Difference between revisions of "Term paper wiki"

From GcatWiki
Jump to: navigation, search
 
(30 intermediate revisions by the same user not shown)
Line 1: Line 1:
<center>[[Davidson Missouri W| <span style="color:black">Home</span>]] | [[Davidson Missouri W/Background Information| <span style="color:red">Background Information</span>]] | [[Davidson Missouri W/Solving the HPP in vivo| <span style="color:red">Current Project: Solving the Hamiltonian Path Problem ''in vivo''</span>]] | [[Davidson Missouri W/Mathematical Modeling| <span style="color:red">Mathematical Modeling</span>]] | [[Davidson Missouri W/Gene splitting| <span style="color:red">Gene Splitting</span>]] | [[Davidson Missouri W/Results| <span style="color:red">Results</span>]] |  [[Davidson Missouri W/Traveling Salesperson Problem| <span style="color:red">Traveling Salesperson Problem</span> ]] | [[Davidson Missouri W/Software|<span style="color:red">Software</span>]] | [[Davidson Missouri W/Resources and Citations|<span style="color:red">Resources and Citations</span>]]</center>
+
<center>[[Term Paper Wiki| <span style="color:red">Home</span>]] | [[Origins and Characterization of Stochasticity| <span style="color:red">Origins and Characterization of Stochasticity</span>]] | [[Modeling Stochasticity| <span style="color:red">Modeling Stochasticity</span>]] | [[Manipulation of Stochasticity| <span style="color:red">Manipulation of Stochasticity</span>]] | [[Evolved Stochasticity? | <span style="color:red">Evolved Stochasticity?</span>]] |  [[Concluding Remarks | <span style="color:red">Concluding Remarks </span> ]] | [[Citations|<span style="color:red">Citations</span>]]</center>
  
  
Line 12: Line 12:
 
|-
 
|-
 
|style="color: black; background-color: black;" align="center"|
 
|style="color: black; background-color: black;" align="center"|
[[Davidson Missouri W/Background Information|<span style="color:red">Background Information</span>]]
+
[[Origins and Characterization of Stochasticity|<span style="color:red">Origins and Characterization of Stochasticity</span>]]
 
<br><br><br>
 
<br><br><br>
[[Davidson Missouri W/Solving the HPP in vivo|<span style="color:red">Current Project: Solving the Hamiltonian Path Problem ''in vivo''</span>]]
+
[[Modeling Stochasticity|<span style="color:red">Modeling Stochasticity</span>]]
 
<br><br><br>
 
<br><br><br>
[[Davidson Missouri W/Mathematical Modeling|<span style="color:red">Mathematical Modeling</span>]]
+
[[Manipulation of Stochasticity|<span style="color:red">Manipulation of Stochasticity</span>]]
 
<br><br><br>
 
<br><br><br>
[[Davidson Missouri W/Gene splitting|<span style="color:red">Gene Splitting</span>]]
+
[[Evolved Stochasticity?|<span style="color:red">Evolved Stochasticity?</span>]]
 
<br><br><br>
 
<br><br><br>
[[Davidson Missouri W/Results|<span style="color:red">Results</span>]]
+
[[Concluding Remarks|<span style="color:red">Concluding Remarks</span>]]
 
<br><br><br>
 
<br><br><br>
[[Davidson Missouri W/Traveling Salesperson Problem|<span style="color:red">Traveling Salesperson Problem</span>]]
+
[[Citations|<span style="color:red">Citations</span>]]
<br><br><br>
 
[[Davidson Missouri W/Software|<span style="color:red">Software</span>]]
 
<br><br><br>
 
[[Davidson Missouri W/Resources and Citations|<span style="color:red">Resources and Citations</span>]]
 
 
<br><br><Br>
 
<br><br><Br>
|Hamiltonian Path Problem
+
|<br> <center>[[Image:Sblogo-small.jpg| 350 px]] <br>Image from Synthetic Biology 2.0 http://pbd.lbl.gov/sbconf/agenda.php permission pending</center><br>The goal of synthetic biology is to create synthetic biological constructs from an engineering perspective. Synthetic biology has implications in many fields such as healthcare, fuel production, and data processing. An exciting component of the field is its integration of biology, chemistry, mathematics and computer science; in order to construct devices from the bottom up, synthetic teams have to be able to amalgamate knowledge from many different fields. Problems arise however when synthetic biologists regard synthetic devices as analogous to electronic circuitry. The stochastic nature of biological processes lead to heterogenic responses for a single input. While these stochastic processes pose a problem for synthetic biology they do not prohibit the successful construction of synthetic biological devices all together. This is because characterization of stochastic processes can lead to dry lab design strategies for implementation <i>in vivo</i>. Here is a characterization of the origin of stochasticity, the devices used to model stochasticity, the effect of stochasticity in gene networks, and a section on why stochastic processes might exist in the cell.  
As a part of iGEM2006, a combined team from Davidson College and Missouri Western State University reconstituted a hin/''hix'' DNA recombination mechanism which exists in nature in ''Salmonella'' as standard biobricks for use in ''E. coli''. The purpose of the 2006 combined team was to provide a proof of concept for a bacterial computer in using this mechanism to solve a variation of The Pancake Problem from Computer Science. This task utilized both biology and mathematics students and faculty from the two institutions.
 
  
For 2007, we successfully continued our collaboration and our efforts to manipulate ''E. coli'' into mathematics problem solvers as we refine our efforts with the hin/''hix'' mechanism to explore another mathematics problem, the Hamiltonian Path Problem. This problem was the subject of a groundbreaking paper by Adleman in 1994 (see [[Davidson_Missouri_W/Resources_and_Citations | citations]]) where a unique Hamiltonian path was found ''in vitro'' for a particular directed graph on seven nodes. We were able to use bacterial computers to solve the Hamiltonian path problem ''in vivo''. ([[Davidson Missouri W/Background Information#Why Use Bacteria?|Why use a bacterial computer?]])
 
 
<br>
 
 
 
[[Image:Adelman.png|thumb|300px|center|The Adleman graph.]] 
 
 
<center> For the graph used in Adleman's paper (shown above), the Hamiltonian Path Problem would ask: can you find a path along the directed edges that travels from node 1 (green) to node 5 (red) and visits each node on the graph exactly once? <br>
 
[http://parts.mit.edu/igem07/images/6/6f/Adelmansolution.png Click here] for the solution.
 
</center>
 
 
|}
 
|}
  
 +
<br><br><br>
  
<Previous Section | [[Davidson Missouri W/Background Information | Next Section>]]
+
<center><Previous Section | [[Origins and Characterization of Stochasticity | Next Section>]]</center>
</center>
 

Latest revision as of 14:23, 6 December 2007

Home | Origins and Characterization of Stochasticity | Modeling Stochasticity | Manipulation of Stochasticity | Evolved Stochasticity? | Concluding Remarks | Citations


Stochasticity in Gene Expression

In Depth Introduction

Origins and Characterization of Stochasticity


Modeling Stochasticity


Manipulation of Stochasticity


Evolved Stochasticity?


Concluding Remarks


Citations



Sblogo-small.jpg
Image from Synthetic Biology 2.0 http://pbd.lbl.gov/sbconf/agenda.php permission pending

The goal of synthetic biology is to create synthetic biological constructs from an engineering perspective. Synthetic biology has implications in many fields such as healthcare, fuel production, and data processing. An exciting component of the field is its integration of biology, chemistry, mathematics and computer science; in order to construct devices from the bottom up, synthetic teams have to be able to amalgamate knowledge from many different fields. Problems arise however when synthetic biologists regard synthetic devices as analogous to electronic circuitry. The stochastic nature of biological processes lead to heterogenic responses for a single input. While these stochastic processes pose a problem for synthetic biology they do not prohibit the successful construction of synthetic biological devices all together. This is because characterization of stochastic processes can lead to dry lab design strategies for implementation in vivo. Here is a characterization of the origin of stochasticity, the devices used to model stochasticity, the effect of stochasticity in gene networks, and a section on why stochastic processes might exist in the cell.




<Previous Section | Next Section>