Team:AUC TURKEY/Project/Modelling

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~~{{AUC_TURKEY}}~~

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~~<div class=WordSection1>~~

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~~<span lang=EN-GB style='font-size:14.0pt;line-height:~~

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~~115%'>A KINETIC MODEL IN MATLAB~~

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~~<span lang=EN-GB style='font-size:12.0pt;line-height:~~

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~~115%;color:red'>How did we build it???~~

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~~Using the SimBiology toolbox for MATLAB we~~

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~~created a framework of the enzyme kinetic modelling(Figure 1).~~

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~~HRP + H2O2 → ES1 (HRP compound I)~~

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~~+ MG → ES2(MGox +HRP compound II)~~

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~~<img width=590 height=260 id="Picture 5"~~

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~~src="https://static.igem.org/mediawiki/2014hs/1/1d/Mimage001.jpg">~~

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~~After creating the basic framework for the~~

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~~model we needed to create mathematical equations for each reaction with~~

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~~appropriate rate constants. These equations and the corresponding values are~~

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~~shown below in Tables 1 and 2.~~

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~~<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0~~

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~~style='border-collapse:collapse;border:none'>~~

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~~<tr>~~

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~~<td width=205 valign=top style='width:153.5pt;border:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>Reaction Name:~~

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~~</td>~~

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~~<td width=205 valign=top style='width:153.55pt;border:solid windowtext 1.0pt;~~

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~~border-left:none;padding:0cm 5.4pt 0cm 5.4pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>Reaction Scheme:~~

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~~</td>~~

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~~<td width=205 valign=top style='width:153.55pt;border:solid windowtext 1.0pt;~~

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~~border-left:none;padding:0cm 5.4pt 0cm 5.4pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>Reaction Rate:~~

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~~</td>~~

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~~</tr>~~

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~~<tr>~~

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~~<td width=205 valign=top style='width:153.5pt;border:solid windowtext 1.0pt;~~

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~~border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>oxidation reaction~~

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~~</td>~~

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~~<td width=205 valign=top style='width:153.55pt;border-top:none;border-left:~~

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~~none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>H2O2 + HRP -> ES1~~

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~~</td>~~

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~~<td width=205 valign=top style='width:153.55pt;border-top:none;border-left:~~

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~~none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>k1*H2O2*HRP~~

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~~</td>~~

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~~</tr>~~

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~~<tr>~~

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~~<td width=205 valign=top style='width:153.5pt;border:solid windowtext 1.0pt;~~

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~~border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>decolourization reaction~~

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~~</td>~~

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~~<td width=205 valign=top style='width:153.55pt;border-top:none;border-left:~~

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~~none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>ES1 + MG -> ES2~~

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~~</td>~~

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~~<td width=205 valign=top style='width:153.55pt;border-top:none;border-left:~~

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~~none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>k2*ES1*MG~~

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~~</td>~~

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~~</tr>~~

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~~</table>~~

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~~Table1: Mathematical~~

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~~representation of enzyme kinetic reaction expression and the subsequent~~

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~~production of the oxidized dye. Constants are described in Table 2.~~

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~~<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0~~

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~~style='border-collapse:collapse;border:none'>~~

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~~<tr style='height:13.1pt'>~~

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~~<td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>Constant:~~

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~~</td>~~

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~~<td width=137 valign=top style='width:102.6pt;border:solid windowtext 1.0pt;~~

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~~border-left:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>Value:~~

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~~</td>~~

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~~<td width=124 valign=top style='width:93.35pt;border:solid windowtext 1.0pt;~~

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~~border-left:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>Units:~~

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~~</td>~~

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~~<td width=124 valign=top style='width:93.35pt;border:solid windowtext 1.0pt;~~

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~~border-left:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>References:~~

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~~</td>~~

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~~</tr>~~

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~~<tr style='height:12.15pt'>~~

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~~<td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;~~

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~~border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:12.15pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>k1~~

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~~</td>~~

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~~<td width=137 valign=top style='width:102.6pt;border-top:none;border-left:~~

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~~none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt;height:12.15pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>0.0018~~

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~~</td>~~

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~~<td width=124 valign=top style='width:93.35pt;border-top:none;border-left:~~

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~~none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt;height:12.15pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>1/(µmolarity*min)~~

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~~</td>~~

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~~<td width=124 valign=top style='width:93.35pt;border-top:none;border-left:~~

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~~none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt;height:12.15pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>Viridiana S. Ferreira-Leitão (2002)~~

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~~</td>~~

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~~</tr>~~

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~~<tr style='height:13.1pt'>~~

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~~<td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;~~

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~~border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>k1r~~

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~~</td>~~

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~~<td width=137 valign=top style='width:102.6pt;border-top:none;border-left:~~

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~~none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>neglected~~

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~~</td>~~

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~~<td width=124 valign=top style='width:93.35pt;border-top:none;border-left:~~

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~~none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>~~

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~~<p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;~~

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~~text-align:center;line-height:normal'>-~~

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~~</td>~~

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~~<td width=124 valign=top style='width:93.35pt;border-top:none;border-left:~~

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~~none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>~~

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~~<p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;~~

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~~text-align:center;line-height:normal'> ~~

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~~</td>~~

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~~</tr>~~

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~~<tr style='height:13.1pt'>~~

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~~<td width=136 valign=top style='width:101.9pt;border:solid windowtext 1.0pt;~~

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~~border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>k2~~

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~~</td>~~

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~~<td width=137 valign=top style='width:102.6pt;border-top:none;border-left:~~

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~~none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>0.004~~

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~~</td>~~

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~~<td width=124 valign=top style='width:93.35pt;border-top:none;border-left:~~

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~~none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>1/(µmolarity*min)~~

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~~</td>~~

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~~<td width=124 valign=top style='width:93.35pt;border-top:none;border-left:~~

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~~none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;~~

-

~~padding:0cm 5.4pt 0cm 5.4pt;height:13.1pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>Viridiana S. Ferreira-Leitão (2002)~~

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~~</td>~~

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~~</tr>~~

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~~<tr style='height:14.05pt'>~~

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~~<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'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>k2r~~

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~~</td>~~

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~~<td width=137 valign=top style='width:102.6pt;border-top:none;border-left:~~

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~~none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>neglected~~

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~~</td>~~

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~~<td width=124 valign=top style='width:93.35pt;border-top:none;border-left:~~

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~~none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>~~

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~~<p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;~~

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~~text-align:center;line-height:normal'>-~~

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~~</td>~~

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~~<td width=124 valign=top style='width:93.35pt;border-top:none;border-left:~~

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~~none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt;height:14.05pt'>~~

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~~<p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt;~~

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~~text-align:center;line-height:normal'> ~~

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~~</td>~~

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~~</tr>~~

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~~</table>~~

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~~Table 2: Values~~

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~~assigned to kinetic parameters described in Table 1. We ignored k1r and k2r~~

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~~values because of k1>>>>k1r and k2>>>k2r, so our both~~

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~~reactions act as irreversible.~~

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~~<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0~~

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~~style='border-collapse:collapse;border:none'>~~

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~~<tr>~~

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~~<td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>Rule Name:~~

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~~</td>~~

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~~<td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;~~

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~~border-left:none;padding:0cm 5.4pt 0cm 5.4pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

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~~normal'>Rate Rules:~~

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~~</td>~~

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~~</tr>~~

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~~<tr>~~

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~~<td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;~~

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~~border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

-

~~normal'>HRP~~

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~~</td>~~

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~~<td width=307 valign=top style='width:230.3pt;border-top:none;border-left:~~

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~~none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

-

~~normal'>dE/dt = - k1[E][S1]+k1r[ES1]~~

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~~</td>~~

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~~</tr>~~

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~~<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'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

-

~~normal'>H2O2~~

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~~</td>~~

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~~<td width=307 valign=top style='width:230.3pt;border-top:none;border-left:~~

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~~none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

-

~~normal'>dS1/dt = -k1[E][S1]+k1r[ES1]~~

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~~</td>~~

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~~</tr>~~

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~~<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'>ES1 (HRP compound I)~~

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~~</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'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

-

~~normal'>dES1/dt =k1[E][S1]~~

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~~–k1r[ES1]-k2[ES1][S2]+k2r[ES2]~~

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~~</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'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

-

~~normal'>Methyl Green (MG)~~

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~~</td>~~

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~~<td width=307 valign=top style='width:230.3pt;border-top:none;border-left:~~

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~~none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt'>~~

-

~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

-

~~normal'>dS2/dt = -k2[ES1][S2] +k2r[ES2]~~

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~~</td>~~

-

~~</tr>~~

-

~~<tr>~~

-

~~<td width=307 valign=top style='width:230.3pt;border:solid windowtext 1.0pt;~~

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~~border-top:none;padding:0cm 5.4pt 0cm 5.4pt'>~~

-

~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

-

~~normal'>ES2 (MGox +LiP compound II)~~

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~~</td>~~

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~~<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;~~

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~~padding:0cm 5.4pt 0cm 5.4pt'>~~

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~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

-

~~normal'>dES2/dt = k2[ES1][S2] – k2r[ES2]~~

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~~</td>~~

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~~</tr>~~

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~~</table>~~

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~~<span lang=EN-GB style='font-size:12.0pt;line-height:~~

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~~115%'>Table3: <span lang=EN-GB style='font-size:12.0pt;line-height:~~

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~~115%'>Differential equations of reactions. ~~

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~~<span lang=EN-GB style='font-size:12.0pt;line-height:~~

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~~115%;color:red'>What did it show???~~

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~~Before running~~

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~~the model we needed to decide what an appropriate endpoint of reaction would~~

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~~be. Therefore, concentrations of species were determined from the literature~~

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~~and necessary assumptions were made to check our cascade reactions work~~

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~~correctly. ~~

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~~According to chosen~~

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~~references points, we were trying to determine how quickly we could get a decolourization.~~

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~~Decolourization depends on final [ES2] (MGox +HRP compound II)~~

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~~concentration and degradation of MB. ~~

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~~Decolourization~~

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~~starts in 40 minutes.~~

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~~ ~~

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~~<img width=666 height=335 src="https://static.igem.org/mediawiki/2014hs/3/35/Mimage002.jpg">~~

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~~<table class=MsoTableGrid border=1 cellspacing=0 cellpadding=0~~

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~~style='border-collapse:collapse;border:none'>~~

-

~~<tr>~~

-

~~<td width=205 valign=top style='width:153.5pt;border:solid windowtext 1.0pt;~~

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~~padding:0cm 5.4pt 0cm 5.4pt'>~~

-

~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

-

~~normal'>Reaction Name:~~

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~~</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'>Reaction Scheme:~~

-

~~</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'>Reaction Rate:~~

-

~~</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'>oxidation reaction~~

-

~~</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'>H2O2 + HRP -> ES1~~

-

~~</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'>k1*H2O2*HRP~~

-

~~</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'>decolorization reaction~~

-

~~</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'>ES1 + MB -> ES2~~

-

~~</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'>k2*ES1*MB~~

-

~~</td>~~

-

~~</tr>~~

-

~~</table>~~

-

~~Table 4: Mathematical~~

-

~~representation of enzyme kinetic reaction expression and the subsequent~~

-

~~production of the oxidized dye. Constants are described in Table 5.~~

-

~~ ~~

-

~~<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'>Constant:~~

-

~~</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'>Value:~~

-

~~</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'>Units:~~

-

~~</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'>References:~~

-

~~</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'>k1~~

-

~~</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'>0.0018~~

-

~~</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'>1/(µmolarity*min)~~

-

~~</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'>Viridiana S. Ferreira-Leitão (2002)~~

-

~~</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'>k1r~~

-

~~</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'>neglected~~

-

~~</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'>-~~

-

~~</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'> ~~

-

~~</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'>k2~~

-

~~</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'>0.004~~

-

~~</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'>1/(µmolarity*min)~~

-

~~</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'>Viridiana S. Ferreira-Leitão (2002)~~

-

~~</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'>k2r~~

-

~~</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'>neglected~~

-

~~</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'>-~~

-

~~</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'> ~~

-

~~</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'> ~~

-

~~</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'> ~~

-

~~</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'> ~~

-

~~</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'> ~~

-

~~</td>~~

-

~~</tr>~~

-

~~</table>~~

-

~~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.~~

-

~~ ~~

-

~~<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'>Rule Name:~~

-

~~</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'>Rate Rules:~~

-

~~</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'>HRP~~

-

~~</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'>dE/dt = - k1[E][S1]+k1r[ES1]~~

-

~~</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'>H2O2~~

-

~~</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'>dS1/dt = -k1[E][S1]+k1r[ES1]~~

-

~~</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'>ES1 (HRP compound I)~~

-

~~</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'>dES1/dt =k1[E][S1]~~

-

~~–k1r[ES1]-k2[ES1][S2]+k2r[ES2]~~

-

~~</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'>Methylen Blue (MB)~~

-

~~</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'>dS2/dt = -k2[ES1][S2] +k2r[ES2]~~

-

~~</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'>ES2 (MBox +LiP compound II)~~

-

~~</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'>dES2/dt = k2[ES1][S2] – k2r[ES2]~~

-

~~</td>~~

-

~~</tr>~~

-

~~</table>~~

-

~~<span lang=EN-GB style='font-size:12.0pt;line-height:~~

-

~~115%'>Table6: <span lang=EN-GB style='font-size:12.0pt;line-height:~~

-

~~115%'>Differential equations of reactions. ~~

-

~~ ~~

-

~~<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 lang=EN-GB style='font-size:12.0pt;line-height:~~

-

~~115%;color:red'>1hour of HRP- MB decolourization~~

-

~~<span lang=EN-GB style='font-size:12.0pt;line-height:~~

-

~~115%;color:red'>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] <span~~

-

~~style='color:#7030A0'>(MBox +LiP compound II)<span~~

-

~~style='color:#7030A0'> concentration and degradation of MB. ~~

-

~~Decolourization~~

-

~~starts in 40 minutes.~~

-

~~LiP + H2O2 →ES1 (LiP compound I )~~

-

~~+ MB → ES2 (MBox +LiP compound II)~~

-

~~<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">~~

-

~~<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'>Reaction Name:~~

-

~~</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'>Reaction Scheme:~~

-

~~</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'>Reaction Rate:~~

-

~~</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'>oxidation reaction~~

-

~~</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'>H2O2 + LiP -> ES1~~

-

~~</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'>k1*H2O2*LiP~~

-

~~</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'>decolorization reaction~~

-

~~</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'>ES1 + MB -> ES2~~

-

~~</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'>k2*ES1*MB~~

-

~~</td>~~

-

~~</tr>~~

-

~~</table>~~

-

~~Table7: Mathematical~~

-

~~representation of enzyme kinetic reaction expression and the subsequent~~

-

~~production of the oxidized dye. Constants are described in Table 8.~~

-

~~<span lang=EN-GB style='font-size:12.0pt;line-height:~~

-

~~115%;color:red'> ~~

-

~~<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'>Constant:~~

-

~~</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'>Value:~~

-

~~</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'>Units:~~

-

~~</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'>References:~~

-

~~</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'>k1~~

-

~~</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'>1.0E-4~~

-

~~</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'>1/(µmolarity*min)~~

-

~~</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'>Paulı Ollıkka, Kırsı Alhonmakı ~~

-

~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

-

~~normal'>(1993)~~

-

~~</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'>k1r~~

-

~~</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'>neglected~~

-

~~</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'>-~~

-

~~</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'> ~~

-

~~</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'>k2~~

-

~~</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'>2.0E-4~~

-

~~</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'>1/(µmolarity*min)~~

-

~~</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'>Paulı Ollıkka, Kırsı Alhonmakı ~~

-

~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

-

~~normal'>(1993)~~

-

~~</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'>k2r~~

-

~~</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'>neglected~~

-

~~</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'>-~~

-

~~</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'> ~~

-

~~</td>~~

-

~~</tr>~~

-

~~</table>~~

-

~~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.~~

-

~~<span lang=EN-GB style='font-size:12.0pt;line-height:~~

-

~~115%;color:red'> ~~

-

~~<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'>Rule Name:~~

-

~~</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'>Rate Rules:~~

-

~~</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'>HRP~~

-

~~</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'>dE/dt = - k1[E][S1]+k1r[ES1]~~

-

~~</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'>H2O2~~

-

~~</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'>dS1/dt = -k1[E][S1]+k1r[ES1]~~

-

~~</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'>ES1 (HRP compound I)~~

-

~~</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'>dES1/dt =k1[E][S1]~~

-

~~–k1r[ES1]-k2[ES1][S2]+k2r[ES2]~~

-

~~</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'>Methylen Blue (MB)~~

-

~~</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'>dS2/dt = -k2[ES1][S2] +k2r[ES2]~~

-

~~</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'>ES2 (MBox +LiP compound II)~~

-

~~</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'>dES2/dt = k2[ES1][S2] – k2r[ES2]~~

-

~~</td>~~

-

~~</tr>~~

-

~~</table>~~

-

~~<span lang=EN-GB style='font-size:12.0pt;line-height:~~

-

~~115%'>Table9: <span lang=EN-GB style='font-size:12.0pt;line-height:~~

-

~~115%'>Differential equations of reactions. ~~

-

~~<span lang=EN-GB style='font-size:12.0pt;line-height:~~

-

~~115%;color:red'> ~~

-

~~<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 lang=EN-GB style='font-size:12.0pt;line-height:~~

-

~~115%;color:red'>6 hours of Lip- MG decolourization~~

-

~~<span lang=EN-GB style='font-size:12.0pt;line-height:~~

-

~~115%;color:red'>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] <span~~

-

~~style='color:#7030A0'>(Mgox +Lip compound II)~~

-

~~concentration and degradation of MG. ~~

-

~~Decolourization~~

-

~~starts in 40 minutes.~~

-

~~<span lang=EN-GB style='font-size:12.0pt;line-height:~~

-

~~115%;color:red'> ~~

-

~~<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'>Reaction Name:~~

-

~~</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'>Reaction Scheme:~~

-

~~</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'>Reaction Rate:~~

-

~~</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'>oxidation reaction~~

-

~~</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'>H2O2 + LiP -> ES1~~

-

~~</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'>k1*H2O2*LiP~~

-

~~</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'>decolourization reaction~~

-

~~</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'>ES1 + MG -> ES2~~

-

~~</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'>k2*ES1*MG~~

-

~~</td>~~

-

~~</tr>~~

-

~~</table>~~

-

~~Table10: Mathematical~~

-

~~representation of enzyme kinetic reaction expression and the subsequent~~

-

~~production of the oxidized dye. Constants are described in Table 11.~~

-

~~<span lang=EN-GB style='font-size:12.0pt;line-height:~~

-

~~115%;color:red'> ~~

-

~~<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'>Constant:~~

-

~~</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'>Value:~~

-

~~</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'>Units:~~

-

~~</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'>References:~~

-

~~</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'>k1~~

-

~~</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'>1.0E-4~~

-

~~</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'>1/(µmolarity*min)~~

-

~~</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'>Paulı Ollıkka, Kırsı Alhonmakı ~~

-

~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

-

~~normal'>(1993)~~

-

~~</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'>k1r~~

-

~~</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'>neglected~~

-

~~</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'>-~~

-

~~</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'> ~~

-

~~</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'>k2~~

-

~~</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'>2.0E-4~~

-

~~</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'>1/(µmolarity*min)~~

-

~~</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'>Paulı Ollıkka, Kırsı Alhonmakı ~~

-

~~<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height:~~

-

~~normal'>(1993)~~

-

~~</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'>k2r~~

-

~~</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'>neglected~~

-

~~</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'>-~~

-

~~</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'> ~~

-

~~</td>~~

-

~~</tr>~~

-

~~</table>~~

-

~~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~~

-

~~<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'>Rule Name:~~

-

~~</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'>Rate Rules:~~

-

~~</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'>HRP~~

-

~~</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'>dE/dt = - k1[E][S1]+k1r[ES1]~~

-

~~</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'>H2O2~~

-

~~</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'>dS1/dt = -k1[E][S1]+k1r[ES1]~~

-

~~</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'>ES1 (HRP compound I)~~

-

~~</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'>dES1/dt =k1[E][S1]~~

-

~~–k1r[ES1]-k2[ES1][S2]+k2r[ES2]~~

-

~~</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'>Methyl Green (MG)~~

-

~~</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'>dS2/dt = -k2[ES1][S2] +k2r[ES2]~~

-

~~</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'>ES2 (MGox +LiP compound II)~~

-

~~</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'>dES2/dt = k2[ES1][S2] – k2r[ES2]~~

-

~~</td>~~

-

~~</tr>~~

-

~~</table>~~

-

~~<span lang=EN-GB style='font-size:12.0pt;line-height:~~

-

~~115%'>Table12: <span lang=EN-GB style='font-size:12.0pt;line-height:~~

-

~~115%'>Differential equations of reactions. ~~

-

~~<span lang=EN-GB style='font-size:12.0pt;line-height:~~

-

~~115%;color:red'> ~~

-

~~<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 lang=EN-GB style='font-size:12.0pt;line-height:~~

-

~~115%;color:red'>LiP – MB 5 hours of decolorization~~

-

~~<span lang=EN-GB style='font-size:12.0pt;line-height:~~

-

~~115%;color:red'>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] (MBox +Lip~~

-

~~compound II) concentration and degradation of MB. ~~

-

~~Decolourization~~

-

~~starts in 40 minutes.~~

-

~~<span lang=EN-GB style='font-size:12.0pt;line-height:~~

-

~~115%;color:red'> ~~

-

~~<span lang=EN-GB style='font-size:12.0pt;line-height:~~

-

~~115%;color:red'>Future plans~~

-

~~<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 lang=EN-GB style='font-family:"Arial","sans-serif";~~

-

~~color:black; '>Thanks to Ayşe Çelik for her support.~~

-

~~</div>~~

-

~~</body>~~

-

~~</head>~~

-

~~</html>~~

@@ Line 1: / Line 1: @@
-{{AUC_TURKEY}}
-{{:Vertical:AUC_TURKEY}}
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-</head>
-<body lang=TR>
-<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>

Team:AUC TURKEY/Project/Modelling

From 2014hs.igem.org

Revision as of 21:42, 18 February 2015