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</p>
<hr>
<h2 style="text-align:center">How to Access Our Vcell Models</h2>
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<p>Our most up-to-date models can be found in a table on the experiments page. These models are free for anyone
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See our Engineering page for more details on how we constructed and refined our models, and see our
Contributions page for how to access our models.
</p>
<h2>Constructs Table</h2>
<h2>Vcell Rate Constants</h2>
<h3>Construct3_Cycle3_dgl</h3>
<table style="font-size: 10px;">
<tr></tr>
<th>Reaction Name</th>
<th>Kf Value</th>
<th>Kr Value</th>
<th>Annotations</th>
</tr>
<tr>
<td>PFAS_DiffusionAndMessenger</td>
<td>0.001 s<sup>-1</sup></td>
<td>0.001 s<sup>-1</sup></td>
<td>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8913905/
it is not well known if PFAS interact with proteins for cell transport. in absence of better evidence,
we assume it acts by simple diffusion</td>
</tr>
<tr>
<td>PFAS_Bind_Syntran</td>
<td>1.0 s<sup>-1</sup>.&mu;M<sup>-1</sup></td>
<td>7.195E-5 s<sup>-1</sup></td>
<td>https://www.sciencedirect.com/science/article/pii/S016041201932759X
Kd is 71.95 uM
kr/kf=71.95*10^-6
if kf=1
kr=71.95*10^-6
https://pubs.acs.org/doi/abs/10.1021/es304030x
this says kd=107 ??M
about the same</td>
</tr>
<tr>
<td>Syntran_Degr</td>
<td>9.62704417444E-6 s<sup>-1</sup></td>
<td>0 s<sup>-1</sup></td>
<td>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6660218/
protein half lives range from 2-20 hours in e. coli. since our e coli are likely in the stationary
phase, their protein turnover rate is much lower and therefore is closer to 20 hours.
k=ln(2)/(20*60*60)=9.62704417444E-6</td>
</tr>
<tr>
<td>SynTRan_Production</td>
<td>0.00155709342561 s<sup>-1</sup></td>
<td>0 s<sup>-1</sup>.&mu;M<sup>-1</sup></td>
<td>https://bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=100059&ver=26&hlid=56413
12 for slower rates
synthetic transcription factor is 1734/3 aa
(12.0 / (1734.0 / 3.0))
https://www.nature.com/articles/s41467-023-41176-y at slow growth rates elongation can fall to 9 aa
so 9 /(1734/3)=0.0155709342561
also says translation initiation time is about 10 s so
.1*0.0155709342561=0.00155709342561</td>
</tr>
<tr>
<td>Production</td>
<td>0.00763650248 s<sup>-1</sup></td>
<td>0 s<sup>-1</sup>.&mu;M<sup>-1</sup></td>
<td>https://book.bionumbers.org/what-is-faster-transcription-or-translation/ transcription 40-80 nt/sec.
syntrans is 1734 nt
rbs is 12
40/1746=0.0229095074456
https://bionumbers.hms.harvard.edu/bionumber.aspx?id=111997&ver=5 initiation about 20 genes per minute
so 1/3 gene per second
0.0229095074456/3=0.00763650248187</td>
</tr>
<tr>
<td>degrade_synt_pfas_cplx</td>
<td>9.62704417444E-6 s<sup>-1</sup></td>
<td>0 s<sup>-1</sup>.&mu;M<sup>-1</sup></td>
<td>same as protein degradation</td>
</tr>
<tr>
<td>mRNA_Degr</td>
<td>3.85E-4 s<sup>-1</sup></td>
<td>0 s<sup>-1</sup></td>
<td>https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02811-x
https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2020.02111/full
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6660218/
Half life of mRNA is about 0.5 hour, so k=ln(2)/(0.5*60*60)</td>
</tr>
<tr>
<td>Syntran_bind_pLex</td>
<td>4 s<sup>-1</sup>.&mu;M<sup>-1</sup></td>
<td>1 s<sup>-1</sup></td>
<td>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5873372/
In figure 4 our promoter has strength of about 80%. assuming that full strength means all DNA is taken,
you could roughly approximate K as 80/20 = 4/1=kf/kr</td>
</tr>
<tr>
<td>Leak</td>
<td>4.553734E-4 s<sup>-1</sup></td>
<td>0 s<sup>-1</sup>.&mu;M<sup>-1</sup></td>
<td>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5873372/
inducibility is 40 times leak, so rate of leak transcription is roughly 1/40 of induced
0.01821493624/40=0.0004553734</td>
</tr>
<tr>
<td>make GFP_mRNA</td>
<td>0.01821493624 s<sup>-1</sup></td>
<td>0 s<sup>-1</sup>.&mu;M<sup>-1</sup></td>
<td>https://book.bionumbers.org/what-is-faster-transcription-or-translation/ transcription 40-80 nt/sec.
gfp + rbs is 732 nt
40/732=0.0546448087432
https://bionumbers.hms.harvard.edu/bionumber.aspx?id=111997&ver=5 initiation about 20 genes per minute
so 1/3 gene per second
0.0546448087432/3=0.01821493624</td>
</tr>
<tr>
<td>Degr_GFP_mRNA</td>
<td>0.01821493624 s<sup>-1</sup></td>
<td>0 s<sup>-1</sup>.&mu;M<sup>-1</sup></td>
<td>https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02811-x
https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2020.02111/full
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6660218/
Half life of mRNA is about 0.5 hour, so k=ln(2)/(0.5*60*60)</td>
</tr>
<tr>
<td>SF_GFP_degr</td>
<td>1.83E-5 s<sup>-1</sup></td>
<td>0 s<sup>-1</sup></td>
<td>Was halflife of 2 hrs but substituted for 4.15/hr or 0.00115/s From
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4162443/</td>
</tr>
</table>
<h3>FAB_GFP_Construct_v1.1_Douglas</h3>
<table style="font-size: 10px;">
<tr>
<th>Reaction Name</th>
<th>Kf Value</th>
<th>Kr Value</th>
<th>Annotations</th>
</tr>
<tr>
<td>PFAS_DiffusionAndMessenger</td>
<td>0.001 s<sup>-1</sup></td>
<td>0.001 s<sup>-1</sup></td>
<td>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8913905/
it is not well known if PFAS interact with proteins for cell transport. in absence of better evidence,
we assume it acts by simple diffusion (probably slowly)</td>
</tr>
<tr>
<td>Fab_GFP_Production</td>
<td>0.0116652085156 s<sup>-1</sup></td>
<td>0 s<sup>-1</sup>.&mu;M<sup>-1</sup></td>
<td>https://book.bionumbers.org/what-is-faster-transcription-or-translation/ transcription 40-80 nt/sec.
fabgfp is 1143 nt with rbs
40/1143=0.0349956255468
https://bionumbers.hms.harvard.edu/bionumber.aspx?id=111997&ver=5 initiation about 20 genes per minute
so 1/3 gene per second
0.0349956255468/3=0.0116652085156</td>
</tr>
<tr>
<td>FAB_GFP_mRNA_degredation</td>
<td>3.85E-4 s<sup>-1</sup></td>
<td>0 s<sup>-1</sup></td>
<td>https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02811-x
https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2020.02111/full
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6660218/
Half life of mRNA is about 0.5 hour, so k=ln(2)/(0.5*60*60)</td>
</tr>
<tr>
<td>FAB_GFP_mRNA translation</td>
<td>0.00238726790451 s<sup>-1</sup></td>
<td>0 s<sup>-1</sup>.&mu;M<sup>-1</sup></td>
<td>https://bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=100059&ver=26&hlid=56413
12nt/s for slower rates
https://www.nature.com/articles/s41467-023-41176-y at slow growth rates elongation can fall to 9 aa
fab gfp is 377 aa so
9/377=0.0238726790451
above paper also says translation initiation time is about 10 s so
=0.00238726790451</td>
</tr>
<tr>
<td>FAB_GFP_Protein_degr</td>
<td>9.62704417444E-6 s<sup>-1</sup></td>
<td>0 s<sup>-1</sup></td>
<td>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6660218/
protein half lives range from 2-20 hours in e. coli. since our e coli are likely in the stationary
phase, their protein turnover rate is much lower and therefore is closer to 20 hours.
k=ln(2)/(20*60*60)=9.62704417444E-6</td>
</tr>
<tr>
<td>PFAS_and_FAB_GFP_ bind</td>
<td>192.4 s<sup>-1</sup>.&mu;M<sup>-1</sup></td>
<td>9.99E-4 s<sup>-1</sup></td>
<td>calculated using graph and table from paper: https://www.nature.com/articles/s41598-023-41953-1</td>
</tr>
<tr>
<td>PFAS_FAB_GFP_degr</td>
<td>9.62704417444E-6 s<sup>-1</sup></td>
<td>0 s<sup>-1</sup>.&mu;M<sup>-1</sup></td>
<td>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6660218/
protein half lives range from 2-20 hours in e. coli. since our e coli are likely in the stationary
phase, their protein turnover rate is much lower and therefore is closer to 20 hours.
k=ln(2)/(20*60*60)=9.62704417444E-6</td>
</tr>
</table>
<h3>pRMA_GFP construct 1 v1.3</h3>
<table style="font-size: 10px;">
<tr>
<th>Reaction Name</th>
<th>Kf Value</th>
<th>Kr Value</th>
<th>Annotations</th>
</tr>
<tr>
<td>PFAS_DiffusionAndMessenger</td>
<td>0.1 s<sup>-1</sup></td>
<td>0.1 s<sup>-1</sup></td>
<td>This is a rough first approximation of the unknown mechanisms for
activating prmA</td>
</tr>
<tr>
<td>PFAS_bind_pRMA</td>
<td>1 s<sup>-1</sup>.&mu;M<sup>-1</sup></td>
<td>0.01 s<sup>-1</sup></td>
<td>Taken from PFAS_Detectorv4_pillow, original had no source</td>
</tr>
<tr>
<td>Make_GFP_mRNA</td>
<td><sup>50</sup>&frasl;<sub>1200</sub> s<sup>-1</sup></td>
<td> 0 s<sup>-1</sup>.&mu;M<sup>-1</sup></td>
<td> estimated 643 bp, transcription rate of 10bp/sec</td>
</tr>
<tr>
<td>pRMA_Leak</td>
<td><sup>50</sup>&frasl;<sub>3600</sub> s<sup>-1</sup></td>
<td>0 s<sup>-1</sup>.&mu;M<sup>-1</sup></td>
<td>Leakiness rate constant taken from PFAS Detectorv4_pillow, original had no source</td>
</tr>
<tr>
<td>Degr_GFP_mRNA</td>
<td>3.85E-4 s<sup>-1</sup></td>
<td>0 s<sup>-1</sup></td>
<td>https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02811-x
https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2020.02111/full
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6660218//
Half life of mRNA is about 0.5 hour, so k=ln(2)/(0.5*60*60)</td>
</tr>
<tr>
<td>Make_SF_GFP</td>
<td>0.04201680672 s<sup>-1</sup></td>
<td>0 s<sup>-1</sup>.&mu;M<sup>-1</sup></td>
<td> From the paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4162443/ GFP
protein production from gene to immature (?) GFP with active promoter was
150/hr and another 3.6 /hr to get to the mature version I will use 150/hr
= 150/hr *1hr/3600 sec= 0.04166/sec</td>
</tr>
<tr>
<td>SF_GFP_degr</td>
<td>1.83E-5 s<sup>-1</sup></td>
<td>0 s<sup>-1</sup></td>
<td>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6660218/
https://www.mdpi.com/2073-4409/12/14/1846</td>
</tr>
<tr>
<td>SF_GFP_dimerization</td>
<td>0.83333 s<sup>-1</sup></td>
<td>0.01666 s<sup>-1</sup></td>
<td>https://pubmed.ncbi.nlm.nih.gov/18601531/</td>
</tr>
<tr>
<td>SF_GFP_dimer_degr</td>
<td>3.33333333333E-5 s<sup>-1</sup></td>
<td>0 s<sup>-1</sup></td>
<td>Rate constant used from PFAS Detectorv4_pillow, from similar dimerization degradation reaction,
original had no source</td>
</tr>
</table>
<h2>Constructs Table</h2>
<table>
<tr>
<th>Construct Name</th>
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<img style src="https://static.igem.wiki/teams/5114/team-members-page/labteam.png"
alt="Names from front to back prioritized more than left to right: Aryan Shah, Vishwaa Kannan, Leon Guo, Gowshik Ramanathan, Akhila Nalladimma, Edward Kim, James Marshall, Daniel Jiang, Sabine Waigel, Chaturya Sree Paladugu, Kalina Andreeva-Stallard">
<div class="group-card-info">
<h4>Names from front to back prioritized more than left to right: Aryan Shah, Vishwaa Kannan, Leon Guo, Gowshik Ramanathan, Akhila Nalladimma, Edward Kim, James Marshall, Daniel Jiang, Sabine Waigel, Chaturya Sree Paladugu, Kalina Andreeva-Stallard</h4>
<h4>Names from front to back prioritized more than left to right: Aryan Shah, Vishwaa Kannan, Leon Guo,
Gowshik Ramanathan, Akhila Nalladimma, Edward Kim, James Marshall, Daniel Jiang, Sabine Waigel, Chaturya
Sree Paladugu, Kalina Andreeva-Stallard</h4>
</div>
</div>
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