Biomod/2011/UTAustin/Hook'em Hybridizers

From OpenWetWare

< Biomod | 2011(Difference between revisions)
Jump to: navigation, search
Current revision (01:37, 3 November 2011) (view source)
 
(28 intermediate revisions not shown.)
Line 1: Line 1:
-
<div id="outerbox" style="background-color:#042358; padding-top:10px; padding-bottom:10px;">
+
<html><head>
 +
<style type="text/css">
 +
#outerbox{
 +
//background-image:url( 'http://openwetware.org/images/7/75/Utbiomodbg1.png' );
 +
//background-repeat:repeat-x;
 +
background-image: linear-gradient(bottom, rgb(0,0,0) 9%, rgb(204,85,0) 55%);
 +
background-image: -o-linear-gradient(bottom, rgb(0,0,0) 9%, rgb(204,85,0) 55%);
 +
background-image: -moz-linear-gradient(bottom, rgb(0,0,0) 9%, rgb(204,85,0) 55%);
 +
background-image: -webkit-linear-gradient(bottom, rgb(0,0,0) 9%, rgb(204,85,0) 55%);
 +
background-image: -ms-linear-gradient(bottom, rgb(0,0,0) 9%, rgb(204,85,0) 55%);
-
<div id="innerbox" style="width: 800px; padding: 5px; margin: auto; background-color:#ffffff; border-radius: 5px">
+
background-image: -webkit-gradient(
 +
linear,
 +
left bottom,
 +
left top,
 +
color-stop(0.09, rgb(0,0,0)),
 +
color-stop(0.55, rgb(204,85,0))
 +
);
 +
}
-
<div id="header" style="background-color:#FFFFFF;">
+
.navbox {
 +
position: relative;
 +
float: left;
 +
}
 +
 
 +
ul#nav {
 +
    list-style: none;
 +
    display: block;
 +
    width: 200px;
 +
    left: -29px;
 +
    top: -20px;
 +
    position: relative;
 +
    padding: 60px 0 60px 0;
 +
    width: 200px;
 +
    background: url( 'http://openwetware.org/images/6/6f/Shad2.png' ) no-repeat;
 +
    background-size: 50% 100%;
 +
}
 +
 
 +
li {
 +
margin: 5px 0 0 0;
 +
}
 +
 
 +
ul#nav a:hover {
 +
    text-decoration: none;
 +
}
 +
 
 +
ul#nav li span {
 +
    -webkit-transition: all 0.3s ease-out;
 +
    -moz-transition: all 0.3s ease-out;
 +
    -o-transition: all 0.3s ease-out;
 +
    background: #E07020 url( 'http://openwetware.org/images/4/46/Border.png' ) no-repeat;
 +
    color: #174867;
 +
    padding: 7px 15px 7px 15px;
 +
    border-top-right-radius: 10px;
 +
    border-bottom-right-radius: 10px;
 +
    width: 100px;
 +
    display: block;
 +
    text-decoration: none;
 +
    box-shadow: 2px 2px 4px #BB4400;
 +
}
 +
 
 +
ul#nav li span:hover {
 +
    background: #F08030 url( 'http://openwetware.org/images/4/46/Border.png' ) no-repeat;
 +
    color: #67a5cd;
 +
    padding: 7px 15px 7px 30px;
 +
    display: block;
 +
}
 +
 
 +
</style>
 +
</head>
 +
</html>
 +
 
 +
<div id="outerbox" style="padding-top:10px; padding-bottom:10px;">
 +
 
 +
<div id="innerbox" style="width: 820px; padding: 15px; margin: auto; background-color:#000000; border-radius: 5px">
 +
 
 +
<div id="header" style="background-color:#000000;">
<center>
<center>
-
[[Image:Ut_longhorn_logo2_png_800x1000_q100.png‎|200px]]
+
[[Image:UTBiomodBanner2.png|780px]]
-
<span style="font-size:40px; font-family: Arial; font-weight:bold; color:#CC5500; vertical-align: middle;">The Hook'em Hybridizers</span>
+
</center>
</center>
</div>
</div>
-
<div style="padding: 10px; color: #FFFFFF; background-color: #CC5500; width: 130px; height: 800px; float: left;">
+
<div style="padding: 10px; color: #FFFFFF; background-color: #CC5500; width: 130px; height: 1025px; float: left;">
-
<div>
+
<div id="navbox">
-
[[Biomod/2011/UTAustin/Hook'em_Hybridizers | <span style='font-size:16px; font-family: "trebuchet ms"; font-weight:bold; color:#FFFFFF; vertical-align: middle; text-decoration: none;'>'''Home'''</span> ]]
+
<ul id="nav">
-
</div>
+
<li>
-
<div>
+
[[Biomod/2011/UTAustin/Hook'em_Hybridizers | <span style='font-size:16px; font-family: "trebuchet ms"; font-weight:bold; color:#FFFFFF; vertical-align: middle; text-decoration: none;'>'''Home'''</span> ]]
 +
</li>
 +
<li>
[[Biomod/2011/UTAustin/Hook'em_Hybridizers:Rationale | <span style='font-size:16px; font-family: "trebuchet ms"; font-weight:bold; color:#FFFFFF; vertical-align: middle; text-decoration: none;'>'''Rationale'''</span> ]]
[[Biomod/2011/UTAustin/Hook'em_Hybridizers:Rationale | <span style='font-size:16px; font-family: "trebuchet ms"; font-weight:bold; color:#FFFFFF; vertical-align: middle; text-decoration: none;'>'''Rationale'''</span> ]]
-
</div>
+
</li>
-
<div>
+
<li>
[[Biomod/2011/UTAustin/Hook'em Hybridizers:Simulation | <span style='font-size:16px; font-family: "trebuchet ms"; font-weight:bold; color:#FFFFFF; vertical-align: middle; text-decoration: none;'>'''Simulation'''</span> ]]
[[Biomod/2011/UTAustin/Hook'em Hybridizers:Simulation | <span style='font-size:16px; font-family: "trebuchet ms"; font-weight:bold; color:#FFFFFF; vertical-align: middle; text-decoration: none;'>'''Simulation'''</span> ]]
-
</div>
+
</li>
-
<div>
+
<li>
[[Biomod/2011/UTAustin/Hook'em Hybridizers:Methods | <span style='font-size:16px; font-family: "trebuchet ms"; font-weight:bold; color:#FFFFFF; vertical-align: middle; text-decoration: none;'>'''Methods'''</span> ]]
[[Biomod/2011/UTAustin/Hook'em Hybridizers:Methods | <span style='font-size:16px; font-family: "trebuchet ms"; font-weight:bold; color:#FFFFFF; vertical-align: middle; text-decoration: none;'>'''Methods'''</span> ]]
-
</div>
+
</li>
-
<div>
+
<li>
[[Biomod/2011/UTAustin/Hook'em Hybridizers:Results | <span style='font-size:16px; font-family: "trebuchet ms"; font-weight:bold; color:#FFFFFF; vertical-align: middle; text-decoration: none;'>'''Results'''</span> ]]
[[Biomod/2011/UTAustin/Hook'em Hybridizers:Results | <span style='font-size:16px; font-family: "trebuchet ms"; font-weight:bold; color:#FFFFFF; vertical-align: middle; text-decoration: none;'>'''Results'''</span> ]]
-
</div>
+
</li>
-
<div>
+
<li>
 +
[[Biomod/2011/UTAustin/Hook'em Hybridizers:Tools | <span style='font-size:16px; font-family: "trebuchet ms"; font-weight:bold; color:#FFFFFF; vertical-align: middle; text-decoration: none;'>'''Tools'''</span> ]]
 +
</li>
 +
<li>
[[Biomod/2011/UTAustin/Hook'em Hybridizers:People | <span style='font-size:16px; font-family: "trebuchet ms"; font-weight:bold; color:#FFFFFF; vertical-align: middle; text-decoration: none;'>'''People'''</span> ]]
[[Biomod/2011/UTAustin/Hook'em Hybridizers:People | <span style='font-size:16px; font-family: "trebuchet ms"; font-weight:bold; color:#FFFFFF; vertical-align: middle; text-decoration: none;'>'''People'''</span> ]]
-
</div>
+
</li>
-
<div>
+
</ul>
-
[[Biomod/2011/UTAustin/Hook'em Hybridizers:Contact | <span style='font-size:16px; font-family: "trebuchet ms"; font-weight:bold; color:#FFFFFF; vertical-align: middle; text-decoration: none;'>'''Contact'''</span> ]]
+
</div>
</div>
</div>
</div>
-
<div style="width: 650px; float: left; padding: 0px">
+
<div style="width: 650px; float: left; padding: 0px; background-color: #000000;">
<div style="width: 320px; text-align: left; float: left; margin-left: 5px">
<div style="width: 320px; text-align: left; float: left; margin-left: 5px">
<div style="height: 30px; background-color: #3F70C3; padding: 10px 10px 10px;">
<div style="height: 30px; background-color: #3F70C3; padding: 10px 10px 10px;">
-
<span style="font-size: 20px; font-family: Verdana; color:#FFFFFF; vertical-align: middle;">Team</span>
+
<span style="font-size: 20px; font-family: Verdana; color:#FFFFFF; vertical-align: middle;">Objective</span>
</div>
</div>
-
<div style="padding: 10px; background-color:#eeeeee; margin-top: 5px; height: 745px;">
+
<div style="padding: 10px; background-color:#000000; color: #FFFFFF; margin-top: 5px; height: 345px;">
-
*Team name: The Hook'em Hybridizers
+
-
*Institution: The University of Texas at Austin
+
-
*Team Members
+
<center>'''Counting Events with a DNA Processor'''</center>
-
**[[User:Ben_Braun|Ben Braun]]
+
-
**[[User:Victor J. Kronberg|Victor Kronberg]]
+
-
**[[User:Jeremy R. McLain|Jeremy McLain]]
+
-
**[[User:Daniel Winkler|Daniel Winkler]]
+
-
*Postdoc Mentors
+
A major goal in nanotechnology is the find useful forms of DNA computation. This broad definition includes amplifiers, logic gates, oscillators, structural manipulations, and many more forms of controlled responses. We believe an enzyme-free, DNA toehold exchange catalyzed system that preforms the computation of “counting” can be useful in various fields of biotechnology. Counting, by our definition, relies on two main principles. The first is the input that is being counted must be the same with each pulse and the second is the output of the counter must be independent of the input quantity or concentration. That is, regardless of the amount of input used, the counter must only reach completion after the specified number of counts, or pulses.
-
**Dr. Peter Allen
+
-
**[[User:Xi_Chen|Dr. Xi Chen]]
+
-
*Faculty mentors
 
-
**[http://ellingtonlab.org/ Dr. Andrew Ellington]
 
</div>
</div>
Line 65: Line 130:
<div style="height: 30px; width: 320px; text-align: left; float: right; margin-left: 5px;">
<div style="height: 30px; width: 320px; text-align: left; float: right; margin-left: 5px;">
-
<div style="background-color: #51D535; padding: 10px 10px 10px;">
+
<div style="background-color: #3F70C3; padding: 10px 10px 10px;">
-
<span style="font-size: 20px; font-family: Verdana; color:#FFFFFF; vertical-align: middle;">About</span>
+
<span style="font-size: 20px; font-family: Verdana; color:#FFFFFF; vertical-align: middle;">The essence of a counter</span>
</div>
</div>
-
<div style="padding: 10px; background-color:#eeeeee; margin-top: 5px; height: 745px;">
+
<div style="padding: 10px; background-color:#000000; margin-top: 5px; height: 345px;">
-
====The Counting Machine as a Modular Nanoscale DNA Component.====
+
<center>[[Image:Counteressence.png|300px]]</center>
 +
</div>
 +
 
 +
</div>
 +
 
 +
<div style="width: 645px; text-align: left; float: left; margin-left: 5px">
 +
 
 +
<div style="padding: 10px; background-color:#000000; margin-top: 5px; height: 600px;">
 +
 
 +
<html><object style="height: 390px; width: 640px"><param name="movie" value="http://www.youtube.com/v/hFEjbkRfkL0?version=3&feature=player_detailpage"><param name="allowFullScreen" value="true"><param name="allowScriptAccess" value="always"><embed src="http://www.youtube.com/v/hFEjbkRfkL0?version=3&feature=player_detailpage" type="application/x-shockwave-flash" allowfullscreen="true" allowScriptAccess="always" width="640" height="360"></object></html>
-
One major goal of nanotechnology is to control chemical
 
-
reactions pera logical specification. Nano-biological devices have
 
-
been"programmed" to function as AND / OR gates, timed oscillators,
 
-
motors,and to have other forms of controlled responses to their
 
-
environment.We have engineered a prototype of an enzyme-free DNA
 
-
circuit based on toeholdexchange to 'count' signal pulses
 
-
corresponding to additions of adefined chemical. Counting, by our
 
-
definition, needs to meet twocriteria: First, the input being being
 
-
counted is a single chemicalused for each pulse. Second, the counter
 
-
should output an ON signalonly when some fixed number of pulses have
 
-
been encountered,regardless of the amount of input added in any pulse,
 
-
and the strengthof the ON signal should be independent of the amount
 
-
of input addedeach pulse. The molecular basis of our prototype
 
-
count-to-two unitincludes (1) a time-delayedsignal transduction series
 
-
coupled to an AND gate and (2) a mechanism forconstant input
 
-
degradation.  In theory such units can be connected seriallyto make a
 
-
counter that is capable to count to any pre-specified finitenumber.
 
</div>
</div>

Current revision

Objective

Counting Events with a DNA Processor

A major goal in nanotechnology is the find useful forms of DNA computation. This broad definition includes amplifiers, logic gates, oscillators, structural manipulations, and many more forms of controlled responses. We believe an enzyme-free, DNA toehold exchange catalyzed system that preforms the computation of “counting” can be useful in various fields of biotechnology. Counting, by our definition, relies on two main principles. The first is the input that is being counted must be the same with each pulse and the second is the output of the counter must be independent of the input quantity or concentration. That is, regardless of the amount of input used, the counter must only reach completion after the specified number of counts, or pulses.

The essence of a counter

Personal tools