Difference between revisions of "Team:SEU/Model"

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                                       <div>
 
                                       <div>
 
                                           <h2>Model</h2>
 
                                           <h2>Model</h2>
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                                           <p>In this part, we provide our computation model in chemical reactions and prove the validity via kinetic analysis. The whole proof is based on mass action kinetics. The corresponding DNA strand displacement reaction implementation is given as well. As only addition, subtraction and multiplication are required in our project, we only provide the implementation of such computation. </p>
+
                                           <p>In this part, we provide our computation model in chemical reactions and prove the validity via kinetic analysis.</p>
 +
                                          <p>According to [1], formal reactions such as \(A+B \xrightarrow{k} C\) can be mapped to DNA strand displacement (DSD) reactions [2] without losing the kinetic features of the reaction. We borrow such a model in our project to implement calculation operations.</p>
 +
                                          <p> The whole proof is based on mass action kinetics. The corresponding DSD reaction implementation is given as well. As only addition, subtraction and multiplication are required in our project, we only provide the implementation of such computation. For each calculation operation, we firstly provide formal reactions, then provide kinetic analysis and finally propose DSD reaction implementation.</p>
 
                                           <!-- <h3>Computation method</h3> -->
 
                                           <!-- <h3>Computation method</h3> -->
 
                                           <h4>Addition:</h4>  
 
                                           <h4>Addition:</h4>  
 
                                           <p>\(A_1 \xrightarrow{k_1} O,\quad A_2 \xrightarrow{k_2} O\)</p>
 
                                           <p>\(A_1 \xrightarrow{k_1} O,\quad A_2 \xrightarrow{k_2} O\)</p>
 
                                           <h5> Proof:</h5> <p>\(\dfrac{d [A_i](t)}{d t}=-k_i[A_i](t)\) \(\Rightarrow [A_i](t)=[A_i](0)e^{-k_it}, \) \(\dfrac{d [O](t)}{d t}=\sum_{i=1}^2 k_i[A_i](t)\) \(\Rightarrow [O](\infty)=\int_0^\infty \sum_{i=1}^2 k_i[A_i](t)dt = [A_1](0)/k_1+[A_2](0)/k_2.\) If \(k_1\approx k_2\), then addition is successfully implemented.</p>
 
                                           <h5> Proof:</h5> <p>\(\dfrac{d [A_i](t)}{d t}=-k_i[A_i](t)\) \(\Rightarrow [A_i](t)=[A_i](0)e^{-k_it}, \) \(\dfrac{d [O](t)}{d t}=\sum_{i=1}^2 k_i[A_i](t)\) \(\Rightarrow [O](\infty)=\int_0^\infty \sum_{i=1}^2 k_i[A_i](t)dt = [A_1](0)/k_1+[A_2](0)/k_2.\) If \(k_1\approx k_2\), then addition is successfully implemented.</p>
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                                           <p style="font-size=18px">The DNA strand displacement implementation:</p>
+
                                           <p style="font-size=18px">The DSD implementation:</p>
 
                                           <img src="https://static.igem.org/mediawiki/2019/8/8f/T--SEU--additionDNA.png"  width="620" height="175" >
 
                                           <img src="https://static.igem.org/mediawiki/2019/8/8f/T--SEU--additionDNA.png"  width="620" height="175" >
 
                                           <h4>Subtraction:</h4>
 
                                           <h4>Subtraction:</h4>
 
                                           <p style="font-size=1px">\(A+B \xrightarrow{k_1} \phi\)</p>
 
                                           <p style="font-size=1px">\(A+B \xrightarrow{k_1} \phi\)</p>
−
                                           <h5> Proof:</h5> <p>It is identical with [2]. Apparently, \([A](t)=[B](t)+\Delta \). <br>If \(\Delta \neq 0\), \(\dfrac{d [A](t)}{d t}=-[A](t)([A](t)-\Delta)\) \(\Rightarrow [A](t)=\dfrac{[A](0)\Delta}{-[A](0)+[A](0)e^{\Delta t}+\Delta e^{\Delta t}} (\Delta \neq 0).\) If \(\Delta > 0\), \([A](\infty)=\Delta\). Otherwise \([A](\infty)=0\).
+
                                           <h5> Proof:</h5> <p>It is identical with [4]. Apparently, \([A](t)=[B](t)+\Delta \). <br>If \(\Delta \neq 0\), \(\dfrac{d [A](t)}{d t}=-[A](t)([A](t)-\Delta)\) \(\Rightarrow [A](t)=\dfrac{[A](0)\Delta}{-[A](0)+[A](0)e^{\Delta t}+\Delta e^{\Delta t}} (\Delta \neq 0).\) If \(\Delta > 0\), \([A](\infty)=\Delta\). Otherwise \([A](\infty)=0\).
 
                                           <br>If \(\Delta =0\), \([A](t)=\dfrac{[A](0)}{1+[A](0)t}\). \([A](\infty)=0\). Hence substraction is implemented.</p>
 
                                           <br>If \(\Delta =0\), \([A](t)=\dfrac{[A](0)}{1+[A](0)t}\). \([A](\infty)=0\). Hence substraction is implemented.</p>
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                                           <p style="font-size=18px">The DNA strand displacement implementation:</p>
+
                                           <p style="font-size=18px">The DSD implementation:</p>
 
                                           <img src="https://static.igem.org/mediawiki/2019/b/bf/T--SEU--subtractionDNA.png"  width="620" height="235" >
 
                                           <img src="https://static.igem.org/mediawiki/2019/b/bf/T--SEU--subtractionDNA.png"  width="620" height="235" >
 
                                           <h4>Multiplication: </h4>
 
                                           <h4>Multiplication: </h4>
 
                                           <p style="font-size=18px">\(\alpha \xrightarrow{k_1} \phi, A+B+\alpha \xrightarrow{k_2} A+B+\alpha+C\)</p>
 
                                           <p style="font-size=18px">\(\alpha \xrightarrow{k_1} \phi, A+B+\alpha \xrightarrow{k_2} A+B+\alpha+C\)</p>
 
                                           <h5> Proof:</h5> <p>\(\dfrac{d [\alpha](t)}{d t}=-k_1[\alpha](t)\) \(\Rightarrow [\alpha](t)=[\alpha](0)e^{-k_1t},\) \(\dfrac{d [A](t)}{d t}=\dfrac{d [B](t)}{d t}=0, \dfrac{d [C](t)}{d t}=k_2[A](t)[B](t)[\alpha](t)\) \(\Rightarrow [C](\infty)=\int_0^\infty [A](0)[B](0)[\alpha](t)=k_2/k_1[\alpha](0)[A](0)[B](0)\). Hence multiplication is implemented.</p>
 
                                           <h5> Proof:</h5> <p>\(\dfrac{d [\alpha](t)}{d t}=-k_1[\alpha](t)\) \(\Rightarrow [\alpha](t)=[\alpha](0)e^{-k_1t},\) \(\dfrac{d [A](t)}{d t}=\dfrac{d [B](t)}{d t}=0, \dfrac{d [C](t)}{d t}=k_2[A](t)[B](t)[\alpha](t)\) \(\Rightarrow [C](\infty)=\int_0^\infty [A](0)[B](0)[\alpha](t)=k_2/k_1[\alpha](0)[A](0)[B](0)\). Hence multiplication is implemented.</p>
−
                                           <p style="font-size=18px">The DNA strand displacement implementation:</p>
+
                                           <p style="font-size=18px">The DSD implementation:</p>
 
                                           <img src="https://static.igem.org/mediawiki/2019/d/d6/T--SEU--multiplicationDNA.png"  width="620" height="339" >
 
                                           <img src="https://static.igem.org/mediawiki/2019/d/d6/T--SEU--multiplicationDNA.png"  width="620" height="339" >
 
                                           <h3>References</h3>
 
                                           <h3>References</h3>
−
                                           <p>[1]C. Fang, Z. Shen, Z. Zhang, X. You and C. Zhang, "Synthesizing a Neuron Using Chemical Reactions," 2018 IEEE International Workshop on Signal Processing Systems (SiPS), Cape Town, 2018, pp. 187-192.</p>
+
                                           <p>[1] D. Soloveichik, G. Seelig, E. Winfree, "DNA as a universal substrate for chemical kinetics," Proceedings of the National Academy of Sciences, vol. 107, no. 12, pp. 5393–5398, 2010.</p>
−
                                           <p>[2]M. Vasic, D. Soloveichik, S. Khurshid, "CRN++: Molecular Programming Language." arXiv preprint arXiv:1809.07430.</p>
+
                                           <p>[2] <a href="https://www.youtube.com/watch?v=zjC_0PW9A4c&feature=youtu.be&tdsourcetag=s_pctim_aiomsg">DNA Strand Displacement.</a></p>
 +
                                          <p>[3] M. Vasic, D. Soloveichik, S. Khurshid, "CRN++: Molecular Programming Language," arXiv preprint arXiv:1809.07430.</p>
 +
                                          <p>[4] C. Fang, Z. Shen, Z. Zhang, X. You and C. Zhang, "Synthesizing a Neuron Using Chemical Reactions," 2018 IEEE International Workshop on Signal Processing Systems (SiPS), Cape Town, 2018, pp. 187-192.</p>
 
                                                                              
 
                                                                              
 
                                       </div>
 
                                       </div>

Revision as of 02:53, 3 October 2019





Model

In this part, we provide our computation model in chemical reactions and prove the validity via kinetic analysis.

According to [1], formal reactions such as \(A+B \xrightarrow{k} C\) can be mapped to DNA strand displacement (DSD) reactions [2] without losing the kinetic features of the reaction. We borrow such a model in our project to implement calculation operations.

The whole proof is based on mass action kinetics. The corresponding DSD reaction implementation is given as well. As only addition, subtraction and multiplication are required in our project, we only provide the implementation of such computation. For each calculation operation, we firstly provide formal reactions, then provide kinetic analysis and finally propose DSD reaction implementation.

Addition:

\(A_1 \xrightarrow{k_1} O,\quad A_2 \xrightarrow{k_2} O\)

Proof:

\(\dfrac{d [A_i](t)}{d t}=-k_i[A_i](t)\) \(\Rightarrow [A_i](t)=[A_i](0)e^{-k_it}, \) \(\dfrac{d [O](t)}{d t}=\sum_{i=1}^2 k_i[A_i](t)\) \(\Rightarrow [O](\infty)=\int_0^\infty \sum_{i=1}^2 k_i[A_i](t)dt = [A_1](0)/k_1+[A_2](0)/k_2.\) If \(k_1\approx k_2\), then addition is successfully implemented.

The DSD implementation:

Subtraction:

\(A+B \xrightarrow{k_1} \phi\)

Proof:

It is identical with [4]. Apparently, \([A](t)=[B](t)+\Delta \).
If \(\Delta \neq 0\), \(\dfrac{d [A](t)}{d t}=-[A](t)([A](t)-\Delta)\) \(\Rightarrow [A](t)=\dfrac{[A](0)\Delta}{-[A](0)+[A](0)e^{\Delta t}+\Delta e^{\Delta t}} (\Delta \neq 0).\) If \(\Delta > 0\), \([A](\infty)=\Delta\). Otherwise \([A](\infty)=0\).
If \(\Delta =0\), \([A](t)=\dfrac{[A](0)}{1+[A](0)t}\). \([A](\infty)=0\). Hence substraction is implemented.

The DSD implementation:

Multiplication:

\(\alpha \xrightarrow{k_1} \phi, A+B+\alpha \xrightarrow{k_2} A+B+\alpha+C\)

Proof:

\(\dfrac{d [\alpha](t)}{d t}=-k_1[\alpha](t)\) \(\Rightarrow [\alpha](t)=[\alpha](0)e^{-k_1t},\) \(\dfrac{d [A](t)}{d t}=\dfrac{d [B](t)}{d t}=0, \dfrac{d [C](t)}{d t}=k_2[A](t)[B](t)[\alpha](t)\) \(\Rightarrow [C](\infty)=\int_0^\infty [A](0)[B](0)[\alpha](t)=k_2/k_1[\alpha](0)[A](0)[B](0)\). Hence multiplication is implemented.

The DSD implementation:

References

[1] D. Soloveichik, G. Seelig, E. Winfree, "DNA as a universal substrate for chemical kinetics," Proceedings of the National Academy of Sciences, vol. 107, no. 12, pp. 5393–5398, 2010.

[2] DNA Strand Displacement.

[3] M. Vasic, D. Soloveichik, S. Khurshid, "CRN++: Molecular Programming Language," arXiv preprint arXiv:1809.07430.

[4] C. Fang, Z. Shen, Z. Zhang, X. You and C. Zhang, "Synthesizing a Neuron Using Chemical Reactions," 2018 IEEE International Workshop on Signal Processing Systems (SiPS), Cape Town, 2018, pp. 187-192.