Difference between revisions of "Team:NCKU Tainan/Model"

 
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                     <h1 class="mb-0 pl-2 headtitle" >
 
                         Model
 
                         Model
 
                         <!--<span class="text-primary">Taylor</span>-->
 
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                         In one word, Laplace transform
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                         Surfactant between Experimental Data and Theories
 
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                         <p>   Experiment alone is not enough to prove the effectiveness of Eye kNOw. By building mathematical models with scientific theories, we’re able to understand how contact lens deformation induces bNOS production and further delivers nitric oxide into the eye.</p>
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                         <p> There are three critical parts in our project that crucially affect our final design of Eye kNOw: <b>IOP-elevation induced contact lens deformation, NO diffusion efficiency in ocular system, and seeking for higher effectiveness.</b> Experiment alone is not enough to provide the answers. To build a bridge between experimental data and scientific theories, we built three models that fully describe the whole working process of Eye kNOw:</p>
 
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                      <ol class="mb-4">
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                        <li><p><b>Contact Lens Deformation Model</b>: Provide quantitative result of contact lens deformation caused by IOP elevation.</p></li>
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                        <li><p><b>NO Ocular Diffusion Model</b>: Obtain the initial parameters needed for Eye kNOw design, and describe NO ocular diffusion with quantitative simulation.</p></li>
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                    <li><p><b>NO Ocular Diffusion Model</b>: Utilize model 1, model 2 and experimental data to precisely calculate the effectiveness of Eye kNOw.</p></li>
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                      </ol>
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              </div>         
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             <h4 class="mb-3">Background</h4>  
 
             <h4 class="mb-3">Background</h4>  
 
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                         <p>   As aforementioned, we aim to provide a new treatment that can release ocular hypotensive agents (nitric oxide) according to patients’ IOP in a contact lens system—Eye kNOw. Eye kNOw contains a designed chamber filled with L-arginine, IPTG, and our engineered bacteria. Here are the three main principles we used to design our contact lens:</p>
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                         <p> This year, We aim to provide a real-time treatment that can release ocular hypotensive agents (nitric oxide) according to patients’ IOP in a contact lens system—Eye kNOw. Eye kNOw contains a designed chamber filled with L-arginine, IPTG, and our engineered bacteria. Here are the three main principles we used to design Eye kNOw:</p>
 
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                         <li><p>bNOS produced by our engineered bacteria turns L-arginine into NO.</p></li>
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                         <li><p>NOS produced by our engineered bacteria turns L-arginine into NO.</p></li>
                         <li><p>Different concentrations of IPTG induces different production rates of bNOS.</p></li>
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                         <li><p>Different concentrations of IPTG induces different production rates of NOS.</p></li>
                     <li><p>The proportional relationship between IOP and cornea’s radius of curvature.</p></li>
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                     <li><p>IOP elevation causes corneal radius of curvature to change, leading to deformation of Eye kNOw.</p></li>
 
                       </ol>
 
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                       <p>   Below are the steps showing how it works:</p>
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                       <p> Below are the workflows of Eye kNOw:</p>
 
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                     <li><p>Elevated IPTG leads to higher production rate of NOS by engineered bacteria.</p></li>
 
                     <li><p>Elevated IPTG leads to higher production rate of NOS by engineered bacteria.</p></li>
 
                         <li><p>The more NOS produced, the more L-arginine turned into NO.</p></li>
 
                         <li><p>The more NOS produced, the more L-arginine turned into NO.</p></li>
                         <li><p>More NO is released into the patients’ eyes, relaxing Trabecular Meshwork.</p></li>
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                         <li><p>More NO is released into the eyes, relaxing trabecular meshwork.</p></li>
                         <li><p>Finally, patients’ IOP will be lowered to normal.</p></li>
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                         <li><p>Finally, IOP will be lowered to normal level.</p></li>
 
                       </ol>
 
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                       <p>   We will need to set up two models: cornea deformation model and NO ocular delivery model. WIth the two models above, we can calculate the efficiency of Eye kNOw.</p>
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                       <p> We establish three models to simulate the whole process above: contact lens deformation model and NO ocular diffusion model. Model 3 combines model 1, model 2 and experimental data, which precisely calculate the effectiveness of Eye kNOw.</p>
 
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                 <a href="https://static.igem.org/mediawiki/2020/2/20/T--NCKU_Tainan--Model_IOP.png" target="_blank" style="width:60%"><img src="https://static.igem.org/mediawiki/2020/2/20/T--NCKU_Tainan--Model_IOP.png" alt="" title="" style="width:100%"></a>
 
                 <a href="https://static.igem.org/mediawiki/2020/2/20/T--NCKU_Tainan--Model_IOP.png" target="_blank" style="width:60%"><img src="https://static.igem.org/mediawiki/2020/2/20/T--NCKU_Tainan--Model_IOP.png" alt="" title="" style="width:100%"></a>
                 <figcaption class="caption-design">Fig. 0. Steps from IOP elevation to NO diffusion</figcaption>
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                 <figcaption class="caption-design">Fig. 0A. Eye kNOw workflow chart.</figcaption>
 
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                     <ol class="mb-4">
 
                     <ol class="mb-4">
                         <li><p>To set up a correct model that can mimic nitric oxide ocular delivery system.</p></li>
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                         <li><p>To build a model that describes the deformation of contact lens quantitatively.</p></li>
                         <li><p>To set up a correct model that can calculate the deformation of contact lens.</p></li>
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                         <li><p>To establish a model that simulates nitric oxide ocular diffusion system.</p></li>
                     <li><p>To calculate the efficiency of Eye kNOw, and prove that Eye kNOw will work effectively.</p></li>
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                     <li><p>To precisely calculate the effectiveness of Eye kNOw by taking both experimental data and model theories into consideration.</p></li>
 
                       </ol>
 
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                         <p>   This model is used to predict the deformation of our contact lens under varying intraocular pressure (IOP), and research suggested that the radius of curvature of cornea increases linearly with respect to the increment of IOP, and there are no known compound to serve as a suitable biomarker that is able to be detected without invasion into the eyeball when the IOP varies, we took advantage of it and  designed Eye kNOw. (See Description page)</p>
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                         <p> This model is used to describe the <b>deformation of the contact lens under varying intraocular pressure (IOP) with quantitative estimation.</b> Research suggested that the radius of cornea curvature increases linearly with the increment of IOP<sup>[<a href = "#ref1" class = "linklink">1</a>]</sup>. However, the pressure exerted on the contact lens while being worn is not fully studied, not to mention the volume difference of contact lens with respect to different IOP. Therefore, to build this model from scratch, we first made the following assumptions:</p>
 
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                        <p> Table 1A shows the parameters of cornea that will be used in our model.</p>
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                              <th scope="col" style="font-size:1.2rem; text-align: center;"></th>
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                              <th scope="col" style="font-size:1.2rem; text-align: center;">Description</th>
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                              <th scope="col" style="font-size:1.2rem; text-align: center;">Value</th>
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                              <td scope="row" style="font-size:1.1rem; text-align: center;">E<sub>Cornea</sub></td>
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                              <td style="font-size:1.1rem; text-align: center;">Elastic modulus of the cornea</td>
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                              <td style="font-size:1.1rem; text-align: center;">15.3 mPa</td>
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                            </tr>
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                              <td scope="row" style="font-size:1.1rem; text-align: center;">t<sub>Cornea</sub></td>
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                              <td style="font-size:1.1rem; text-align: center;">Thickness of the cornea</td>
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                              <td style="font-size:1.1rem; text-align: center;">0.666 mm</td>
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                            </tr>
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                              <td scope="row" style="font-size:1.1rem; text-align: center;">R<sub>Cornea_0</sub></td>
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                              <td style="font-size:1.1rem; text-align: center;">Corneal radius of curvature</td>
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                              <td style="font-size:1.1rem; text-align: center;">8.45 mm</td>
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                        <figcaption class="caption-design" style="margin-bottom:1rem; text-align: center">Table 1A. Parameters of cornea used in model 1<sup>[<a href = "#ref2" class = "linklink">2</a>][<a href = "#ref3" class = "linklink">3</a>]</sup>.</figcaption>
 
                
 
                
 
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                         <p>   Considering the force equilibrium equation between the pressure of fluid and the membrane (cornea) in the section, as you can see in the figure below, we would be able to obtain equation (1)</p>
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                         <p> First, we need to obtain the relationship between IOP and radius Eye kNOw. Considering the force equilibrium equation between the pressure of fluid and the membrane (cornea) in the section, we obtain Equation 1.1:</p>
 
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                       <p>   According to Hooke’s Law, we have (2)</p>
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                       <p> According to Hooke’s Law, we have Equation 1.2:</p>
 
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                 <a style="width:35%"><img src="https://static.igem.org/mediawiki/2020/c/c7/T--NCKU_Tainan--model2.png" alt="" title="" style="width:100%"></a>
 
                 <figcaption class="caption-design">Equation 1.2</figcaption>
 
                 <figcaption class="caption-design">Equation 1.2</figcaption>
 
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                         <p>   Under proportional limit, the radius difference - ΔR, is given by (3)</p>
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                         <p> Under proportional limit, the radius difference (ΔR), is given by Equation 1.3:</p>
 
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                       <p>   From (1), (2), (3), we obtain (4)</p>
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                       <p> From the equations listed above, we obtain Equation 1.4:</p>
 
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                         <p>   For a thick membrane, which means the thickness of the membrane is too large to be neglected in comparison to the radius. Thus, we have a constant term that is related to the poisson ratio, ν, in the equation (5). [1] [2]</p>
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                         <p> For a thick membrane, which means the thickness of the membrane is too large to be neglected in comparison to the radius. Thus, we have a constant term that is related to the poisson ratio, ν, in the Equation 1.5<sup>[<a href = "#ref1" class = "linklink">1</a>][<a href = "#ref4" class = "linklink">4</a>]</sup>.</p>
 
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                    <p style="position: relative;left: 2rem;">E: Elastic modulus of the membrane (cornea of porcine in this case).</p>
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                    <p style="position: relative;left: 2rem;">t: Thickness of the membrane (cornea of porcine ).</p>
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                     <div class="flex-grow-1">                       
 
                     <div class="flex-grow-1">                       
                         <p>   Notice that the p in (4) and (5) represents the pressure difference with respect to the initial pressure (IOP difference) instead of the pressure itself. We adopted the initial IOP to be 10 mmHg.</p>
+
                         <p> Notice that the p in Equation 1.4 and Equation 1.5  represents the pressure difference with respect to the initial pressure instead of the pressure itself. We assumed the initial IOP to be 10 mmHg. By Equation 1.5, <b>we predict the relation between IOP and the radius difference, or the strain, is linear, which fits the results of digital image correlation experiment. </b>(See <a href="https://2020.igem.org/Team:NCKU_Tainan/Proof_Of_Concept" alt="" target="_blank">Proof of concept</a>: step 1 )</p>  
 
               </div>
 
               </div>
 
               </div>
 
               </div>
 
               <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
               <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                     <div class="flex-grow-1">                       
 
                     <div class="flex-grow-1">                       
                         <p>   By equation (5), we predict the relation between IOP and the radius difference, or the strain, is linear.(See Proof of concept: step 1)</p>
+
                         <p> Second, we calculate the relationship between IOP and volume difference of the chamber in Eye kNOw. Table 1B lists all the parameters of Eye kNOw used in the following calculation.</p>
 
               </div>
 
               </div>
 
               </div>
 
               </div>
 +
              <table class="table table-Border">
 +
                          <thead>
 +
                            <tr style="border:3px solid #7E3B40;">
 +
                              <th scope="col" style="font-size:1.2rem; text-align: center;"></th>
 +
                              <th scope="col" style="font-size:1.2rem; text-align: center;">Description</th>
 +
                              <th scope="col" style="font-size:1.2rem; text-align: center;">Value</th>
 +
                            </tr>
 +
                          </thead>
 +
                          <tbody>
 +
                            <tr> 
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">R<sub>Eye_kNOw_0</sub></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">Inner radius of curvature</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">8.2 mm</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">E<sub>Eye_kNOw</sub></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">Elastic modulus of Eye kNOw</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">3.10<sup>6</sup> dyne/mm<sup>2</sup></td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">d</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">Diameter of Eye kNOw</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">14 mm</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">d<sub>1</sub></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">Inner diameters of the chamber</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">10 mm</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">d<sub>2</sub></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">Outer diameters of the chamber</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">12 mm</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">t<sub>Eye_kNOw</sub></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">Thickness of Eye kNOw</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">2.10<sup>-4</sup> mm</td>
 +
                            </tr>
 +
                          </tbody>
 +
                        </table>
 +
              <figcaption class="caption-design" style="margin-bottom:1rem; text-align: center">Table 1B. Parameters of Eye kNOw used in model 1.</figcaption>
 +
             
 
               <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
               <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
                     <div class="flex-grow-1">                    
+
                     <div class="flex-grow-1">
                         <p>   The volume of the ring-like compartment in Eye kNOw is calculated by the same method of the volume of revolution in calculus. Volume of compartment equals 4.4 cubic millimeters.</p>
+
                     
 +
     
 +
                         <p> The volume of the chamber in Eye kNOw , which is a ring-like compartment, is calculated by the same method of the volume of revolution in calculus. After calculation, the volume of the chamber  equals 4.4 cubic millimeters initially.</p>
 
               </div>
 
               </div>
 
               </div>
 
               </div>
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                 <div class="col-lg ">
 
                 <div class="col-lg ">
 
                 <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3">
 
                 <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3">
                 <a style="width:60%"><img src="https://static.igem.org/mediawiki/2020/4/41/T--NCKU_Tainan--model_schematic_of_lens.png" alt="" title="" style="width:100%"></a>
+
                 <a style="width:40%"><img src="https://static.igem.org/mediawiki/2020/a/a7/T--NCKU_Tainan--Model_chamber.png" alt="" title="" style="width:100%"></a>
                 <figcaption class="caption-design">Fig. 2. Structure design of Eye kNOw.</figcaption>
+
                 <figcaption class="caption-design">Fig. 1B. Structure design of Eye kNOw.</figcaption>
 
                 </figure>
 
                 </figure>
 
                 </div>
 
                 </div>
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               <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
               <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                     <div class="flex-grow-1">                       
 
                     <div class="flex-grow-1">                       
                         <p>   The volume difference is given by the elongation of the part above the compartment in meridional direction, which is given by the formula list below:</p>
+
                         <p> The volume difference is given by the elongation of the part above the compartment in meridional direction, which is given by the formula list below:</p>
 
               </div>
 
               </div>
 
               </div>
 
               </div>
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                 <div class="col-lg ">
 
                 <div class="col-lg ">
 
                 <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3">
 
                 <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3">
                 <a style="width:30%"><img src="https://static.igem.org/mediawiki/2020/0/0b/T--NCKU_Tainan--model6.png" alt="" title="" style="width:100%"></a>
+
                 <a style="width:35%"><img src="https://static.igem.org/mediawiki/2020/0/0b/T--NCKU_Tainan--model6.png" alt="" title="" style="width:100%"></a>
                   <figcaption class="caption-design">Equation 1.6.</figcaption>
+
                   <figcaption class="caption-design">Equation 1.6</figcaption>
 
                 </figure>
 
                 </figure>
 
                 </div>
 
                 </div>
Line 521: Line 635:
 
               <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
               <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                     <div class="flex-grow-1">                       
 
                     <div class="flex-grow-1">                       
                       <p>   while</p>
+
                       <p> while</p>
 
               </div>
 
               </div>
 
               </div>
 
               </div>
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                 <div class="col-lg ">
 
                 <div class="col-lg ">
 
                 <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3">
 
                 <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3">
                 <a style="width:30%"><img src="https://static.igem.org/mediawiki/2020/3/3f/T--NCKU_Tainan--model7.png" alt="" title="" style="width:100%"></a>
+
                 <a style="width:12%"><img src="https://static.igem.org/mediawiki/2020/f/f0/T--NCKU_Tainan--Thick_Epsilon.png" alt="" title="" style="width:100%"></a>
                   <figcaption class="caption-design">Equation 1.7.</figcaption>
+
                   <figcaption class="caption-design">Equation 1.7</figcaption>
 
                 </figure>
 
                 </figure>
 
                 </div>
 
                 </div>
 
                 </div>
 
                 </div>
 
                 </div>
 
                 </div>
             
 
             
 
              <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                    <div class="flex-grow-1">                     
 
                        <p>  and</p>
 
              </div>
 
              </div>
 
 
                
 
                
 
               <div class="container-fluid p-0">
 
               <div class="container-fluid p-0">
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                 <div class="col-lg ">
 
                 <div class="col-lg ">
 
                 <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3">
 
                 <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3">
                 <a style="width:30%"><img src="https://static.igem.org/mediawiki/2020/8/8a/T--NCKU_Tainan--model8.png" alt="" title="" style="width:100%"></a>
+
                 <a style="width:12%"><img src="https://static.igem.org/mediawiki/2020/a/a8/T--NCKU_Tainan--Thick_VE.png" alt="" title="" style="width:100%"></a>
                   <figcaption class="caption-design">Equation 1.7.</figcaption>
+
                   <figcaption class="caption-design">Equation 1.8</figcaption>
 +
                </figure>
 +
                </div>
 +
                </div>
 +
                </div>
 +
              <p> The ratio of volume difference is given by Equation 1.9:</p>
 +
              <div class="container-fluid p-0">
 +
                <div class="row no-gutters">
 +
                <div class="col-lg ">
 +
                <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3">
 +
                <a style="width:55%"><img src="https://static.igem.org/mediawiki/2020/8/8d/T--NCKU_Tainan--Final1_9.png" alt="" title="" style="width:100%"></a>
 +
                <figcaption class="caption-design">Equation 1.9</figcaption>
 
                 </figure>
 
                 </figure>
 
                 </div>
 
                 </div>
 
                 </div>
 
                 </div>
 
                 </div>
 
                 </div>
             
 
 
               <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
               <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                     <div class="flex-grow-1">                       
 
                     <div class="flex-grow-1">                       
                         <p>   By doing so, the ratio of volume difference is approximated to be 1% when the IOP has an increment of 1 mmHg.</p>
+
                         <p> After calculation with the parameters listed above, <b>the result is approximately 1% when the IOP has an increment of 1 mmHg.</b></p>
 
               </div>
 
               </div>
 
               </div>
 
               </div>
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                 <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                 <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                     <div class="flex-grow-1">                       
 
                     <div class="flex-grow-1">                       
                         <p>   Eye is a complicated organ with various tissues. In other ocular delivery models, they consider the whole eye as one compartment since their drugs are stable and large enough that the difference of tissues can be ignored. However, we use NO as our drug, which is small and unstable. Thus, we need to set up a new model to simulate NO ocular delivery system.</p>
+
                         <p> Eye is a complicated organ consisting of various tissues with different physical properties. In most of the ocular delivery models, they consider the whole eye as one compartment since their drugs are stable and large enough that the difference of tissue characteristics can be ignored. However, we use NO as our drug, which is small and unstable. Thus, we need to set up a new model to simulate NO ocular delivery system.</p>
 +
                </div>
 +
                </div>
 +
              <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 +
                    <div class="flex-grow-1">                     
 +
                        <p> This model <b>divides the eye system into three different compartment</b> according to the tissues differences, and provide <b>quantitative NO concentration profiles dynamically.</b> This model can be applied on ocular drug delivery system of other small and unstable drugs.</p>
 
                 </div>
 
                 </div>
 
                 </div>
 
                 </div>
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                 <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                 <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                     <div class="flex-grow-1">                       
 
                     <div class="flex-grow-1">                       
                         <p>   Eye structure can be divided into three main compartments: cornea, anterior chamber, and posterior chamber. Target site of NO is trabecular meshwork, which is located at the posterior angle of anterior chamber. We simplify the eye structures into one dimension as below:</p>
+
                         <p> Eye structure can be divided into three main compartments: cornea, anterior chamber, and posterior chamber. <b>Target site of NO is trabecular meshwork</b>, which is located at the posterior angle of anterior chamber. We simplify the eye structures into one dimension as below:</p>
 
                 </div>
 
                 </div>
 
                 </div>
 
                 </div>
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                 <div class="col-lg ">
 
                 <div class="col-lg ">
 
                 <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3">
 
                 <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3">
                 <a style="width:60%"><img src="https://static.igem.org/mediawiki/2020/2/2a/T--NCKU_Tainan--model_schematic.png" alt="" title="" style="width:100%"></a>
+
                 <a style="width:60%"><img src="https://static.igem.org/mediawiki/2020/4/47/T--NCKU_Tainan--SchematicNew.png" alt="" title="" style="width:100%"></a>
                 <figcaption class="caption-design">Fig. 2B. One dimensional schematic graph for NO ocular delivery model</figcaption>
+
                 <figcaption class="caption-design">Fig. 2B. One dimensional schematic graph for NO ocular delivery model.</figcaption>
 
                 </figure>
 
                 </figure>
 
                 </div>
 
                 </div>
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                 <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                 <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                     <div class="flex-grow-1">                       
 
                     <div class="flex-grow-1">                       
                       <p> Since the tissue characteristics of the three compartments varies a lot, we need to calculate them separately by different partial differentiation equations (PDEs).</p>
+
                       <p> Since the tissue characteristics of the three compartments varies a lot, we need to simulate the behavior of NO in them separately, by different partial differential equations (PDEs).</p>
 
                 </div>
 
                 </div>
 
             </div>
 
             </div>
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               <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
               <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                     <div class="flex-grow-1">                       
 
                     <div class="flex-grow-1">                       
                       <p> First, we calculated the initial state of NO distribution in the eye before the production of NO by Eye kNOw. After ensuring the initial state, we can calculate the NO distribution after the production of NO by Eye kNOw, which is a formula of position and time. Before all these things, we should set up the PDEs that can describe the distribution of NO. Refer table below for abbreviations and variables:</p>
+
                       <p> First, <b>we establish the initial state of NO distribution in the eye</b> before Eye kNOw being triggered. Second, we build the <b>dynamic NO concentration profile according to time and distance</b> after Eye kNOw activation. We use several partial differential equations(PDEs) to describe the behavior of NO. Table 2A lists all the abbreviations used in PDEs.</p>
 
</div>
 
</div>
 
             </div>
 
             </div>
 +
              <table class="table table-Border">
 +
                          <thead>
 +
                            <tr style="border:3px solid #7E3B40;">
 +
                              <th scope="col" style="font-size:1.2rem; text-align: center;"></th>
 +
                              <th scope="col" style="font-size:1.2rem; text-align: center;">Full Name</th>
 +
                              <th scope="col" style="font-size:1.2rem; text-align: center;">Unit</th>
 +
                            </tr>
 +
                          </thead>
 +
                          <tbody>
 +
                            <tr> 
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">C</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">Concentration of NO</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">M</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">x</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">distance (from outside of the eye to inside)</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">cm</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">t</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">time (t=0 resembles the time when Eye kNOw start to produce NO)</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">s</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">D</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">Diffusion coefficient</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">cm<sup>2</sup>/s</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">R</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">Flow rate of liquid</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">L/s</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">k</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">Degradation coefficient of NO</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">M<sup>-2</sup>/s</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">Pro</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">Production rate of NO in the compartment</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">mol/s</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">V</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">Volume of the compartment</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">L</td>
 +
                            </tr>
 +
                          </tbody>
 +
                        </table>
 +
              <figcaption class="caption-design" style="margin-bottom:1rem; text-align: center">Table 2A. Abbreviations and variables used in PDEs.</figcaption>
 
                
 
                
 
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                     <p>1. Setting up PDEs:</p>
 
                     <p>1. Setting up PDEs:</p>
 
                  
 
                  
                     <p style="position: relative;left: 2rem;">PDEs are used to describe the factors that will affect the concentration of NO. Factors are listed below:</p>
+
                     <p style="position: relative;left: 2rem;"> PDEs take the factors that may affect the concentration of NO into consideration to describe the behavior of NO. Factors are listed below:</p>
                     <p style="position: relative;left: 2rem;">(1) Degradation</p>
+
                     <p style="position: relative;left: 2rem;"><b>(1) Degradation</b></p>
 
                      
 
                      
                         <p style="position: relative;left: 4rem;">The two main factors that will cause degradation of nitric oxide are Hemoglobin and oxygen. Hemoglobin doesn’t exist in the eye system, thus we only need to consider oxygen to calculate the amount of nitric oxide degradation.</p>
+
                         <p style="position: relative;left: 4rem;"> The two main factors that will cause degradation of nitric oxide in the human body are hemoglobin and oxygen. Hemoglobin doesn’t exist in the eye system, thus we only need to consider oxygen as the factor causing NO degradation.</p>
                         <p style="position: relative;left: 4rem;">According to papers, the formula can be written as below:</p>
+
                         <p style="position: relative;left: 4rem;"> According to current studies, the formula can be written as below:</p>
 
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                 </div>
 
                   </div>
 
                   </div>
                     <p style="position: relative;left: 2rem;">(2) Diffusion</p>
+
                     <p style="position: relative;left: 2rem;"><b>(2) Diffusion</b></p>
 
                                            
 
                                            
                           <p style="position: relative;left: 4rem;">By Fick's second law, the diffusion formula can be written as below:</p>                             
+
                           <p style="position: relative;left: 4rem;"> By <b>Fick's second law</b>, the diffusion of chemicals can be described as below:</p>                             
 
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                     <p style="position: relative;left: 2rem;">(3) Endogenous production</p>
+
                     <p style="position: relative;left: 2rem;"><b>(3) Endogenous production</b></p>
               <p style="position: relative;left: 4rem;">Since aqueous humor has an initial concentration of NO around 53.4uM, there should exist endogenous NO production. There are three different types of NOS in human eyes: e-NOS, n-NOS, and i-NOS.</p>
+
               <p style="position: relative;left: 4rem;"><b> Glaucoma patients’ aqueous humor has an initial average concentration of NO around 53.4uM<sup>[<a href = "#ref7" class = "linklink">7</a>]</b>, which is maintained by endogenous NO produced by NO synthase (NOS). There are three different types of NOS in human eyes: e-NOS, n-NOS, and i-NOS<sup>[<a href = "#ref7" class = "linklink">7</a>]</sup>.</p>
                     <p style="position: relative;left: 4rem;">e-NOS and n-NOS work constantly, which are expressed on iris, cornea, vascular endothelium, etc. i-NOS only works when inflammation happens, which is not a common symptom for glaucoma, thus we can ignore it. We assume that these NOS produce NO in a constant rate, so the formula can be written as below:</p>
+
                     <p style="position: relative;left: 4rem;"> e-NOS and n-NOS work constantly, which are expressed on iris, cornea, vascular endothelium, etc. i-NOS only works when ocular inflammation happens, which is not a common symptom for glaucoma, thus we can ignore it. We assume that these NOS produce NO in a constant rate, so the formula can be written as below:</p>
 
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                   </div>
 
                   </div>
                     <p style="position: relative;left: 2rem;">(4) Convection</p>
+
                     <p style="position: relative;left: 2rem;"><b>(4) Convection</b></p>
                     <p style="position: relative;left: 4rem;">There’s a flow of aqueous humor in the anterior chamber, which is 2.4 uL/min. Convection will affect the distribution of nitric oxide, which can be written as below:</p>
+
                     <p style="position: relative;left: 4rem;"> There’s a flow of aqueous humor in the anterior chamber, which is 2.4 uL/min<sup>[8]</sup>. Convection will affect the distribution of nitric oxide, which can be written as below:</p>
 
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                   </div>
 
                   </div>
                    <p style="position: relative;left: 4rem;">Combining the factors listed above, the PDE for describing the distribution of NO can be written as below:</p>
+
                    <p style="position: relative;left: 4rem;"> Combining the factors listed above, the PDE for describing the distribution of NO can be written as below:</p>
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+
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                 </div>
 
                 </div>
 
                 </div>
 
                 </div>
                  </div>
+
              </div>
                    <p style="position: relative;left: 4rem;">To make the calculation easier, we need to <b>simplify Equation 1 into homogeneous form</b>.
+
                    <p style="position: relative;left: 4rem;"> Equation 2.5 is a heterogeneous PDE, which is very hard to solve. We need to <b>simplify Equation 2.5 into homogeneous form for further calculation.</b></p>
                    <p style="position: relative;left: 4rem;">First, since the concentration of oxygen can be maintained by oxygen in the air( oxygen in the air can dissolve and penetrate into our eyes), <b>we can set k[Oxygen] as a constant</b>.
+
                    <p style="position: relative;left: 4rem;"> First, since the concentration of oxygen can be maintained by oxygen in the air( oxygen in the air can dissolve and penetrate into our eyes), <b>we can set k[Oxygen] as a constant.</b></p>
              <p style="position: relative;left: 4rem;">Second, we want to simplify C^2 into C. In order to prevent over-estimation of nitric oxide concentration, <b>we change C^2 into C(max)*C, where C(max) is the max concentration of nitric oxide in the compartment</b>. Since C(max)*C is always larger than (or same as) C^2, we can make sure that we won’t over-estimate the concentration of nitric oxide. Since C(max) is a constant, we can set <b>constant B = k[Oxygen]C(max)</b>.
+
                    <p style="position: relative;left: 4rem;"> Second, we want to simplify the C<sup>2</sup> term into C. In order to prevent over-estimation of nitric oxide concentration, <b>we change C<sup>2</sup> into C<sub>max</sub>.C, where C<sub>max</sub> is the max concentration of nitric oxide in the compartment.</b> Since C<sub>max</sub>.C is always larger than (or same as) C<sup>2</sup>, we can make sure that we won’t over-estimate the concentration of nitric oxide. Since C<sub>max</sub> is a constant, we can consider <b>constant B = k[Oxygen]C<sub>max</sub>.</b></p>
                    <p style="position: relative;left: 4rem;">So, the modified form of PDE will be:</p>
+
                    <p style="position: relative;left: 4rem;"> Therefore, the modified form of PDE will be:</p>
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                 </div>
 
                 </div>
 
                 </div>
 
                 </div>
                  </div>
+
                  </div>
                    </div>
+
                  </div>
 
                     </div>
 
                     </div>
 
                  
 
                  
 
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                     <p>2. Parameters: </p>
+
                     <p>2. Obtaining parameters from current studies: </p>
                         <p style="position: relative;left: 2rem;">Parameters used are listed below. We collected them from different papers.<p>
+
                         <p style="position: relative;left: 2rem;"> Parameters used are listed in table 2B. We collected them from current studies.</p>
                         <p style="position: relative;left: 2rem;">We're still lacking some of the parameters. We can <b>estimate them by solving the steady state of NO distribution</b>.</p>
+
                    <table class="table table-Border">
 +
                          <thead>
 +
                            <tr style="border:3px solid #7E3B40;">
 +
                              <th scope="col" style="font-size:1.2rem; text-align: center;"></th>
 +
                              <th scope="col" style="font-size:1.2rem; text-align: center;">Contact Lens</th>
 +
                              <th scope="col" style="font-size:1.2rem; text-align: center;">Cornea</th>
 +
                              <th scope="col" style="font-size:1.2rem; text-align: center;">Aqueous Humor</th>
 +
                              <th scope="col" style="font-size:1.2rem; text-align: center;">Unit</th>
 +
                            </tr>
 +
                          </thead>
 +
                          <tbody>
 +
                            <tr> 
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">D</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">1.8.10<sup>-6</sup><sup>[<a href = "#ref9" class = "linklink">9</a>]</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">2.81.10<sup>-5</sup><sup>[<a href = "#ref10" class = "linklink">10</a>]</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">3.10<sup>-5</sup><sup>[<a href = "#ref11" class = "linklink">11</a>]</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">cm<sup>2</sup>/s</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">B</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">?</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">?</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">?</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">1/s</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">R</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">0</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">0</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">4.10<sup>-8</sup><sup>[<a href = "#ref8" class = "linklink">8</a>]</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">L/s</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">V</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">2.77.10<sup>-5</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">1.6.10<sup>-5</sup><sup>[<a href = "#ref12" class = "linklink">12</a>]</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">2.5.10<sup>-4</sup><sup>[<a href = "#ref13" class = "linklink">13</a>]</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">L</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">Pro</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">?</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">?</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">?</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">mol/s</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">Initial Average [NO]</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">?</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">?</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">5.34.10<sup>-5</sup><sup>[<a href = "#ref6" class = "linklink">6</a>]</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">M</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">Maximum Distance</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">0.02</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">0.055<sup>[<a href = "#ref14" class = "linklink">14</a>]</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">1.122<sup>[<a href = "#ref15" class = "linklink">15</a>]</sup><sup>[<a href = "#ref16" class = "linklink">16</a>]</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">cm</td>
 +
                            </tr>
 +
                          </tbody>
 +
                        </table>
 +
              <figcaption class="caption-design" style="margin-bottom:1rem; text-align: center">Table 2B. Parameters of Eye kNOw used in model 2.</figcaption>
 +
                         <p style="position: relative;left: 2rem;"> We're still lacking some of the parameters. We can <b>estimate them by solving the steady state of NO distribution</b>.</p>
 
          
 
          
 
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                     <p>3. Calculating steady state:</p>
 
                     <p>3. Calculating steady state:</p>
                         <p style="position: relative;left: 2rem;">We start from the contact lens compartment. When in steady state,  concentration of NO won't change by time. Thus, Equation 2.6 can be written as below:<p>
+
                         <p style="position: relative;left: 2rem;"> We start from the contact lens compartment. When in steady state,  NO concentration won't change by time. Thus, Equation 2.6 can be written as below:<p>
 
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                     <p style="position: relative;left: 2rem;">Where subscript 1 stands for the parameters and variables of the contact lens compartment. By solving this equation, we can get the solution of C1 in steady state:</p>
+
                     <p style="position: relative;left: 2rem;"> Where subscript 1 stands for the parameters and variables of the contact lens compartment. By solving Equation 2.7, we can get the solution of C<sub>1</sub> in steady state:</p>
 
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                     <p style="position: relative;left: 2rem;">We use the approximation:</p>
+
                     <p style="position: relative;left: 2rem;"> We use the approximation:</p>
 
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                       <p style="position: relative;left: 2rem;">Thus turning equation 2.8 into linear form:</p>
+
                       <p style="position: relative;left: 2rem;"> Thus turning Equation 2.8 into linear form:</p>
 
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                   <a style="width:60%"><img src="https://static.igem.org/mediawiki/2020/6/64/T--NCKU_Tainan--model_1_10.png" alt="" title="" style="width:100%"></a>
+
                   <a style="width:60%"><img src="https://static.igem.org/mediawiki/2020/7/73/T--NCKU_Tainan--Revised_Formula_Kelvin.png" alt="" title="" style="width:100%"></a>
 
               <figcaption class="caption-design">Equation 2.10</figcaption>
 
               <figcaption class="caption-design">Equation 2.10</figcaption>
 
             </figure>
 
             </figure>
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                         <p style="position: relative;left: 2rem;">Since C1(0)=0 (one of the boundary conditions), the final form of C1 in steady state can be written as below:</p>
+
                         <p style="position: relative;left: 2rem;"> Since C<sub>1</sub>(0)=0 (one of the boundary conditions), the final form of C<sub>1</sub> in steady state can be written as below:</p>
 
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                   <p style="position: relative;left: 2rem;">By the same method, we can simplify the concentration of NO in cornea and aqueous humor compartments as a linear formula of position. To simplify the formulas, we set the outer surface of every compartment as the starting position of that compartment. For example, for cornea compartment, the interface of cornea and contact lens is considered the starting position, namely x=0.</p>
+
                   <p style="position: relative;left: 2rem;"> By the same method, we can simplify the concentration of NO in cornea and aqueous humor compartments as a linear formula of x. To simplify the formulas, <b>we set the outer surface of every compartment as the starting position of that compartment.</b> For example, for cornea compartment, the interface of cornea and contact lens is considered the starting position, namely x=0.</p>
                           <p style="position: relative;left: 2rem;">As for the boundary conditions, the interfaces should have only one concentration. For example, the formula of C1 at x=0.02 should have the same value as C2 at x=0. Combining these conditions, we can get the function of C2 and C3:</p>
+
                           <p style="position: relative;left: 2rem;"> As for the boundary conditions, the interfaces should have only one concentration. For example, the formula of C<sub>1</sub> at x=0.02 should have the same value as C<sub>2</sub> at x=0. Combining these conditions, we can get the function of C<sub>2</sub> and C<sub>3</sub>:</p>
 
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                   <p style="position: relative;left: 2rem;">Now we need to solve the slope of NO concentration, namely a1, a2, a3. Here, we use Fick’s first law as boundary conditions, that is at the interfaces, input of NO from one compartment should be the same as output of another compartment. For example, at the interface of cornea and contact lens, input of NO to contact lens should be the same as output of NO from cornea.</p>
+
                   <p style="position: relative;left: 2rem;"> Now we need to solve the slope of NO concentration, namely a<sub>1</sub>, a<sub>2</sub>, a<sub>3</sub>. Here, we use Fick’s first law as boundary conditions, that is <b>at the interfaces, input of NO from one compartment should be the same as output of another compartment.</b> For example, at the interface of cornea and contact lens, input of NO to contact lens should be the same as output of NO from cornea.</p>
                             <p style="position: relative;left: 2rem;">The input of NO to contact lens can be written as below, according to Fick’s first law:</p>
+
                             <p style="position: relative;left: 2rem;"> The input of NO to contact lens can be written as below, according to Fick’s first law:</p>
 
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        <p style="position: relative;left: 2rem;">The output of NO from cornea can be written as below:</p>
+
        <p style="position: relative;left: 2rem;"> The output of NO from cornea can be written as below:</p>
 
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                     <p style="position: relative;left: 2rem;">Applying the solution we’d found before, we can get the relationship of slopes of each compartment:</p>
+
                     <p style="position: relative;left: 2rem;"> Applying the solution we’d obtained, we can get the relationship of slopes of each compartment:</p>
 
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                     <p style="position: relative;left: 2rem;">Therefore, we can draw the graph of NO concentration in steady state:</p>         
+
                     <p style="position: relative;left: 2rem;"> Therefore, we can draw the steady-state-graph of NO distribution in the eye:</p>  
                    <p style="position: relative;left: 2rem;">Red line represents the NO concentration in contact lens, blue one represents cornea compartment, and green one represents aqueous humor compartment.</p>
+
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                            <p style="position: relative;left: 2rem;">Now, there are just B and Pro not determined yet. Recall that B = k[Oxygen]C(max), we can calculator them. As for Pro, we can calculate each compartment’s total input and output, they should be the same since we’re dealing with steady state. After some calculations, the table can be filled completely:</p>
+
                                               
+
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                   <a style="width:60%"><img src="https://static.igem.org/mediawiki/2020/d/d1/T--NCKU_Tainan--Model_NO_3_parts.png" alt="" title="" style="width:100%"></a>
+
                   <a style="width:60%"><img src="https://static.igem.org/mediawiki/2020/3/3e/T--NCKU_Tainan--Model_NOABCABC.png" alt="" title="" style="width:100%"></a>
               <figcaption class="caption-design">Fig. 2C. NO Concentration Profile in Steady State. </figcaption>
+
               <figcaption class="caption-design">Fig. 2C. NO Concentration Profile in Steady State. A stands for contact lens compartment, B stands for cornea comparment, C stands for aqueous humor compartment.</figcaption>
 
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                 </div>
 
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+
                 </div>        
 +
                    <p style="position: relative;left: 2rem;"> Now, there are just B and Pro not determined yet. Recall that <b>B = k[Oxygen]C<sub>max</sub></b>, we can calculate them. <b>As for Pro, we can calculate each compartment’s total input and output, they should be the same since we’re dealing with steady state.</b> After calculations, Table 2B can be filled completely as Table 2C.</p>
 +
                            <table class="table table-Border">
 +
                          <thead>
 +
                            <tr style="border:3px solid #7E3B40;">
 +
                              <th scope="col" style="font-size:1.2rem; text-align: center;"></th>
 +
                              <th scope="col" style="font-size:1.2rem; text-align: center;">Contact Lens</th>
 +
                              <th scope="col" style="font-size:1.2rem; text-align: center;">Cornea</th>
 +
                              <th scope="col" style="font-size:1.2rem; text-align: center;">Aqueous Humor</th>
 +
                              <th scope="col" style="font-size:1.2rem; text-align: center;">Unit</th>
 +
                            </tr>
 +
                          </thead>
 +
                          <tbody>
 +
                            <tr> 
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">D</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">1.8.10<sup>-6</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">2.81.10<sup>-5</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">3.10<sup>-5</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">cm<sup>2</sup>/s</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">B</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">2.84.10<sup>-2</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">1.03.10<sup>-2</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">1.566.10<sup>-2</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">1/s</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">R</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">0</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">0</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">4.10<sup>-8</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">L/s</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">V</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">2.77.10<sup>-5</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">1.6.10<sup>-5</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">2.5.10<sup>-4</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">L</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">Pro</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">7.10<sup>-6</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">1.52.10<sup>-5</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">1.239.10<sup>-3</sup></td>
 +
                              <td style="font-size:1.1rem; text-align: center;">mol/s</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">Initial Average [NO]</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">C<sub>1</sub> = 933.7x</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">C<sub>2</sub> = 59.818x + 18.674</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">C<sub>3</sub> = 56.063x + 21.964</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">uM</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">Maximum Distance</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">0.02</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">0.055</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">1.122</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">cm</td>
 +
                            </tr>
 +
                          </tbody>
 +
                        </table>
 +
              <figcaption class="caption-design" style="margin-bottom:1rem; text-align: center">Table 2C. Complete table of parameters used for model 2.</figcaption>                 
 +
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 +
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 +
               
 
               <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
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                   <div class="flex-grow-1">
 
                   <div class="flex-grow-1">
 
                     <p>4. Calculating NO concentration after production of NO by Eye kNOw (non-steady state):</p>
 
                     <p>4. Calculating NO concentration after production of NO by Eye kNOw (non-steady state):</p>
                     <p style="position: relative;left: 2rem;">After confirming all the parameters, we went on to calculate the NO concentration of each compartment when Eye kNOw senses the change of IOP. We assume that <b>the production rate of Eye kNOw raised j% compared with steady state</b>.</p>
+
                     <p style="position: relative;left: 2rem;"> After confirming all the parameters, we continue to calculate the NO concentration of each compartment when Eye kNOw is activated by elevation of IPTG concentration. We assume that <b>the production rate of Eye kNOw raised j% after activation compared with steady state.</b> Table 2D. Shows the PDEs, initial conditions, and boundary conditions:</p>
                     <p style="position: relative;left: 2rem;">Start from the contact lens compartment. Below are the PDE, initial conditions, and boundary conditions:</p>
+
                     <table class="table table-Border">
                  <p style="position: relative;left: 2rem;">After taking Laplace transform and inverse Laplace transform, we obtained the solutions for each compartment:</p>
+
                          <thead>
 +
                            <tr style="border:3px solid #7E3B40;">
 +
                              <th scope="col" style="font-size:1.2rem; text-align: center;"></th>
 +
                              <th scope="col" style="font-size:1.2rem; text-align: center;">PDE</th>
 +
                              <th scope="col" style="font-size:1.2rem; text-align: center;">Initial Condition</th>
 +
                              <th scope="col" style="font-size:1.2rem; text-align: center;">Boundary Condition</th>
 +
                            </tr>
 +
                          </thead>
 +
                          <tbody>
 +
                            <tr> 
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">Contact Lens</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">
 +
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 +
                  <a style="width:70%"><img src="https://static.igem.org/mediawiki/2020/6/61/T--NCKU_Tainan--Gan1.png" alt="" title="" style="width:100%"></a>
 +
            </figure>
 +
                </div>
 +
                </div>
 +
                </div>
 +
                              </td>
 +
                              <td style="font-size:1.1rem; text-align: center;">
 +
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 +
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 +
                  <a style="width:55%"><img src="https://static.igem.org/mediawiki/2020/c/cf/T--NCKU_Tainan--Gan2.png" alt="" title="" style="width:100%"></a>
 +
            </figure>
 +
                </div>
 +
                </div>
 +
                </div>
 +
                              </td>
 +
                              <td style="font-size:1.1rem; text-align: center;">
 +
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 +
                  <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3" style = "background:white; margin-bottom:0">
 +
                  <a style="width:55%"><img src="https://static.igem.org/mediawiki/2020/e/e6/T--NCKU_Tainan--Gan3.png" alt="" title="" style="width:100%"></a>
 +
            </figure>
 +
                </div>
 +
                </div>
 +
                </div>
 +
                              </td>
 +
                            </tr>
 +
                            <tr> 
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">Cornea</td>
 +
                              <td style="font-size:1.1rem; text-align: center;">
 +
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 +
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 +
                  <a style="width:70%"><img src="https://static.igem.org/mediawiki/2020/f/f6/T--NCKU_Tainan--Gan4.png" alt="" title="" style="width:100%"></a>
 +
            </figure>
 +
                </div>
 +
                </div>
 +
                </div>
 +
                              </td>
 +
                              <td style="font-size:1.1rem; text-align: center;">
 +
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 +
                  <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3" style = "background:white; margin-bottom:0">
 +
                  <a style="width:70%"><img src="https://static.igem.org/mediawiki/2020/5/59/T--NCKU_Tainan--Gan5.png" alt="" title="" style="width:100%"></a>
 +
            </figure>
 +
                </div>
 +
                </div>
 +
                </div>
 +
                              </td>
 +
                              <td style="font-size:1.1rem; text-align: center;">
 +
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 +
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 +
                  <a style="width:70%"><img src="https://static.igem.org/mediawiki/2020/e/e5/T--NCKU_Tainan--Gan6.png" alt="" title="" style="width:100%"></a>
 +
            </figure>
 +
                </div>
 +
                </div>
 +
                </div>
 +
                                <p>  </p>
 +
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 +
                  <a style="width:75%"><img src="https://static.igem.org/mediawiki/2020/9/92/T--NCKU_Tainan--Gan7.png" alt="" title="" style="width:100%"></a>
 +
                                  </figure>
 +
                </div>
 +
                </div>
 +
                </div>
 +
                              </td>
 +
                            </tr>
 +
                            <tr> 
 +
                              <td scope="row" style="font-size:1.1rem; text-align: center;">Aqueous Humor</td>
 +
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 +
                  <a style="width:80%"><img src="https://static.igem.org/mediawiki/2020/9/97/T--NCKU_Tainan--Gan8.png" alt="" title="" style="width:100%"></a>
 +
            </figure>
 +
                </div>
 +
                </div>
 +
                </div>
 +
                              </td>
 +
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 +
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 +
                  <a style="width:80%"><img src="https://static.igem.org/mediawiki/2020/e/e4/T--NCKU_Tainan--Gan9.png" alt="" title="" style="width:100%"></a>
 +
            </figure>
 +
                </div>
 +
                </div>
 +
                </div>
 +
                              </td>
 +
                              <td style="font-size:1.1rem; text-align: center;">
 +
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 +
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 +
                  <a style="width:70%"><img src="https://static.igem.org/mediawiki/2020/7/71/T--NCKU_Tainan--Gan10.png" alt="" title="" style="width:100%"></a>
 +
            </figure>
 +
                </div>
 +
                </div>
 +
                </div>
 +
                                <p>  </p>
 +
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 +
                  <a style="width:75%"><img src="https://static.igem.org/mediawiki/2020/f/f2/T--NCKU_Tainan--Gan11.png" alt="" title="" style="width:100%"></a>
 +
            </figure>
 +
                </div>
 +
                </div>
 +
                </div>
 +
                              </td>
 +
                            </tr>
 +
                          </tbody>
 +
                        </table>
 +
              <figcaption class="caption-design" style="margin-bottom:1rem; text-align: center">Table 2D. PDEs, initial conditions, boundary conditions of each compartment.</figcaption>
 +
                    <p style="position: relative;left: 2rem;"> However, we found the PDEs hard to solve by current methods, including Fourier transform and separation of variables. After lots of effort, we finally solved the PDEs by means of <b>double Laplace transform and inverse double Laplace transform.</b></p>
 +
                  <p style="position: relative;left: 2rem;"> We developed two MATLAB programs, one of them functioning as PDE solver utilizes double Laplace transform, and another one working as Laplace transform estimator for functions which cannot be transformed by current method. These programs are available on the internet with clear documentation, see modeling <a href="https://2020.igem.org/Team:NCKU_Tainan/Software" alt="" target="_blank">software</a> for more information.</p>
 +
                    <p style="position: relative;left: 2rem;"> The dynamic NO concentration profiles can be described by three formulas as follow:</p>
 
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                   <a style="width:60%"><img src="https://static.igem.org/mediawiki/2020/7/7f/T--NCKU_Tainan--model_2_9.png" alt="" title="" style="width:100%"></a>
+
                   <a style="width90%"><img src="https://static.igem.org/mediawiki/2020/7/7f/T--NCKU_Tainan--model_2_9.png" alt="" title="" style="width:100%"></a>
 
               <figcaption class="caption-design">Equation 2.18</figcaption>
 
               <figcaption class="caption-design">Equation 2.18</figcaption>
 
             </figure>
 
             </figure>
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                   <a style="width:60%"><img src="https://static.igem.org/mediawiki/2020/6/63/T--NCKU_Tainan--model_2_14.png" alt="" title="" style="width:100%"></a>
+
                   <a style="width:100%"><img src="https://static.igem.org/mediawiki/2020/a/ae/T--NCKU_Tainan--RevisedAns3.png" alt="" title="" style="width:100%"></a>
 
               <figcaption class="caption-design">Equation 2.19</figcaption>
 
               <figcaption class="caption-design">Equation 2.19</figcaption>
 
             </figure>
 
             </figure>
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                 </div>   
 
                 </div>   
                     <p style="position: relative;left: 2rem;">Notice that there is an undefined parameter r in our solutions. Parameter r is correlated with the interfaces’ properties in our eyes, namely the interface of cornea and contact lens, and the interface of cornea and aqueous humor. Since we cannot do experiments on living animals, we cannot obtain the value of r. In fact, the value of r varies individually, so we just pick some of the r to demonstrate the result.</p>
+
                     <p style="position: relative;left: 2rem;"> Notice that there is an undefined parameter r in our solutions. Parameter r is correlated with the interfaces’ properties in our eyes, namely the interface of cornea and contact lens, and the interface of cornea and aqueous humor. Since we cannot do experiments on living animals, we cannot obtain the value of r. In fact, the value of r varies individually, so we just pick some of the r to demonstrate the result.</p>
                     <p style="position: relative;left: 2rem;">We use MATLAB to plot the final graph of NO distribution in our eyes according to time:</p>
+
                     <p style="position: relative;left: 2rem;"> We use MATLAB to plot the dynamic NO concentration profile of each compartment according to time:</p>
 
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+
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                 <source src="https://static.igem.org/mediawiki/2020/6/62/T--NCKU_Tainan--model_animation.mp4" type="video/mp4" style="width:100%" />
+
                 <source src="https://static.igem.org/mediawiki/2020/6/6a/T--NCKU_Tainan--Non_Steady_Movie_Final.mp4" type="video/mp4" style="width:100%" />
 
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                     <p>This model is a combination of model 1 and model 2, aiming to calculate the time needed from IOP elevation to NO reaching minimum effective concentration</p>
+
                     <p> As a new developing treatment of Glaucoma, it's important to show that the effectiveness of Eye kNOw is better than current treatment. Effectiveness reflects how a drug actually works in the patient's body, which can be evaluated by time and drug amount needed to cause therapeutic effect. Particularly, <b>the minimum concentration of a drug that can cause therapeutic effect is called minimum effective concentration (MEC).</b></p>
                     <p>We assume that contact lens deformation happens immediately after IOP elevation, and [IPTG] elevation happens immediately after contact lens deformation, too. Therefore, the only two steps we should take in concern are how fast will NOS be produced after [IPTG] elevation, and how fast will [NO] at trabecular meshwork be raised to minimum effective concentration (MEC). We’ll discuss them one by one.</p>
+
                    <p> To prove that Eye kNOw can help treat glaucoma more effectively, this model combines model 1, model 2, and experimental data, aiming to precisely quantify Eye kNOw's MEC and the time needed to reach it. Noted that <b>there's no MEC data of NO since current treatment utilizes NO donor instead of NO directly</b>, but estimation can be made by adopting data from current NO prodrug. Here, we adopt data of <b>Latanoprostene Bunod</b> to estimate the MEC of NO, approximately <b>1.182.10<sup>-8</sup>M.</b><sup>[<a href = "#ref17" class = "linklink">17</a>]</sup><sup>[<a href = "#ref18" class = "linklink">18</a>]</sup><sup>[<a href = "#ref19" class = "linklink">19</a>]</sup></p>
                     <p>First, we calculate the speed of NOS production after [IPTG] elevation. By wet team’s results (NO kinetics experiment and IPTG induction experiment), we can calculate the NO production rate according to [IPTG] and time:</p>
+
                     <p> We assume that contact lens deformation happens immediately after IOP elevation, and [IPTG] elevation happens immediately after contact lens deformation, too. Therefore, the only two steps we should concern are <b>how fast will NOS be produced after [IPTG] elevates, and how fast will [NO] at trabecular meshwork reach MEC</b>. We’ll discuss them one by one.</p>
 +
                     <p> First, we calculate the speed of NOS production after [IPTG] elevation. By wet team’s results (<a href="https://2020.igem.org/Team:NCKU_Tainan/Results" alt="" target="_blank">NO kinetics experiment and IPTG induction experiment</a>), we can calculate the NO production rate according to [IPTG] and time:</p>
 
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                   <a style="width:60%"><img src="https://static.igem.org/mediawiki/2020/3/34/T--NCKU_Tainan--model_3_1.png" alt="" title="" style="width:100%"></a>
+
                   <a style="width:90%"><img src="https://static.igem.org/mediawiki/2020/3/34/T--NCKU_Tainan--model_3_1.png" alt="" title="" style="width:100%"></a>
 
               <figcaption class="caption-design">Equation 3.1</figcaption>
 
               <figcaption class="caption-design">Equation 3.1</figcaption>
 
             </figure>
 
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                     <p>Notice that the unit of equation 3.1 is nmol/hr, and the reaction volume is 60uL. Since the volume of contact lens’ chamber is 4.4uL, the production rate in Eye kNOw with certain concentration of IPTG can be written as below:</p>
+
                     <p> Notice that the unit of Equation 3.1 is nmol/hr, and the reaction volume of the experiments is 60uL. Since the volume of Eye kNOw’s chamber is 4.4uL, the production rate in Eye kNOw can be written as below: </p>
 
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                   <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3">
 
                   <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3">
                   <a style="width:60%"><img src="https://static.igem.org/mediawiki/2020/d/d8/T--NCKU_Tainan--model_3_2.png" alt="" title="" style="width:100%"></a>
+
                   <a style="width:90%"><img src="https://static.igem.org/mediawiki/2020/d/d8/T--NCKU_Tainan--model_3_2.png" alt="" title="" style="width:100%"></a>
 
               <figcaption class="caption-design">Equation 3.2</figcaption>
 
               <figcaption class="caption-design">Equation 3.2</figcaption>
 
             </figure>
 
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                     <p>Notice that the production rate depends on not only the efficiency of NOS, but also the concentration of NOS in the solution. We set IOP = 15mmHg, [IPTG] = 0.1mM as initial conditions. By model 2, the initial production rate should be 7umol/s to maintain steady state. Therefore, by elevating bacteria concentration in Eye kNOw, we can rewrite equation as below:</p>
+
                     <p> Notice that the production rate depends on not only the efficiency of NOS, but also the concentration of NOS in the solution. <b>We set IOP = 15mmHg, [IPTG] = 0.1mM as initial conditions.</b> By model 2, the <b>initial production rate should be 7.10<sup>-6</sup> mol/s to maintain steady state.</b> Therefore, by <b>elevating bacteria concentration in Eye kNOw</b>, the initial production rate of NOS in Eye kNOw can be written as Equation 3.3:</p>
 
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                   <a style="width:60%"><img src="https://static.igem.org/mediawiki/2020/a/a1/T--NCKU_Tainan--model_3_3.png" alt="" title="" style="width:100%"></a>
+
                   <a style="width:90%"><img src="https://static.igem.org/mediawiki/2020/a/a1/T--NCKU_Tainan--model_3_3.png" alt="" title="" style="width:100%"></a>
 
               <figcaption class="caption-design">Equation 3.3</figcaption>
 
               <figcaption class="caption-design">Equation 3.3</figcaption>
 
             </figure>
 
             </figure>
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                 </div>
 
                 </div>
 
                 </div>   
 
                 </div>   
                     <p>Since in initial state, NOS has already been made for a long time, so we can neglect the time-related term in equation 3.2. Assume that patient’s IOP raised i mmHg, we can calculate the production rate of NO by Eye kNOw after IPTG induction as below:</p>
+
                     <p> Since in initial state, NOS has already been made, so we can neglect the time-related term in Equation 3.2. <b>Assume that patient’s IOP raises i mmHg</b>, the production rate of NOS can be written as below:</p>
                     <P>Second, we calculate the time needed to reach MEC of NO at trabecular meshwork. We use MATLAB to plot out the concentration change of NO at trabecular meshwork according to time after induction. Below are the results:</p>  
+
                    <div class="container-fluid p-0">
 +
                <div class="row no-gutters">
 +
                <div class="col-lg ">
 +
                  <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3">
 +
                  <a style="width:90%"><img src="https://static.igem.org/mediawiki/2020/8/82/T--NCKU_Tainan--Final_Func_3_3.png" alt="" title="" style="width:100%"></a>
 +
              <figcaption class="caption-design">Equation 3.4</figcaption>
 +
            </figure>
 +
                </div>
 +
                </div>
 +
                </div>
 +
                     <P> Second, we calculate the time needed for Eye kNOw to raise the [NO] at the trabecular meshwork to MEC once the IOP is elevated. We use MATLAB to plot out the concentration change of NO at trabecular meshwork according to time after induction. Below are the results:</p>  
 
                     <div class="container-fluid p-0">
 
                     <div class="container-fluid p-0">
 
                 <div class="row no-gutters">
 
                 <div class="row no-gutters">
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                   <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3">
 
                   <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3">
 
                   <a style="width:60%"><img src="https://static.igem.org/mediawiki/2020/8/82/T--NCKU_Tainan--Model_NO_TM_big1.png" alt="" title="" style="width:100%"></a>
 
                   <a style="width:60%"><img src="https://static.igem.org/mediawiki/2020/8/82/T--NCKU_Tainan--Model_NO_TM_big1.png" alt="" title="" style="width:100%"></a>
               <figcaption class="caption-design">Fig. 3A. NO concentration at trabecular meshwork in different volume change-large time scale</figcaption>
+
               <figcaption class="caption-design">Fig. 3A. NO concentration at trabecular meshwork in different volume change-large time scale.</figcaption>
 
             </figure>
 
             </figure>
 
                 </div>
 
                 </div>
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                   <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3">
 
                   <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3">
 
                   <a style="width:60%"><img src="https://static.igem.org/mediawiki/2020/c/c9/T--NCKU_Tainan--Model_NO_TM.png" alt="" title="" style="width:100%"></a>
 
                   <a style="width:60%"><img src="https://static.igem.org/mediawiki/2020/c/c9/T--NCKU_Tainan--Model_NO_TM.png" alt="" title="" style="width:100%"></a>
               <figcaption class="caption-design">Fig. 3B. NO concentration at trabecular meshwork in different volume change-small time scale</figcaption>
+
               <figcaption class="caption-design">Fig. 3B. NO concentration at trabecular meshwork in different volume change-small time scale.</figcaption>
 
             </figure>
 
             </figure>
 
                 </div>
 
                 </div>
 
                 </div>
 
                 </div>
 
                 </div>   
 
                 </div>   
                     <p>We can obtain that time needed for Eye kNOw to raise trabecular meshwork’s NO concentration up to MEC is very short, which theoretically proves that Eye kNOw can treat glaucoma with high efficiency and accuracy.</p>
+
                     <p> We can obtain that <b>time needed for Eye kNOw to raise trabecular meshwork’s NO concentration up to MEC is very short</b>, which theoretically proves that Eye kNOw can treat glaucoma with high efficiency and accuracy.</p>
 
                   </div>
 
                   </div>
 
               </div>
 
               </div>
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             <h2>References</h2>
 
             <h2>References</h2>
 
               <ol>
 
               <ol>
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                 <li id="ref1">Chen G-Z, Chan I-S, Leung LKK, Lam DCC. Soft wearable contact lens sensor for continuous intraocular pressure monitoring. <i>Medical Engineering & Physics.</i> 2014;36(9):1134-1139.</li>
                 <li id="ref2">Berest P, Nguyen-Minh D. Response of a spherical cavity in an elastic viscoplastic medium under a variable internal pressure. International Journal of Solids and Structures.</li>
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                 <li id="ref2">Berest P, Nguyen-Minh D. Response of a spherical cavity in an elastic viscoplastic medium under a variable internal pressure. <i>International Journal of Solids and Structures.</i></li>
 
                 <li id="ref3">Sanchez I, Martin R, Ussa F, Fernandez-Bueno I. The parameters of the porcine eyeball. Graefe’s Archive for Clinical and Experimental Ophthalmology. 2011;249(4):475-482.</li>
 
                 <li id="ref3">Sanchez I, Martin R, Ussa F, Fernandez-Bueno I. The parameters of the porcine eyeball. Graefe’s Archive for Clinical and Experimental Ophthalmology. 2011;249(4):475-482.</li>
                 <li id="ref4">Dupps WJ, Netto MV, Herekar S, Krueger RR. Surface wave elastometry of the cornea in porcine and human donor eyes. Journal of refractive surgery (Thorofare, NJ : 1995). 2007;23(1):66-75. Accessed October 24, 2020.</li>
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                 <li id="ref4">Dupps WJ, Netto MV, Herekar S, Krueger RR. Surface wave elastometry of the cornea in porcine and human donor eyes. <i>Journal of refractive surgery</i> (Thorofare, NJ : 1995). 2007;23(1):66-75. Accessed October 24, 2020.</li>
                 <li id="ref5">Cerviño A, Gonzalez-Meijome JM, Ferrer-Blasco T, Garcia-Resua C, Montes-Mico R, Parafita M. Determination of corneal volume from anterior topography and topographic pachymetry: application to healthy and keratoconic eyes. Ophthalmic and Physiological Optics. 2009;29(6):652-660.</li>
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                 <li id="ref6">Ford PC, Wink DA, Stanbury DM. Autoxidation kinetics of aqueous nitric oxide. FEBS Letters. 1993;326(1-3):1-3.</li>
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                 <li id="ref5">Ford PC, Wink DA, Stanbury DM. Autoxidation kinetics of aqueous nitric oxide. FEBS Letters. 1993;326(1-3):1-3.</li>
                 <li id="ref7">MGoel M. Aqueous Humor Dynamics: A Review~!2010-03-03~!2010-06-17~!2010-09-02~! The Open Ophthalmology Journal. 2010;4(1):52-59.</li>
+
                <li id="ref6">Ghanem AA, Elewa AM, Arafa LF. Endothelin-1 and Nitric Oxide Levels in Patients with Glaucoma. Ophthalmic Research. 2011;46(2):98-102.</li>
              <li id="ref8">Larrea X, Bu¨chler P. A Transient Diffusion Model of the Cornea for the Assessment of Oxygen Diffusivity and Consumption. Investigative Opthalmology & Visual Science. 2009;50(3):1076.</li>
+
 
                 <li id="ref9">Cunanan C. Ophthalmologic Applications: Glaucoma Drains and Implants. Biomaterials Science. Published online 2013:940-946.</li>
+
                 <li id="ref7">Forstermann U, Sessa WC. Nitric oxide synthases: regulation and function. European Heart Journal. 2011;33(7):829-837. </li>
            <li id="ref10">Pozuelo J, Compañ V, Gonzalez-Meijome JM, Mollá S. Oxygen and ionic transport in hydrogel and silicone-hydrogel contact lens materials: An experimental and... ResearchGate. Published February 2014. Accessed October 25, 2020.</li>
+
 
                <li id="ref11">
+
                  
                <li id="ref12">
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              <li id="ref8"> Goel M. Aqueous Humor Dynamics: A Review~!2010-03-03~!2010-06-17~!2010-09-02~! The Open Ophthalmology Journal. 2010;4(1):52-59. </li>
                 <li id="ref13">
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                <li id="ref14">Cerviño A, Gonzalez-Meijome JM, Ferrer-Blasco T, Garcia-Resua C, Montes-Mico R, Parafita M. Determination of corneal volume from anterior topography and topographic pachymetry: application to healthy and keratoconic eyes. Ophthalmic and Physiological Optics. 2009;29(6):652-660.</li>
+
                 <li id="ref9">Pozuelo J, Compañ V, Gonzalez-Meijome JM, Mollá S. Oxygen and ionic transport in hydrogel and silicone-hydrogel contact lens materials: An experimental and... ResearchGate. Published February 2014. Accessed October 25, 2020. </li>
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                <li id="ref16">
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            <li id="ref10">Larrea X, Bu¨chler P. A Transient Diffusion Model of the Cornea for the Assessment of Oxygen Diffusivity and Consumption. Investigative Opthalmology & Visual Science. 2009;50(3):1076.</li>
                 <li id="ref17">Classify corneas simply as average, thin or thick. Healio.com. Published 2020. Accessed October 25, 2020.</li>
+
                 <li id="ref11">Borland C, Moggridge G, Patel R, Patel S, Zhu Q, Vuylsteke A. Permeability and diffusivity of nitric oxide in human plasma and red cells. Nitric Oxide. 2018;78:51-59. </li>
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              <li id="ref12">Cerviño A, Gonzalez-Meijome JM, Ferrer-Blasco T, Garcia-Resua C, Montes-Mico R, Parafita M. Determination of corneal volume from anterior topography and topographic pachymetry: application to healthy and keratoconic eyes. Ophthalmic and Physiological Optics. 2009;29(6):652-660.</li>
 +
 
 +
                <li id="ref13">Cunanan C. Ophthalmologic Applications: Glaucoma Drains and Implants. Biomaterials Science. Published online 2013:940-946.</li>
 +
         
 +
                 <li id="ref14">Classify corneas simply as average, thin or thick. Healio.com. Published 2020. Accessed October 25, 2020.</li>
 +
                <li id="ref15">Mashige KP. A review of corneal diameter, curvature and  thickness values and influencing factors*. African Vision and Eye Health. 2013;72(4).</li>
 +
 
 +
                <li id="ref16">Huang G. Anterior Chamber Depth, Iridocorneal Angle Width, and Intraocular Pressure Changes After Phacoemulsification. Archives of Ophthalmology. 2011;129(10):1283. </li>
 +
                <li id="ref17">Vyzulta (Latanoprostene Bunod) Ophthalmic Solution. Fda.gov. Published 2017. Accessed October 27, 2020.</li>
 +
 
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 +
                 <li id="ref18">Addis VM, Miller E. Latanoprostene bunod ophthalmic solution 0.024% in the treatment of open-angle glaucoma: design, development, and place in therapy. Clinical Ophthalmology. 2018;Volume 12:2649-2657.
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</li>
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                <li id="ref19">Karki R, Meena M, Prakash T, Rajeswari T, Goli D, Kumar S. Reduction in drop size of ophthalmic topical drop preparations and the impact of treatment. Journal of Advanced Pharmaceutical Technology & Research. 2011;2(3):192.</li>
 +
 
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Latest revision as of 03:34, 28 October 2020


Model

Surfactant between Experimental Data and Theories

Overview

There are three critical parts in our project that crucially affect our final design of Eye kNOw: IOP-elevation induced contact lens deformation, NO diffusion efficiency in ocular system, and seeking for higher effectiveness. Experiment alone is not enough to provide the answers. To build a bridge between experimental data and scientific theories, we built three models that fully describe the whole working process of Eye kNOw:

  1. Contact Lens Deformation Model: Provide quantitative result of contact lens deformation caused by IOP elevation.

  2. NO Ocular Diffusion Model: Obtain the initial parameters needed for Eye kNOw design, and describe NO ocular diffusion with quantitative simulation.

  3. NO Ocular Diffusion Model: Utilize model 1, model 2 and experimental data to precisely calculate the effectiveness of Eye kNOw.

Background

This year, We aim to provide a real-time treatment that can release ocular hypotensive agents (nitric oxide) according to patients’ IOP in a contact lens system—Eye kNOw. Eye kNOw contains a designed chamber filled with L-arginine, IPTG, and our engineered bacteria. Here are the three main principles we used to design Eye kNOw:

  1. NOS produced by our engineered bacteria turns L-arginine into NO.

  2. Different concentrations of IPTG induces different production rates of NOS.

  3. IOP elevation causes corneal radius of curvature to change, leading to deformation of Eye kNOw.

Below are the workflows of Eye kNOw:

  1. IOP elevates, causing the cornea's radius of curvature to change.

  2. Chamber’s volume decreased due to the deformation of the cornea.

  3. The semipermeable chamber only allows water and gas to pass. Therefore, the concentration of IPTG inside the chamber elevates.

  4. Elevated IPTG leads to higher production rate of NOS by engineered bacteria.

  5. The more NOS produced, the more L-arginine turned into NO.

  6. More NO is released into the eyes, relaxing trabecular meshwork.

  7. Finally, IOP will be lowered to normal level.

We establish three models to simulate the whole process above: contact lens deformation model and NO ocular diffusion model. Model 3 combines model 1, model 2 and experimental data, which precisely calculate the effectiveness of Eye kNOw.

Fig. 0A. Eye kNOw workflow chart.

Our goals

  1. To build a model that describes the deformation of contact lens quantitatively.

  2. To establish a model that simulates nitric oxide ocular diffusion system.

  3. To precisely calculate the effectiveness of Eye kNOw by taking both experimental data and model theories into consideration.


Model 1: Deformation of Contact Lens

This model is used to describe the deformation of the contact lens under varying intraocular pressure (IOP) with quantitative estimation. Research suggested that the radius of cornea curvature increases linearly with the increment of IOP[1]. However, the pressure exerted on the contact lens while being worn is not fully studied, not to mention the volume difference of contact lens with respect to different IOP. Therefore, to build this model from scratch, we first made the following assumptions:

  1. The contact lens fits on the cornea perfectly no matter it deforms or not.

  2. The contact lens remains in the shape of a sphere during the whole process of deformation.

  3. Deformation of the contact lens is not changing with time, which is a static model.

Fig. 1A. Cross-section diagram of pressure balance.

Table 1A shows the parameters of cornea that will be used in our model.

Description Value
ECornea Elastic modulus of the cornea 15.3 mPa
tCornea Thickness of the cornea 0.666 mm
RCornea_0 Corneal radius of curvature 8.45 mm
Table 1A. Parameters of cornea used in model 1[2][3].

First, we need to obtain the relationship between IOP and radius Eye kNOw. Considering the force equilibrium equation between the pressure of fluid and the membrane (cornea) in the section, we obtain Equation 1.1:

Equation 1.1

According to Hooke’s Law, we have Equation 1.2:

Equation 1.2

Under proportional limit, the radius difference (ΔR), is given by Equation 1.3:

Equation 1.3

From the equations listed above, we obtain Equation 1.4:

Equation 1.4

For a thick membrane, which means the thickness of the membrane is too large to be neglected in comparison to the radius. Thus, we have a constant term that is related to the poisson ratio, ν, in the Equation 1.5[1][4].

Equation 1.5

Notice that the p in Equation 1.4 and Equation 1.5 represents the pressure difference with respect to the initial pressure instead of the pressure itself. We assumed the initial IOP to be 10 mmHg. By Equation 1.5, we predict the relation between IOP and the radius difference, or the strain, is linear, which fits the results of digital image correlation experiment. (See Proof of concept: step 1 )

Second, we calculate the relationship between IOP and volume difference of the chamber in Eye kNOw. Table 1B lists all the parameters of Eye kNOw used in the following calculation.

Description Value
REye_kNOw_0 Inner radius of curvature 8.2 mm
EEye_kNOw Elastic modulus of Eye kNOw 3.106 dyne/mm2
d Diameter of Eye kNOw 14 mm
d1 Inner diameters of the chamber 10 mm
d2 Outer diameters of the chamber 12 mm
tEye_kNOw Thickness of Eye kNOw 2.10-4 mm
Table 1B. Parameters of Eye kNOw used in model 1.

The volume of the chamber in Eye kNOw , which is a ring-like compartment, is calculated by the same method of the volume of revolution in calculus. After calculation, the volume of the chamber equals 4.4 cubic millimeters initially.

Fig. 1B. Structure design of Eye kNOw.

The volume difference is given by the elongation of the part above the compartment in meridional direction, which is given by the formula list below:

Equation 1.6

while

Equation 1.7
Equation 1.8

The ratio of volume difference is given by Equation 1.9:

Equation 1.9

After calculation with the parameters listed above, the result is approximately 1% when the IOP has an increment of 1 mmHg.


Model 2: Nitric Oxide Diffusion Model

Overview

Eye is a complicated organ consisting of various tissues with different physical properties. In most of the ocular delivery models, they consider the whole eye as one compartment since their drugs are stable and large enough that the difference of tissue characteristics can be ignored. However, we use NO as our drug, which is small and unstable. Thus, we need to set up a new model to simulate NO ocular delivery system.

This model divides the eye system into three different compartment according to the tissues differences, and provide quantitative NO concentration profiles dynamically. This model can be applied on ocular drug delivery system of other small and unstable drugs.

Background

Fig. 2A. Eye structure of human.

Eye structure can be divided into three main compartments: cornea, anterior chamber, and posterior chamber. Target site of NO is trabecular meshwork, which is located at the posterior angle of anterior chamber. We simplify the eye structures into one dimension as below:

Fig. 2B. One dimensional schematic graph for NO ocular delivery model.

Since the tissue characteristics of the three compartments varies a lot, we need to simulate the behavior of NO in them separately, by different partial differential equations (PDEs).

Model

First, we establish the initial state of NO distribution in the eye before Eye kNOw being triggered. Second, we build the dynamic NO concentration profile according to time and distance after Eye kNOw activation. We use several partial differential equations(PDEs) to describe the behavior of NO. Table 2A lists all the abbreviations used in PDEs.

Full Name Unit
C Concentration of NO M
x distance (from outside of the eye to inside) cm
t time (t=0 resembles the time when Eye kNOw start to produce NO) s
D Diffusion coefficient cm2/s
R Flow rate of liquid L/s
k Degradation coefficient of NO M-2/s
Pro Production rate of NO in the compartment mol/s
V Volume of the compartment L
Table 2A. Abbreviations and variables used in PDEs.

1. Setting up PDEs:

PDEs take the factors that may affect the concentration of NO into consideration to describe the behavior of NO. Factors are listed below:

(1) Degradation

The two main factors that will cause degradation of nitric oxide in the human body are hemoglobin and oxygen. Hemoglobin doesn’t exist in the eye system, thus we only need to consider oxygen as the factor causing NO degradation.

According to current studies, the formula can be written as below:

Equation 2.1

(2) Diffusion

By Fick's second law, the diffusion of chemicals can be described as below:

Equation 2.2

(3) Endogenous production

Glaucoma patients’ aqueous humor has an initial average concentration of NO around 53.4uM[7], which is maintained by endogenous NO produced by NO synthase (NOS). There are three different types of NOS in human eyes: e-NOS, n-NOS, and i-NOS[7].

e-NOS and n-NOS work constantly, which are expressed on iris, cornea, vascular endothelium, etc. i-NOS only works when ocular inflammation happens, which is not a common symptom for glaucoma, thus we can ignore it. We assume that these NOS produce NO in a constant rate, so the formula can be written as below:

Equation 2.3

(4) Convection

There’s a flow of aqueous humor in the anterior chamber, which is 2.4 uL/min[8]. Convection will affect the distribution of nitric oxide, which can be written as below:

Equation 2.4

Combining the factors listed above, the PDE for describing the distribution of NO can be written as below:

Equation 2.5

Equation 2.5 is a heterogeneous PDE, which is very hard to solve. We need to simplify Equation 2.5 into homogeneous form for further calculation.

First, since the concentration of oxygen can be maintained by oxygen in the air( oxygen in the air can dissolve and penetrate into our eyes), we can set k[Oxygen] as a constant.

Second, we want to simplify the C2 term into C. In order to prevent over-estimation of nitric oxide concentration, we change C2 into Cmax.C, where Cmax is the max concentration of nitric oxide in the compartment. Since Cmax.C is always larger than (or same as) C2, we can make sure that we won’t over-estimate the concentration of nitric oxide. Since Cmax is a constant, we can consider constant B = k[Oxygen]Cmax.

Therefore, the modified form of PDE will be:

Equation 2.6

2. Obtaining parameters from current studies:

Parameters used are listed in table 2B. We collected them from current studies.

Contact Lens Cornea Aqueous Humor Unit
D 1.8.10-6[9] 2.81.10-5[10] 3.10-5[11] cm2/s
B ? ? ? 1/s
R 0 0 4.10-8[8] L/s
V 2.77.10-5 1.6.10-5[12] 2.5.10-4[13] L
Pro ? ? ? mol/s
Initial Average [NO] ? ? 5.34.10-5[6] M
Maximum Distance 0.02 0.055[14] 1.122[15][16] cm
Table 2B. Parameters of Eye kNOw used in model 2.

We're still lacking some of the parameters. We can estimate them by solving the steady state of NO distribution.

3. Calculating steady state:

We start from the contact lens compartment. When in steady state, NO concentration won't change by time. Thus, Equation 2.6 can be written as below:

Equation 2.7

Where subscript 1 stands for the parameters and variables of the contact lens compartment. By solving Equation 2.7, we can get the solution of C1 in steady state:

Equation 2.8

We use the approximation:

Equation 2.9

Thus turning Equation 2.8 into linear form:

Equation 2.10

Since C1(0)=0 (one of the boundary conditions), the final form of C1 in steady state can be written as below:

Equation 2.11

By the same method, we can simplify the concentration of NO in cornea and aqueous humor compartments as a linear formula of x. To simplify the formulas, we set the outer surface of every compartment as the starting position of that compartment. For example, for cornea compartment, the interface of cornea and contact lens is considered the starting position, namely x=0.

As for the boundary conditions, the interfaces should have only one concentration. For example, the formula of C1 at x=0.02 should have the same value as C2 at x=0. Combining these conditions, we can get the function of C2 and C3:

Equation 2.12
Equation 2.13

Now we need to solve the slope of NO concentration, namely a1, a2, a3. Here, we use Fick’s first law as boundary conditions, that is at the interfaces, input of NO from one compartment should be the same as output of another compartment. For example, at the interface of cornea and contact lens, input of NO to contact lens should be the same as output of NO from cornea.

The input of NO to contact lens can be written as below, according to Fick’s first law:

Equation 2.14

The output of NO from cornea can be written as below:

Equation 2.15

Applying the solution we’d obtained, we can get the relationship of slopes of each compartment:

Equation 2.16

Therefore, we can draw the steady-state-graph of NO distribution in the eye:

Fig. 2C. NO Concentration Profile in Steady State. A stands for contact lens compartment, B stands for cornea comparment, C stands for aqueous humor compartment.

Now, there are just B and Pro not determined yet. Recall that B = k[Oxygen]Cmax, we can calculate them. As for Pro, we can calculate each compartment’s total input and output, they should be the same since we’re dealing with steady state. After calculations, Table 2B can be filled completely as Table 2C.

Contact Lens Cornea Aqueous Humor Unit
D 1.8.10-6 2.81.10-5 3.10-5 cm2/s
B 2.84.10-2 1.03.10-2 1.566.10-2 1/s
R 0 0 4.10-8 L/s
V 2.77.10-5 1.6.10-5 2.5.10-4 L
Pro 7.10-6 1.52.10-5 1.239.10-3 mol/s
Initial Average [NO] C1 = 933.7x C2 = 59.818x + 18.674 C3 = 56.063x + 21.964 uM
Maximum Distance 0.02 0.055 1.122 cm
Table 2C. Complete table of parameters used for model 2.

4. Calculating NO concentration after production of NO by Eye kNOw (non-steady state):

After confirming all the parameters, we continue to calculate the NO concentration of each compartment when Eye kNOw is activated by elevation of IPTG concentration. We assume that the production rate of Eye kNOw raised j% after activation compared with steady state. Table 2D. Shows the PDEs, initial conditions, and boundary conditions:

PDE Initial Condition Boundary Condition
Contact Lens
Cornea

Aqueous Humor

Table 2D. PDEs, initial conditions, boundary conditions of each compartment.

However, we found the PDEs hard to solve by current methods, including Fourier transform and separation of variables. After lots of effort, we finally solved the PDEs by means of double Laplace transform and inverse double Laplace transform.

We developed two MATLAB programs, one of them functioning as PDE solver utilizes double Laplace transform, and another one working as Laplace transform estimator for functions which cannot be transformed by current method. These programs are available on the internet with clear documentation, see modeling software for more information.

The dynamic NO concentration profiles can be described by three formulas as follow:

Equation 2.17
Equation 2.18
Equation 2.19

Notice that there is an undefined parameter r in our solutions. Parameter r is correlated with the interfaces’ properties in our eyes, namely the interface of cornea and contact lens, and the interface of cornea and aqueous humor. Since we cannot do experiments on living animals, we cannot obtain the value of r. In fact, the value of r varies individually, so we just pick some of the r to demonstrate the result.

We use MATLAB to plot the dynamic NO concentration profile of each compartment according to time:

Video 1. NO Distribution. (r=0.0156 j=20)

Model 3: Effectiveness of Eye kNOw

As a new developing treatment of Glaucoma, it's important to show that the effectiveness of Eye kNOw is better than current treatment. Effectiveness reflects how a drug actually works in the patient's body, which can be evaluated by time and drug amount needed to cause therapeutic effect. Particularly, the minimum concentration of a drug that can cause therapeutic effect is called minimum effective concentration (MEC).

To prove that Eye kNOw can help treat glaucoma more effectively, this model combines model 1, model 2, and experimental data, aiming to precisely quantify Eye kNOw's MEC and the time needed to reach it. Noted that there's no MEC data of NO since current treatment utilizes NO donor instead of NO directly, but estimation can be made by adopting data from current NO prodrug. Here, we adopt data of Latanoprostene Bunod to estimate the MEC of NO, approximately 1.182.10-8M.[17][18][19]

We assume that contact lens deformation happens immediately after IOP elevation, and [IPTG] elevation happens immediately after contact lens deformation, too. Therefore, the only two steps we should concern are how fast will NOS be produced after [IPTG] elevates, and how fast will [NO] at trabecular meshwork reach MEC. We’ll discuss them one by one.

First, we calculate the speed of NOS production after [IPTG] elevation. By wet team’s results (NO kinetics experiment and IPTG induction experiment), we can calculate the NO production rate according to [IPTG] and time:

Equation 3.1

Notice that the unit of Equation 3.1 is nmol/hr, and the reaction volume of the experiments is 60uL. Since the volume of Eye kNOw’s chamber is 4.4uL, the production rate in Eye kNOw can be written as below:

Equation 3.2

Notice that the production rate depends on not only the efficiency of NOS, but also the concentration of NOS in the solution. We set IOP = 15mmHg, [IPTG] = 0.1mM as initial conditions. By model 2, the initial production rate should be 7.10-6 mol/s to maintain steady state. Therefore, by elevating bacteria concentration in Eye kNOw, the initial production rate of NOS in Eye kNOw can be written as Equation 3.3:

Equation 3.3

Since in initial state, NOS has already been made, so we can neglect the time-related term in Equation 3.2. Assume that patient’s IOP raises i mmHg, the production rate of NOS can be written as below:

Equation 3.4

Second, we calculate the time needed for Eye kNOw to raise the [NO] at the trabecular meshwork to MEC once the IOP is elevated. We use MATLAB to plot out the concentration change of NO at trabecular meshwork according to time after induction. Below are the results:

Fig. 3A. NO concentration at trabecular meshwork in different volume change-large time scale.
Fig. 3B. NO concentration at trabecular meshwork in different volume change-small time scale.

We can obtain that time needed for Eye kNOw to raise trabecular meshwork’s NO concentration up to MEC is very short, which theoretically proves that Eye kNOw can treat glaucoma with high efficiency and accuracy.



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