Team:Hong Kong CUHK/modelling

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  <h2>Modeling</h2>
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<h2>Modelling</h2>
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   <h1>Overview</h1>
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   <h3>Overview</h3>
   <p2><p> The hypothesis for this  project is that the voltage sensor can help increase the rate of reaction.<br />
   <p2><p> The hypothesis for this  project is that the voltage sensor can help increase the rate of reaction.<br />
     The aim of this  simulation is to check the effect of change in structure of the voltage switch  on the overall reaction rate. The commercial software COMSOL, which was made  for finite element analysis, is used. The overall model is separated into three  models. Model 1 is a simulation of the bending of the voltage switch by a  piezoelectric model. Model 2 is a simulation of the reaction in a 0D  environment. Model 3 is a simulation of the flow and diffusion of the fluid and  reactants around the enzymes. Several areas of physics are touched upon,  including piezoelectric devices, reaction engineering, laminar flow and  transport of diluted species.</p></p2>
     The aim of this  simulation is to check the effect of change in structure of the voltage switch  on the overall reaction rate. The commercial software COMSOL, which was made  for finite element analysis, is used. The overall model is separated into three  models. Model 1 is a simulation of the bending of the voltage switch by a  piezoelectric model. Model 2 is a simulation of the reaction in a 0D  environment. Model 3 is a simulation of the flow and diffusion of the fluid and  reactants around the enzymes. Several areas of physics are touched upon,  including piezoelectric devices, reaction engineering, laminar flow and  transport of diluted species.</p></p2>
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   <h1>Model 1: Bending  of Voltage Switch</h1>
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   <h3>Model 1: Bending  of Voltage Switch</h3>
     <img width="695" height="469" src="https://static.igem.org/mediawiki/igem.org/8/80/6.JPG" align="middle"/> <br />
     <img width="695" height="469" src="https://static.igem.org/mediawiki/igem.org/8/80/6.JPG" align="middle"/> <br />
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     The geometry of the  model is two identical rectangular plates representing the voltage-sensing S4  protein (VS), each with a box at the bottom to represent the enzymes, laccase  and dioxygenase. The bending of the voltage switch is simulated by the bending  of piezoelectric material when there is a voltage applied across two surfaces.  The angle of bending is set to be about 4 degree, as shown in literature[1].  As the two VS proteins are linked by PDZ domain and PDZ ligand, the top  boundary of the proteins are set to be static. The &ldquo;Form Union&rdquo; function is  used to link the VS-representing part and the enzyme-representing part together.  Configuration 1, with the two plates bent, represents the structure of the  protein when it is the natural position. Configuration 2, with the two plates  straight, represents the structure of the protein when there is a change in  membrane potential.<br />
     The geometry of the  model is two identical rectangular plates representing the voltage-sensing S4  protein (VS), each with a box at the bottom to represent the enzymes, laccase  and dioxygenase. The bending of the voltage switch is simulated by the bending  of piezoelectric material when there is a voltage applied across two surfaces.  The angle of bending is set to be about 4 degree, as shown in literature[1].  As the two VS proteins are linked by PDZ domain and PDZ ligand, the top  boundary of the proteins are set to be static. The &ldquo;Form Union&rdquo; function is  used to link the VS-representing part and the enzyme-representing part together.  Configuration 1, with the two plates bent, represents the structure of the  protein when it is the natural position. Configuration 2, with the two plates  straight, represents the structure of the protein when there is a change in  membrane potential.<br />
     The material used to  simulate the voltage switch is Lead Zirconate Titanate (PZT-5H). Voltage is  applied across the x-y planes of the plates, with higher voltage applied on the  inner side. We solved for a stationary solution. </p></p2>
     The material used to  simulate the voltage switch is Lead Zirconate Titanate (PZT-5H). Voltage is  applied across the x-y planes of the plates, with higher voltage applied on the  inner side. We solved for a stationary solution. </p></p2>
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   <h1>Model 2: BaP  Degradation</h1>
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   <h3>Model 2: BaP  Degradation</h3>
     <img width="691" height="397" src="https://static.igem.org/mediawiki/igem.org/7/7d/7.JPG" /> <br />
     <img width="691" height="397" src="https://static.igem.org/mediawiki/igem.org/7/7d/7.JPG" /> <br />
     <p2><p>The physics module  used here is Reaction Engineering. Since the actual chemical equations for  degradation of benzo(α)-pyrene (BaP) are not known, the overall reaction is represented by the  following two step reaction. <br />
     <p2><p>The physics module  used here is Reaction Engineering. Since the actual chemical equations for  degradation of benzo(α)-pyrene (BaP) are not known, the overall reaction is represented by the  following two step reaction. <br />
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     where I represents intermediate, S represents the  second product and P represents the final harmless product.<br />
     where I represents intermediate, S represents the  second product and P represents the final harmless product.<br />
     This is set to be an irreversible reaction with  forward rate constant of 1. The temperature and pressure in which the reaction  is carried out is 298K and 1atm respectively. It is a surface reaction with a  constant volume of liquid mixture. We solved for a time-dependent solution.</p></p2>
     This is set to be an irreversible reaction with  forward rate constant of 1. The temperature and pressure in which the reaction  is carried out is 298K and 1atm respectively. It is a surface reaction with a  constant volume of liquid mixture. We solved for a time-dependent solution.</p></p2>
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   <h1>Model 3: Diffusion and Fluid Flow</h1>
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   <h3>Model 3: Diffusion and Fluid Flow</h3>
     <img width="691" height="469" src="https://static.igem.org/mediawiki/igem.org/a/a5/Model8.JPG" /> <br />
     <img width="691" height="469" src="https://static.igem.org/mediawiki/igem.org/a/a5/Model8.JPG" /> <br />
     <p2><p>The physics module used here is Transport of  Diluted Species and Laminar Flow.<br />
     <p2><p>The physics module used here is Transport of  Diluted Species and Laminar Flow.<br />
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Latest revision as of 10:51, 27 October 2013

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