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| Line 4: |
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| | <html> | | <html> |
| | | | |
| − | <head>
| + | <head> |
| − | <link href="https://fonts.googleapis.com/css?family=Roboto+Mono" rel="stylesheet">
| + | <link href="https://fonts.googleapis.com/css?family=Roboto+Mono" rel="stylesheet"> |
| − | </head> | + | |
| − |
| + | <style> |
| − | <!-- start of content -->
| + | /* Show & hide */ |
| − | <body>
| + | .expandable { |
| − | <div class = "igem_2017_content_wrapper">
| + | /* overflow set to hidden to hide the expanded text */ |
| | + | overflow: hidden; |
| | + | /* all style changes will ease-in-out for 1s */ |
| | + | -moz-transition: all 1s ease-in-out; |
| | + | -ms-transition: all 1s ease-in-out; |
| | + | -o-transition: all 1s ease-in-out; |
| | + | -webkit-transition: all 1s ease-in-out; |
| | + | transition: all 1s; |
| | + | } |
| | | | |
| − | <center> | + | .panel { |
| − | <h1>Modeling</h1> | + | background-color: #eaf2ae; |
| − | </center> | + | border: 1px solid transparent; |
| | + | border-radius: 4px; |
| | + | border-color: #424017; |
| | + | -webkit-box-shadow: 0 1px 1px rgba(0, 0, 0, .05); |
| | + | box-shadow: 0 1px 1px rgba(0, 0, 0, .05); |
| | + | padding:15px; |
| | + | width:85%; |
| | + | margin: auto; |
| | + | margin-top:10px; |
| | + | } |
| | | | |
| − | <!--Growth curve of Chlorella vulgaris--> | + | /* IF THE SCREEN IS LESS THAN 1300PX */ |
| − | <h3></h3> | + | @media only screen and (max-width: 1300px) { |
| − | <h3>Growth curve of <i>Chlorella vulgaris</i></h3> | + | .panel {width:92%} |
| | + | } |
| | | | |
| − | <p>The timing of adding engineering E.coli or purified protein to Chlorella vulgaris culture is critical for our project. Through the initial, final biomass concentration data, the instantaneous rate of a reference time and other lab environment datas, we simulate the change in biomass concentration throughout the culture cycle. The status information in the culture medium at each point is then obtained through the other calculus to obtain the best timing point and the corresponding state.</p>
| |
| − |
| |
| − | <h6 style='color:#bc0101; font-family:"Roboto Mono", monospace;'>ln(Xt/X0)/t=A+Bexp(-C(t-M))=μ(specific growth rate)</h6>
| |
| | | | |
| − | <blockquote> | + | /* IF THE SCREEN IS LESS THAN 1200PX */ |
| − | <p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'> | + | @media only screen and (max-width: 1200px) { |
| − | X: biomass concentration(g/l)
| + | .panel {width:96%} |
| − | <br>t: time(hr)
| + | } |
| − | <br>A: the asymptotic of ln Xt/Xo as t decrese indefinitely | + | |
| − | <br>B: the asymptotic of ln Xt/Xo as t increase indefinitely
| + | |
| − | <br>C: the relative growth rate at time M
| + | |
| − | </p>
| + | |
| − | </blockquote>
| + | |
| | | | |
| − | <!--
| + | </style> |
| − | <p></p>
| + | |
| − | <p>If there are some key condition changed, we use following equation to correct the model.
| + | <script> |
| − | (we culture the microalgae in incubator ,it surrounding temperature is stable.)</p> | + | function toggleHeight1(e, maxHeight) { |
| | + | e = document.getElementById("s1"); // e = the gray div |
| | + | |
| | + | if(e.style.height != '30px') { |
| | + | e.style.height = '30px'; // height of one line: 20px |
| | + | } else { |
| | + | e.style.height = maxHeight + 'px'; |
| | + | } |
| | + | } |
| | | | |
| − | <h6 style='color:#bc0101; font-family:"Roboto Mono", monospace;'>μ=KI/(Ki+I+I^2/Kii); | + | function toggleHeight2(e, maxHeight) { |
| − | <br>
| + | e = document.getElementById("s2"); // e = the gray div |
| − | <br>=μmS/(Ks+S+S^2/Kss);
| + | |
| − | <br>
| + | if(e.style.height != '30px') { |
| − | <br>μm=μm*/(Kn+N+N^2/Knn);
| + | e.style.height = '30px'; // height of one line: 20px |
| − | </h6>
| + | } else { |
| − | <blockquote>
| + | e.style.height = maxHeight + 'px'; |
| − | <p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'>K: constant.
| + | } |
| − | <br>Ki: saturation constant of light intensity
| + | } |
| − | <br>Kii: inhibition constant of light intensity
| + | |
| − | <br>Ks: inhibition constant of substrate
| + | |
| − | <br>Kss: saturation constant of substrate
| + | |
| − | <br>μm: maximum specific growth rate
| + | |
| − | <br>Kn: inhibition constant of nitrogen
| + | |
| − | <br>Knn: saturation constant of nitrogen
| + | |
| − | <br>μm*: constant
| + | |
| − | </p>
| + | |
| − | </blockquote>
| + | |
| − | -->
| + | |
| − | | + | |
| − | <p></p>
| + | |
| − | <center>
| + | |
| − | <img src='https://static.igem.org/mediawiki/2017/0/04/T--NYMU-Taipei--model_growth_curve.gif'
| + | |
| − | alt='Growth curve of Chlorella vulgaris'
| + | |
| − | style='width:65%'>
| + | |
| − | <p style='font-size:20px'>fig.1-1 Growth curve of <i>Chlorella vulgaris</i></p>
| + | |
| − | </center>
| + | |
| − | <p></p> | + | |
| | | | |
| − | <center> | + | function toggleHeight3(e, maxHeight) { |
| − | <img src='https://static.igem.org/mediawiki/2017/e/e5/T--NYMU-Taipei--model_growth_rate.gif'
| + | e = document.getElementById("s3"); // e = the gray div |
| − | alt='Growth rate of Chlorella vulgaris'
| + | |
| − | style='width:65%'>
| + | if(e.style.height != '30px') { |
| − | <p style='font-size:20px'>fig.1-2 Growth rate of <i>Chlorella vulgaris</i></p>
| + | e.style.height = '30px'; // height of one line: 20px |
| − | </center>
| + | } else { |
| − | <p></p>
| + | e.style.height = maxHeight + 'px'; |
| − |
| + | } |
| − | <!-- oil accumulation and nitrogen source consumption -->
| + | } |
| − | <h3></h3>
| + | |
| − | <h3>Oil accumulation & Nirogen source consumption</h3>
| + | |
| − |
| + | |
| − | <p>Simulating common system of oil accumulation and nitrogen source consumption, not only get the reference of state before the improvement as well as the stage information, but also as a basic equation after some parameters or organisms join into the system.</p>
| + | |
| − |
| + | |
| − | <h6 style='color:#bc0101; font-family:"Roboto Mono", monospace;'>
| + | |
| − | dP/dt=*dX/dt+*X;
| + | |
| − | <br>
| + | |
| − | <br>dN/dt=-V*X;
| + | |
| − | <br>
| + | |
| − | <br>V=((qM-Q)/(qM-q))*((Vm*N)/(N+Vh)); | + | |
| − | <br>
| + | |
| − | <br>Q=(X0*Q0+N0-N)/X;
| + | |
| − | </h6>
| + | |
| − |
| + | |
| − | <blockquote>
| + | |
| − | <p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'>
| + | |
| − | P: lipid
| + | |
| − | <br>N: nitrogen
| + | |
| − | <br>X: biomass
| + | |
| − | <br>
| + | |
| − | <br>α: the instantaneous yield coefficient of product formation due to cell growth
| + | |
| − | <br>β: the specific formation rate of product
| + | |
| − | <br>
| + | |
| − | <br>q: Minimum N quota
| + | |
| − | <br>qM: Maximum N quota
| + | |
| − | <br>Q: N quota
| + | |
| − | <br>Vm: Maximum uptake rate of nitrogen
| + | |
| − | <br>Vh: Half-saturation coefficient
| + | |
| − | </p>
| + | |
| − | </blockquote>
| + | |
| − |
| + | |
| − | <p></p>
| + | |
| − | <center>
| + | |
| − | <img src='https://static.igem.org/mediawiki/2017/c/ca/T--NYMU-Taipei--model_L%26N.gif'
| + | |
| − | alt='Oil accumulation and nirogen source consumption at normal situation'
| + | |
| − | style='width:90%'>
| + | |
| − | <p style='font-size:20px'>fig.2 Oil accumulation and nirogen source consumption at normal situation</p>
| + | |
| − | </center>
| + | |
| − | <p></p>
| + | |
| − |
| + | |
| − |
| + | |
| − | <!-- Biomass in different nitrogen concentration-->
| + | |
| − | <h3></h3>
| + | |
| − | <h3>Biomass in different nitrogen concentration</h3>
| + | |
| − |
| + | |
| − | <p>To find the optimal amount of nitrogen removal, we model biomass decrease in different nitrogen concentration environments, and then we can find the best productivity.
| + | |
| − | </p>
| + | |
| − |
| + | |
| − | <h6 style='color:#bc0101; font-family:"Roboto Mono", monospace;'>
| + | |
| − | n2=exp((A+C*exp(-exp(-B(t-M))))*(t2-t1))*n1; | + | |
| − | <br>
| + | |
| − | <br>x2=x1+(n2-n1)*((k(ln(b(ns+a))^-1))-e);
| + | |
| − | </h6>
| + | |
| − |
| + | |
| − | <blockquote>
| + | |
| − | <p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'>
| + | |
| − | n1: biomass at frist state
| + | |
| − | <br>n2: biomass at secind state | + | |
| − | <br>x: biomass concentration(g/l)
| + | |
| − | <br>t: time(hr)
| + | |
| − | <br>
| + | |
| − | <br>A: the asymptotic of ln Xt/Xo as t decrese indefinitely //-39.9532
| + | |
| − | <br>B: the asymptotic of ln Xt/Xo as t increase indefinitely //-0.0222
| + | |
| − | <br>C: the relative growth rate at time M hr //45.6931
| + | |
| − | <br>
| + | |
| − | <br>k: constant //8.15229
| + | |
| − | <br>b:yield coefficient//1207.569
| + | |
| − | <br>ns:initial nitrogen concentration
| + | |
| − | <br>a:regression constant//0.01
| + | |
| − | <br>e:a perturbation//0.50678
| + | |
| − | </p>
| + | |
| − | </blockquote>
| + | |
| | | | |
| − | <p></p> | + | function toggleHeight4(e, maxHeight) { |
| − | <center>
| + | e = document.getElementById("s4"); // e = the gray div |
| − | <img src='https://static.igem.org/mediawiki/2017/e/e1/T--NYMU-Taipei--model_biomass.gif'
| + | |
| − | alt='Biomass in different nitrogen concentration'
| + | if(e.style.height != '30px') { |
| − | style='width:65%'>
| + | e.style.height = '30px'; // height of one line: 20px |
| − | <p style='font-size:20px'>fig.3 Biomass in different nitrogen concentration</p>
| + | } else { |
| − | </center>
| + | e.style.height = maxHeight + 'px'; |
| − | <p></p>
| + | } |
| − |
| + | } |
| − | <!-- Nitrogen source in nitrogen starvation -->
| + | |
| − | <h3></h3>
| + | |
| − | <h3>Nitrogen concentration in nitrogen starvation</h3>
| + | |
| − |
| + | |
| − | <p>Put normal and modified nitrogen source system together,see their demonstration, like speed and occasion.by constructing this model,we can find out the declining rate of each state,then adjust experiment.
| + | |
| − | </p>
| + | |
| − |
| + | |
| − | <h6 style='color:#bc0101; font-family:"Roboto Mono", monospace;'>
| + | |
| − | dn/dt=Yxn*dx/dt+m*x | + | |
| − | </h6>
| + | |
| − |
| + | |
| − | <blockquote>
| + | |
| − | <p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'>
| + | |
| − | n: nitrogen concentration
| + | |
| − | <br>Yxn: nitrate coefficient g/g 0.21016 | + | |
| − | <br>m: maintenance parameter hr^-1 0.0014393
| + | |
| − | <br>x: biomass concentration
| + | |
| − | </p>
| + | |
| − | </blockquote>
| + | |
| | | | |
| − | <p></p> | + | function toggleHeight5(e, maxHeight) { |
| − | <center>
| + | e = document.getElementById("s5"); // e = the gray div |
| − | <img src='https://static.igem.org/mediawiki/2017/5/5b/T--NYMU-Taipei--model_ns_nitrogen.gif'
| + | |
| − | alt='Nitrogen source in nitrogen starvation'
| + | if(e.style.height != '30px') { |
| − | style='width:65%'>
| + | e.style.height = '30px'; // height of one line: 20px |
| − | <p style='font-size:20px'>fig.4 Nitrogen source in nitrogen starvation</p>
| + | } else { |
| − | </center>
| + | e.style.height = maxHeight + 'px'; |
| − | <p></p> | + | } |
| | + | } |
| | + | </script> |
| | + | |
| | + | </head> |
| | + | |
| | + | <body> |
| | + | <div class='igem_2017_content_wrapper'> |
| | + | |
| | + | <center><h1>Modeling</h1></center> |
| | | | |
| | + | <div class='panel'> |
| | + | <div id="s1" class="expandable" style='height: 30px;padding-top:15px;'> |
| | + | <a href="#!" onclick="toggleHeight1(this, 620); return false" |
| | + | style="font-family:'Acme', sans-serif;font-size:34px;color:#205e1a;height: 30px;"> |
| | + | Growth curve of <i>Chlorella vulgaris</i> |
| | + | </a> |
| | + | <p style="padding-top:10px;"></p> |
| | + | |
| | + | <p>The timing of adding engineering <i>E.coli</i> or purified protein to <i>Chlorella vulgaris</i> culture is critical for our project. Through the initial, final biomass concentration data, the instantaneous rate of a reference time and other lab environment datas, we simulate the change in biomass concentration throughout the culture cycle. The status information in the culture medium at each point is then obtained through the other calculus to obtain the best timing point and the corresponding state.</p> |
| | + | |
| | + | <h6 style='color:#bc0101; font-family:"Roboto Mono", monospace;'>ln(Xt/X0)/t=A+Bexp(-C(t-M))=μ(specific growth rate)</h6> |
| | + | |
| | + | <blockquote> |
| | + | <p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'> |
| | + | X: biomass concentration(g/l) |
| | + | <br>t: time(hr) |
| | + | <br>A: the asymptotic of ln Xt/Xo as t decrese indefinitely |
| | + | <br>B: the asymptotic of ln Xt/Xo as t increase indefinitely |
| | + | <br>C: the relative growth rate at time M |
| | + | </p> |
| | + | </blockquote> |
| | + | |
| | + | <p></p> |
| | + | <center> |
| | + | <img src='https://static.igem.org/mediawiki/2017/0/04/T--NYMU-Taipei--model_growth_curve.gif' |
| | + | alt='Growth curve of Chlorella vulgaris' |
| | + | style='width:65%'> |
| | + | <p style='font-size:20px'>fig.1-1 Growth curve of <i>Chlorella vulgaris</i></p> |
| | + | </center> |
| | + | <p></p> |
| | | | |
| − | <!-- Oil accumulation in nitrogen starvation -->
| + | <center> |
| − | <h3></h3>
| + | <img src='https://static.igem.org/mediawiki/2017/e/e5/T--NYMU-Taipei--model_growth_rate.gif' |
| − | <h3>Oil accumulation in nitrogen starvation</h3> | + | alt='Growth rate of Chlorella vulgaris' |
| | + | style='width:65%'> |
| | + | <p style='font-size:20px'>fig.1-2 Growth rate of <i>Chlorella vulgaris</i></p> |
| | + | </center> |
| | + | <p></p> |
| | + | |
| | + | </div> |
| | + | </div> |
| | | | |
| − | <p>We predict total lipid increase under nitrogen starvation. The model provide theoretical information of top yield. This graph show that if we use symbiotic microbe isolating nitrogen source temporarily and successfully, the productivity will be enhanced. | + | <div class='panel'> |
| − | </p> | + | <div id="s2" class="expandable" style='height: 30px;padding-top:15px;'> |
| − |
| + | |
| − | <h6 style='color:#bc0101; font-family:"Roboto Mono", monospace;'>
| + | <a href="#!" onclick="toggleHeight2(this, 620); return false" |
| − | dp/dt=k1(dx/dt)^2+k2(dx/dt)(x)+e | + | style="font-family:'Acme', sans-serif;font-size:34px;color:#205e1a;height: 30px;"> |
| − | </h6>
| + | Growth curve of |
| − |
| + | </a> |
| − | <blockquote>
| + | |
| − | <p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'>
| + | <p style="padding-top:10px;"></ p> |
| − | p: lipid concentrtion
| + | |
| − | <br>K1: growth correlation coefficient g^2/g^2 //122.40085
| + | |
| − | <br>K2: non-growth correlation coefficient g^-1 //0.28736
| + | |
| − | <br>e: a perturbation g/l*hr //-0.078
| + | |
| − | </p>
| + | |
| − | </blockquote>
| + | |
| | | | |
| − | <p></p>
| |
| − | <center>
| |
| − | <img src='https://static.igem.org/mediawiki/2017/e/e8/T--NYMU-Taipei--model_ns_oil.gif'
| |
| − | alt='Oil accumulation in nitrogen starvation'
| |
| − | style='width:65%'>
| |
| − | <p style='font-size:20px'>fig.5 Oil accumulation in nitrogen starvation</p>
| |
| − | </center>
| |
| − | <p></p>
| |
| | | | |
| − | <!-- Population of co-cultured Chlorella and modified E.coli --> | + | </div> |
| − | <h3></h3>
| + | </div> |
| − | <h3>Population of co-cultured Chlorella and modified E.coli</h3> | + | |
| | | | |
| − | <p>According to our reference experiment data, we find that e.coli can build a relationship with chlorella like symbiosis. So we build a model and use 3 kinds of situations’ value to simulate their change when they are co-cultured. According to it,we get the proper experimental proportion of them at each need.
| |
| − | </p>
| |
| − |
| |
| − | <h6 style='color:#bc0101; font-family:"Roboto Mono", monospace;'>
| |
| − | x2=(ax-x^2/(1+b*x*z))/Rx+x/Yx
| |
| − | <br>
| |
| − | <br>z2=(cz-z^2/(1+g*z*x))/Rz+z/Yz
| |
| − | </h6>
| |
| − |
| |
| − | <blockquote>
| |
| − | <p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'>
| |
| − | X: chlorella vugaris
| |
| − | <br>Z: e.coil
| |
| − | <br>Rx: symbiosis coefficient g/hr //1.0000023
| |
| − | <br>Rz: symbiosis coefficient g/hr //1.178
| |
| − | <br>Yx: correlation coefficient//12.576
| |
| − | <br>Yz: correlation coefficient//2.276
| |
| − | <br>a: population constant //0.80467
| |
| − | <br>c: population constant//0.61198
| |
| − | <br>b: relative parameter //0.00027
| |
| − | <br>g: relative parameter //0.0013
| |
| − | </p>
| |
| − | </blockquote>
| |
| − |
| |
| − | <p></p>
| |
| − | <center>
| |
| − | <img src='https://static.igem.org/mediawiki/2017/a/a5/T--NYMU-Taipei--model_population1.gif'
| |
| − | alt='Population of co-cultured Chlorella and modified E.coli'
| |
| − | style='width:65%'>
| |
| − | <p style='font-size:20px'>fig.5-1 Population of co-cultured Chlorella and modified E.coli</p>
| |
| − | </center>
| |
| − | <p></p>
| |
| − |
| |
| − | <center>
| |
| − | <img src='https://static.igem.org/mediawiki/2017/e/eb/T--NYMU-Taipei--model_population2.gif'
| |
| − | alt='Population of co-cultured Chlorella and modified E.coli'
| |
| − | style='width:65%'>
| |
| − | <p style='font-size:20px'>fig.5-2 Population of co-cultured Chlorella and modified E.coli</p>
| |
| − | </center>
| |
| − | <p></p>
| |
| − |
| |
| − | <center>
| |
| − | <img src='https://static.igem.org/mediawiki/2017/b/b0/T--NYMU-Taipei--model_populaiton3.gif'
| |
| − | alt='Population of co-cultured Chlorella and modified E.coli'
| |
| − | style='width:65%'>
| |
| − | <p style='font-size:20px'>fig.5-3 Population of co-cultured Chlorella and modified E.coli</p>
| |
| − | </center>
| |
| − | <p></p>
| |
| − |
| |
| − | <!-- Nitrogen-lipid plot -->
| |
| − | <h3></h3>
| |
| − | <h3>Nitrogen-lipid plot</h3>
| |
| − |
| |
| − | <p>This chart demonstrate the connection between initial nitrogen concentration and final lipid proportion in algae cell.tell us the approximately trend of it.
| |
| − | </p>
| |
| − |
| |
| − | <h6 style='color:#bc0101; font-family:"Roboto Mono", monospace;'>
| |
| − | l=k(ln(b(ns+a))^-1)-e
| |
| − | </h6>
| |
| − |
| |
| − | <blockquote>
| |
| − | <p style='color:#702828;font-size:16px; font-family:"Roboto Mono", monospace;'>
| |
| − | l: lipid proportion in cell
| |
| − | <br>k: constant g/100g //1.13372
| |
| − | <br>b: yield coefficient//1.57172
| |
| − | <br>ns: initial nitrogen concentration
| |
| − | <br>a: regression constant//0.51653
| |
| − | <br>e: a perturbation g/100g//-55.2776
| |
| − | </p>
| |
| − | </blockquote>
| |
| − |
| |
| − | <p></p>
| |
| − | <center>
| |
| − | <img src='https://static.igem.org/mediawiki/2017/c/ce/T--NYMU-Taipei--model_nitrogen%2Blipid.png'
| |
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