Team:Dundee/Project/NetlogoSec

From 2013.igem.org

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       <!-- Title -->
       <!-- Title -->
       <div class="page-header">
       <div class="page-header">
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           <h2><b>NetLogo </b> - SECGATE Transportation</h2>
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           <h2><b>NetLogo </b> - SECGATE Transport</h2>
           <p style="text-align:justify">
           <p style="text-align:justify">
                 The applet requires Java 5 or higher. Java must be enabled in your browser settings. Mac users must have Mac OS X 10.4 or higher. Windows and Linux users may obtain the latest Java from Oracle's Java site.
                 The applet requires Java 5 or higher. Java must be enabled in your browser settings. Mac users must have Mac OS X 10.4 or higher. Windows and Linux users may obtain the latest Java from Oracle's Java site.
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       <div class="span12" style="margin-left:0px;margin-top: 10px;">
       <div class="span12" style="margin-left:0px;margin-top: 10px;">
             <applet code="org.nlogo.lite.Applet"
             <applet code="org.nlogo.lite.Applet"
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                     codebase="http://www.kyleharrison.co.uk/netlogo/"  
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                     codebase="http://www.kyleharrison.co.uk/igem/netlogo/SecNetlogoApplet/"  
                     archive="NetLogoLite.jar"
                     archive="NetLogoLite.jar"
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                     width="1330" height="556">
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                     width="1330" height="800">
               <param name="DefaultModel"
               <param name="DefaultModel"
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                     value="SECGATEcoloursprobabilities.nlogo">
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                     value="SECGATEcommented.nlogo">
               <param name="java_arguments"
               <param name="java_arguments"
                     value="-Djnlp.packEnabled=true">
                     value="-Djnlp.packEnabled=true">
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         </div>
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        <div class="row" >
 
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            <div class="span12">
 
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              <h2>WHAT IS IT?</h2>
 
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              <p style="text-align:justify">
 
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                This model follows on the Simple Kinetics 2 model. In Simple Kinetics 2, we saw how changes to variables such as temperature, volume, and concentration affected the rate at which a chemical reaction reached an equilibrium state. Here we model the same phenomenon based upon a physical separation.
 
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                This model investigates some laboratory methods that chemists use to purify chemicals. Most of these methods are based upon physical properties of molecular separation. The same principles that affect chemical equilibrium affect physical equilibrium as well. By changing the variables of temperature, volume, and concentration, we can affect not only the speed at which a system reaches equilibrium, but also the nature of the distribution ratio. In this model, we watch how these factors affect the physical distribution of red molecules that are considered “dissolved” in a blue solvent.
 
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              <h2>HOW TO USE IT</h2>
 
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              <p style="text-align:justify">
 
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                Setup the model by pressing either the SETUP-RANDOM or the SETUP-SIDE buttons at the top of the Interface tab. SETUP-RANDOM distributes all the molecules randomly around the world. SETUP-SIDE distributes the blue molecules evenly, while placing the red molecules on the right side of the world.<br>
 
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                Press GO to watch the molecules move about the world as they achieve equilibrium. The plot tracks the relative concentrations of each color molecule on each side of the central divider. If the red line dips below 0, there are more red molecules on the left side of the divider than on the right. If it rises above 0, there are more red molecules on the right side of the divider than on the left. The blue line plots the same relationship for blue molecules.<br>
 
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                You can add more red molecules to the right side of the world by pressing ADD RED.<br>
 
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                Similarly, you can shrink or expand the right side of the box with the buttons SHRINK RIGHT and EXPAND RIGHT, respectively.<br>
 
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                Finally, to change the size of the connection window, move the WINDOW slider to your desired size and then press the CHANGE WINDOW button.<br>
 
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              </p>
 
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              <h2>Things to Notice</h2>
 
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              <p style="text-align:justify">
 
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                Pay attention to the plot and compare it what you see in the world. Is there an equal number of blue and red molecules on each side of the divider according to the plot and according to what you see in the view?</p>
 
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              <h2>Things to Try</h2>
 
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              <p style="text-align:justify">
 
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                Run the model with several different states for each variable. Do you observe similar equilibrium effects to those seen in Simple Kinetics 2? Are there significant differences?<br>
 
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                Does the temperature affect the system in the same way it affected the chemical reaction in Simple Kinetics 2? Why or why not?<br>
 
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                How does changing the concentration affect the rate at which the molecules achieve equilibrium? Does this make sense?<br></p>
 
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Latest revision as of 20:08, 3 October 2013

iGEM Dundee 2013 · ToxiMop

Retrieved from "http://2013.igem.org/Team:Dundee/Project/NetlogoSec"