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Team:ZJU-China/Modeling
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<div class="zju_sec"> | <div class="zju_sec"> | ||
<h3 id="nav1" name="nav1">1. The Whole Genetic Pathways</h3> | <h3 id="nav1" name="nav1">1. The Whole Genetic Pathways</h3> | ||
| - | <p>ODE equations:</p> | + | <p><b>ODE equations: </b></p> |
<p>Before recombination:</p> | <p>Before recombination:</p> | ||
<table class="img" style="float:right;width:100%;text-align:center"> | <table class="img" style="float:right;width:100%;text-align:center"> | ||
| Line 60: | Line 60: | ||
<p>Formulary:</p> | <p>Formulary:</p> | ||
<p>Take GFP for example</p> | <p>Take GFP for example</p> | ||
| - | <table> | + | <table border=1px cellspacing="0" width="50%" bordercolorlight="#333333" bordercolordark="#efefef" style="word-break: break-all;"> |
| - | <tr><th>Name</th><th>description</th></tr> | + | <tr bgcolor=#cccccc><th>Name</th><th>description</th></tr> |
| - | <tr><td><em>m<sub>gfp</sub></em></td><td>The number of GFP mRNA | + | <tr bgcolor=#eafeff><td><em>m<sub>gfp</sub></em></td><td>The number of GFP mRNA |
</td></tr> | </td></tr> | ||
| - | <tr><td><em>p<sub>gfp</sub></em></td><td>The number of GFP protein | + | <tr bgcolor=#eafeff><td><em>p<sub>gfp</sub></em></td><td>The number of GFP protein |
</td></tr> | </td></tr> | ||
| - | <tr><td><em>N<sub>pla</sub></em></td><td>The number of plasmid | + | <tr bgcolor=#eafeff><td><em>N<sub>pla</sub></em></td><td>The number of plasmid |
</td></tr> | </td></tr> | ||
| - | <tr><td><em>α<sub>gfp</sub></em></td><td>The maximal transcription rate of GFP | + | <tr bgcolor=#eafeff><td><em>α<sub>gfp</sub></em></td><td>The maximal transcription rate of GFP |
</td></tr> | </td></tr> | ||
| - | <tr><td><em>α<sub>0<sub>gfp</sub></sub></em></td><td>The leak of the promoter | + | <tr bgcolor=#eafeff><td><em>α<sub>0<sub>gfp</sub></sub></em></td><td>The leak of the promoter |
</td></tr> | </td></tr> | ||
| - | <tr><td><em>α<sub>m<sub>gfp</sub></sub></em></td><td>The degradation rate of mRNA | + | <tr bgcolor=#eafeff><td><em>α<sub>m<sub>gfp</sub></sub></em></td><td>The degradation rate of mRNA |
</td></tr> | </td></tr> | ||
| - | <tr><td><em>β<sub>m<sub>gfp</sub></sub></em></td><td>The translate rate of mRNA | + | <tr bgcolor=#eafeff><td><em>β<sub>m<sub>gfp</sub></sub></em></td><td>The translate rate of mRNA |
</td></tr> | </td></tr> | ||
| - | <tr><td><em>β<sub>p<sub>gfp</sub></sub></em></td><td>The degradation rate of GFP protein | + | <tr bgcolor=#eafeff><td><em>β<sub>p<sub>gfp</sub></sub></em></td><td>The degradation rate of GFP protein |
</td></tr> | </td></tr> | ||
</table> | </table> | ||
<h3 id="nav2" name="nav2">2. Recombination</h3> | <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><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 | + | <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> | 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> | <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> | 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><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>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> |
| - | Some basic biology facts and simulation parameter choice:</p><table class="img" style="float:right;width:100%;text-align:center"> | + | <p><b>Some basic biology facts and simulation parameter choice:</b></p> |
| + | <table class="img" style="float:right;width:100%;text-align:center"> | ||
<tr> | <tr> | ||
<td><img src="https://static.igem.org/mediawiki/2014/8/8e/ZJU_mol_p1.png" style="float:none" width="600px"/></td> | <td><img src="https://static.igem.org/mediawiki/2014/8/8e/ZJU_mol_p1.png" style="float:none" width="600px"/></td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| - | <td> | + | <td><b>figure.1</b> E.coli cell</td> |
</tr> | </tr> | ||
</table> | </table> | ||
<ol> | <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 , height is 2 . </li> | + | <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> | 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> | 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> | </ol> | ||
| Line 106: | Line 110: | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| - | <td></td> | + | <td>results</td> |
</tr> | </tr> | ||
</table> | </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> | <h3 id="nav3" name="nav3">3. Bistable Switch</h3> | ||
| - | <p>ODE equtions：</p> | + | <p><a href="https://2014.igem.org/Team:ZJU-China/B_Switch">background link</a></p> |
| + | <p><b>ODE equtions：</b></p> | ||
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<p>Formulary:</p> | <p>Formulary:</p> | ||
| - | <table> | + | <table border=1px cellspacing="0" width="80%" bordercolorlight="#333333" bordercolordark="#efefef" style="word-break: break-all;"> |
| - | <tr><th>Name</th><th>description</th></tr> | + | <tr bgcolor=#cccccc><th>Name</th><th>description</th></tr> |
| - | <tr><td>[ ]</td><td>[ ] stands for the concentration | + | <tr bgcolor=#eafeff><td>[ ]</td><td>[ ] stands for the concentration |
</td></tr> | </td></tr> | ||
| - | <tr><td><em>k<sub>c</sub></em></td><td>Inversion rate constant | + | <tr bgcolor=#eafeff><td><em>k<sub>c</sub></em></td><td>Inversion rate constant |
</td></tr> | </td></tr> | ||
| - | <tr><td><em>k<sub>di</sub></em></td><td>dissociation equilibrium constant of int dimer-recombination site complex | + | <tr bgcolor=#eafeff><td><em>k<sub>di</sub></em></td><td>dissociation equilibrium constant of int dimer-recombination site complex |
</td></tr> | </td></tr> | ||
| - | <tr><td><em>k<sub>i</sub></em></td><td>dissociation equilibrium constant of int-int dimer | + | <tr bgcolor=#eafeff><td><em>k<sub>i</sub></em></td><td>dissociation equilibrium constant of int-int dimer |
</td></tr> | </td></tr> | ||
| - | <tr><td><em>k<sub>dix</sub></em></td><td>dissociation equilibrium constant of int-xis dimer complex on a recombination site | + | <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> | </td></tr> | ||
| - | <tr><td><em>α<sub>set</sub></em></td><td>The transcription rate of input set | + | <tr bgcolor=#eafeff><td><em>α<sub>set</sub></em></td><td>The transcription rate of input set |
</td></tr> | </td></tr> | ||
| - | <tr><td><em>α<sub>reset</sub></em></td><td>The transcription rate of input reset | + | <tr bgcolor=#eafeff><td><em>α<sub>reset</sub></em></td><td>The transcription rate of input reset |
</td></tr> | </td></tr> | ||
| - | <tr><td><em>α<sub>I</sub></em></td><td>The maximal transcription rate of int | + | <tr bgcolor=#eafeff><td><em>α<sub>I</sub></em></td><td>The maximal transcription rate of int |
</td></tr> | </td></tr> | ||
| - | <tr><td><em>α<sub>X</sub></em></td><td>The maximal transcription rate of xis | + | <tr bgcolor=#eafeff><td><em>α<sub>X</sub></em></td><td>The maximal transcription rate of xis |
</td></tr> | </td></tr> | ||
| - | <tr><td><em>γ<sub>I</sub></em></td><td>The degradation rate of int | + | <tr bgcolor=#eafeff><td><em>γ<sub>I</sub></em></td><td>The degradation rate of int |
</td></tr> | </td></tr> | ||
| - | <tr><td><em>γ<sub>X</sub></em></td><td>The degradation rate of xis | + | <tr bgcolor=#eafeff><td><em>γ<sub>X</sub></em></td><td>The degradation rate of xis |
</td></tr> | </td></tr> | ||
| - | <tr><td><em>k<sub>d</sub></em></td><td>The dissociation equilibrium constant | + | <tr bgcolor=#eafeff><td><em>k<sub>d</sub></em></td><td>The dissociation equilibrium constant |
</td></tr></table> | </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>.γ<sub>i</sub>=γ<sub>x</sub>=K<sub>i</sub>K<sub>c</sub>.</p> | ||
| + | </table> | ||
<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/ | + | <td><img src="https://static.igem.org/mediawiki/2014/f/f3/1.jpg" style="float:none" width="400px"/></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| - | <td></td> | + | <td><b>figure.2</b>The response to set input</td> |
</tr> | </tr> | ||
</table> | </table> | ||
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| + | <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> | ||
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</div> | </div> | ||
</html> | </html> | ||
Latest revision as of 03:33, 18 October 2014
| Team Sponsor | Contact us | ||
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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 |
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1. The Whole Genetic Pathways
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
| Name | description |
|---|---|
| mgfp | The number of GFP mRNA |
| pgfp | The number of GFP protein |
| Npla | The number of plasmid |
| αgfp | The maximal transcription rate of GFP |
| α0gfp | The leak of the promoter |
| αmgfp | The degradation rate of mRNA |
| βmgfp | The translate rate of mRNA |
| βpgfp | The degradation rate of GFP protein |
2. Recombination
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 |
- 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.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.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 |
3. Bistable Switch
ODE equtions：
 |
| Formular.5 |
 |
| Formular.6 |
Formulary:
| Name | description |
|---|---|
| [ ] | [ ] stands for the concentration |
| kc | Inversion rate constant |
| kdi | dissociation equilibrium constant of int dimer-recombination site complex |
| ki | dissociation equilibrium constant of int-int dimer |
| kdix | dissociation equilibrium constant of int-xis dimer complex on a recombination site |
| αset | The transcription rate of input set |
| αreset | The transcription rate of input reset |
| αI | The maximal transcription rate of int |
| αX | The maximal transcription rate of xis |
| γI | The degradation rate of int |
| γX | The degradation rate of xis |
| kd | The 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.
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