Team:Tsinghua-A/Modeling

From 2011.igem.org

(Difference between revisions)
Line 102: Line 102:
</div>
</div>
<p>&nbsp;</p>
<p>&nbsp;</p>
-
<!-- end #menu -->
+
<!-- end #menu --><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
-
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+
<HTML>
<HTML>
<HEAD>
<HEAD>
Line 112: Line 111:
<META NAME="CREATED" CONTENT="20110930;20563600">
<META NAME="CREATED" CONTENT="20110930;20563600">
<META NAME="CHANGEDBY" CONTENT="Sl Y">
<META NAME="CHANGEDBY" CONTENT="Sl Y">
-
<META NAME="CHANGED" CONTENT="20111001;22404000">
+
<META NAME="CHANGED" CONTENT="20111002;1083700">
<META NAME="CHANGEDBY" CONTENT="Sl Y">
<META NAME="CHANGEDBY" CONTENT="Sl Y">
<META NAME="CHANGEDBY" CONTENT="Sl Y">
<META NAME="CHANGEDBY" CONTENT="Sl Y">
<META NAME="CHANGEDBY" CONTENT="Sl Y">
<META NAME="CHANGEDBY" CONTENT="Sl Y">
<META NAME="CHANGEDBY" CONTENT="Sl Y">
<META NAME="CHANGEDBY" CONTENT="Sl Y">
-
 
-
 
</HEAD>
</HEAD>
-
<BODY LANG="zh-CN" BGCOLOR="#E7F2D5" DIR="LTR">
+
<BODY LANG="zh-CN" BGCOLOR="#ffffff" DIR="LTR">
<P><FONT FACE="Arial, sans-serif"><FONT SIZE=5 STYLE="font-size: 20pt"><SPAN LANG="en-US">Modeling
<P><FONT FACE="Arial, sans-serif"><FONT SIZE=5 STYLE="font-size: 20pt"><SPAN LANG="en-US">Modeling
Section</SPAN></FONT></FONT></P>
Section</SPAN></FONT></FONT></P>
Line 154: Line 151:
Model </FONT></FONT></FONT></SPAN></FONT>
Model </FONT></FONT></FONT></SPAN></FONT>
</P>
</P>
-
<P ALIGN=RIGHT><FONT FACE="Times New Roman, serif"><SPAN LANG="en-US"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US"><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/P1A">construction</A>
+
<P ALIGN=RIGHT><FONT FACE="Times New Roman, serif"><SPAN LANG="en-US"><FONT COLOR="#666600"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US"><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/P1A">construction</A>
-
</SPAN></FONT></FONT><FONT COLOR="#6b4794"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">|</SPAN></FONT></FONT></FONT><FONT FACE="Times New Roman, serif"><SPAN LANG="en-US">
+
</SPAN></FONT></FONT></FONT><FONT COLOR="#6b4794"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">|</SPAN></FONT></FONT></FONT><FONT FACE="Times New Roman, serif"><SPAN LANG="en-US">
-
</SPAN></FONT><FONT COLOR="#000000"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US"><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/P1B">parameters</A>
+
</SPAN></FONT><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/P1B"><FONT COLOR="#666600"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">parameters</SPAN></FONT></FONT></FONT></A><FONT COLOR="#000000"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">
</SPAN></FONT></FONT></FONT><FONT COLOR="#6b4794"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">|
</SPAN></FONT></FONT></FONT><FONT COLOR="#6b4794"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">|
-
</SPAN></FONT></FONT></FONT><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/P1C"><FONT COLOR="#000000"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">results</SPAN></FONT></FONT></FONT></A></SPAN></FONT></P>
+
</SPAN></FONT></FONT></FONT><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/P1C"><FONT COLOR="#666600"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">results</SPAN></FONT></FONT></FONT></A></SPAN></FONT></P>
<P STYLE="margin-left: 1.53cm"><FONT FACE="Arial, sans-serif"><SPAN LANG="en-US">In
<P STYLE="margin-left: 1.53cm"><FONT FACE="Arial, sans-serif"><SPAN LANG="en-US">In
our first step, we wanted to describe the system thoroughly without
our first step, we wanted to describe the system thoroughly without
Line 169: Line 166:
<P><FONT FACE="Arial, sans-serif"><FONT SIZE=5 STYLE="font-size: 20pt"><SPAN LANG="en-US"><FONT SIZE=4 STYLE="font-size: 15pt"><I>PART
<P><FONT FACE="Arial, sans-serif"><FONT SIZE=5 STYLE="font-size: 20pt"><SPAN LANG="en-US"><FONT SIZE=4 STYLE="font-size: 15pt"><I>PART
2</I></FONT> <FONT COLOR="#dc2300">Simplified Model</FONT></SPAN></FONT></FONT></P>
2</I></FONT> <FONT COLOR="#dc2300">Simplified Model</FONT></SPAN></FONT></FONT></P>
-
<P ALIGN=RIGHT><FONT FACE="Times New Roman, serif"><SPAN LANG="en-US"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US"><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/P2A">preparation</A>
+
<P ALIGN=RIGHT><FONT FACE="Times New Roman, serif"><SPAN LANG="en-US"><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/P2A"><FONT COLOR="#c5000b"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">preparation</SPAN></FONT></FONT></FONT></A><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">
</SPAN></FONT></FONT><FONT COLOR="#6b4794"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">|</SPAN></FONT></FONT></FONT><FONT FACE="Times New Roman, serif"><SPAN LANG="en-US">
</SPAN></FONT></FONT><FONT COLOR="#6b4794"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">|</SPAN></FONT></FONT></FONT><FONT FACE="Times New Roman, serif"><SPAN LANG="en-US">
-
</SPAN></FONT><FONT COLOR="#000000"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US"><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/P2B">parameters</A>
+
</SPAN></FONT><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/P2B"><FONT COLOR="#c5000b"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">parameters</SPAN></FONT></FONT></FONT></A><FONT COLOR="#000000"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">
</SPAN></FONT></FONT></FONT><FONT COLOR="#6b4794"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">|
</SPAN></FONT></FONT></FONT><FONT COLOR="#6b4794"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">|
-
</SPAN></FONT></FONT></FONT><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/P2C"><FONT COLOR="#000000"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">results</SPAN></FONT></FONT></FONT></A></SPAN></FONT></P>
+
</SPAN></FONT></FONT></FONT><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/P2C"><FONT COLOR="#c5000b"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">results</SPAN></FONT></FONT></FONT></A></SPAN></FONT></P>
<P STYLE="margin-left: 1.53cm"><FONT FACE="Arial, sans-serif"><SPAN LANG="en-US">Although
<P STYLE="margin-left: 1.53cm"><FONT FACE="Arial, sans-serif"><SPAN LANG="en-US">Although
ODEs provide a thorough, precise description of the whole system,
ODEs provide a thorough, precise description of the whole system,
Line 184: Line 181:
</P>
</P>
<P><FONT FACE="Arial, sans-serif"><SPAN LANG="en-US"><FONT SIZE=4 STYLE="font-size: 15pt"><I>PART
<P><FONT FACE="Arial, sans-serif"><SPAN LANG="en-US"><FONT SIZE=4 STYLE="font-size: 15pt"><I>PART
-
3 </I></FONT><FONT COLOR="#0099ff"><FONT SIZE=5 STYLE="font-size: 20pt">Dimensionless
+
3 </I></FONT><FONT COLOR="#006b6b"><FONT SIZE=5 STYLE="font-size: 20pt">Dimensionless
Model</FONT></FONT></SPAN></FONT></P>
Model</FONT></FONT></SPAN></FONT></P>
-
<P ALIGN=RIGHT><FONT FACE="Times New Roman, serif"><SPAN LANG="en-US"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US"><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/P3A">preparation</A>
+
<P ALIGN=RIGHT><FONT FACE="Times New Roman, serif"><SPAN LANG="en-US"><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/P3A"><FONT COLOR="#198a8a"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">preparation</SPAN></FONT></FONT></FONT></A><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">
</SPAN></FONT></FONT><FONT COLOR="#6b4794"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">|</SPAN></FONT></FONT></FONT><FONT FACE="Times New Roman, serif"><SPAN LANG="en-US">
</SPAN></FONT></FONT><FONT COLOR="#6b4794"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">|</SPAN></FONT></FONT></FONT><FONT FACE="Times New Roman, serif"><SPAN LANG="en-US">
-
</SPAN></FONT><FONT COLOR="#000000"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US"><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/P3B">parameters</A>
+
</SPAN></FONT><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/P3B"><FONT COLOR="#006b6b"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">parameters</SPAN></FONT></FONT></FONT></A><FONT COLOR="#000000"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">
</SPAN></FONT></FONT></FONT><FONT COLOR="#6b4794"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">|
</SPAN></FONT></FONT></FONT><FONT COLOR="#6b4794"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">|
-
</SPAN></FONT></FONT></FONT><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/P3C"><FONT COLOR="#000000"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">results</SPAN></FONT></FONT></FONT></A></SPAN></FONT></P>
+
</SPAN></FONT></FONT></FONT><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/P3C"><FONT COLOR="#006b6b"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">results</SPAN></FONT></FONT></FONT></A></SPAN></FONT></P>
<P STYLE="margin-left: 1.56cm"><FONT FACE="Arial, sans-serif"><SPAN LANG="en-US">In
<P STYLE="margin-left: 1.56cm"><FONT FACE="Arial, sans-serif"><SPAN LANG="en-US">In
order to make a further analysis on stability of the system,
order to make a further analysis on stability of the system,
Line 203: Line 200:
4 </I></FONT><FONT COLOR="#666600"><FONT SIZE=5 STYLE="font-size: 20pt">Quorum-sensing
4 </I></FONT><FONT COLOR="#666600"><FONT SIZE=5 STYLE="font-size: 20pt">Quorum-sensing
Effect</FONT></FONT></SPAN></FONT></P>
Effect</FONT></FONT></SPAN></FONT></P>
-
<P ALIGN=RIGHT><FONT FACE="Times New Roman, serif"><SPAN LANG="en-US"><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/P4"><FONT COLOR="#000000"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">results</SPAN></FONT></FONT></FONT></A></SPAN></FONT></P>
+
<P ALIGN=RIGHT><FONT COLOR="#663300"><FONT FACE="Times New Roman, serif"><SPAN LANG="en-US"><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/P4"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">results</SPAN></FONT></FONT></A></SPAN></FONT></FONT></P>
<P STYLE="margin-left: 1.59cm"><FONT FACE="Arial, sans-serif"><SPAN LANG="en-US">What
<P STYLE="margin-left: 1.59cm"><FONT FACE="Arial, sans-serif"><SPAN LANG="en-US">What
we have done insofar is focused on two-cell oscillation.
we have done insofar is focused on two-cell oscillation.
Line 214: Line 211:
<P><FONT FACE="Arial, sans-serif"><SPAN LANG="en-US"><FONT SIZE=4 STYLE="font-size: 15pt"><I>PART
<P><FONT FACE="Arial, sans-serif"><SPAN LANG="en-US"><FONT SIZE=4 STYLE="font-size: 15pt"><I>PART
5</I></FONT> <FONT COLOR="#c5000b"><FONT SIZE=5 STYLE="font-size: 20pt">Reference</FONT></FONT></SPAN></FONT></P>
5</I></FONT> <FONT COLOR="#c5000b"><FONT SIZE=5 STYLE="font-size: 20pt">Reference</FONT></FONT></SPAN></FONT></P>
-
<P ALIGN=RIGHT><FONT FACE="Times New Roman, serif"><SPAN LANG="en-US"><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/REF"><FONT COLOR="#000000"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">reference</SPAN></FONT></FONT></FONT></A></SPAN></FONT></P>
+
<P ALIGN=RIGHT><FONT COLOR="#b84700"><FONT FACE="Times New Roman, serif"><SPAN LANG="en-US"><A HREF="https://2011.igem.org/Team:Tsinghua-A/Modeling/REF"><FONT FACE="Arial, sans-serif"><FONT SIZE=4 STYLE="font-size: 16pt"><SPAN LANG="en-US">reference</SPAN></FONT></FONT></A></SPAN></FONT></FONT></P>
<P ALIGN=CENTER><BR><BR>
<P ALIGN=CENTER><BR><BR>
</P>
</P>

Revision as of 17:09, 1 October 2011


Republic by Free CSS Templates

 

Modeling Section

Overview | Accurate Model | Simplified Model | Dimensionless Model | Quorum-sensing Effect | Reference



PART 0 Intro

In our project, we are dedicated to design a quorum-sensing oscillator which consists of two types of cells. Cells of the same type can fluctuate synchronously and certain designs were made to adjust the phase and the amplitude of oscillation. These are the things that our modeling part aims to simulate. We built and simplified our simulation system step by step and deepened into further characteristics of the system, which would provide firm evidence proving that our design does work.



PART 1 Accurate Model

construction | parameters | results

In our first step, we wanted to describe the system thoroughly without leaving out any seemingly unimportant actions and factors. As a result, the description of the system contains every possible mass actions as well as some hill kinetics, Henri-Michaelis-Menten. We came up a set of ODEs with 19 equations.



PART 2 Simplified Model

preparation | parameters | results

Although ODEs provide a thorough, precise description of the whole system, they contain too many equations and parameters which would act as a barrier for simulation and further analysis. A simplification of complicated ODEs is necessary. We simplify every single ODE according to certain appropriate assumptions. Finally, we came up with a set of DDE equations.



PART 3 Dimensionless Model

preparation | parameters | results

In order to make a further analysis on stability of the system, sensitivity of parameters, feedback factors-we manipulate all the arguments and parameters to make them dimensionless. Analysis of this part is crucial since parameters in vivo experiment may be different and even at odds with modeling ones but a proper dimensionless can reveal the mathematical essence of our model.



PART 4 Quorum-sensing Effect

results

What we have done insofar is focused on two-cell oscillation. Quorum-sensing oscillator is not simply a matter of expansion in magnitude, but a matter of robustness in allowing difference of each individual cell. Moreover, we test the adjustment of phase and amplitude of oscillation in this part.



PART 5 Reference

reference