Team:Carnegie Mellon/Modeling

<!-- *** What falls between these lines is the Alert Box!  You can remove it from your pages once you have read and understood the alert *** -->

<html>
<div id="box" style="width: 700px; margin-left: 137px; padding: 5px; border: 3px solid #000; background-color: #fe2b33;">
<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;">
This is a template page. READ THESE INSTRUCTIONS.
</div>
<div id="instructions" style="text-align: center; font-weight: normal; font-size: small; color: #f6f6f6; padding: 5px;">
You are provided with this team page template with which to start the iGEM season.  You may choose to personalize it to fit your team but keep the same "look." Or you may choose to take your team wiki to a different level and design your own wiki.  You can find some examples <a href="https://2008.igem.org/Help:Template/Examples">HERE</a>.
</div>
<div id="warning" style="text-align: center; font-weight: bold; font-size: small; color: #f6f6f6; padding: 5px;">
You <strong>MUST</strong>  have all of the pages listed in the menu below with the names specified.  PLEASE keep all of your pages within your teams namespace.  
</div>
</div>
</html>

<!-- *** End of the alert box *** -->


{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
!align="center"|[[Team:Carnegie_Mellon|Home]]
!align="center"|[[Team:Carnegie_Mellon/Team|Team]]
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Carnegie_Mellon Official Team Profile]
!align="center"|[[Team:Carnegie_Mellon/Project|Project]]
!align="center"|[[Team:Carnegie_Mellon/Parts|Parts Submitted to the Registry]]
!align="center"|[[Team:Carnegie_Mellon/Modeling|Modeling]]
!align="center"|[[Team:Carnegie_Mellon/Notebook|Notebook]]
!align="center"|[[Team:Carnegie_Mellon/Safety|Safety]]
!align="center"|[[Team:Carnegie_Mellon/Attributions|Attributions]]
|}


'''Intracellular model'''

The intracellular model attempts to simulate the synthesis and action of KillerRed using ordinary differential equations over three stages of a typical photobleaching expeiment: induction at 37degC, storage at 4degC to allow for protein maturation, and photobleaching at room temperature. It includes:

mRNA synthesis and degradation

KillerRed synthesis, maturation, and degradation

KillerRed states: singlet, singlet excited, triplet excited, and deactivated

Superoxide production (by KillerRed)

Superoxide elimination (by superoxide dismutase)

Parameters:

mRNA synthesis: adapted from Kennell and Riezman 1977.

mRNA degradation: Bernstein, Lin, Cohen, and Lin-Chao 2002.

KillerRed synthesis: from Kennell and Riezman 1977 and our own fluorescence data

Superoxide production: adapted from Tsien and Waggoner 1995; Song, Hennink, Young, and Tanke 1995; and our own fluorescence data.