Biomod/2014/Kyutech/Design: Difference between revisions
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<h3>Membrane Design Group</h3> | <h3>Membrane Design Group</h3> | ||
<figure class="centered"><img src="http://openwetware.org/images/ | <figure class="centered"><img src="http://openwetware.org/images/7/7a/Bioanime_2014kyutech_design.gif" width="400" height="266" alt=""/> | ||
<figcaption></figcaption> | <figcaption></figcaption> | ||
</figure> | </figure> | ||
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<p><h4>Membrane as a key element in our devise</h4> | <p><h4>Membrane as a key element in our devise</h4> | ||
A technical highlight of our product is to realize an integral controller for regulating a concentration of a specific DNA strand as an output signal to be a desired level by using a series of DNA strand displacement reactions in combination with a membrane. Therefore we attempted to design of osmosis membrane that DNA strand can move. (Fig.1) | A technical highlight of our product is to realize an integral controller for regulating a concentration of a specific DNA strand as an output signal to be a desired level by using a series of DNA strand displacement reactions in combination with a membrane. Therefore we attempted to design of osmosis membrane that DNA strand can move. (Fig.1) | ||
<figure class="centered"><img src="http://openwetware.org/images/ | <figure class="centered"><img src="http://openwetware.org/images/e/e8/Molecule_2014kyutech_design.png" width="400" height="266" alt=""/> | ||
<figcaption></figcaption> | <figcaption></figcaption> | ||
</figure> | </figure> | ||
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<p><h4>How to design the membrane</h4> | <p><h4>How to design the membrane</h4> | ||
<b>Size of DNA strand</b><BR> | |||
First, we have to inquire into a size of DNA strand that is a solute through the membrane. We suppose that a DNA strand that is used in a series of reactions for realizing the integral controller has 10-40 bases. Here, for the sake of simplicity a DNA strand is approximated by spherical object with a radius of 3 nm as illustrated in Fig.2. | |||
<figure class="centered"><img src="http://openwetware.org/images/f/f4/Design_dna_2014kyutech_design.png" width="400" height="266" alt=""/> | |||
<figure class="centered"><img src="http://openwetware.org/images/f/ | |||
<figcaption>Fig2. Size of DNA we use in this present</figcaption> | <figcaption>Fig2. Size of DNA we use in this present</figcaption> | ||
</figure> | </figure> | ||
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Property of membrane<BR> | <b>Property of membrane</b><BR> | ||
We need some formula to determine the structure of the membrane. Transmission phenomenon of osmosis membrane is described following equations. | We need some formula to determine the structure of the membrane. Transmission phenomenon of osmosis membrane is described following equations. | ||
<figure class="centered"><img src="http://openwetware.org/images/ | <figure class="centered"><img src="http://openwetware.org/images/9/9d/No1equation_2014kyutech_design.png" width="192" height="75" alt=""/> | ||
</figure> | </figure> | ||
where R is a rejection rate of solute, Cb, Cp and Cm are concentrations[M] of solution, permeated liquid, solute in near membrane, respectively. When solute permeates membrane with impurities, Cm increases with pressure. In this present, since we use solution without impurity, we can assume that Cm almost equals to Cb. | where R is a rejection rate of solute, Cb, Cp and Cm are concentrations[M] of solution, permeated liquid, solute in near membrane, respectively. When solute permeates membrane with impurities, Cm increases with pressure. In this present, since we use solution without impurity, we can assume that Cm almost equals to Cb. <BR> | ||
where Jv is the flux of solvent [mol/(s•m^3)], Lp is the permeated coefficient, ∆p is the pressure difference of both of membrane [kPa], σ is the reflection coefficient of solute. Where Js is the flux of solute [m^3/(s•m^2)], P is the permeated coefficient.C ̅ is the differences between Cb and Cm. | |||
The key elements of the above transmission equation relate to such three transmission coefficients as Lp, σ, and P. We used general model called “pore model” to combine these transmission coefficient. In this model, we assume that DNA strand is hard sphere, pore is cylinder and flow in pore is “Poiseuille flow”. | The key elements of the above transmission equation relate to such three transmission coefficients as Lp, σ, and P. We used general model called “pore model” to combine these transmission coefficient. In this model, we assume that DNA strand is hard sphere, pore is cylinder and flow in pore is “Poiseuille flow”. | ||
<figure class="centered"><img src="http://openwetware.org/images/ | <figure class="centered"><img src="http://openwetware.org/images/7/77/Design_membrane_2014kyutech_design.png" width="400" height="266" alt=""/> | ||
<figcaption>Fig3. Pore model</figcaption> | <figcaption>Fig3. Pore model</figcaption> | ||
</figure> | </figure> | ||
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The radius of solution is given below expression. | The radius of solution is given below expression. | ||
<figure class="centered"><img src="http://openwetware.org/images/d/dd/No2equation_2014kyutech_design.png" width="65" height="32" alt=""/> | |||
</figure> | |||
where rs is the radius of solute [nm], rp is the radius of pore [nm], ∆x is the membrane thickness [nm], D is the diffusion coefficient of solute, K is the Boltzmann's constant, T is the absolute temperature [℃], μ is the viscosity of solute. | |||
Three transport coefficients are given by following equation. | Three transport coefficients are given by following equation. | ||
<figure class="centered"><img src="http://openwetware.org/images/5/53/No3equation_2014kyutech_design.png" width="139" height="54" alt=""/> | |||
</figure> | |||
where q is the ratio of rs to rp, Ak is the value that the unit area of the total area of pores divides the unit area of area of membrane, S_F and S_D are steric hindrance. | |||
These are given by following equation. | These are given by following equation. | ||
<figure class="centered"><img src="http://openwetware.org/images/9/9a/No4equation_2014kyutech_design.png" width="131" height="38" alt=""/> | |||
</figure> | |||
</p> | </p> | ||
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As we mentioned above, we can use formulas as a design theory of membrane. In this present, we designed membrane to satisfy the concentration of a specific DNA strand as an output signal to be a desired level. Therefore, we need to adjust parameters of membrane such as rp, ∆x , and Ak. We define x2 and x4 as concentration of input single, output single, respectively. We assume that Jv is zero in our design. Table 1 shows the each parameter used in our design of membrane. | As we mentioned above, we can use formulas as a design theory of membrane. In this present, we designed membrane to satisfy the concentration of a specific DNA strand as an output signal to be a desired level. Therefore, we need to adjust parameters of membrane such as rp, ∆x , and Ak. We define x2 and x4 as concentration of input single, output single, respectively. We assume that Jv is zero in our design. Table 1 shows the each parameter used in our design of membrane. | ||
<figure class="centered"><img src="http://openwetware.org/images/ | <figure class="centered"><img src="http://openwetware.org/images/0/09/Table_2014kyutech_design.png" width="322" height="241" alt=""/> | ||
<figcaption></figcaption> | <figcaption></figcaption> | ||
</figure> | </figure> | ||
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<figure class="centered"><img src="http://openwetware.org/images/ | <figure class="centered"><img src="http://openwetware.org/images/e/e9/Simux2x4_2014kyutech_design.png" width="400" height="266" alt=""/> | ||
<figcaption>Table 1 Parameter and Hypothetical condition</figcaption> | <figcaption>Table 1 Parameter and Hypothetical condition</figcaption> | ||
</figure> | </figure> | ||
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We omit the calculation process, however, we calculated following parameters. | We omit the calculation process, however, we calculated following parameters. | ||
rp is 4. | rp is 4.97×10^(-9)[m], Js is 4.79×10^(-14)[m^3/(s•m^2)] | ||
As Figure 4 shows, we estimated that x4 becomes steady state at approximately 200 second. Therefore, we simulated size of membrane at 200 second.(Fig.5) | As Figure 4 shows, we estimated that x4 becomes steady state at approximately 200 second. Therefore, we simulated size of membrane at 200 second.(Fig.5) | ||
<figure class="centered"><img src="http://openwetware.org/images/ | <figure class="centered"><img src="http://openwetware.org/images/9/97/Simuakdx_2014kyutech_design.png" width="400" height="266" alt=""/> | ||
<figcaption>Table 1 Parameter and Hypothetical condition</figcaption> | <figcaption>Table 1 Parameter and Hypothetical condition</figcaption> | ||
</figure> | </figure> | ||
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<li><a href="/wiki/Biomod/2014/Kyutech">TOP</a></li>
<li><a href="/wiki/Biomod/2014/Kyutech/Introduction">INTRODUCTION</a></li>
<li><a href="/wiki/Biomod/2014/Kyutech/Design">DESIGN</a></li>
<li><a href="/wiki/Biomod/2014/Kyutech/Experiment">EXPERIMENT</a></li>
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<h2>DESIGN</h2>
<h3>Membrane Design Group</h3>
<figure class="centered"><img src="http://openwetware.org/images/7/7a/Bioanime_2014kyutech_design.gif" width="400" height="266" alt=""/>
<figcaption></figcaption>
</figure>
<p><h4>Membrane as a key element in our devise</h4>
A technical highlight of our product is to realize an integral controller for regulating a concentration of a specific DNA strand as an output signal to be a desired level by using a series of DNA strand displacement reactions in combination with a membrane. Therefore we attempted to design of osmosis membrane that DNA strand can move. (Fig.1)
<figure class="centered"><img src="http://openwetware.org/images/e/e8/Molecule_2014kyutech_design.png" width="400" height="266" alt=""/>
<figcaption></figcaption>
</figure>
Fig.1 indicates that flow of a single DNA strand and multi-stranded DNA through a membrane. As shown in Fig.1, a specific single-stranded DNA can permeate membrane since the size of single-stranded DNA is enough to move the pore of membrane. However, the multi-stranded DNA can’t permeate membrane since it is much longer than single-stranded DNA. Because of the membrane, we can regulate a concentration of DNA strand. </p>
<p><h4>How to design the membrane</h4>
<b>Size of DNA strand</b><BR>
First, we have to inquire into a size of DNA strand that is a solute through the membrane. We suppose that a DNA strand that is used in a series of reactions for realizing the integral controller has 10-40 bases. Here, for the sake of simplicity a DNA strand is approximated by spherical object with a radius of 3 nm as illustrated in Fig.2.
<figure class="centered"><img src="http://openwetware.org/images/f/f4/Design_dna_2014kyutech_design.png" width="400" height="266" alt=""/>
<figcaption>Fig2. Size of DNA we use in this present</figcaption>
</figure>
<b>Property of membrane</b><BR>
We need some formula to determine the structure of the membrane. Transmission phenomenon of osmosis membrane is described following equations. <figure class="centered"><img src="http://openwetware.org/images/9/9d/No1equation_2014kyutech_design.png" width="192" height="75" alt=""/> </figure>
where R is a rejection rate of solute, Cb, Cp and Cm are concentrations[M] of solution, permeated liquid, solute in near membrane, respectively. When solute permeates membrane with impurities, Cm increases with pressure. In this present, since we use solution without impurity, we can assume that Cm almost equals to Cb. <BR> where Jv is the flux of solvent [mol/(s•m^3)], Lp is the permeated coefficient, ∆p is the pressure difference of both of membrane [kPa], σ is the reflection coefficient of solute. Where Js is the flux of solute [m^3/(s•m^2)], P is the permeated coefficient.C ̅ is the differences between Cb and Cm.
The key elements of the above transmission equation relate to such three transmission coefficients as Lp, σ, and P. We used general model called “pore model” to combine these transmission coefficient. In this model, we assume that DNA strand is hard sphere, pore is cylinder and flow in pore is “Poiseuille flow”.
<figure class="centered"><img src="http://openwetware.org/images/7/77/Design_membrane_2014kyutech_design.png" width="400" height="266" alt=""/>
<figcaption>Fig3. Pore model</figcaption> </figure>
The radius of solution is given below expression.
<figure class="centered"><img src="http://openwetware.org/images/d/dd/No2equation_2014kyutech_design.png" width="65" height="32" alt=""/> </figure>
where rs is the radius of solute [nm], rp is the radius of pore [nm], ∆x is the membrane thickness [nm], D is the diffusion coefficient of solute, K is the Boltzmann's constant, T is the absolute temperature [℃], μ is the viscosity of solute. Three transport coefficients are given by following equation.
<figure class="centered"><img src="http://openwetware.org/images/5/53/No3equation_2014kyutech_design.png" width="139" height="54" alt=""/> </figure>
where q is the ratio of rs to rp, Ak is the value that the unit area of the total area of pores divides the unit area of area of membrane, S_F and S_D are steric hindrance. These are given by following equation.
<figure class="centered"><img src="http://openwetware.org/images/9/9a/No4equation_2014kyutech_design.png" width="131" height="38" alt=""/> </figure>
</p>
<p><h4>Determination of the structure</h4>
As we mentioned above, we can use formulas as a design theory of membrane. In this present, we designed membrane to satisfy the concentration of a specific DNA strand as an output signal to be a desired level. Therefore, we need to adjust parameters of membrane such as rp, ∆x , and Ak. We define x2 and x4 as concentration of input single, output single, respectively. We assume that Jv is zero in our design. Table 1 shows the each parameter used in our design of membrane.
<figure class="centered"><img src="http://openwetware.org/images/0/09/Table_2014kyutech_design.png" width="322" height="241" alt=""/>
<figcaption></figcaption>
</figure>
Figure 4 shows the simulation results by using parameters of Table 1.
<figure class="centered"><img src="http://openwetware.org/images/e/e9/Simux2x4_2014kyutech_design.png" width="400" height="266" alt=""/>
<figcaption>Table 1 Parameter and Hypothetical condition</figcaption> </figure>
We omit the calculation process, however, we calculated following parameters. rp is 4.97×10^(-9)[m], Js is 4.79×10^(-14)[m^3/(s•m^2)] As Figure 4 shows, we estimated that x4 becomes steady state at approximately 200 second. Therefore, we simulated size of membrane at 200 second.(Fig.5)
<figure class="centered"><img src="http://openwetware.org/images/9/97/Simuakdx_2014kyutech_design.png" width="400" height="266" alt=""/>
<figcaption>Table 1 Parameter and Hypothetical condition</figcaption> </figure>
As a result, there are several combinations of rp,∆x and Ak. In other words, we can design membrane of different size.
<p><h4>Future Perspectives</h4>
We mentioned design theory of membrane and calculated some pattern of membrane. However, we still have problems to make membrane actually. The problem which we must consider next is below.<BR>
・What is the material to make membrane easily and efficiently?<BR> ・What is the best size of membrane that DNA strand permeates ?<BR> ・How do we make hole in membrane? We are planning to study about membrane engineering and design membrane by experiment to solve the problems.
</p>
</article> <aside id="sideber"> <h2></h2> <p></p> <p></p> </aside> <footer> <p> BIOMOD 2014</p> </footer>
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