"
Team:NTU-Taida/Modeling/Parameters
From 2012.igem.org
(Difference between revisions)
(→Single-Cell/ System analysis Model) |
(→Fatty Acid Reaction Absorption Model Model) |
||
| Line 179: | Line 179: | ||
<html> | <html> | ||
| - | <table | + | <table> |
| - | + | <thead> | |
| - | + | <tr> | |
| - | + | <td> <b>Parameter</b> </td> | |
| - | + | <td> <b>Description</b> </td> | |
| - | + | <td> <b>Value</b> </td> | |
| - | + | <td> <b>Reference</b> </td> | |
| - | + | </tr> | |
| - | + | </thead> | |
| - | + | <tbody> | |
| - | + | <tr> | |
| - | + | <td> \([E]_t \) </td> | |
| - | + | <td> Total active enzyme </td> | |
| - | + | <td> \(50~\mu\text{M} \) </td> | |
| - | + | <td> [8] </td> | |
| - | + | </tr> | |
| - | + | <tr> | |
| - | + | <td> \(K_m \) </td> | |
| - | + | <td> Reaction rate constant </td> | |
| - | + | <td> 47.9 </td> | |
| - | + | <td> [6][7] </td> | |
| - | + | </tr> | |
| - | </ | + | <tr> |
| - | + | <td> \(D_{FA} \) </td> | |
| - | + | <td> FA Diffusion Constant </td> | |
| - | + | <td> \( 6.46 \cdot 10^{-10} \cdot \text{m}^2 \cdot \text{s}^{-1} \) </td> | |
| - | + | <td> </td> | |
| - | + | </tr> | |
| - | + | <tr> | |
| - | + | <td> \(d\) </td> | |
| - | + | <td> Thickness of the unstirred water layer </td> | |
| - | + | <td> \( 190~\mu\text{m} \) </td> | |
| - | + | <td> [9] </td> | |
| - | + | </tr> | |
| - | + | <tr> | |
| - | + | <td> \( \frac{K_{cat}}{\text{molecular weight}} \)</td> | |
| - | + | <td> Catalytic Rate constant </td> | |
| - | + | <td> \(1.8\cdot10^{-3}\) </td> | |
| - | + | <td> [6][7] </td> | |
| - | + | </tr> | |
| - | + | </tbody> | |
| - | + | </table> | |
| - | + | ||
| - | + | </html> | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | </tbody></table></html> | + | |
==Cell-Cell Communication Model== | ==Cell-Cell Communication Model== | ||
Revision as of 18:59, 25 October 2012
Cell Population Response Model
Parameters
Contents |
Single-Cell/ System analysis Model
| Parameter | Description | Value | Reference |
| \(\alpha_{TetR} \) | TetR max. production rate | \(0.8~\mu \text{M}\cdot\text{min}^{-1} \) | [5] |
| \(\alpha_{FadR} \) | FadR max. production rate | \(100~\mu\text{M}\cdot\text{min}^{-1} \) | a. |
| \(\alpha_{GLP-1} \) | GLP-1 max. production rate | \(1.23~\mu\text{M}\cdot\text{min}^{-1} \) | a. |
| \(\alpha_{LacI} \) | LacI max. production rate | \(0.8~\mu\text{M}\cdot\text{min}^{-1} \) | [1] |
| \(k_{s1} \) | AHL i production rate | \(0.01~\text{min}^{-1} \) | [2] |
| \(\rho_R \) | LuxR-AHL dimerization rate | \(0.5~\mu\text{M}^{-3}\cdot min^{-1} \) | [1] |
| \(\beta_{TetR} \) | TetR repression coefficient | \(0.13~\mu\text{M} \) | a. |
| \(\beta_{FA} \) | FA repression coefficient | \(10~\mu\text{M} \) | [1] |
| \(\beta_{FadR} \) | FadR repression coefficient | \(0.13~\mu\text{M} \) | [1] |
| \(\beta_{LacI} \) | LacI repression coefficient | \(0.8~\mu\text{M} \) | [1] |
| \(\beta_R \) | LuxR-AHL repression coefficient | \(0.01~\mu\text{M} \) | [1] |
| \(\gamma_{TetR} \) | TetR degradation rate | \(0.0692~\text{min}^{-1} \) | a. |
| \(\gamma_{LacI} \) | LacI degradation rate | \(0.0231~\text{min}^{-1} \) | [1] |
| \(\gamma_{GLP-1} \) | GLP-1 degradation rate | \(0.0731~\text{min}^{-1} \) | [1] |
| \(\gamma_{LuxI} \) | LuxI degradation rate | \(0.0167~\text{min}^{-1} \) | [3] |
| \(k_{s0} \) | AHLi degradation rate | \(1~\text{min}^{-1} \) | [2] |
| \(k_{se} \) | AHLe degradation rate | \(1~\text{min}^{-1} \) | [2] |
| \(\gamma_R \) | LuxR-AHL degradation rate | \(0.0231~\text{min}^{-1} \) | [1] |
| \(\gamma_{RFP} \) | RFP degradation rate | \(0.0041~\text{min}^{-1} \) | [4] |
| \(n_1\) | FadR cooperativity coefficient | \(3\) | a. |
| \(n_2\) | FA cooperativity coefficient | \(2\) | a. |
| \(n_3\) | LuxR-AHL cooperativity coefficient | \(3\) | [1] |
| \(n_5\) | TetR cooperativity coefficient | \(2\) | [2] |
| \(n_6\) | LacI cooperativity coefficient | \(4\) | [1] |
| \(\eta\) | AHL Diffusion rate across the cell membrane | \(2\) | [2] |
| \(\eta\)ext | Average diffusion rate for all cells | \(1\) | [2] |
Fatty Acid Reaction Absorption Model Model
| Parameter | Description | Value | Reference |
| \([E]_t \) | Total active enzyme | \(50~\mu\text{M} \) | [8] |
| \(K_m \) | Reaction rate constant | 47.9 | [6][7] |
| \(D_{FA} \) | FA Diffusion Constant | \( 6.46 \cdot 10^{-10} \cdot \text{m}^2 \cdot \text{s}^{-1} \) | |
| \(d\) | Thickness of the unstirred water layer | \( 190~\mu\text{m} \) | [9] |
| \( \frac{K_{cat}}{\text{molecular weight}} \) | Catalytic Rate constant | \(1.8\cdot10^{-3}\) | [6][7] |
Cell-Cell Communication Model
|
Parameter |
Description |
Value |
Reference |
|
cd |
E.
coli Cell Density |
0.1 |
|
|
DFA |
FA Diffusion Constant |
6.46* 10^-10m^2 /s |
|
|
DAHL |
AHL Diffusion Constant |
4.9e-6 cm2/s |
[9] |
|
γAHL,ext |
AHL cell-external degradation |
8.0225e-006/s |
Derived from 1 day half-life at pH 7 [7] |
Reference
|
Source |
|
|
[1] |
Subhayu Basu, Yoram
Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss.A
synthetic multicellular system for programmed pattern formation, Nature
Vol. 434, 2005 |
|
[2] |
Garcia-Ojalvo, Michael B. Elowitz,
and Steven H. Strogatz. Modeling a synthetic multicellular clock:
Repressilators coupled by quorum sensing, PNAS vol. 101 no. 30, 2004 |
|
[3] |
MIT igem 2010 |
|
[4] |
Michael Halter, Alex Tona,
Kiran Bhadriraju, Anne L. Plant, John T. Elliott, Automated Live Cell
Imaging of Green Fluorescent Protein Degradation in Individual Fibroblasts,
Cytometry Part A, Volume 71A Issue 10, 2007 |
|
[5] |
Wilfried Weber, Markus
Rimann, Manuela Spielmann, Bettina Keller, Marie Daoud-El Baba, Dominique
Aubel, Cornelia C Weber & Martin Fussenegger, Gas-inducible
transgene expression in mammalian cells and mice, Nature Biotechnology, volume
22, number 11, 2004 |
|
[6] |
Sulaiman Al-Zuhair,
Masitah Hasan, K.B. Ramachandran, Kinetics of the enzymatic hydrolysis of
palm oil by lipase, Process Biochemistry Volume 38, Issue 8, 2003 |
|
[7] |
Ho-Shing Wu, Ming-Ju Tsai,
Kinetics of tributyrin hydrolysis by
lipase, Enzyme and Microbial Technology, Volume 35, Issues 6–7, 2004 |
|
[8] |
Bengt Borgstrom, Luminal Digestion of Fats, Handbook
of Physiology, The Gastrointestinal System, Intestinal Absorption and
Secretion, 1991 |
|
[9] |
Sallee VL, Dietschy JM., Determinants of intestinal mucosal uptake
of short- and medium-chain fatty acids and alcohols, Journal of Lipid
Research, 1973 |
