Team:AUC TURKEY/Project/Modelling

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Latest revision as of 17:35, 26 April 2015

A KINETIC MODEL IN MATLAB

How did we build it???

Using the SimBiology toolbox for MATLAB we created a framework of the enzyme kinetic modelling(Figure 1).

HRP + H2O2 → ES1 (HRP compound I) + MG → ES2(MG_ox+HRP compound II)

After creating the basic framework for the model we needed to create mathematical equations for each reaction with appropriate rate constants. These equations and the corresponding values are shown below in Tables 1 and 2.

Reaction Name:	Reaction Scheme:	Reaction Rate:
oxidation reaction	H2O2 + HRP -> ES1	k1H2O2HRP
decolourization reaction	ES1 + MG -> ES2	k2ES1MG

Table1: Mathematical representation of enzyme kinetic reaction expression and the subsequent production of the oxidized dye. Constants are described in Table 2.

Constant:	Value:	Units:	References:
k1	0.0018	1/(µmolarity*min)	Viridiana S. Ferreira-Leitão (2002)
k1r	neglected	-
k2	0.004	1/(µmolarity*min)	Viridiana S. Ferreira-Leitão (2002)
k2r	neglected	-

Table 2: Values assigned to kinetic parameters described in Table 1. We ignored k1r and k2r values because of k1>>>>k1r and k2>>>k2r, so our both reactions act as irreversible.

Rule Name:	Rate Rules:
HRP	dE/dt = - k1[E][S1]+k1r[ES1]
H2O2	dS1/dt = -k1[E][S1]+k1r[ES1]
ES1 (HRP compound I)	dES1/dt =k1[E][S1] –k1r[ES1]-k2[ES1][S2]+k2r[ES2]
Methyl Green (MG)	dS2/dt = -k2[ES1][S2] +k2r[ES2]
ES2 (MGox +LiP compound II)	dES2/dt = k2[ES1][S2] – k2r[ES2]

Table3: Differential equations of reactions.

What did it show???

Before running the model we needed to decide what an appropriate endpoint of reaction would be. Therefore, concentrations of species were determined from the literature and necessary assumptions were made to check our cascade reactions work correctly.

According to chosen references points, we were trying to determine how quickly we could get a decolourization. Decolourization depends on final [ES2] (MG_ox+HRP compound II) concentration and degradation of MB.

Decolourization starts in 40 minutes.

Reaction Name:	Reaction Scheme:	Reaction Rate:
oxidation reaction	H2O2 + HRP -> ES1	k1H2O2HRP
decolorization reaction	ES1 + MB -> ES2	k2ES1MB

Table 4: Mathematical representation of enzyme kinetic reaction expression and the subsequent production of the oxidized dye. Constants are described in Table 5.

Constant:	Value:	Units:	References:
k1	0.0018	1/(µmolarity*min)	Viridiana S. Ferreira-Leitão (2002)
k1r	neglected	-
k2	0.004	1/(µmolarity*min)	Viridiana S. Ferreira-Leitão (2002)
k2r	neglected	-

Table 5: Values assigned to kinetic parameters described in Table 4. We ignored k1r and k2r values because of k1>>>>k1r and k2>>>k2r, so our both reactions act as irreversible.

Rule Name:	Rate Rules:
HRP	dE/dt = - k1[E][S1]+k1r[ES1]
H2O2	dS1/dt = -k1[E][S1]+k1r[ES1]
ES1 (HRP compound I)	dES1/dt =k1[E][S1] –k1r[ES1]-k2[ES1][S2]+k2r[ES2]
Methylen Blue (MB)	dS2/dt = -k2[ES1][S2] +k2r[ES2]
ES2 (MBox +LiP compound II)	dES2/dt = k2[ES1][S2] – k2r[ES2]

Table6: Differential equations of reactions.

1hour of HRP- MB decolourization

What did it show???

Before running the model we needed to decide what an appropriate endpoint of reaction would be. Therefore, concentrations of species were determined from the literature and necessary assumptions were made to check our cascade reactions work correctly.

According to chosen references points, we were trying to determine how quickly we could get a decolourization. Decolourization depends on final [ES2] (MB_ox+LiP compound II) concentration and degradation of MB.

Decolourization starts in 40 minutes.

LiP + H2O2 →ES1 (LiP compound I ) + MB → ES2 (MB_ox+LiP compound II)

Reaction Name:	Reaction Scheme:	Reaction Rate:
oxidation reaction	H2O2 + LiP -> ES1	k1H2O2LiP
decolorization reaction	ES1 + MB -> ES2	k2ES1MB

Table7: Mathematical representation of enzyme kinetic reaction expression and the subsequent production of the oxidized dye. Constants are described in Table 8.

Constant:	Value:	Units:	References:
k1	1.0E-4	1/(µmolarity*min)	Paulı Ollıkka, Kırsı Alhonmakı (1993)
k1r	neglected	-
k2	2.0E-4	1/(µmolarity*min)	Paulı Ollıkka, Kırsı Alhonmakı (1993)
k2r	neglected	-

Table 8: Values assigned to kinetic parameters described in Table 7. We ignored k1r and k2r values because of k1>>>>k1r and k2>>>k2r, so our both reactions act as irreversible.

Rule Name:	Rate Rules:
HRP	dE/dt = - k1[E][S1]+k1r[ES1]
H2O2	dS1/dt = -k1[E][S1]+k1r[ES1]
ES1 (HRP compound I)	dES1/dt =k1[E][S1] –k1r[ES1]-k2[ES1][S2]+k2r[ES2]
Methylen Blue (MB)	dS2/dt = -k2[ES1][S2] +k2r[ES2]
ES2 (MBox +LiP compound II)	dES2/dt = k2[ES1][S2] – k2r[ES2]

Table9: Differential equations of reactions.

6 hours of Lip- MG decolourization

What did it show???

Before running the model we needed to decide what an appropriate endpoint of reaction would be. Therefore, concentrations of species were determined from the literature and necessary assumptions were made to check our cascade reactions work correctly.

According to chosen references points, we were trying to determine how quickly we could get a decolourization. Decolourization depends on final [ES2] (Mg_ox+Lip compound II) concentration and degradation of MG.

Decolourization starts in 40 minutes.

Reaction Name:	Reaction Scheme:	Reaction Rate:
oxidation reaction	H2O2 + LiP -> ES1	k1H2O2LiP
decolourization reaction	ES1 + MG -> ES2	k2ES1MG

Table10: Mathematical representation of enzyme kinetic reaction expression and the subsequent production of the oxidized dye. Constants are described in Table 11.

Constant:	Value:	Units:	References:
k1	1.0E-4	1/(µmolarity*min)	Paulı Ollıkka, Kırsı Alhonmakı (1993)
k1r	neglected	-
k2	2.0E-4	1/(µmolarity*min)	Paulı Ollıkka, Kırsı Alhonmakı (1993)
k2r	neglected	-

Table 11: Values assigned to kinetic parameters described in Table 10. We ignored k1r and k2r values because of k1>>>>k1r and k2>>>k2r, so our both reactions act as irreversible

Rule Name:	Rate Rules:
HRP	dE/dt = - k1[E][S1]+k1r[ES1]
H2O2	dS1/dt = -k1[E][S1]+k1r[ES1]
ES1 (HRP compound I)	dES1/dt =k1[E][S1] –k1r[ES1]-k2[ES1][S2]+k2r[ES2]
Methyl Green (MG)	dS2/dt = -k2[ES1][S2] +k2r[ES2]
ES2 (MGox +LiP compound II)	dES2/dt = k2[ES1][S2] – k2r[ES2]

Table12: Differential equations of reactions.

LiP – MB 5 hours of decolorization

What did it show???

Before running the model we needed to decide what an appropriate endpoint of reaction would be. Therefore, concentrations of species were determined from the literature and necessary assumptions were made to check our cascade reactions work correctly.

According to chosen references points, we were trying to determine how quickly we could get a decolourization. Decolourization depends on final [ES2] (MB_ox+Lip compound II) concentration and degradation of MB.

Decolourization starts in 40 minutes.

Future plans

The most important results that we were able to achieve were the correlation between the functional assays the modelling results of our MATLAB kinetic model. In the modelling, the decolourizations start at the approximately 40 minutes while these are 60 minutes for the assay. These differences were due to the consideration of the used HRP and LIP enzymes in the modelling as purified allowing more direct interaction in between the hydrogen peroxide and the dyes. The assay was not conducted with purified enzymes but with lysate acquired from liquid culture containing impurities which slow down the conduction of the reaction. In the future, we hope to extract the enzymes from the bacteria to allow the direct contact of the enzymes and the dyes to increase spontaneity.

Thanks to Ayşe Çelik for her support.

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+<div class=WordSection1>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:14.0pt;line-height:
+%'>A KINETIC MODEL IN MATLAB</span></b></p>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%;color:red'>How did we build it???</span></b></p>
+<p class=MsoNormal><span lang=EN-GB>Using the SimBiology toolbox for MATLAB we
+created a framework of the enzyme kinetic modelling(Figure 1).</span></p>
+<p class=MsoNormal><b><span lang=EN-GB>HRP + H2O2 &#8594; ES1 (HRP compound I)
++ MG &#8594; ES2(MG<sub>ox </sub>+HRP compound II)</span></b></p>
+<p class=MsoNormal><img width=590 height=260 id="Picture 5"
+src="https://static.igem.org/mediawiki/2014hs/1/1d/Mimage001.jpg"></p>
+<p class=MsoNormal><span lang=EN-GB>After creating the basic framework for the
+model we needed to create mathematical equations for each reaction with
+appropriate rate constants. These equations and the corresponding values are
+shown below in Tables 1 and 2.</span></p>
+<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0
+ style='border-collapse:collapse;border:none'>
+ <tr>
+  <td width=205 valign=top style='width:153.5pt;border:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Reaction Name:</span></b></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Reaction Scheme:</span></b></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Reaction Rate:</span></b></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=205 valign=top style='width:153.5pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>oxidation reaction</span></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>H2O2 + HRP -&gt; ES1</span></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>k1*H2O2*HRP</span></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=205 valign=top style='width:153.5pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>decolourization reaction</span></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>ES1 + MG -&gt; ES2</span></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>k2*ES1*MG</span></p>
+  </td>
+ </tr>
+</table>
+<p class=MsoNormal><b><span lang=EN-GB>Table1: </span></b><span lang=EN-GB>Mathematical
+representation of enzyme kinetic reaction expression and the subsequent
+production of the oxidized dye. Constants are described in Table 2.</span></p>
+<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0
+ style='border-collapse:collapse;border:none'>
+ <tr style='height:13.1pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Constant:</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Value:</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Units:</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>References:</span></b></p>
+  </td>
+ </tr>
+ <tr style='height:12.15pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:12.15pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>k1</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:12.15pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>0.0018</span></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:12.15pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>1/(µmolarity*min)</span></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:12.15pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>Viridiana S. Ferreira-Leitão (2002)</span></p>
+  </td>
+ </tr>
+ <tr style='height:13.1pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB style='color:#C00000'>k1r</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>neglected</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;
+  text-align:center;line-height:normal'><b><span lang=EN-GB>-</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;
+  text-align:center;line-height:normal'><b><span lang=EN-GB>&nbsp;</span></b></p>
+  </td>
+ </tr>
+ <tr style='height:13.1pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>k2</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>0.004</span></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>1/(µmolarity*min)</span></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>Viridiana S. Ferreira-Leitão (2002)</span></p>
+  </td>
+ </tr>
+ <tr style='height:14.05pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB style='color:#C00000'>k2r</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>neglected</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>
+  <p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;
+  text-align:center;line-height:normal'><b><span lang=EN-GB>-</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>
+  <p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;
+  text-align:center;line-height:normal'><b><span lang=EN-GB>&nbsp;</span></b></p>
+  </td>
+ </tr>
+</table>
+<p class=MsoNormal><b><span lang=EN-GB>Table 2: </span></b><span lang=EN-GB>Values
+assigned to kinetic parameters described in Table 1. We ignored k1r and k2r
+values because of k1&gt;&gt;&gt;&gt;k1r and k2&gt;&gt;&gt;k2r, so our both
+reactions act as irreversible.</span></p>
+<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0
+ style='border-collapse:collapse;border:none'>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB style='font-size:12.0pt;color:black'>Rule Name:</span></b></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB style='font-size:12.0pt;color:black'>Rate Rules:</span></b></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>HRP</span></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>dE/dt = - k1[E][S1]+k1r[ES1]</span></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>H2O2</span></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>dS1/dt = -k1[E][S1]+k1r[ES1]</span></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>ES1 (HRP compound I)</span></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>dES1/dt =k1[E][S1]
+  –k1r[ES1]-k2[ES1][S2]+k2r[ES2]</span></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>Methyl Green (MG)</span></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>dS2/dt = -k2[ES1][S2] +k2r[ES2]</span></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>ES2 (MGox +LiP compound II)</span></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>dES2/dt = k2[ES1][S2] – k2r[ES2]</span></p>
+  </td>
+ </tr>
+</table>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%'>Table3: </span></b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%'>Differential equations of reactions. </span></p>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%;color:red'>What did it show???</span></b></p>
+<p class=MsoNormal style='text-align:justify'><span lang=EN-GB>Before running
+the model we needed to decide what an appropriate endpoint of reaction would
+be. Therefore, concentrations of species were determined from the literature
+and necessary assumptions were made to check our cascade reactions work
+correctly. </span></p>
+<p class=MsoNormal style='text-align:justify'><span lang=EN-GB>According to chosen
+references points, we were trying to determine how quickly we could get a decolourization.
+Decolourization depends on final [ES2]<b> (MG<sub>ox </sub>+HRP compound II)</b>
+concentration and degradation of MB. </span></p>
+<p class=MsoNormal style='text-align:justify'><span lang=EN-GB>Decolourization
+starts in 40 minutes.</span></p>
+<p class=MsoNormal><span lang=EN-GB>&nbsp;</span></p>
+<p class=MsoNormal><img width=666 height=335 src="https://static.igem.org/mediawiki/2014hs/3/35/Mimage002.jpg"></p>
+<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0
+ style='border-collapse:collapse;border:none'>
+ <tr>
+  <td width=205 valign=top style='width:153.5pt;border:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Reaction Name:</span></b></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Reaction Scheme:</span></b></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Reaction Rate:</span></b></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=205 valign=top style='width:153.5pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>oxidation reaction</span></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>H2O2 + HRP -&gt; ES1</span></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>k1*H2O2*HRP</span></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=205 valign=top style='width:153.5pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>decolorization reaction</span></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>ES1 + MB -&gt; ES2</span></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>k2*ES1*MB</span></p>
+  </td>
+ </tr>
+</table>
+<p class=MsoNormal><b><span lang=EN-GB>Table 4: </span></b><span lang=EN-GB>Mathematical
+representation of enzyme kinetic reaction expression and the subsequent
+production of the oxidized dye. Constants are described in Table 5.</span></p>
+<p class=MsoNormal><span lang=EN-GB>&nbsp;</span></p>
+<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0
+ style='border-collapse:collapse;border:none'>
+ <tr style='height:13.1pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Constant:</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Value:</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Units:</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>References:</span></b></p>
+  </td>
+ </tr>
+ <tr style='height:12.15pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:12.15pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>k1</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:12.15pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>0.0018</span></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:12.15pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>1/(µmolarity*min)</span></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:12.15pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>Viridiana S. Ferreira-Leitão (2002)</span></p>
+  </td>
+ </tr>
+ <tr style='height:13.1pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB style='color:#C00000'>k1r</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>neglected</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;
+  text-align:center;line-height:normal'><b><span lang=EN-GB>-</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;
+  text-align:center;line-height:normal'><b><span lang=EN-GB>&nbsp;</span></b></p>
+  </td>
+ </tr>
+ <tr style='height:13.1pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>k2</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>0.004</span></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>1/(µmolarity*min)</span></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>Viridiana S. Ferreira-Leitão (2002)</span></p>
+  </td>
+ </tr>
+ <tr style='height:14.05pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB style='color:#C00000'>k2r</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>neglected</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>
+  <p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;
+  text-align:center;line-height:normal'><b><span lang=EN-GB>-</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>
+  <p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;
+  text-align:center;line-height:normal'><b><span lang=EN-GB>&nbsp;</span></b></p>
+  </td>
+ </tr>
+ <tr style='height:14.05pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB style='color:#C00000'>&nbsp;</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>&nbsp;</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>
+  <p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;
+  text-align:center;line-height:normal'><b><span lang=EN-GB>&nbsp;</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>
+  <p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;
+  text-align:center;line-height:normal'><b><span lang=EN-GB>&nbsp;</span></b></p>
+  </td>
+ </tr>
+</table>
+<p class=MsoNormal><b><span lang=EN-GB>Table 5: </span></b><span lang=EN-GB>Values
+assigned to kinetic parameters described in Table 4. We ignored k1r and k2r
+values because of k1&gt;&gt;&gt;&gt;k1r and k2&gt;&gt;&gt;k2r, so our both
+reactions act as irreversible.</span></p>
+<p class=MsoNormal><span lang=EN-GB>&nbsp;</span></p>
+<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0
+ style='border-collapse:collapse;border:none'>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB style='font-size:12.0pt;color:black'>Rule Name:</span></b></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB style='font-size:12.0pt;color:black'>Rate Rules:</span></b></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>HRP</span></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>dE/dt = - k1[E][S1]+k1r[ES1]</span></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>H2O2</span></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>dS1/dt = -k1[E][S1]+k1r[ES1]</span></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>ES1 (HRP compound I)</span></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>dES1/dt =k1[E][S1]
+  –k1r[ES1]-k2[ES1][S2]+k2r[ES2]</span></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>Methylen Blue (MB)</span></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>dS2/dt = -k2[ES1][S2] +k2r[ES2]</span></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>ES2 (MBox +LiP compound II)</span></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>dES2/dt = k2[ES1][S2] – k2r[ES2]</span></p>
+  </td>
+ </tr>
+</table>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%'>Table6: </span></b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%'>Differential equations of reactions. </span></p>
+<p class=MsoNormal><span lang=EN-GB>&nbsp;</span></p>
+<p class=MsoNormal><b><span style='font-size:12.0pt;line-height:115%;
+color:red'><img width=687 height=328 id="Picture 1"
+src="https://static.igem.org/mediawiki/2014hs/5/50/Mimage003.jpg"></span></b></p>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%;color:red'>1hour of HRP- MB decolourization</span></b></p>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%;color:red'>What did it show???</span></b></p>
+<p class=MsoNormal style='text-align:justify'><span lang=EN-GB>Before running
+the model we needed to decide what an appropriate endpoint of reaction would
+be. Therefore, concentrations of species were determined from the literature
+and necessary assumptions were made to check our cascade reactions work
+correctly. </span></p>
+<p class=MsoNormal style='text-align:justify'><span lang=EN-GB>According to
+chosen references points, we were trying to determine how quickly we could get
+a decolourization. Decolourization depends on final [ES2]<b> <span
+style='color:#7030A0'>(MB<sub>ox </sub>+LiP compound II)</span></b><span
+style='color:#7030A0'> </span>concentration and degradation of MB. </span></p>
+<p class=MsoNormal style='text-align:justify'><span lang=EN-GB>Decolourization
+starts in 40 minutes.</span></p>
+<p class=MsoNormal><b><span lang=EN-GB>LiP + H2O2 &#8594;ES1 (LiP compound I )
++ MB &#8594; ES2 (MB<sub>ox </sub>+LiP compound II)</span></b></p>
+<p class=MsoNormal><b><span style='font-size:12.0pt;line-height:115%;
+color:red'><img width=605 height=270 id="Picture 2"
+src="https://static.igem.org/mediawiki/2014hs/0/0c/Mimage004.jpg"></span></b></p>
+<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0
+ style='border-collapse:collapse;border:none'>
+ <tr>
+  <td width=205 valign=top style='width:153.5pt;border:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Reaction Name:</span></b></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Reaction Scheme:</span></b></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Reaction Rate:</span></b></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=205 valign=top style='width:153.5pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>oxidation reaction</span></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>H2O2 + LiP -&gt; ES1</span></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>k1*H2O2*LiP</span></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=205 valign=top style='width:153.5pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>decolorization reaction</span></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>ES1 + MB -&gt; ES2</span></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>k2*ES1*MB</span></p>
+  </td>
+ </tr>
+</table>
+<p class=MsoNormal><b><span lang=EN-GB>Table7: </span></b><span lang=EN-GB>Mathematical
+representation of enzyme kinetic reaction expression and the subsequent
+production of the oxidized dye. Constants are described in Table 8.</span></p>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%;color:red'>&nbsp;</span></b></p>
+<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0
+ style='border-collapse:collapse;border:none'>
+ <tr style='height:13.1pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Constant:</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Value:</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Units:</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>References:</span></b></p>
+  </td>
+ </tr>
+ <tr style='height:12.15pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:12.15pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>k1</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:12.15pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>1.0E-4</span></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:12.15pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>1/(µmolarity*min)</span></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:12.15pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>Paulı Ollıkka, Kırsı Alhonmakı </span></p>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>(1993)</span></p>
+  </td>
+ </tr>
+ <tr style='height:13.1pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB style='color:#C00000'>k1r</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>neglected</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;
+  text-align:center;line-height:normal'><b><span lang=EN-GB>-</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;
+  text-align:center;line-height:normal'><b><span lang=EN-GB>&nbsp;</span></b></p>
+  </td>
+ </tr>
+ <tr style='height:13.1pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>k2</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>2.0E-4</span></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>1/(µmolarity*min)</span></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>Paulı Ollıkka, Kırsı Alhonmakı </span></p>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>(1993)</span></p>
+  </td>
+ </tr>
+ <tr style='height:14.05pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB style='color:#C00000'>k2r</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>neglected</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>
+  <p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;
+  text-align:center;line-height:normal'><b><span lang=EN-GB>-</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>
+  <p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;
+  text-align:center;line-height:normal'><b><span lang=EN-GB>&nbsp;</span></b></p>
+  </td>
+ </tr>
+</table>
+<p class=MsoNormal><b><span lang=EN-GB>Table 8: </span></b><span lang=EN-GB>Values
+assigned to kinetic parameters described in Table 7. We ignored k1r and k2r
+values because of k1&gt;&gt;&gt;&gt;k1r and k2&gt;&gt;&gt;k2r, so our both
+reactions act as irreversible.</span></p>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%;color:red'>&nbsp;</span></b></p>
+<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0
+ style='border-collapse:collapse;border:none'>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB style='font-size:12.0pt;color:black'>Rule Name:</span></b></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB style='font-size:12.0pt;color:black'>Rate Rules:</span></b></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>HRP</span></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>dE/dt = - k1[E][S1]+k1r[ES1]</span></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>H2O2</span></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>dS1/dt = -k1[E][S1]+k1r[ES1]</span></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>ES1 (HRP compound I)</span></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>dES1/dt =k1[E][S1]
+  –k1r[ES1]-k2[ES1][S2]+k2r[ES2]</span></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>Methylen Blue (MB)</span></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>dS2/dt = -k2[ES1][S2] +k2r[ES2]</span></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>ES2 (MBox +LiP compound II)</span></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>dES2/dt = k2[ES1][S2] – k2r[ES2]</span></p>
+  </td>
+ </tr>
+</table>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%'>Table9: </span></b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%'>Differential equations of reactions. </span></p>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%;color:red'>&nbsp;</span></b></p>
+<p class=MsoNormal><b><span style='font-size:12.0pt;line-height:115%;
+color:red'><img width=604 height=254 id="Picture 3"
+src="https://static.igem.org/mediawiki/2014hs/0/02/Mimage005.jpg"></span></b></p>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%;color:red'>6 hours of Lip- MG decolourization</span></b></p>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%;color:red'>What did it show???</span></b></p>
+<p class=MsoNormal style='text-align:justify'><span lang=EN-GB>Before running
+the model we needed to decide what an appropriate endpoint of reaction would
+be. Therefore, concentrations of species were determined from the literature
+and necessary assumptions were made to check our cascade reactions work
+correctly. </span></p>
+<p class=MsoNormal style='text-align:justify'><span lang=EN-GB>According to
+chosen references points, we were trying to determine how quickly we could get
+a decolourization. Decolourization depends on final [ES2]<b> <span
+style='color:#7030A0'>(Mg<sub>ox </sub>+Lip compound II)</span></b>
+concentration and degradation of MG. </span></p>
+<p class=MsoNormal style='text-align:justify'><span lang=EN-GB>Decolourization
+starts in 40 minutes.</span></p>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%;color:red'>&nbsp;</span></b></p>
+<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0
+ style='border-collapse:collapse;border:none'>
+ <tr>
+  <td width=205 valign=top style='width:153.5pt;border:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Reaction Name:</span></b></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Reaction Scheme:</span></b></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Reaction Rate:</span></b></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=205 valign=top style='width:153.5pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>oxidation reaction</span></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>H2O2 + LiP -&gt; ES1</span></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>k1*H2O2*LiP</span></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=205 valign=top style='width:153.5pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>decolourization reaction</span></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>ES1 + MG -&gt; ES2</span></p>
+  </td>
+  <td width=205 valign=top style='width:153.55pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>k2*ES1*MG</span></p>
+  </td>
+ </tr>
+</table>
+<p class=MsoNormal><b><span lang=EN-GB>Table10: </span></b><span lang=EN-GB>Mathematical
+representation of enzyme kinetic reaction expression and the subsequent
+production of the oxidized dye. Constants are described in Table 11.</span></p>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%;color:red'>&nbsp;</span></b></p>
+<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0
+ style='border-collapse:collapse;border:none'>
+ <tr style='height:13.1pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Constant:</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Value:</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>Units:</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>References:</span></b></p>
+  </td>
+ </tr>
+ <tr style='height:12.15pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:12.15pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>k1</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:12.15pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>1.0E-4</span></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:12.15pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>1/(µmolarity*min)</span></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:12.15pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>Paulı Ollıkka, Kırsı Alhonmakı </span></p>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>(1993)</span></p>
+  </td>
+ </tr>
+ <tr style='height:13.1pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB style='color:#C00000'>k1r</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>neglected</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;
+  text-align:center;line-height:normal'><b><span lang=EN-GB>-</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;
+  text-align:center;line-height:normal'><b><span lang=EN-GB>&nbsp;</span></b></p>
+  </td>
+ </tr>
+ <tr style='height:13.1pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>k2</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>2.0E-4</span></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>1/(µmolarity*min)</span></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>Paulı Ollıkka, Kırsı Alhonmakı </span></p>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB>(1993)</span></p>
+  </td>
+ </tr>
+ <tr style='height:14.05pt'>
+  <td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB style='color:#C00000'>k2r</span></b></p>
+  </td>
+  <td width=137 valign=top style='width:102.6pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB>neglected</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>
+  <p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;
+  text-align:center;line-height:normal'><b><span lang=EN-GB>-</span></b></p>
+  </td>
+  <td width=124 valign=top style='width:93.35pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>
+  <p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;
+  text-align:center;line-height:normal'><b><span lang=EN-GB>&nbsp;</span></b></p>
+  </td>
+ </tr>
+</table>
+<p class=MsoNormal><b><span lang=EN-GB>Table 11: </span></b><span lang=EN-GB>Values
+assigned to kinetic parameters described in Table 10. We ignored k1r and k2r
+values because of k1&gt;&gt;&gt;&gt;k1r and k2&gt;&gt;&gt;k2r, so our both
+reactions act as irreversible</span></p>
+<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0
+ style='border-collapse:collapse;border:none'>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB style='font-size:12.0pt;color:black'>Rule Name:</span></b></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-left:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><b><span lang=EN-GB style='font-size:12.0pt;color:black'>Rate Rules:</span></b></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>HRP</span></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>dE/dt = - k1[E][S1]+k1r[ES1]</span></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>H2O2</span></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>dS1/dt = -k1[E][S1]+k1r[ES1]</span></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>ES1 (HRP compound I)</span></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>dES1/dt =k1[E][S1]
+  –k1r[ES1]-k2[ES1][S2]+k2r[ES2]</span></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>Methyl Green (MG)</span></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>dS2/dt = -k2[ES1][S2] +k2r[ES2]</span></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;
+  border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>ES2 (MGox +LiP compound II)</span></p>
+  </td>
+  <td width=307 valign=top style='width:230.3pt;border-top:none;border-left:
+  none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;
+  padding:0cm 5.4pt 0cm 5.4pt'>
+  <p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:
+  normal'><span lang=EN-GB style='color:black'>dES2/dt = k2[ES1][S2] – k2r[ES2]</span></p>
+  </td>
+ </tr>
+</table>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%'>Table12: </span></b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%'>Differential equations of reactions. </span></p>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%;color:red'>&nbsp;</span></b></p>
+<p class=MsoNormal><b><span style='font-size:12.0pt;line-height:115%;
+color:red'><img width=669 height=296 id="Picture 4"
+src="https://static.igem.org/mediawiki/2014hs/5/5d/Mimage006.jpg"></span></b></p>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%;color:red'>LiP – MB 5 hours of decolorization</span></b></p>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%;color:red'>What did it show???</span></b></p>
+<p class=MsoNormal style='text-align:justify'><span lang=EN-GB>Before running
+the model we needed to decide what an appropriate endpoint of reaction would
+be. Therefore, concentrations of species were determined from the literature
+and necessary assumptions were made to check our cascade reactions work
+correctly. </span></p>
+<p class=MsoNormal style='text-align:justify'><span lang=EN-GB>According to
+chosen references points, we were trying to determine how quickly we could get
+a decolourization. Decolourization depends on final [ES2]<b> (MB<sub>ox </sub>+Lip
+compound II)</b> concentration and degradation of MB. </span></p>
+<p class=MsoNormal style='text-align:justify'><span lang=EN-GB>Decolourization
+starts in 40 minutes.</span></p>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%;color:red'>&nbsp;</span></b></p>
+<p class=MsoNormal><b><span lang=EN-GB style='font-size:12.0pt;line-height:
+%;color:red'>Future plans</span></b></p>
+<p class=MsoNormal><span lang=EN-GB style='font-family:"Arial","sans-serif";
+color:black; '>The most important results that we were able to
+achieve were the correlation between the functional assays the modelling
+results of our MATLAB kinetic model. In the modelling, the decolourizations
+start at the approximately 40 minutes while these are 60 minutes for the assay.
+These differences were due to the consideration of the used HRP and LIP enzymes
+in the modelling as purified allowing more direct interaction in between the
+hydrogen peroxide and the dyes. The assay was not conducted with purified
+enzymes but with lysate acquired from liquid culture containing impurities
+which slow down the conduction of the reaction. In the future, we hope to
+extract the enzymes from the bacteria to allow the direct contact of the enzymes
+and the dyes to increase spontaneity.</span></p>
+<p class=MsoNormal><span lang=EN-GB style='font-family:"Arial","sans-serif";
+color:black; '>Thanks to Ayşe Çelik for her support.</span></p>
+</div>
+</body>
+</head>
+</html>