Team:Tokyo Tech/Modeling/Overview

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                   <td><p class="info-18">The equations above describe how cells grow in the culture. Equation (1), (2), (3) describe populations of Bank, Company, and Customer for each of them. All first terms of the equations are considered carrying capacity. Second terms of (2) and (3) describe the effect of chloramphenicol and chloramphenicol resistance gene. Note that in second terms <a href="https://2014.igem.org/File:Tokyo_Tech_Cm.png"><img width="114" height="19" src="https://static.igem.org/mediawiki/2014/c/c9/Tokyo_Tech_Cm.png" alt="说明: Macintosh HD:Users:takuya:Documents:iGEM:projectBank:wiki_modeling:equations:equationsForBank1005chlorampheicol.jpg" /></a> are set to 0 once the value becomes minus.</p></td>
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                   <td><p class="info-18">The equations above describe how cells grow in the culture. Equation (1), (2), (3) describe the populations of Bank, Company, and Customer . All first terms of the equations are considered carrying capacity. Second terms of (2) and (3) describe the effect of chloramphenicol and chloramphenicol resistance gene. Note that in second terms <a href="https://2014.igem.org/File:Tokyo_Tech_Cm.png"><img width="114" height="19" src="https://static.igem.org/mediawiki/2014/c/c9/Tokyo_Tech_Cm.png" alt="说明: Macintosh HD:Users:takuya:Documents:iGEM:projectBank:wiki_modeling:equations:equationsForBank1005chlorampheicol.jpg" /></a> are set to 0 once the value becomes minus.</p></td>
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                   <td><p class="info-18">These equations describe concentrations of C4HSL and 3OC12HSL.<br />
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                   <td><p class="info-18">These equations describe the concentrations of C4HSL and 3OC12HSL.<br />
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                   First and Second terms of (4) describe production of C4HSL from RhlI in Bank and Customers cells. Third term is meant for decomposition of C4HSL by AiiA in Bank cell. Fourth term is for degradation of C4HSL.</p>
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                   First and Second terms of (4) describe the  production of C4HSL from RhlI in Bank and Customers cells. Third term is meant for the decomposition of C4HSL by AiiA in Bank cell. Fourth term is for the degradation of C4HSL.</p>
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                   <p class="info-18">Same goes on for 3OC12HSL. First term describes the production of 3OC12HSL from LasI in Company. Second term is for decomposition of 3OC12HSL by AiiA in Bank cell. Third term is for degradation of 3OC12HSL.</p></td>
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                   <p class="info-18">Same goes on for 3OC12HSL. First term describes the production of 3OC12HSL from LasI in Company. Second term is for the decomposition of 3OC12HSL by AiiA in Bank cell. Third term is for the degradation of 3OC12HSL.</p></td>
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                   <td class="info-18"><p class="info-18">Bank has two states changing during the cultivation. (6) and (7) describe Distribution state. LacI represses the translation of TetR as described in first term of (8). RhlI will distribute C4HSL which represents money. On the other hand, (8) and (9) describe Collection state. TetR represses LacI. AiiA decomposes C4HSL. </p>
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                   <td class="info-18"><p class="info-18">Bank switches to two states during the cultivation. (6) and (7) describe the Distribution state. LacI represses the translation of TetR as described in first term of (8). RhlI will distribute C4HSL which represents money. On the other hand, (8) and (9) describe the Collection state. TetR represses LacI. AiiA decomposes C4HSL. </p>
                   <p class="info-18">In order to achieve the state switching depend on the concentration of C4HSL, TetR and AiiA are regulated not only by LacI, but also by C4HSL. This makes the system be able to switch depends on the concentration of C4HSL.</p></td>
                   <p class="info-18">In order to achieve the state switching depend on the concentration of C4HSL, TetR and AiiA are regulated not only by LacI, but also by C4HSL. This makes the system be able to switch depends on the concentration of C4HSL.</p></td>
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                   <td><h2>2. Story simulation details</h2></td>
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                   <td><h2>2. Story Stimulation details</h2></td>
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                   <td class="info-18"><p class="info-18">The system which includes only Company and Customer was simulated before our experiments. From the analysis we performed, we noticed that strength levels of Prhl and Plux promoters should be equally strong as shown in Fig. 4-1-2-1-1.(Detail analysis is shown in other modeling page.)</p></td>
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                   <td class="info-18"><p class="info-18">The system which includes only Company and Customer was simulated before our experiments. From the analysis we performed, we noticed that strength levels of Prhl and Plux promoters should be equally strong as shown in Fig. 4-1-2-1-1.(Detailed analysis is shown in another modeling page.)</p></td>
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                   <td><p class="info-18">When the strength levels of Prhl and Plux promoters are in the red area, Company and Customer can grow well. Otherwise when strength levels are in the blue area, either Company or Customer cannot grow well. </p>
                   <td><p class="info-18">When the strength levels of Prhl and Plux promoters are in the red area, Company and Customer can grow well. Otherwise when strength levels are in the blue area, either Company or Customer cannot grow well. </p>
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                   <p class="info-18">With the optimized parameter values, Company and Customer grows well as shown in Fig. 4-1-2-1-1. </p></td>
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                   <p class="info-18">With the optimized parameter values, Company and Customer can  grow well as shown in Fig. 4-1-2-1-1. </p></td>
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Revision as of 21:12, 17 October 2014

Tokyo_Tech

Modeling

Overview
 
Contents
 

1. Mathematical model

1.1 Introduction

1.2 Cell population

1.3 Signaling molecules

1.4 Bank

1.5 Company

1.6 Customer

2. Story simulation details

2.1 Company and Customer co-culture simulation

2.2 Introduction of Bank

2.3 Economic wave
 
 

1. Mathematical model

1.1 Introduction

Since our genetic circuit is complex, it is very difficult to predict the system’s behavior intuitively. Thus we constructed mathematical models to predict the behavior.
Fig. 4-1-1-1. Genetic circuit design
 
Fig. 4-1-1-2. Corresponding mathematical model
 
 

・Table 4-1-1-1 Meaning of parameters
 
 

Detailed designs are shown below.

1.2 Cell population
Fig. 4-1-1-3. Equations for cell population
 

The equations above describe how cells grow in the culture. Equation (1), (2), (3) describe the populations of Bank, Company, and Customer . All first terms of the equations are considered carrying capacity. Second terms of (2) and (3) describe the effect of chloramphenicol and chloramphenicol resistance gene. Note that in second terms 说明: Macintosh HD:Users:takuya:Documents:iGEM:projectBank:wiki_modeling:equations:equationsForBank1005chlorampheicol.jpg are set to 0 once the value becomes minus.

1.3 Signaling molecules
Fig. 4-1-1-4. Equations for signaling molecules
 

These equations describe the concentrations of C4HSL and 3OC12HSL.
First and Second terms of (4) describe the production of C4HSL from RhlI in Bank and Customers cells. Third term is meant for the decomposition of C4HSL by AiiA in Bank cell. Fourth term is for the degradation of C4HSL.

Same goes on for 3OC12HSL. First term describes the production of 3OC12HSL from LasI in Company. Second term is for the decomposition of 3OC12HSL by AiiA in Bank cell. Third term is for the degradation of 3OC12HSL.

1.4 Bank
Fig. 4-1-1-5. Equations for Bank
 

Bank switches to two states during the cultivation. (6) and (7) describe the Distribution state. LacI represses the translation of TetR as described in first term of (8). RhlI will distribute C4HSL which represents money. On the other hand, (8) and (9) describe the Collection state. TetR represses LacI. AiiA decomposes C4HSL.

In order to achieve the state switching depend on the concentration of C4HSL, TetR and AiiA are regulated not only by LacI, but also by C4HSL. This makes the system be able to switch depends on the concentration of C4HSL.

1.5 Company

Fig. 4-1-1-6. Equations for Company
 

In the presence of C4HSL, LasI and CmR will be expressed.

1.6 Customer

Fig. 4-1-1-7. Equations for Customer
 

In the presence of 3OC12HSL, RhlI and CmR will be expressed.

2. Story Stimulation details

2.1 Company and Customer co-culture simulation

The system which includes only Company and Customer was simulated before our experiments. From the analysis we performed, we noticed that strength levels of Prhl and Plux promoters should be equally strong as shown in Fig. 4-1-2-1-1.(Detailed analysis is shown in another modeling page.)
Fig. 4-1-2-1-1. Company and Customer growth dependency of Prhl and Plux promoters strength levels
 

When the strength levels of Prhl and Plux promoters are in the red area, Company and Customer can grow well. Otherwise when strength levels are in the blue area, either Company or Customer cannot grow well.

With the optimized parameter values, Company and Customer can grow well as shown in Fig. 4-1-2-1-1.

Fig. 4-1-2-1-2. Company and Customer can grow well with optimized parameters
 

2.2 Introduction of Bank

Company and Customer cannot grow well with less initial amounts than previous simulation as shown in Fig. 4-1-2-2-1.
Fig. 4-1-2-2-1. Company and Customer cannot grow with less initial amounts
 

But once we add the Bank to the system, they can grow well with the C4HSL produced by the Bank as shown in Fig. 4-1-2-2-2.
Fig. 4-1-2-2-2. Addition of Bank make the system grow well
 

Along with the growth of the system, Bank eventually changes its state from distribution state to collection state. This is shown in Fig. 4-1-2-2-3.
Fig. 4-1-2-2-3. Bank changes its state from Distribution State to Collection State
 

RhlI is expressed mainly in Distribution State. And AiiA is expressed mainly in collection state. Fig. 4-1-2-2-3 shows the Bank was first in Distribution State and in the following changed to Collection State.
 

2.3 Economic wave

With the advice from entrepreneurs, we introduced economic wave to our system. Detail is shown in Economic Wave page in the modeling.

Once the economic wave is introduced to our system, Company and Customer cannot grow well because of the recession during the economic wave. This is shown in Fig. 4-1-2-3-1.

Fig. 4-1-2-3-1. Company and Customer cannot grow with economic wave
 

As in the real economy, we also introduced Bank to this system. The result was different depending on the harshness of the economic wave. If the economic wave is moderate, then the Bank can help Company and Customer to grow well even in the presence of economic wave. This is shown in Fig. 4-1-2-3-2.
Fig. 4-1-2-3-2. Bank can help Company and Customer even in the presence of economic wave
 

But if the economic wave is harsher than the previous one, then Bank cannot help Company and Customer enough. The result is shown in Fig. 4-1-2-3-3.
Fig. 4-1-2-3-3. Bank cannot help Company and Customer enough in the presence of harsh economic wave

 

 

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