Difference between revisions of "Team:Heidelberg/Modeling"

(Prototype team page)
 
 
(18 intermediate revisions by 3 users not shown)
Line 1: Line 1:
−
{{Heidelberg}}
+
{{Heidelberg/Header}}
 +
{{Heidelberg/js/zitator.js}}
 +
{{Heidelberg/navbar}}
 
<html>
 
<html>
 +
<script type="text/javascript">var bibfile = "</html>{{filepath:Heidelberg_citations_michael.txt|nowiki}}<html>".replace("&#58;",":");
 +
new Zitator(".basictext",bibfile).zitiere();
 +
</script>
 +
</html>
 +
<html>
 +
<head/>
 +
<body>
 +
<div class="container">
 +
<div class="content">
 +
<img src="https://static.igem.org/mediawiki/2015/5/5f/Heidelberg_media_banner_sextant.svg" style="width:100%; top:70px; margin-top: -10px;margin-left:-20px;">
 +
</div>
 +
</div>
 +
</body>
 +
</html>
 +
<html>
 +
<head></head>
 +
<body>
 +
<div class="container">
 +
<div class="content">
 +
<div class="row">
 +
<div class="col-lg-12">
 +
<div class="panel panel‐default">
 +
<div class="panel‐heading">
 +
<h3 class="basicheader"> Overview Modeling</h3>
 +
</div> <!-- panel-heading -->
 +
<div class="panel‐body">
 +
<div class="row">
 +
<div class="col-lg-12">
 +
<p class="basictext">
 +
In our subprojects on the development of switchable aptamer sensors and on aptamer-based small-molecule sensing, we wanted to determine affinities and kinetic parameters of enzymes. For this purpose, we constructed mathematical models of coupled ordinary differential equations (ODEs) and used experimental data for parameter estimations.
 +
Thereby, we could successfully characterize affinities of switchable aptamer sensors to their targets and the switching behavior of software-designed stems. With regard to our in-vitro transcription subproject, we could test different hypotheses on the function of a polymerase based on model selection. We learned that the binding kinetics of the polymerase to its target is an important determinant for the transcription kinetics. The surprising result that increasing the concentration of the polymerase results in a hyper-linear gain of products could be mechanistically verified by a decrease of polymerase accuracy at higher ATP to polymerase ratios. In the following sections the two models shall be described. <br/> <br/>
  
−
<h2> Modeling</h2>
 
  
 +
Assisting the optimization of switchable <a href="https://2015.igem.org/Team:Heidelberg/Modeling/aptakinetics">aptamer sensors</a> by mathematical modeling <br/> <br/>
  
−
<div class="highlightBox">
+
Studying <a href="https://2015.igem.org/Team:Heidelberg/Modeling/rtsms">determinants of polymerase efficiency</a> based on an aptamer sensor
−
<h4>Note</h4>
+
−
<p>In order to be considered for the <a href="https://2015.igem.org/Judging/Awards#SpecialPrizes">Best Model award</a>, you must fill out this page.</p>
+
−
</div>
+
  
−
 
−
<p>Mathematical models and computer simulations provide a great way to describe the function and operation of BioBrick Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior in conjunction with experiments in the wetlab.</p>
 
−
 
−
<p>
 
−
Here are a few examples from previous teams:
 
 
</p>
 
</p>
−
<ul>
+
</div> <!-- col-lg-12 -->
−
<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">ETH Zurich 2014</a></li>
+
</div> <!-- row -->
−
<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">Waterloo 2014</a></li>
+
</div> <!-- panel-body -->
−
</ul>
+
</div> <!-- panel panel‐default -->
−
 
+
</div> <!-- col-lg-12 -->
−
 
+
</div> <!-- row -->
−
</div>
+
<div class="row">
−
 
+
        <div class="col-lg-12">
 +
            <div class="panel panel‐default" style="min-height:318px;">
 +
<div class="panel‐heading">
 +
<h3 class="basicheader"> </h3>
 +
</div> <!-- panel-heading -->
 +
                <!-- panel-heading -->
 +
                <div class="panel‐body">
 +
                    <div class="row">
 +
                        <div class="col-lg-12">
 +
                            <p class="basictext" id="references"></p>
 +
                        </div>
 +
                    </div>
 +
                    <!-- row -->
 +
                </div>
 +
                <!-- panel-body -->
 +
            </div>
 +
            <!-- panel panel‐default -->
 +
        </div>
 +
        <!-- col-lg-12 -->
 +
    </div>
 +
    <!-- row -->
 +
</div> <!-- content -->
 +
</div> <!-- container -->
 +
</body>
 
</html>
 
</html>

Latest revision as of 05:13, 2 October 2015

Overview Modeling

In our subprojects on the development of switchable aptamer sensors and on aptamer-based small-molecule sensing, we wanted to determine affinities and kinetic parameters of enzymes. For this purpose, we constructed mathematical models of coupled ordinary differential equations (ODEs) and used experimental data for parameter estimations. Thereby, we could successfully characterize affinities of switchable aptamer sensors to their targets and the switching behavior of software-designed stems. With regard to our in-vitro transcription subproject, we could test different hypotheses on the function of a polymerase based on model selection. We learned that the binding kinetics of the polymerase to its target is an important determinant for the transcription kinetics. The surprising result that increasing the concentration of the polymerase results in a hyper-linear gain of products could be mechanistically verified by a decrease of polymerase accuracy at higher ATP to polymerase ratios. In the following sections the two models shall be described.

Assisting the optimization of switchable aptamer sensors by mathematical modeling

Studying determinants of polymerase efficiency based on an aptamer sensor