Difference between revisions of "Team:Heidelberg/Modeling"

 
(10 intermediate revisions by the same user not shown)
Line 1: Line 1:
 
{{Heidelberg/Header}}
 
{{Heidelberg/Header}}
 +
{{Heidelberg/js/zitator.js}}
 
{{Heidelberg/navbar}}
 
{{Heidelberg/navbar}}
 +
<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>
 
<html>
 
<head/>
 
<head/>
Line 6: Line 12:
 
<div class="container">
 
<div class="container">
 
<div class="content">
 
<div class="content">
−
<!-- Button trigger modal -->
+
<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;">
−
<button type="button" class="btn btn-primary btn-lg" data-toggle="modal" data-target="#myModal">
+
−
  Launch demo modal
+
−
</button>
+
−
 
+
−
<!-- Modal -->
+
−
<div class="modal fade" id="myModal" tabindex="-1" role="dialog" aria-labelledby="myModalLabel">
+
−
  <div class="modal-dialog" role="document">
+
−
    <div class="modal-content">
+
−
      <div class="modal-header">
+
−
        <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
+
−
        <h4 class="modal-title" id="myModalLabel">Modal title</h4>
+
−
      </div>
+
−
      <div class="modal-body">
+
−
        ...
+
−
      </div>
+
−
      <div class="modal-footer">
+
−
        <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
+
−
        <button type="button" class="btn btn-primary">Save changes</button>
+
−
      </div>
+
−
    </div>
+
−
  </div>
+
−
</div>
+
 
</div>
 
</div>
 
</div>
 
</div>
 
</body>
 
</body>
 
</html>
 
</html>
−
{{Heidelberg/pages/Modeling}}
+
<html>
−
{{Heidelberg/Footer}}
+
<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/>
 +
 
 +
 
 +
Assisting the optimization of switchable <a href="https://2015.igem.org/Team:Heidelberg/Modeling/aptakinetics">aptamer sensors</a> by mathematical modeling <br/> <br/>
 +
 
 +
Studying <a href="https://2015.igem.org/Team:Heidelberg/Modeling/rtsms">determinants of polymerase efficiency</a> based on an aptamer sensor
 +
 
 +
</p>
 +
</div> <!-- col-lg-12 -->
 +
</div> <!-- row -->
 +
</div> <!-- panel-body -->
 +
</div> <!-- panel panel‐default -->
 +
</div> <!-- col-lg-12 -->
 +
</div> <!-- row -->
 +
<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>

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