Difference between revisions of "Team:MIT/ModelingCHutch"

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<p>In the absence of chromate, \(C_{V}\)<!--Content surrounded by \(\) represents inline equations and symbols from mathjax, they will be displayed as the latex output symbols and equations.-->, the \(ChrB\) protein forms a dimer, \(D\), which then binds the pChr promoter, forming a closed promoter, \(P_{c}\). This promoter cannot function so no green fluorescent protein, \(GFP\), is produced. In the presence of chromate, the \(ChrB\) dimer instead binds to chromate forming a complex, \([C_{V} \cdot D]\). This allows the open promoter, \(P_{o}\) to function and produce \(GFP\). The reactions can be described as chemical equations, where the parameters \(k\) are the kinetic rates:</p>
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<p>This system was written as a system of ODEs and simulations were run with chromate added at specific times to investigate change in concentration over time. The steady state in the presence of chromate was calculated as the \(GFP\) reached a steady level and did not change once there.  Once chromate was removed from the system the \(GFP\) decreased again as expected. The steady state analysis showed that there was a 18927.20% increase of \(GFP\) concentration from the initial concentration.</p>
 
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<p>We wish to compare the modified pathway with the original pathway, where only one plasmid is used:</p>
 
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<img  src='https://static.igem.org/mediawiki/2015/5/58/TeamDundee_plasmid_wt_tiny.png' height="40%" width="auto"/>
 
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<figcaption>Figure 2: Plasmid map of the original biobrick system, <a href="http://parts.igem.org/Part:BBa_K1058008"><u><b>(BBa_K1058008)</b></u></a>.</figcaption>
 
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Revision as of 05:30, 18 September 2015


Detailed Description of Modeling Methods
Equations test
\(\require{mhchem}\) \ce{C6H5-CHO} \ce{$A$ ->[\ce{+H2O}] $B$} \ce{SO4^2- + Ba^2+ -> BaSO4 v}
$$ \ce{ ->[k_{1}] ChrB ->[k_{2}]}\\ \ce{ ChrB + ChrB <=>[k_{3}][k_{-3}] D ->[k_{5}]}\\ \ce{ D + \text{\(C_{V}\)} <=>[k_{4}][k_{-4}] [D \cdot C_{V}]}\\ \ce{ D + P_{o} <=>[k_{6}][k_{-6}] P_{c} }\\ \ce{ P_{o} ->[k_{7}] GFP + P_{o} }\\ \ce{GFP ->[k_{8}] } $$