Team:ZJU-China/Modeling

From 2014.igem.org

(Difference between revisions)
 
(30 intermediate revisions not shown)
Line 6: Line 6:
<html>
<html>
-
 
+
<!-- side navigation bar -->
 +
<ul id="side_nav">
 +
    <li id="first_item" href="#top"><b>Home</b></li>
 +
    <li href="#nav1"><b>The Whole Genetic Pathways</b></li>
 +
    <li href="#nav2"><b>Recombination</b></li>
 +
    <li href="#nav3"><b>Bistable Swicth</b></li>
 +
</ul>
 +
<!-- side navigation end -->
<div class="zju_frame">
<div class="zju_frame">
<p class="cutline">&nbsp;</p>
<p class="cutline">&nbsp;</p>
<div class="zju_sec">
<div class="zju_sec">
-
    <!--Put content here -->
+
<h3 id="nav1" name="nav1">1. The Whole Genetic Pathways</h3>
-
    <p>hello!</p>
+
<p><b>ODE equations: </b></p>
-
 
+
<p>Before recombination:</p>
-
<!--main content -->
+
<table class="img" style="float:right;width:100%;text-align:center">
<table class="img" style="float:right;width:100%;text-align:center">
<tr>
<tr>
-
     <td><img src="https://static.igem.org/mediawiki/2014/8/85/ZJU_mol_formular1.png" style="float:none" width="400px"/></td>
+
     <td><img src="https://static.igem.org/mediawiki/2014/e/e9/ZJU_mol_f0.png" style="float:none" width="400px"/></td>
</tr>
</tr>
<tr>
<tr>
     <td>Formular.1</td>
     <td>Formular.1</td>
</tr>
</tr>
 +
</table>
 +
 +
<p>After combination, if combination succeeds.</p>
 +
<table class="img" style="float:right;width:100%;text-align:center">
 +
<tr>
 +
    <td><img src="https://static.igem.org/mediawiki/2014/6/69/ZJU_mol_f1.png" style="float:none" width="400px"/></td>
 +
</tr>
 +
<tr>
 +
    <td>Formular.2</td>
 +
</tr>
 +
</table>
 +
<table class="img" style="float:right;width:100%;text-align:center">
 +
<tr>
 +
    <td><img src="https://static.igem.org/mediawiki/2014/f/fe/ZJU_mol_f2.png" style="float:none" width="400px"/></td>
 +
</tr>
 +
<tr>
 +
    <td>Formular.3</td>
 +
</tr>
 +
</table>
 +
 +
<p>After putting in Ara</p>
 +
<table class="img" style="float:right;width:100%;text-align:center">
 +
<tr>
 +
    <td><img src="https://static.igem.org/mediawiki/2014/c/c3/ZJU_mol_f3.png" style="float:none" width="400px"/></td>
 +
</tr>
 +
<tr>
 +
    <td>Formular.4</td>
 +
</tr>
 +
</table>
 +
 +
 +
<p>Formulary:</p>
 +
<p>Take GFP for example</p>
 +
<table border=1px cellspacing="0" width="50%" bordercolorlight="#333333" bordercolordark="#efefef"  style="word-break: break-all;">
 +
<tr bgcolor=#cccccc><th>Name</th><th>description</th></tr>
 +
<tr bgcolor=#eafeff><td><em>m<sub>gfp</sub></em></td><td>The number of GFP mRNA
 +
</td></tr>
 +
<tr bgcolor=#eafeff><td><em>p<sub>gfp</sub></em></td><td>The number of GFP protein
 +
</td></tr>
 +
<tr bgcolor=#eafeff><td><em>N<sub>pla</sub></em></td><td>The number of plasmid
 +
</td></tr>
 +
<tr bgcolor=#eafeff><td><em>&alpha;<sub>gfp</sub></em></td><td>The maximal transcription rate of GFP
 +
</td></tr>
 +
<tr bgcolor=#eafeff><td><em>&alpha;<sub>0<sub>gfp</sub></sub></em></td><td>The leak of the promoter
 +
</td></tr>
 +
<tr bgcolor=#eafeff><td><em>&alpha;<sub>m<sub>gfp</sub></sub></em></td><td>The degradation rate of mRNA
 +
</td></tr>
 +
<tr bgcolor=#eafeff><td><em>&beta;<sub>m<sub>gfp</sub></sub></em></td><td>The translate rate of mRNA
 +
</td></tr>
 +
<tr bgcolor=#eafeff><td><em>&beta;<sub>p<sub>gfp</sub></sub></em></td><td>The degradation rate of GFP protein
 +
</td></tr>
 +
</table>
 +
<h3 id="nav2" name="nav2">2. Recombination</h3>
 +
<p><a href="https://2014.igem.org/Team:ZJU-China/SSR">background link</a></p>
 +
<p><b>description: </b></p>
 +
<p>In this part, what we want to do is to find out the probability of the recombination of gene of interest through simple molecular dynamics simulation. Although this simulation is quite simple, it certainly can tell us something right in some aspects within a certain accuracy.</p>
 +
The most important things for simulation are initial conditions and boundary conditions. Next, I will describe the initial conditions and boundary conditions in detail.</p>
 +
<p><b>Initial conditions:</b> </p>
 +
What is initial condition? Simply, initial condition is the condition when your simulation starts. More simply, initial condition is that you know every molecular coordinate as well as velocity if needs.</p>
 +
<p><b>Boundary conditions:</b></p>
 +
<p>What is boundary condition? E coli has a boundary, when the molecule runs out of its boundary, we should adjust it back in the E coli. In this simulation, periodic boundary condition is used.</p>
 +
<p><b>Some basic biology facts and simulation parameter choice:</b></p>
 +
<table class="img" style="float:right;width:100%;text-align:center">
 +
<tr>
 +
    <td><img src="https://static.igem.org/mediawiki/2014/8/8e/ZJU_mol_p1.png" style="float:none" width="600px"/></td>
 +
</tr>
 +
<tr>
 +
    <td><b>figure.1</b> E.coli cell</td>
 +
</tr>
 +
</table>
 +
<ol>
 +
<li>As shown above, the shape of E coli is similar to a cylinder. So in our simulation, we regard E coli as a cylinder whose radius is 0.5 micrometer, height is 2 micrometer. </li>
 +
<li>
 +
2.By looking up some online information, we find the average velocity of protein in cells is about 10 , we estimate the average velocity of gene of interest fragment is the same order of magnitude of the protein for their mass is the same order of magnitude. </li>
 +
<li>
 +
3.E coli replicate its chromosome in 40 minutes, the proceed rate of replication fork is about 10^5 bp/min. A fragment about 1kb needs 0.6s. </li>
 +
</ol>
 +
</table>
 +
<table class="img" style="float:right;width:100%;text-align:center">
 +
<tr>
 +
    <td><img src="https://static.igem.org/mediawiki/2014/c/ca/1-4.JPG" style="float:none" width="400px"/></td>
 +
</tr>
 +
<tr>
 +
    <td>results</td>
 +
</tr>
 +
</table>
 +
<li>We have simulate this for three times.The results are showed above,Which is consistent with our wet lab result.Although our simulation is quite simple,the result is good.</li>
 +
<h3 id="nav3" name="nav3">3. Bistable Switch</h3>
 +
<p><a href="https://2014.igem.org/Team:ZJU-China/B_Switch">background link</a></p>
 +
<p><b>ODE equtions：</b></p>
 +
 +
 +
<table class="img" style="float:right;width:100%;text-align:center">
 +
<tr>
 +
    <td><img src="https://static.igem.org/mediawiki/2014/c/c2/ZJU_mol_f4.png" style="float:none" width="400px"/></td>
 +
</tr>
 +
<tr>
 +
    <td>Formular.5</td>
 +
</tr>
 +
</table>
 +
 +
<table class="img" style="float:right;width:100%;text-align:center">
 +
<tr>
 +
    <td><img src="https://static.igem.org/mediawiki/2014/d/d7/ZJU_mol_f5.png" style="float:none" width="400px"/></td>
 +
</tr>
 +
<tr>
 +
    <td>Formular.6</td>
 +
</tr>
 +
</table>
 +
 +
<p>Formulary:</p>
 +
<table border=1px  cellspacing="0" width="80%" bordercolorlight="#333333" bordercolordark="#efefef" style="word-break: break-all;">
 +
<tr bgcolor=#cccccc><th>Name</th><th>description</th></tr>
 +
<tr bgcolor=#eafeff><td>[ ]</td><td>[ ] stands for the concentration
 +
</td></tr>
 +
<tr bgcolor=#eafeff><td><em>k<sub>c</sub></em></td><td>Inversion rate constant
 +
</td></tr>
 +
<tr bgcolor=#eafeff><td><em>k<sub>di</sub></em></td><td>dissociation equilibrium constant of int dimer-recombination site complex
 +
</td></tr>
 +
<tr bgcolor=#eafeff><td><em>k<sub>i</sub></em></td><td>dissociation equilibrium constant of int-int dimer
 +
</td></tr>
 +
<tr bgcolor=#eafeff><td><em>k<sub>dix</sub></em></td><td>dissociation equilibrium constant of int-xis dimer complex on a recombination site
 +
</td></tr>
 +
<tr bgcolor=#eafeff><td><em>&alpha;<sub>set</sub></em></td><td>The transcription rate of input set
 +
</td></tr>
 +
<tr bgcolor=#eafeff><td><em>&alpha;<sub>reset</sub></em></td><td>The transcription rate of input reset
 +
</td></tr>
 +
<tr bgcolor=#eafeff><td><em>&alpha;<sub>I</sub></em></td><td>The maximal transcription rate of int
 +
</td></tr>
 +
<tr bgcolor=#eafeff><td><em>&alpha;<sub>X</sub></em></td><td>The maximal transcription rate of xis
 +
</td></tr>
 +
<tr bgcolor=#eafeff><td><em>&gamma;<sub>I</sub></em></td><td>The degradation rate of int
 +
</td></tr>
 +
<tr bgcolor=#eafeff><td><em>&gamma;<sub>X</sub></em></td><td>The degradation rate of xis
 +
</td></tr>
 +
<tr bgcolor=#eafeff><td><em>k<sub>d</sub></em></td><td>The dissociation equilibrium constant
 +
</td></tr></table>
 +
<p><b> Parameter non-dimensionalization</b></p>
 +
<p>We nondimensionalize all concentration and time units,in terms of K<sub>i</sub> and K<sub>c</sub><sup>-1</sup>.K<sub>di</sub>=K<sub>dix</sub>=K<sub>i</sub>.&gamma;<sub>i</sub>=&gamma;<sub>x</sub>=K<sub>i</sub>K<sub>c</sub>.</p>
 +
 +
</table>
 +
<table class="img" style="float:right;width:100%;text-align:center">
 +
<tr>
 +
    <td><img src="https://static.igem.org/mediawiki/2014/f/f3/1.jpg" style="float:none" width="400px"/></td>
 +
</tr>
 +
<tr>
 +
    <td><b>figure.2</b>The response to set input</td>
 +
</tr>
 +
</table>
 +
 +
<p>Source code Download:<a href="https://2014.igem.org/File:ZJU_Modeling.zip">ZJU_Modeling.zip</a>
 +
 +
<h3>Reference</h3>
 +
 +
<p>[1]Mosberg, J. A., M. J. Lajoie and G. M. Church (2010). "Lambda red recombineering in Escherichia coli occurs through a fully single-stranded intermediate." Genetics 186(3): 791-799.</p>
 +
 +
<p>[2]Bonnet, J., P. Subsoontorn and D. Endy (2012). "Rewritable digital data storage in live cells via engineered control of recombination directionality." Proceedings of the National Academy of Sciences of the United States of America 109(23): 8884-8889.
 +
</p>
 +
 +
<table>
 +
    <tr>
 +
        <td><img  src="https://static.igem.org/mediawiki/2014/4/47/ZJU_left_arow.png"> </img></td><td> <a href="https://2014.igem.org/Team:ZJU-China/Solution">Previous: Solution</a></td>
 +
        <td width=700px></td>
 +
        <td><a href="https://2014.igem.org/Team:ZJU-China/Results">Next: Results</a> </td><td><img  src="https://static.igem.org/mediawiki/2014/1/19/ZJU_right_arow.png" > </img> </td>
 +
    </tr>
</table>
</table>

Latest revision as of 03:33, 18 October 2014

Team SponsorContact us

Zhejiang University ZJU International Education Fundation College of Life Sciences ZJU School of Medicine Zhejiang University

College of Agriculture & Biotechnology ZJU Faculty of Science Zhejiang University Undergraduate School of ZJU Department of Polymer Sciencce and Engneering Zhejiang University

International Relations Zhejiang University Vazyme Nanking ™ Co.

 Team Forum(BBS): ZJU-China 2014 Team Forum on www.zjubiolab.zju.edu.cn
Post Address: Biolab Center Room 413, ZJU Zijin'gang Campus,
Yuhang Tang Road No.866, Hangzhou, Zhejiang
Powered by . Zhejiang University. Email Address: zjuchina2014 @ 163.com

  • Home
  • The Whole Genetic Pathways
  • Recombination
  • Bistable Swicth

 

ODE equations:

Before recombination:

Formular.1

After combination, if combination succeeds.

Formular.2
Formular.3

After putting in Ara

Formular.4

Formulary:

Take GFP for example

Namedescription
mgfpThe number of GFP mRNA
pgfpThe number of GFP protein
NplaThe number of plasmid
αgfpThe maximal transcription rate of GFP
α0gfpThe leak of the promoter
αmgfpThe degradation rate of mRNA
βmgfpThe translate rate of mRNA
βpgfpThe degradation rate of GFP protein

background link

description:

In this part, what we want to do is to find out the probability of the recombination of gene of interest through simple molecular dynamics simulation. Although this simulation is quite simple, it certainly can tell us something right in some aspects within a certain accuracy.

The most important things for simulation are initial conditions and boundary conditions. Next, I will describe the initial conditions and boundary conditions in detail.

Initial conditions:

What is initial condition? Simply, initial condition is the condition when your simulation starts. More simply, initial condition is that you know every molecular coordinate as well as velocity if needs.

Boundary conditions:

What is boundary condition? E coli has a boundary, when the molecule runs out of its boundary, we should adjust it back in the E coli. In this simulation, periodic boundary condition is used.

Some basic biology facts and simulation parameter choice:

figure.1 E.coli cell
  1. As shown above, the shape of E coli is similar to a cylinder. So in our simulation, we regard E coli as a cylinder whose radius is 0.5 micrometer, height is 2 micrometer.
  2. 2.By looking up some online information, we find the average velocity of protein in cells is about 10 , we estimate the average velocity of gene of interest fragment is the same order of magnitude of the protein for their mass is the same order of magnitude.
  3. 3.E coli replicate its chromosome in 40 minutes, the proceed rate of replication fork is about 10^5 bp/min. A fragment about 1kb needs 0.6s.
results
  • We have simulate this for three times.The results are showed above,Which is consistent with our wet lab result.Although our simulation is quite simple,the result is good.

    • background link

    ODE equtions：

    Formular.5
    Formular.6

    Formulary:

    Namedescription
    [ ][ ] stands for the concentration
    kcInversion rate constant
    kdidissociation equilibrium constant of int dimer-recombination site complex
    kidissociation equilibrium constant of int-int dimer
    kdixdissociation equilibrium constant of int-xis dimer complex on a recombination site
    αsetThe transcription rate of input set
    αresetThe transcription rate of input reset
    αIThe maximal transcription rate of int
    αXThe maximal transcription rate of xis
    γIThe degradation rate of int
    γXThe degradation rate of xis
    kdThe dissociation equilibrium constant

    Parameter non-dimensionalization

    We nondimensionalize all concentration and time units,in terms of Ki and Kc-1.Kdi=Kdix=Ki.γi=γx=KiKc.

    figure.2The response to set input

    Source code Download:ZJU_Modeling.zip

    Reference

    [1]Mosberg, J. A., M. J. Lajoie and G. M. Church (2010). "Lambda red recombineering in Escherichia coli occurs through a fully single-stranded intermediate." Genetics 186(3): 791-799.

    [2]Bonnet, J., P. Subsoontorn and D. Endy (2012). "Rewritable digital data storage in live cells via engineered control of recombination directionality." Proceedings of the National Academy of Sciences of the United States of America 109(23): 8884-8889.

    Previous: Solution Next: Results

    Retrieved from "http://2014.igem.org/Team:ZJU-China/Modeling"