order rate constants are expressed in units of second^-1, nMol^-1*second^-1 and L^2*nMol^-2*second^-1 respectively.

Revision as of 22:00, 11 September 2006

System Diagram of Arsenic Biosensor

Model Diagram2.JPG

Reaction set

No. Name Equation Rate Law Parameters
1 ArsD binding to Arsenic (III) ArsD+2As(III)=ArsD-2As(III)Mass Action K1=1000 K-1=0.65
2 ArsD binding to promoter1 2 ArsD+promoter1=2ArsD-promoter1 Mass ActionK2=10000, K-2=0.65
3 ArsD degradation ArsD->null Mass ActionK3=0.05
4 ArsD production promoter1->promoter1+ArsDMichaelis-Menten V4m=0.5, K4m=75
5 ArsR binding to Arsenic (III) ArsR+2As(III)=ArsR-2As(III) Mass Action K5=1000, K-5=0.65
6 ArsR binding to promoter2 2ArsR+promoter2=2ArsR-promoter2 Mass Action K6=10000, K-6=0.65
7 ArsR degradation ArsR->null Mass Action K7=0.05
8 ArsR production promoter2->promoter2+ArsR Michaelis-Menten V8m=10, K8m=25
9 LacI binding to allolactose LacI+allolactose=LacI-allolactose Mass Action K9=10000, K-9=0.1
10 LacI binding to promoter4 LacI+promoter4 = LacI-promoter4 Mass Action K10=1000, K-10=0.5
11 LacI degradation LacI->null Mass Action K11=0.1
12 LacI production promoter3->promoter3+LacI Michaelis-Menten V12m=0.5, K12m=40
13 lacZ degradation lacZ->null Mass Action K13=0.1
14 lacZ production promoter1->promoter1+lacZ Michaelis-Menten V14m=25, K14m=10
15 LCI binding to promoter 4 LCI+promoter4=LCI-promoter4 Mass Action K15=10000, K-15=0.5
16 LCI degradation LCI->null Mass Action K16=0.1
17 LCI production promoter2->promoter2+LCI Michaelis-Menten V17m=10, K17m=25
18 Urease degradation Urease->null Mass Action K18=0.1
19 Urease production promoter4->promoter4+Urease Michaelis-Menten V19m=10, K19m=40

Note: The units for first, second and third order rate constants are expressed in units of second^-1, nMol^-1*second^-1 and L^2*nMol^-2*second^-1 respectively.

Intial concentration

No. Species Intial Concentration (nMol/L)
1 ArsD 25
2 As(III) 40
3 2ArsD-promoter1 25
4 promoter1 5
5 ArsR 25
6 2ArsR-promoter2 25
7 promoter2 5
8 LCI 4
9 LacI 0.1
10 LacI-allolactose 0.1
11 allolactose 1000
12 LacI-promoter4 0.1
13 promoter4 25
14 LCI-promoter4 0.1
15 Urease 0.1
16 promoter3 5
17 Other species 0
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