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| - | <p><font size="-1">In order for this to work, this file, your model file | + | <!-- Fav and touch icons --> |
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| - | you and download time for your users.)</font></p>
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| - | <p>powered by | + | <li class="dropdown"> |
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| | + | <li><a href="/Team:Dundee/Project">Project Overview</a></li> |
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| - | <p>view/download model file: | + | < li><a href=" /Team:Dundee/Project/LabOverview"> Lab Overview</a></ li> |
| - | <a href="SECGATEcoloursprobabilities.nlogo">SECGATEcoloursprobabilities.nlogo</a></p> | + | < li><a href="/ Team:Dundee/ Project/ Mop"> Mop</a></ li> |
| - | <h2>WHAT IS IT?</h2><p>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.</p><p>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.</p><h2>HOW TO USE IT</h2><p>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.</p><p>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.</p><p>You can add more red molecules to the right side of the world by pressing ADD RED.</p><p>Similarly, you can shrink or expand the right side of the box with the buttons SHRINK RIGHT and EXPAND RIGHT, respectively.</p><p>Finally, to change the size of the connection window, move the WINDOW slider to your desired size and then press the CHANGE WINDOW button.</p><h2>THINGS TO NOTICE</h2><p>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><h2>THINGS TO TRY</h2><p>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?</p><p>Does the temperature affect the system in the same way it affected the chemical reaction in Simple Kinetics 2? Why or why not?</p><p>How does changing the concentration affect the rate at which the molecules achieve equilibrium? Does this make sense?</p><h2>EXTENDING THE MODEL</h2><p>The system we have established here always comes to an approximately identical equilibrium state, no matter how you change the variables. In the lab, this is not useful to chemists, who want to separate one type of molecule from another. Can you extend the model to separate all of the red molecules from the blue molecules?</p><p>Try adding another color of molecule to the system and randomly distributing all the molecules around the world. Can you devise a way to separate the new molecules from the red molecules?</p><p>Add a slider that allows you to alter the temperature of the system. Think about what effect cooling and heating the system would have on the molecules. Be sure to include a command in the procedures window that will execute your proposed effect.</p><h2>RELATED MODELS</h2><p>Simple Kinetics 1, Simple Kinetics 2</p><h2>RELATED MODELS</h2><p>Simple Kinetics 1<br/>Simple Kinetics 2</p><h2>CREDITS AND REFERENCES</h2><p>Thanks to Mike Stieff for his work on this model.</p><h2>HOW TO CITE</h2><p>If you mention this model in a publication, we ask that you include these citations for the model itself and for the NetLogo software:</p> | + | <li><a href=" /Team: Dundee/ Project/ Detector"> Detector - <i>EnvZ</ i> </a></li> |
| - | <ul>
| + | <li><a href=" /Team: Dundee/ Project/ Detector"> Detector - < i> prkC</ i> </ a></ li> |
| - | <li> Stieff, M. and Wilensky, U. (2001). NetLogo Simple Kinetics 3 model. <a href=" http:// ccl.northwestern.edu/netlogo/models/SimpleKinetics3"> http:/ /ccl.northwestern.edu/netlogo/models/SimpleKinetics3</a> . Center for Connected Learning and Computer-Based Modeling, Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL.</li> | + | <li class="divider"></li> |
| - | <li> Wilensky, U. (1999). NetLogo. <a href=" http:// ccl.northwestern.edu/netlogo/"> http://ccl.northwestern.edu/netlogo/</a>. Center for Connected Learning and Computer- Based Modeling, Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL.< /li> | + | <li class="nav-header">Modelling </li> |
| - | </ ul> <h2>COPYRIGHT AND LICENSE</ h2> <p>Copyright 2001 Uri Wilensky.</ p>< p><img src=" http://i.creativecommons.org/l/by-nc-sa/3.0/88x31.png" alt="CC BY-NC-SA 3.0"/></ p>< p>This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 License. To view a copy of this license, visit <a href=" http://creativecommons.org/licenses/by- nc-sa/3.0/"> http://creativecommons.org/licenses/by-nc-sa/3.0/</ a> or send a letter to Creative Commons, 559 Nathan Abbott Way, Stanford, California 94305, USA.< /p><p> Commercial licenses are also available. To inquire about commercial licenses, please contact Uri Wilensky at <a href=" mailto: uri@northwestern.edu"> uri@northwestern.edu</a> .</ p><p>This model was created as part of the projects: PARTICIPATORY SIMULATIONS: NETWORK-BASED DESIGN FOR SYSTEMS LEARNING IN CLASSROOMS and/or INTEGRATED SIMULATION AND MODELING ENVIRONMENT. The project gratefully acknowledges the support of the National Science Foundation (REPP & ROLE programs) – grant numbers REC #9814682 and REC-0126227.</p> | + | < li><a href=" /Team: Dundee/Project/MathOverview"> Modelling Overview</a></ li> |
| | | | |
| - | <h1>CODE</h1> | + | <li><a href="/Team:Dundee/Project/MathTheory">PP1 Capacities</a></li> |
| - | <pre><font color="#007f69">breed</font><font color="#000000"> [PP1s PP1] </font><font color="#5a5a5a">;; red molecules</font><font color="#000000">
| + | <li><a href="/Team:Dundee/Project/MathTheory">Production & Export </a></li> |
| - | </font><font color="#660096">breed</font><font color="#000000"> [degPs degP] </font><font color="#5a5a5a">;; degradation proteins</font><font color="#000000"> | + | <li><a href="/Team:Dundee/Project/MathTheory">Mop Simulation</a></li> |
| - | </font><font color="#660096">breed</font><font color="#000000"> [mcs mc] </font><font color="#5a5a5a">;; microcystin, assuming so small that kinetic interaction is negligible</font><font color="#000000"> | + | <li><a href="/Team:Dundee/Project/MathTheory">Detection Comparison</a></li> |
| - | </font><font color="#660096">breed</font><font color="#000000"> [complexes complex] </font><font color="#5a5a5a">;; PP1 bounded to microcystin</font><font color="#000000"> | + | |
| - | </font><font color="#660096">breed</font><font color="#000000"> [secBs secB] | + | |
| | | | |
| | + | <li class="divider"></li> |
| | + | <li class="nav-header">Software</li> |
| | + | <li><a href="/Team:Dundee/Project/SoftwareOverview">Software Overview</a></li> |
| | + | <li><a href="/Team:Dundee/Project/SoftwareTheory">Mop-toppus</a></li> |
| | + | <li><a href="/Team:Dundee/Project/SoftwareTheory">Toxi-Tweet</a></li> |
| | + | <li><a href="/Team:Dundee/Project/SoftwareTheory">Optical LDR Array</a></li> |
| | + | </ul> |
| | + | </li> |
| | | | |
| - | </font><font color="#007f69">globals</font><font color="#000000"> [ | + | <li class="dropdown"> |
| - | shrink </font><font color="#5a5a5a">;; how many steps right side has been shrunk</font><font color="#000000">
| + | <a href="#" class="dropdown-toggle" data-toggle="dropdown">Parts <b class="caret"></b></a> |
| - | i
| + | <ul class="dropdown-menu"> |
| - | seperation
| + | <li><a href="#">Our Biobricks</a></li> |
| - | j
| + | <li><a href="#">Improvements</a></li> |
| - | current
| + | </ul> |
| - | k
| + | </li> |
| - | l
| + | |
| - | g
| + | |
| - | deg-number
| + | |
| - | PP1-transported
| + | |
| - | init-avg-speed init-avg-energy </font><font color="#5a5a5a">;; initial averages</font><font color="#000000">
| + | |
| - | avg-speed avg-energy </font><font color="#5a5a5a">;; current averages</font><font color="#000000">
| + | |
| - | secBs-dead
| + | |
| - | ]
| + | |
| | | | |
| | + | <li class="dropdown"> |
| | + | <a href="#" class="dropdown-toggle" data-toggle="dropdown">Safety <b class="caret"></b></a> |
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| | + | <li><a href="/Team:Dundee/Safety">Safety Overview</a></li> |
| | + | <li><a href="/Team:Dundee/Safety/InTheLab">In the Lab</a></li> |
| | + | <li><a href="/Team:Dundee/Safety/EnvironmentalSafety">Environmental Safety</a></li> |
| | + | </ul> |
| | + | </li> |
| | | | |
| - | </font><font color="#007f69">turtles-own</font><font color="#000000"> | + | <li class="dropdown"> |
| - | [
| + | <a href="#" class="dropdown-toggle" data-toggle="dropdown">Human Practice <b class="caret"></b></a> |
| - | speed mass energy </font><font color="#5a5a5a">;; particle info</font><font color="#000000">
| + | <ul class="dropdown-menu"> |
| - | last-collision
| + | <li><a href="/Team:Dundee/HumanPractice">Overview</a></li> |
| - | bound
| + | <li><a href="/Team:Dundee/HumanPractice/Collaboration">Collaboration</a></li> |
| - | linked?
| + | <li><a href="/Team:Dundee/HumanPractice/PublicEngagement">Public Engagement</a></li> |
| - | ]
| + | <li><a href="/Team:Dundee/HumanPractice/CaseStudy">Clatto Case Study</a></li> |
| | + | <li><a href="/Team:Dundee/HumanPractice/Interviews">Interviews</a></li> |
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| | + | |
| | | | |
| - | </font><font color="#007f69">to-report</font><font color="#000000"> particles | + | </ul> |
| - | </font><font color="#0000aa">report</font><font color="#000000"> (</font><font color="#660096">turtle-set</font><font color="#000000"> PP1s degPs mcs complexes)
| + | </div><!--/.nav-collapse --> |
| - | </font><font color="#007f69">end</font><font color="#000000"> | + | </div> |
| | + | </div> |
| | + | </div> |
| | | | |
| - | </font><font color="#007f69">to-report</font><font color="#000000"> lefties | + | <!-- Begin page content --> |
| - | </font><font color="#0000aa">report</font><font color="#000000"> (</font><font color="#660096">turtle-set</font><font color="#000000"> degPs mcs complexes)
| + | <div class="container"> |
| - | </font><font color="#007f69">end</font><font color="#000000"> | + | |
| | | | |
| | | | |
| | + | <!-- Title --> |
| | | | |
| | + | <div class="page-header"> |
| | + | <h2><b>NetLogo </b> - SECGATE Transportation</h2> |
| | + | </div> |
| | | | |
| | + | <!-- Title End --> |
| | | | |
| - | </font><font color="#007f69">to</font><font color="#000000"> setup-PP1 </font><font color="#5a5a5a">;; particle procedure</font><font color="#000000"> | + | <div class="span12" style="margin-left:0px;margin-top: 10px;"> |
| - | </font><font color="#0000aa">set</font><font color="#000000"> speed </font><font color="#963700">10</font><font color="#000000">
| + | <applet code="org.nlogo.lite.Applet" |
| - | </font><font color="#0000aa">set</font><font color="#000000"> mass </font><font color="#963700">37500</font><font color="#000000">
| + | archive="NetLogoLite.jar" |
| - | </font><font color="#0000aa">set</font><font color="#000000"> energy (</font><font color="#963700">0.5</font><font color="#000000"> </font><font color="#660096">*</font><font color="#000000"> mass </font><font color="#660096">*</font><font color="#000000"> (speed </font><font color="#660096">^</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">))
| + | width="1330" height="556"> |
| - | </font><font color="#0000aa">set</font><font color="#000000"> last-collision </font><font color="#963700">nobody</font><font color="#000000">
| + | <param name="DefaultModel" |
| - | </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">color</font><font color="#000000"> </font><font color="#963700">red</font><font color="#000000">
| + | value="SECGATEcoloursprobabilities.nlogo"> |
| - | </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">size</font><font color="#000000"> </font><font color="#963700">1.5</font><font color="#000000">
| + | <param name="java_arguments" |
| - | </font><font color="#0000aa">set</font><font color="#000000"> linked? </font><font color="#963700">false</font><font color="#000000">
| + | value="-Djnlp.packEnabled=true"> |
| - | </font><font color="#007f69">end</font><font color="#000000">
| + | </applet> |
| - | | + | </div> |
| - | </font><font color="#007f69">to</font><font color="#000000"> setup-degPs </font><font color="#5a5a5a">;; particle procedure</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> speed </font><font color="#963700">10</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> mass </font><font color="#963700">37500</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> energy (</font><font color="#963700">0.5</font><font color="#000000"> </font><font color="#660096">*</font><font color="#000000"> mass </font><font color="#660096">*</font><font color="#000000"> (speed </font><font color="#660096">^</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">))
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> last-collision </font><font color="#963700">nobody</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">size</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">color</font><font color="#000000"> </font><font color="#963700">black</font><font color="#000000">
| + | |
| - | </font><font color="#007f69">end</font><font color="#000000">
| + | |
| - | | + | |
| - | </font><font color="#007f69">to</font><font color="#000000"> setup-mcs </font><font color="#5a5a5a">;; particle procedure</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> speed </font><font color="#963700">10</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> mass </font><font color="#963700">995</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> energy (</font><font color="#963700">0.5</font><font color="#000000"> </font><font color="#660096">*</font><font color="#000000"> mass </font><font color="#660096">*</font><font color="#000000"> (speed </font><font color="#660096">^</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">))
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> last-collision </font><font color="#963700">nobody</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> bound </font><font color="#963700">false</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">size</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">color</font><font color="#000000"> </font><font color="#963700">114</font><font color="#000000">
| + | |
| - | </font><font color="#007f69">end</font><font color="#000000">
| + | |
| - | | + | |
| - | </font><font color="#007f69">to</font><font color="#000000"> setup-complex </font><font color="#5a5a5a">;; particle procedure</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> speed </font><font color="#963700">10</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> mass </font><font color="#963700">38495</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> energy (</font><font color="#963700">0.5</font><font color="#000000"> </font><font color="#660096">*</font><font color="#000000"> mass </font><font color="#660096">*</font><font color="#000000"> (speed </font><font color="#660096">^</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">))
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> last-collision </font><font color="#963700">nobody</font><font color="#000000">
| + | |
| - | </font><font color="#007f69">end</font><font color="#000000">
| + | |
| - | | + | |
| - | </font><font color="#007f69">to</font><font color="#000000"> setup-secB </font><font color="#5a5a5a">;; particle procedure</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> speed </font><font color="#963700">10</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> mass </font><font color="#963700">17278</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> energy (</font><font color="#963700">0.5</font><font color="#000000"> </font><font color="#660096">*</font><font color="#000000"> mass </font><font color="#660096">*</font><font color="#000000"> (speed </font><font color="#660096">^</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">))
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> last-collision </font><font color="#963700">nobody</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">color</font><font color="#000000"> </font><font color="#963700">55</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">size</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> linked? </font><font color="#963700">false</font><font color="#000000">
| + | |
| - | </font><font color="#007f69">end</font><font color="#000000">
| + | |
| - | | + | |
| - | | + | |
| - | </font><font color="#007f69">to</font><font color="#000000"> setup [both-sides?]
| + | |
| - | </font><font color="#0000aa">clear-all</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set-default-shape</font><font color="#000000"> PP1s </font><font color="#963700">"circle"</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set-default-shape</font><font color="#000000"> degPs </font><font color="#963700">"square"</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set-default-shape</font><font color="#000000"> mcs </font><font color="#963700">"turtle"</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set-default-shape</font><font color="#000000"> secBs </font><font color="#963700">"key"</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> shrink </font><font color="#963700">0</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> i </font><font color="#963700">0</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> k ( </font><font color="#963700">99</font><font color="#000000"> )
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> l ( </font><font color="#660096">-</font><font color="#000000"> </font><font color="#963700">99</font><font color="#000000"> )
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> g </font><font color="#963700">0</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> deg-number </font><font color="#963700">0</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> PP1-transported </font><font color="#963700">0</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> j </font><font color="#963700">0</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> current </font><font color="#963700">0</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> seperation </font><font color="#963700">0</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> init-avg-speed avg-speed
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> init-avg-energy avg-energy
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> secBs-dead </font><font color="#963700">0</font><font color="#000000">
| + | |
| - |
| + | |
| - |
| + | |
| - | walls
| + | |
| - | gates
| + | |
| - |
| + | |
| - | | + | |
| - | create-PP1s initial-PP1 </font><font color="#5a5a5a">;; makes 42 red PP1s</font><font color="#000000">
| + | |
| - | [setup-PP1
| + | |
| - | randomize-right ]
| + | |
| - |
| + | |
| - |
| + | |
| - | create-degPs degP-number </font><font color="#5a5a5a">;; makes xx degradation proteins</font><font color="#000000">
| + | |
| - | [setup-degPs
| + | |
| - | randomize-left ]
| + | |
| - |
| + | |
| - |
| + | |
| - | create-mcs mc-number
| + | |
| - | [ setup-mcs
| + | |
| - | randomize-left]
| + | |
| - |
| + | |
| - | create-secBs initial-secB </font><font color="#5a5a5a">;; makes 42 red PP1s</font><font color="#000000">
| + | |
| - | [setup-secB
| + | |
| - | randomize-right ]
| + | |
| - |
| + | |
| - |
| + | |
| - |
| + | |
| - | </font><font color="#0000aa">reset-ticks</font><font color="#000000">
| + | |
| - | </font><font color="#007f69">end</font><font color="#000000">
| + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | </font><font color="#007f69">to</font><font color="#000000"> randomize-left
| + | |
| - | </font><font color="#0000aa">setxy</font><font color="#000000"> (</font><font color="#660096">-</font><font color="#000000"> (</font><font color="#660096">abs</font><font color="#000000"> </font><font color="#660096">random-xcor</font><font color="#000000">))
| + | |
| - | </font><font color="#660096">random-ycor</font><font color="#000000"> | + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> </font><font color="#660096">any?</font><font color="#000000"> </font><font color="#660096">patches</font><font color="#000000"> </font><font color="#660096">in-radius</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> </font><font color="#660096">with</font><font color="#000000"> [</font><font color="#660096">pcolor</font><font color="#000000"> </font><font color="#660096">!=</font><font color="#000000"> </font><font color="#963700">87</font><font color="#000000">]
| + | |
| - | [ randomize-left ] </font><font color="#5a5a5a">;; try again until we don't land on or near blue</font><font color="#000000">
| + | |
| - | </font><font color="#007f69">end</font><font color="#000000">
| + | |
| - | | + | |
| - | </font><font color="#007f69">to</font><font color="#000000"> randomize-right
| + | |
| - | </font><font color="#0000aa">setxy</font><font color="#000000"> </font><font color="#660096">abs</font><font color="#000000"> </font><font color="#660096">random-xcor</font><font color="#000000">
| + | |
| - | </font><font color="#660096">random-ycor</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> </font><font color="#660096">any?</font><font color="#000000"> </font><font color="#660096">patches</font><font color="#000000"> </font><font color="#660096">in-radius</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> </font><font color="#660096">with</font><font color="#000000"> [</font><font color="#660096">pcolor</font><font color="#000000"> </font><font color="#660096">!=</font><font color="#000000"> </font><font color="#963700">19.9</font><font color="#000000">]
| + | |
| - | [ randomize-right ] </font><font color="#5a5a5a">;; try again until we don't land on or near blue</font><font color="#000000">
| + | |
| - | </font><font color="#007f69">end</font><font color="#000000">
| + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | </font><font color="#007f69">to</font><font color="#000000"> go
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> particles [
| + | |
| - |
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> collide? [check-for-collision]
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> random-walk? [</font><font color="#0000aa">rt</font><font color="#000000"> </font><font color="#660096">random-float</font><font color="#000000"> </font><font color="#963700">360</font><font color="#000000">]
| + | |
| - | bounce
| + | |
| - | </font><font color="#0000aa">fd</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000">
| + | |
| - | ]
| + | |
| - |
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> PP1s [
| + | |
| - | loss-PP1
| + | |
| - | degrade
| + | |
| - | ]
| + | |
| - |
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> </font><font color="#660096">ticks</font><font color="#000000"> </font><font color="#660096">mod</font><font color="#000000"> </font><font color="#963700">5</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">0</font><font color="#000000"> [
| + | |
| - | create-PP1s PP1-production
| + | |
| - | [
| + | |
| - | </font><font color="#0000aa">setxy</font><font color="#000000"> </font><font color="#660096">abs</font><font color="#000000"> </font><font color="#963700">48</font><font color="#000000">
| + | |
| - | </font><font color="#660096">random-ycor</font><font color="#000000">
| + | |
| - | setup-PP1
| + | |
| - | ]
| + | |
| - |
| + | |
| - | create-mcs mc-production
| + | |
| - | [
| + | |
| - | </font><font color="#0000aa">setxy</font><font color="#000000"> ( </font><font color="#660096">-</font><font color="#000000"> </font><font color="#963700">48</font><font color="#000000"> ) | + | |
| - | </font><font color="#660096">random-ycor</font><font color="#000000">
| + | |
| - | setup-mcs
| + | |
| - | ]
| + | |
| - | ]
| + | |
| - |
| + | |
| - |
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> mcs [ | + | |
| - | loss-mc
| + | |
| - | bind
| + | |
| - | ]
| + | |
| - |
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> secBs [
| + | |
| - | stick
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> collide? [check-for-collision]
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> random-walk? [</font><font color="#0000aa">rt</font><font color="#000000"> </font><font color="#660096">random-float</font><font color="#000000"> </font><font color="#963700">360</font><font color="#000000">]
| + | |
| - | bounce
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> linked? </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">false</font><font color="#000000"> [</font><font color="#0000aa">fd</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000">]
| + | |
| - | ]
| + | |
| - |
| + | |
| - | create-secBs (initial-secB </font><font color="#660096">-</font><font color="#000000"> (</font><font color="#660096">count</font><font color="#000000"> secBs)) [
| + | |
| - | setup-secB
| + | |
| - | </font><font color="#0000aa">setxy</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> (</font><font color="#660096">one-of</font><font color="#000000"> [</font><font color="#660096">random-pxcor</font><font color="#000000">] </font><font color="#660096">of</font><font color="#000000"> </font><font color="#660096">patches</font><font color="#000000"> </font><font color="#660096">with</font><font color="#000000"> [</font><font color="#660096">pcolor</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">78</font><font color="#000000">])
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> secBs-dead </font><font color="#963700">0</font><font color="#000000">
| + | |
| - | ]
| + | |
| - |
| + | |
| - | </font><font color="#0000aa">tick</font><font color="#000000">
| + | |
| - | </font><font color="#007f69">end</font><font color="#000000">
| + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | </font><font color="#007f69">to</font><font color="#000000"> walls
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> </font><font color="#660096">patches</font><font color="#000000"> </font><font color="#660096">with</font><font color="#000000"> [</font><font color="#660096">pxcor</font><font color="#000000"> </font><font color="#660096">></font><font color="#000000"> </font><font color="#963700">0</font><font color="#000000"> </font><font color="#660096">and</font><font color="#000000"> </font><font color="#660096">pxcor</font><font color="#000000"> </font><font color="#660096"><</font><font color="#000000"> </font><font color="#963700">50</font><font color="#000000">][ </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">pcolor</font><font color="#000000"> </font><font color="#963700">19.9</font><font color="#000000">]
| + | |
| - | </font><font color="#5a5a5a">;; ask patches with [pxcor = 17 or pxcor = (- 17) or pycor = 17 or pycor = (- 17) or pxcor = 0] [ set pcolor blue ]</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> </font><font color="#660096">patches</font><font color="#000000"> </font><font color="#660096">with</font><font color="#000000"> [ </font><font color="#660096">pxcor</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> (</font><font color="#660096">-</font><font color="#000000"> </font><font color="#963700">50</font><font color="#000000">)] [ </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">pcolor</font><font color="#000000"> </font><font color="#963700">3</font><font color="#000000"> ] | + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> </font><font color="#660096">patches</font><font color="#000000"> </font><font color="#660096">with</font><font color="#000000"> [ </font><font color="#660096">pxcor</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">0</font><font color="#000000">] [ </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">pcolor</font><font color="#000000"> </font><font color="#963700">75</font><font color="#000000"> ]
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> </font><font color="#660096">patches</font><font color="#000000"> </font><font color="#660096">with</font><font color="#000000"> [ </font><font color="#660096">pxcor</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">50</font><font color="#000000"> ] [ </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">pcolor</font><font color="#000000"> </font><font color="#963700">8</font><font color="#000000"> ]
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> k </font><font color="#660096">!=</font><font color="#000000"> </font><font color="#963700">-16</font><font color="#000000"> [
| + | |
| - | periplasm
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> k ( k </font><font color="#660096">-</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> )
| + | |
| - | walls
| + | |
| - |
| + | |
| - | ]
| + | |
| - | </font><font color="#007f69">end</font><font color="#000000">
| + | |
| - | | + | |
| - | </font><font color="#007f69">to</font><font color="#000000"> periplasm
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> l </font><font color="#660096">!=</font><font color="#000000"> </font><font color="#963700">0</font><font color="#000000"> [
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> </font><font color="#660096">patches</font><font color="#000000"> </font><font color="#660096">with</font><font color="#000000"> [</font><font color="#660096">pxcor</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> l </font><font color="#660096">or</font><font color="#000000"> </font><font color="#660096">pycor</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> k ] [ </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">pcolor</font><font color="#000000"> </font><font color="#963700">87</font><font color="#000000"> ]
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> l ( l </font><font color="#660096">+</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> )
| + | |
| - | periplasm
| + | |
| - | ]
| + | |
| - | </font><font color="#007f69">end</font><font color="#000000">
| + | |
| - | | + | |
| - | | + | |
| - | </font><font color="#007f69">to</font><font color="#000000"> gates
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> seperation ( </font><font color="#660096">round</font><font color="#000000"> ( </font><font color="#963700">99</font><font color="#000000"> </font><font color="#660096">/</font><font color="#000000"> ( gate-number </font><font color="#660096">*</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000"> ) ) )
| + | |
| - | | + | |
| - |
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> (gate-number </font><font color="#660096">mod</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000"> ) </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> [
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> seperation ( </font><font color="#660096">round</font><font color="#000000"> ( </font><font color="#963700">99</font><font color="#000000"> </font><font color="#660096">/</font><font color="#000000"> ( (gate-number </font><font color="#660096">+</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000">) </font><font color="#660096">*</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000"> ) ) )
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> j </font><font color="#660096">!=</font><font color="#000000"> ((gate-number </font><font color="#660096">+</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000">) </font><font color="#660096">/</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">) [
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> </font><font color="#660096">patches</font><font color="#000000"> </font><font color="#660096">with</font><font color="#000000"> [ </font><font color="#660096">pxcor</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">0</font><font color="#000000"> </font><font color="#660096">and</font><font color="#000000"> ( </font><font color="#660096">pycor</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">0</font><font color="#000000"> </font><font color="#660096">+</font><font color="#000000"> (seperation </font><font color="#660096">*</font><font color="#000000"> j </font><font color="#660096">*</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">) </font><font color="#660096">or</font><font color="#000000"> </font><font color="#660096">pycor</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">0</font><font color="#000000"> </font><font color="#660096">-</font><font color="#000000"> (seperation </font><font color="#660096">*</font><font color="#000000"> j </font><font color="#660096">*</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">) )] [</font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">pcolor</font><font color="#000000"> </font><font color="#963700">78</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> g </font><font color="#963700">0</font><font color="#000000">
| + | |
| - | gate-width]
| + | |
| - |
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> j (j </font><font color="#660096">+</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000">)
| + | |
| - | gates
| + | |
| - | ]
| + | |
| - | ]
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> (gate-number </font><font color="#660096">mod</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">) </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">0</font><font color="#000000"> [
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> j </font><font color="#660096">!=</font><font color="#000000"> (gate-number </font><font color="#660096">/</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">) [
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> </font><font color="#660096">patches</font><font color="#000000"> </font><font color="#660096">with</font><font color="#000000"> [ </font><font color="#660096">pxcor</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">0</font><font color="#000000"> </font><font color="#660096">and</font><font color="#000000"> ( </font><font color="#660096">pycor</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> ( </font><font color="#660096">-</font><font color="#000000"> seperation) </font><font color="#660096">+</font><font color="#000000"> (seperation </font><font color="#660096">*</font><font color="#000000"> (j </font><font color="#660096">+</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000">) </font><font color="#660096">*</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">) </font><font color="#660096">or</font><font color="#000000"> </font><font color="#660096">pycor</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> seperation </font><font color="#660096">-</font><font color="#000000"> (seperation </font><font color="#660096">*</font><font color="#000000"> (j </font><font color="#660096">+</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000">) </font><font color="#660096">*</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">) )] [</font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">pcolor</font><font color="#000000"> </font><font color="#963700">78</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> g </font><font color="#963700">0</font><font color="#000000">
| + | |
| - | gate-width
| + | |
| - | ]
| + | |
| - |
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> j (j </font><font color="#660096">+</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000">)
| + | |
| - | gates
| + | |
| - | ]
| + | |
| - | ]
| + | |
| - | </font><font color="#007f69">end</font><font color="#000000">
| + | |
| - | | + | |
| - | </font><font color="#007f69">to</font><font color="#000000"> gate-width
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> ( gate-size </font><font color="#660096">mod</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">) </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> [
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> g </font><font color="#660096">!=</font><font color="#000000">(( gate-size </font><font color="#660096">+</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> ) </font><font color="#660096">/</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000"> ) [
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> </font><font color="#660096">patch-at-heading-and-distance</font><font color="#000000"> </font><font color="#963700">0</font><font color="#000000"> g [</font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">pcolor</font><font color="#000000"> </font><font color="#963700">78</font><font color="#000000">]
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> </font><font color="#660096">patch-at-heading-and-distance</font><font color="#000000"> </font><font color="#963700">180</font><font color="#000000"> g [</font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">pcolor</font><font color="#000000"> </font><font color="#963700">78</font><font color="#000000">]
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> g ( g </font><font color="#660096">+</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> )
| + | |
| - | gate-width
| + | |
| - | ]]
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> ( gate-size </font><font color="#660096">mod</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">) </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">0</font><font color="#000000"> [
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> g </font><font color="#660096">!=</font><font color="#000000">(( gate-size ) </font><font color="#660096">/</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000"> ) [
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> </font><font color="#660096">patch-at-heading-and-distance</font><font color="#000000"> </font><font color="#963700">0</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> [</font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">pcolor</font><font color="#000000"> </font><font color="#963700">78</font><font color="#000000">]
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> </font><font color="#660096">patch-at-heading-and-distance</font><font color="#000000"> </font><font color="#963700">0</font><font color="#000000"> (g </font><font color="#660096">+</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000">) [</font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">pcolor</font><font color="#000000"> </font><font color="#963700">78</font><font color="#000000">]
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> </font><font color="#660096">patch-at-heading-and-distance</font><font color="#000000"> </font><font color="#963700">180</font><font color="#000000"> g [</font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">pcolor</font><font color="#000000"> </font><font color="#963700">78</font><font color="#000000">]
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> g ( g </font><font color="#660096">+</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> )
| + | |
| - | gate-width
| + | |
| - |
| + | |
| - | ]
| + | |
| - | ]
| + | |
| - | </font><font color="#007f69">end</font><font color="#000000">
| + | |
| - |
| + | |
| - |
| + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | </font><font color="#007f69">to</font><font color="#000000"> loss-PP1 </font><font color="#5a5a5a">;;loss inside cell</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> [</font><font color="#660096">pcolor</font><font color="#000000">] </font><font color="#660096">of</font><font color="#000000"> </font><font color="#660096">patch-ahead</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">8</font><font color="#000000"> [
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> linked? </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">false</font><font color="#000000"> [</font><font color="#0000aa">die</font><font color="#000000">
| + | |
| - | </font><font color="#5a5a5a">; ask secBs in-radius 2 [</font><font color="#000000">
| + | |
| - | </font><font color="#5a5a5a">; set linked? false</font><font color="#000000">
| + | |
| - | </font><font color="#5a5a5a">; ask links [untie die]</font><font color="#000000">
| + | |
| - | ]
| + | |
| - | ]
| + | |
| - | </font><font color="#007f69">end</font><font color="#000000">
| + | |
| - | | + | |
| - | </font><font color="#007f69">to</font><font color="#000000"> loss-mc </font><font color="#5a5a5a">;;loss inside cell</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> [</font><font color="#660096">pcolor</font><font color="#000000">] </font><font color="#660096">of</font><font color="#000000"> </font><font color="#660096">patch-ahead</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">3</font><font color="#000000"> [</font><font color="#0000aa">die</font><font color="#000000">]
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> [</font><font color="#660096">pcolor</font><font color="#000000">] </font><font color="#660096">of</font><font color="#000000"> </font><font color="#660096">patch-ahead</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">3</font><font color="#000000"> [</font><font color="#0000aa">die</font><font color="#000000">]
| + | |
| - | </font><font color="#007f69">end</font><font color="#000000">
| + | |
| - | | + | |
| - | </font><font color="#007f69">to</font><font color="#000000"> degrade
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> degPs [ </font><font color="#0000aa">let</font><font color="#000000"> prey </font><font color="#660096">one-of</font><font color="#000000"> PP1s-here
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> prey </font><font color="#660096">!=</font><font color="#000000"> </font><font color="#963700">nobody</font><font color="#000000"> [
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> PP1s-here [
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> bound </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">false</font><font color="#000000"> [
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> </font><font color="#660096">random</font><font color="#000000"> </font><font color="#963700">100</font><font color="#000000"> </font><font color="#660096"><=</font><font color="#000000"> degprob [
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> prey [</font><font color="#0000aa">die</font><font color="#000000">] ]
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> deg-number ( deg-number </font><font color="#660096">+</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> )
| + | |
| - | ]]
| + | |
| - | ]
| + | |
| - | ]
| + | |
| - | </font><font color="#5a5a5a">; ask degPs [ let prey one-of complexes-here</font><font color="#000000">
| + | |
| - | </font><font color="#5a5a5a">; if prey != nobody [ </font><font color="#000000">
| + | |
| - | </font><font color="#5a5a5a">; ask complexes-here [ </font><font color="#000000">
| + | |
| - | </font><font color="#5a5a5a">; if bound = false [</font><font color="#000000">
| + | |
| - | </font><font color="#5a5a5a">; ask prey [die] ]</font><font color="#000000">
| + | |
| - | </font><font color="#5a5a5a">; set deg-number ( deg-number + 1 )</font><font color="#000000">
| + | |
| - | </font><font color="#5a5a5a">; ]</font><font color="#000000">
| + | |
| - | </font><font color="#5a5a5a">; ]</font><font color="#000000">
| + | |
| - | </font><font color="#5a5a5a">; ]</font><font color="#000000">
| + | |
| - | </font><font color="#007f69">end</font><font color="#000000">
| + | |
| - | | + | |
| - | | + | |
| - | </font><font color="#007f69">to</font><font color="#000000"> bind
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> </font><font color="#660096">count</font><font color="#000000"> PP1s-here </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> [
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> bound </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">false</font><font color="#000000"> [
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> </font><font color="#660096">random</font><font color="#000000"> </font><font color="#963700">100</font><font color="#000000"> </font><font color="#660096"><=</font><font color="#000000"> bindprob [
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> PP1s-here [
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> bound </font><font color="#963700">true</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">breed</font><font color="#000000"> complexes
| + | |
| - | </font><font color="#5a5a5a">;;set turtle-type "complex"</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">shape</font><font color="#000000"> </font><font color="#963700">"x"</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">color</font><font color="#000000"> </font><font color="#963700">126</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">size</font><font color="#000000"> </font><font color="#963700">3</font><font color="#000000">]
| + | |
| - |
| + | |
| - | </font><font color="#0000aa">die</font><font color="#000000">]
| + | |
| - | ]]
| + | |
| - | | + | |
| - | </font><font color="#007f69">end</font><font color="#000000">
| + | |
| - |
| + | |
| - | | + | |
| - | | + | |
| - | </font><font color="#007f69">to</font><font color="#000000"> bounce </font><font color="#5a5a5a">;; turtle procedure</font><font color="#000000">
| + | |
| - | </font><font color="#5a5a5a">;; or [pcolor] of patch-ahead 1 = 87</font><font color="#000000">
| + | |
| - |
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> [</font><font color="#660096">pcolor</font><font color="#000000">] </font><font color="#660096">of</font><font color="#000000"> </font><font color="#660096">patch-ahead</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">75</font><font color="#000000"> </font><font color="#660096">or</font><font color="#000000"> [</font><font color="#660096">pcolor</font><font color="#000000">] </font><font color="#660096">of</font><font color="#000000"> </font><font color="#660096">patch-ahead</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">3</font><font color="#000000"> [
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">heading</font><font color="#000000"> (</font><font color="#660096">-</font><font color="#000000"> </font><font color="#660096">heading</font><font color="#000000">)
| + | |
| - | ]
| + | |
| - |
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> [</font><font color="#660096">pcolor</font><font color="#000000">] </font><font color="#660096">of</font><font color="#000000"> </font><font color="#660096">patch-ahead</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">78</font><font color="#000000"> </font><font color="#660096">and</font><font color="#000000"> [</font><font color="#660096">pcolor</font><font color="#000000">] </font><font color="#660096">of</font><font color="#000000"> </font><font color="#660096">patch-here</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">87</font><font color="#000000"> [
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">heading</font><font color="#000000"> (</font><font color="#660096">-</font><font color="#000000"> </font><font color="#660096">heading</font><font color="#000000">)
| + | |
| - | ]
| + | |
| - |
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> lefties [
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> [</font><font color="#660096">pcolor</font><font color="#000000">] </font><font color="#660096">of</font><font color="#000000"> </font><font color="#660096">patch-ahead</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> </font><font color="#660096">!=</font><font color="#000000"> </font><font color="#963700">87</font><font color="#000000"> [</font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">heading</font><font color="#000000"> (</font><font color="#660096">-</font><font color="#000000"> </font><font color="#660096">heading</font><font color="#000000">)]
| + | |
| - | ]
| + | |
| - |
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> secBs [
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> [</font><font color="#660096">pcolor</font><font color="#000000">] </font><font color="#660096">of</font><font color="#000000"> </font><font color="#660096">patch-ahead</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">87</font><font color="#000000"> </font><font color="#660096">or</font><font color="#000000"> [</font><font color="#660096">pcolor</font><font color="#000000">] </font><font color="#660096">of</font><font color="#000000"> </font><font color="#660096">patch-ahead</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">8</font><font color="#000000"> [</font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">heading</font><font color="#000000"> (</font><font color="#660096">-</font><font color="#000000"> </font><font color="#660096">heading</font><font color="#000000">)]
| + | |
| - | ]
| + | |
| - |
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> PP1s [
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> [</font><font color="#660096">pcolor</font><font color="#000000">] </font><font color="#660096">of</font><font color="#000000"> </font><font color="#660096">patch-ahead</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">78</font><font color="#000000"> </font><font color="#660096">and</font><font color="#000000"> [</font><font color="#660096">pcolor</font><font color="#000000">] </font><font color="#660096">of</font><font color="#000000"> </font><font color="#660096">patch-here</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">19.9</font><font color="#000000"> [
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> linked? </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">false</font><font color="#000000"> [
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">heading</font><font color="#000000"> (</font><font color="#660096">-</font><font color="#000000"> </font><font color="#660096">heading</font><font color="#000000">)]
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> linked? </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">true</font><font color="#000000"> [
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> gateprob </font><font color="#660096"><=</font><font color="#000000"> (</font><font color="#660096">random</font><font color="#000000"> </font><font color="#963700">100</font><font color="#000000">) [
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">heading</font><font color="#000000"> (</font><font color="#660096">-</font><font color="#000000"> </font><font color="#660096">heading</font><font color="#000000">)
| + | |
| - | ]
| + | |
| - | ]
| + | |
| - | ]
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> [</font><font color="#660096">pcolor</font><font color="#000000">] </font><font color="#660096">of</font><font color="#000000"> </font><font color="#660096">patch-ahead</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">87</font><font color="#000000"> </font><font color="#660096">and</font><font color="#000000"> [</font><font color="#660096">pcolor</font><font color="#000000">] </font><font color="#660096">of</font><font color="#000000"> </font><font color="#660096">patch-here</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">78</font><font color="#000000"> [
| + | |
| - | | + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> linked? </font><font color="#963700">false</font><font color="#000000">
| + | |
| - | unstick
| + | |
| - | | + | |
| - | ]
| + | |
| - | ]
| + | |
| - | </font><font color="#007f69">end</font><font color="#000000">
| + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | </font><font color="#007f69">to</font><font color="#000000"> check-for-collision </font><font color="#5a5a5a">;; PP1 procedure</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> </font><font color="#660096">count</font><font color="#000000"> </font><font color="#660096">other</font><font color="#000000"> </font><font color="#660096">turtles-here</font><font color="#000000"> </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000">
| + | |
| - | [
| + | |
| - | </font><font color="#0000aa">let</font><font color="#000000"> candidate </font><font color="#660096">one-of</font><font color="#000000"> </font><font color="#660096">other</font><font color="#000000"> </font><font color="#660096">turtles-here</font><font color="#000000"> </font><font color="#660096">with</font><font color="#000000">
| + | |
| - | [</font><font color="#660096">who</font><font color="#000000"> </font><font color="#660096"><</font><font color="#000000"> [</font><font color="#660096">who</font><font color="#000000">] </font><font color="#660096">of</font><font color="#000000"> </font><font color="#660096">myself</font><font color="#000000"> </font><font color="#660096">and</font><font color="#000000"> </font><font color="#660096">myself</font><font color="#000000"> </font><font color="#660096">!=</font><font color="#000000"> last-collision]
| + | |
| - |
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> (candidate </font><font color="#660096">!=</font><font color="#000000"> </font><font color="#963700">nobody</font><font color="#000000">) </font><font color="#660096">and</font><font color="#000000"> (speed </font><font color="#660096">></font><font color="#000000"> </font><font color="#963700">0</font><font color="#000000"> </font><font color="#660096">or</font><font color="#000000"> [speed] </font><font color="#660096">of</font><font color="#000000"> candidate </font><font color="#660096">></font><font color="#000000"> </font><font color="#963700">0</font><font color="#000000">)
| + | |
| - | [
| + | |
| - | collide-with candidate
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> last-collision candidate
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> candidate [ </font><font color="#0000aa">set</font><font color="#000000"> last-collision </font><font color="#660096">myself</font><font color="#000000"> ]
| + | |
| - | ]
| + | |
| - | ]
| + | |
| - |
| + | |
| - |
| + | |
| - | </font><font color="#007f69">end</font><font color="#000000">
| + | |
| - | | + | |
| - | | + | |
| - | </font><font color="#007f69">to</font><font color="#000000"> collide-with [ other-particle ] </font><font color="#5a5a5a">;; PP1 colliding with other PP1 proteins</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">let</font><font color="#000000"> mass2 [mass] </font><font color="#660096">of</font><font color="#000000"> other-particle
| + | |
| - | </font><font color="#0000aa">let</font><font color="#000000"> speed2 [speed] </font><font color="#660096">of</font><font color="#000000"> other-particle
| + | |
| - | </font><font color="#0000aa">let</font><font color="#000000"> heading2 [</font><font color="#660096">heading</font><font color="#000000">] </font><font color="#660096">of</font><font color="#000000"> other-particle
| + | |
| - | </font><font color="#0000aa">let</font><font color="#000000"> theta (</font><font color="#660096">random-float</font><font color="#000000"> </font><font color="#963700">360</font><font color="#000000">)
| + | |
| - | </font><font color="#0000aa">let</font><font color="#000000"> v1t (speed </font><font color="#660096">*</font><font color="#000000"> </font><font color="#660096">cos</font><font color="#000000"> (theta </font><font color="#660096">-</font><font color="#000000"> </font><font color="#660096">heading</font><font color="#000000">))
| + | |
| - | </font><font color="#0000aa">let</font><font color="#000000"> v1l (speed </font><font color="#660096">*</font><font color="#000000"> </font><font color="#660096">sin</font><font color="#000000"> (theta </font><font color="#660096">-</font><font color="#000000"> </font><font color="#660096">heading</font><font color="#000000">))
| + | |
| - | </font><font color="#0000aa">let</font><font color="#000000"> v2t (speed2 </font><font color="#660096">*</font><font color="#000000"> </font><font color="#660096">cos</font><font color="#000000"> (theta </font><font color="#660096">-</font><font color="#000000"> heading2))
| + | |
| - | </font><font color="#0000aa">let</font><font color="#000000"> v2l (speed2 </font><font color="#660096">*</font><font color="#000000"> </font><font color="#660096">sin</font><font color="#000000"> (theta </font><font color="#660096">-</font><font color="#000000"> heading2))
| + | |
| - | </font><font color="#0000aa">let</font><font color="#000000"> vcm (((mass </font><font color="#660096">*</font><font color="#000000"> v1t) </font><font color="#660096">+</font><font color="#000000"> (mass2 </font><font color="#660096">*</font><font color="#000000"> v2t)) </font><font color="#660096">/</font><font color="#000000"> (mass </font><font color="#660096">+</font><font color="#000000"> mass2) )
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> v1t (</font><font color="#963700">2</font><font color="#000000"> </font><font color="#660096">*</font><font color="#000000"> vcm </font><font color="#660096">-</font><font color="#000000"> v1t)
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> v2t (</font><font color="#963700">2</font><font color="#000000"> </font><font color="#660096">*</font><font color="#000000"> vcm </font><font color="#660096">-</font><font color="#000000"> v2t)
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> speed </font><font color="#660096">sqrt</font><font color="#000000"> ((v1t </font><font color="#660096">^</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">) </font><font color="#660096">+</font><font color="#000000"> (v1l </font><font color="#660096">^</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">))
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> energy (</font><font color="#963700">0.5</font><font color="#000000"> </font><font color="#660096">*</font><font color="#000000"> mass </font><font color="#660096">*</font><font color="#000000"> speed </font><font color="#660096">^</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">)
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> v1l </font><font color="#660096">!=</font><font color="#000000"> </font><font color="#963700">0</font><font color="#000000"> </font><font color="#660096">or</font><font color="#000000"> v1t </font><font color="#660096">!=</font><font color="#000000"> </font><font color="#963700">0</font><font color="#000000">
| + | |
| - | [ </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">heading</font><font color="#000000"> (theta </font><font color="#660096">-</font><font color="#000000"> (</font><font color="#660096">atan</font><font color="#000000"> v1l v1t)) ]
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> other-particle [
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> speed </font><font color="#660096">sqrt</font><font color="#000000"> ((v2t </font><font color="#660096">^</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">) </font><font color="#660096">+</font><font color="#000000"> (v2l </font><font color="#660096">^</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">))
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> energy (</font><font color="#963700">0.5</font><font color="#000000"> </font><font color="#660096">*</font><font color="#000000"> mass </font><font color="#660096">*</font><font color="#000000"> (speed </font><font color="#660096">^</font><font color="#000000"> </font><font color="#963700">2</font><font color="#000000">))
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> v2l </font><font color="#660096">!=</font><font color="#000000"> </font><font color="#963700">0</font><font color="#000000"> </font><font color="#660096">or</font><font color="#000000"> v2t </font><font color="#660096">!=</font><font color="#000000"> </font><font color="#963700">0</font><font color="#000000">
| + | |
| - | [ </font><font color="#0000aa">set</font><font color="#000000"> </font><font color="#660096">heading</font><font color="#000000"> (theta </font><font color="#660096">-</font><font color="#000000"> (</font><font color="#660096">atan</font><font color="#000000"> v2l v2t)) ]
| + | |
| - | ]
| + | |
| - | </font><font color="#007f69">end</font><font color="#000000">
| + | |
| | | | |
| | + | </div><!-- End Page Content --> |
| | | | |
| - | </font><font color="#007f69">to</font><font color="#000000"> stick
| + | <div id="push"></div> |
| - | </font><font color="#0000aa">if</font><font color="#000000"> </font><font color="#660096">random</font><font color="#000000"> </font><font color="#963700">100</font><font color="#000000"> </font><font color="#660096"><=</font><font color="#000000"> secBprob [
| + | </div> |
| - | </font><font color="#0000aa">if</font><font color="#000000"> (</font><font color="#660096">count</font><font color="#000000"> </font><font color="#660096">other</font><font color="#000000"> PP1s-here </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">1</font><font color="#000000"> ) </font><font color="#660096">and</font><font color="#000000"> (linked? </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">false</font><font color="#000000">)
| + | |
| - | [
| + | |
| - | </font><font color="#0000aa">let</font><font color="#000000"> candidate </font><font color="#660096">one-of</font><font color="#000000"> </font><font color="#660096">other</font><font color="#000000"> PP1s-here </font><font color="#5a5a5a">; with [stick-count = 1]</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> (candidate </font><font color="#660096">!=</font><font color="#000000"> </font><font color="#963700">nobody</font><font color="#000000">)</font><font color="#5a5a5a">; and (speed > 0 or [speed] of candidate > 0)</font><font color="#000000">
| + | |
| - | [
| + | |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> candidate [ | + | |
| - | </font><font color="#0000aa">if</font><font color="#000000"> linked? </font><font color="#660096">=</font><font color="#000000"> </font><font color="#963700">false</font><font color="#000000"> [
| + | |
| - | </font><font color="#0000aa">create-link-to</font><font color="#000000"> </font><font color="#660096">myself</font><font color="#000000">[
| + | |
| - | </font><font color="#0000aa">tie</font><font color="#000000">
| + | |
| - | </font><font color="#0000aa">hide-link</font><font color="#000000">
| + | |
| - | ] </font><font color="#0000aa">ask</font><font color="#000000"> </font><font color="#660096">one-of</font><font color="#000000"> </font><font color="#660096">other</font><font color="#000000"> secBs-here [</font><font color="#0000aa">set</font><font color="#000000"> linked? </font><font color="#963700">true</font><font color="#000000">]
| + | |
| - | </font><font color="#0000aa">set</font><font color="#000000"> linked? </font><font color="#963700">true</font><font color="#000000">
| + | |
| - | ]
| + | |
| - | ]
| + | |
| - |
| + | |
| - | ] | + | |
| - | ]
| + | |
| - | ]
| + | |
| - | </font><font color="#007f69">end</font><font color="#000000"> | + | |
| | | | |
| | + | <div id="footer"> |
| | + | <div class="container"> |
| | + | <p class="muted credit"> Created for <a href="https://igem.org/Main_Page">iGEM 2013</a> Dundee. Based upon <a href ="http://twitter.github.io/bootstrap/">Bootstrap</a> and <a href="http://jquery.com/">JQuery</a>. Design by <a href="www.kyleharrison.co.uk"> Kyle Harrison </a>. </p> |
| | + | </div> |
| | + | </div> |
| | | | |
| - | </font><font color="#007f69">to</font><font color="#000000"> unstick
| |
| - | </font><font color="#0000aa">ask</font><font color="#000000"> </font><font color="#660096">out-link-neighbors</font><font color="#000000"> [
| |
| - | </font><font color="#5a5a5a">; set heading (- heading)</font><font color="#000000">
| |
| - | </font><font color="#5a5a5a">; set linked? false</font><font color="#000000">
| |
| - | </font><font color="#5a5a5a">; fd 1</font><font color="#000000">
| |
| - | </font><font color="#0000aa">die</font><font color="#000000">
| |
| - | ]
| |
| - | </font><font color="#5a5a5a">; set linked? false</font><font color="#000000">
| |
| - |
| |
| - | </font><font color="#007f69">end</font>
| |
| - | </pre>
| |
| | | | |
| - | </body> | + | </body> |
| | </html> | | </html> |
"
