Difference between revisions of "Team:Tec-Chihuahua/Modeling"

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         <section class="text-center">
 
         <section class="text-center">
             <div class="container parts-description">
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             <div class="container modeling-content">
                 <h1 class="arrow">Biobricks</h1>
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                 <h2>Introduction</h2>
                 <p>In our project, we expect that plasmid DNA interacting with a Carbon nanotube will be internalized into the cell and then expressed, this is a system we call “Carbon Carriers.This construction allows us to confirm the success of the experiment: if the resulting cell turns out to be fluorescent, we can confirm in a simple and efficient way the expression of our gene and the success of our    experiment.</p>
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                 <p>Computational chemistry and molecular modeling are considered as prediction tools that give explanation to phenomena and chemical reactions, using approaches that are based on the laws of quantum mechanics and classical mechanics. In this particular case, we could infer whether a reaction may be given spontaneously by conducting experimentation. This minimizes the use of reagents and the generation of hazardous waste.</p>
<p>Our goal is to prove that carbon nanoparticles can be a novel and efficient method for celltransformation and transfection in models such as E.coli and Bos taurus Oocites.</p>
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                <p>The methodology used is based on the electron density of atoms, that’s why only a representative part of the carbon nanotube (CNT) is used, this part contains a carboxyl group which interact directly with the carbodiimide EDC forming an unstable compound with a group which will react with the poliethylamide later, therefore, that’s why only one monomer is used.
                  
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</p>
                <div class="col-md-12">
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                 <h2>Methodology</h2>
                    <h2>BBa_K747096</h2>
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                <p>The theoretical study was carried out using the theory of density functional (DFT) implemented in the Gaussian 09 package, review A.02 and using the graphical display Gauss View 5.0. to make the calculations we use the B3LYP functional and the 6-31G basis set (d). Structures optimizations were conducted using water as the solvent with IEFPCM model. The energy of formation of the amidation reaction was obtained. The optimized structures with their respective energy are in Table 1</p>
                    <div class="col-md-4">
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                 <img class="modeling-equation" src="img/Modeling/table1.PNG" >
                        <img class="biobrick-image" src="img/Biobricks/PartBBa_K747096.png" >
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                <h2>Results</h2>
                    </div>
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                <p>The equation to determinate the energy of reaction is:</p>
                    <div class="col-md-8">
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                <img class="modeling-equation" src="img/Modeling/mod1.png" >
                        <b><p>Aim:</p></b>
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                <p>With thermal correction:</p>
                        <p>The CMV is a promoter, we selected this part for it being the only option as a mammalian promoter. Also, as noted in the iGEM wikis, this is the sole mammalian promoter and is actually part of a lacl-gene. Also, as described in the wiki, we chose this promoter because of its ability to induce fluorescence in bacteria, as accomplished by DTU Denmark.</p>
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                 <img class="modeling-equation" src="img/Modeling/mod2.png" >
 
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                <p>With thermal correction:</p>
                        <p>For our project, since we were working with both mammal and bacterial models, we decided to
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                <img class="modeling-equation" src="img/Modeling/mod3.png" >
 
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                <p>With thermal correction:</p>
include this promoter.</p>
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                <img class="modeling-equation" src="img/Modeling/mod4.png" >
                    </div>
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                <p>The results indicate that the reaction is going to be spontaneous.</p>
                 </div>
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                <h2>Recomendations</h2>
                <div class="col-md-12">
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                <p>It is feasible to establish an equation where the constant value of the reactants and products are set and they are not altered when ethyl-amide units increase or if is necessary to change the molecule that will bind to the CNT.</p>
                    <h2>BBa_E0040</h2>
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                <p>The equations is:</p>
                    <div class="col-md-8">
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                <img class="modeling-equation" src="img/Modeling/mod5.png" >
                        <p>This part codes for a green fluorescent protein. Like other standard parts, it comes with the iGEM prefix and Suffix for a cut-ligation sites with other standard parts the GFP site and a CamR site.</p>
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                        <b><p>Aim:</p></b>
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                        <p>An standard backbone used for biobricks, we decided on its use for its simplicity and high-expression We have selected this backbone part since it’s a high-copy plasmid, which suits our needs. in conjunction with the other selected parts (CMV-promoter and BBa_E0040 Green fluorescent protein) we expect to create a part which will ultimately work as an efficient</p>
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                    </div>
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                    <div class="col-md-4">
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                        <img class="biobrick-image" src="img/Biobricks/PartBBa_E0040.png" >
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                    </div>
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                </div>
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                 <div class="col-md-12">
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                    <h2>pSB1T3</h2>
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                    <div class="col-md-12">
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                        <div class="col-md-4">
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                            <img class="biobrick-image" src="img/Biobricks/pSB1T3.png" >
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                        </div>
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                        <div class="col-md-8">
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                                <img class="biobrick-image" src="img/Biobricks/pSB1T3b.png" >
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+
                        </div>
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                    </div>
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                    <div class="col-md-12">
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                        <p>This is the map of the plasmid backbone with both suffix and prefix, lacl site and tetracycline resistance.</p>
+
                        <b><p>Aim:</p></b>
+
                        <p>An standard backbone used for biobricks, we decided on its use for its simplicity and high-expression. We have selected this backbone part since it’s a high-copy plasmid, which suits our needs. in conjunction with the other selected parts (CMV-promoter and BBa_E0040 Green fluorescent protein) we expect to create a part which will ultimately work as an efficient</p>
+
                    </div>
+
                </div>
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 +
                <p>Conditions:</p>
 +
                <p>To give the reaction spontaneously, it requires that the constant value always presents a negative amount bigger than the sum of the variable values.</p>
 +
                <img    class="modeling-equation" src="img/Modeling/mod5.png" >
 
             </div>
 
             </div>
 
         </section>
 
         </section>

Revision as of 08:19, 17 September 2015

Carbon carriers Carbon carriers

Modeling

Introduction

Computational chemistry and molecular modeling are considered as prediction tools that give explanation to phenomena and chemical reactions, using approaches that are based on the laws of quantum mechanics and classical mechanics. In this particular case, we could infer whether a reaction may be given spontaneously by conducting experimentation. This minimizes the use of reagents and the generation of hazardous waste.

The methodology used is based on the electron density of atoms, that’s why only a representative part of the carbon nanotube (CNT) is used, this part contains a carboxyl group which interact directly with the carbodiimide EDC forming an unstable compound with a group which will react with the poliethylamide later, therefore, that’s why only one monomer is used.

Methodology

The theoretical study was carried out using the theory of density functional (DFT) implemented in the Gaussian 09 package, review A.02 and using the graphical display Gauss View 5.0. to make the calculations we use the B3LYP functional and the 6-31G basis set (d). Structures optimizations were conducted using water as the solvent with IEFPCM model. The energy of formation of the amidation reaction was obtained. The optimized structures with their respective energy are in Table 1

Results

The equation to determinate the energy of reaction is:

With thermal correction:

With thermal correction:

With thermal correction:

The results indicate that the reaction is going to be spontaneous.

Recomendations

It is feasible to establish an equation where the constant value of the reactants and products are set and they are not altered when ethyl-amide units increase or if is necessary to change the molecule that will bind to the CNT.

The equations is:

Conditions:

To give the reaction spontaneously, it requires that the constant value always presents a negative amount bigger than the sum of the variable values.

Address

Av. Heróico Colegio Militar 4700 Col. Nombre de Dios, Zip Code: 31300

Phone Number

+52 (614) 439 5000 (Ext. 3009)

Email

igem_chih@outlook.com