Difference between revisions of "Team:Hong Kong-CUHK/Modeling"
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<center><div style="text-align:justify; text-justify:inter-ideograph; width:1000px"> | <center><div style="text-align:justify; text-justify:inter-ideograph; width:1000px"> | ||
<font face="Times New Roman" size="5pt"> | <font face="Times New Roman" size="5pt"> | ||
− | <h1> Modeling</h1> | + | <h1>Modeling</h1> |
<br> | <br> | ||
− | <p><font face="Times New Roman" size="4pt"> Magnetosome can be used in different | + | <p><font face="Times New Roman" size="4pt"> Magnetosome can be used in different perspectives, thus a great potential to apply in multiple instances. Three applications has been modeled as follows:</p></font> |
− | < | + | <h3> 1) Protein Extraction</h3> |
− | <p><font face="Times New Roman" size="4pt">Magnetosome can be used in microscopic point of view. We | + | <p><font face="Times New Roman" size="4pt">Magnetosome can be used in microscopic point of view. We tried to model the efficiency to bind with <b>(a) different proteins</b> and <b>(b) use GFP-nanobody for immunoprecipitation</b>. The main purpose of this modelling is to stimulate the <b>binding dynamics</b> of a fixed concentration of magnetosome and GFP-nanobody in different initial concentration of antigens.</p></font><br> |
<p><font face="Times New Roman" size="4pt">Various conditions and parameters:</p></font> | <p><font face="Times New Roman" size="4pt">Various conditions and parameters:</p></font> | ||
<center><table><tr> | <center><table><tr> | ||
− | <th>Fixed | + | <th>Fixed Quantity</th> <th>Quantity</th> |
</tr><tr> | </tr><tr> | ||
− | <th>Volume of the mixture</th> <th> | + | <th>Volume of the mixture</th> <th>1000 μl</th> |
</tr></table></center> | </tr></table></center> | ||
− | + | <br> | |
<center><table><tr> | <center><table><tr> | ||
− | <th>Parameters</th> <th> | + | <th>Parameters</th> <th>Quantity</th> |
</tr><tr> | </tr><tr> | ||
− | <th>Molecular Weight of | + | <th>Molecular Weight of Magnetosome</th> <th>6.89 × 10<sup>-8</sup> g</th> |
</tr><tr> | </tr><tr> | ||
− | <th>Number of GFP-nanobody per | + | <th>Number of GFP-nanobody per Magnetosome</th> <th>362</th> |
</tr><tr> | </tr><tr> | ||
− | <th> | + | <th>Association Rate Constant (k<sub>on</sub>; Marta H. Kubala†, 2010)</th> |
− | <th>8. | + | <th>8.84 × 10<sup>4</sup> M<sup>-1</sup> s<sup>-1</sup></th> |
</tr><tr> | </tr><tr> | ||
− | <th> | + | <th>Dissociation Rate Constant (k<sub>off</sub>; Marta H. Kubala†, 2010)</th> |
− | <th>1. | + | <th>1.24 × 10<sup>-4</sup> s<sup>-1</sup></th> |
</tr></table></center> | </tr></table></center> | ||
<center><table><tr> | <center><table><tr> | ||
− | <th>Condition</th> <th> | + | <th>Condition</th> <th>Quantity</th> |
</tr><tr> | </tr><tr> | ||
− | <th>Amount of | + | <th>Amount of Magnetosome</th> <th>1.5 mg</th> |
</tr><tr> | </tr><tr> | ||
− | <th>Weight of GFP-nanobody</th> <th> | + | <th>Weight of GFP-nanobody</th> <th>Negligible</th> |
</tr><tr> | </tr><tr> | ||
− | <th>Initial | + | <th>Initial Molarity of Antigen (GFP)</th> <th>Varying from 0 to 1.6 μM</th> |
</tr><tr> | </tr><tr> | ||
− | <th>Initial | + | <th>Initial Amount of GFP:GFP-nanobody complex</th> <th>0</th> |
</tr></table></center> | </tr></table></center> | ||
− | <p><font face="Times New Roman" size="4pt">First, the molarity of | + | <p><font face="Times New Roman" size="4pt">First, the molarity of magnetosomes is calculated since the amount of magnetosome and its molecular weight are known,</p></font><br> |
− | <Center>Molarity of Magnetosome=(1. | + | <Center>Molarity of Magnetosome=(1.5 mg / 6.89 × 10<sup>-8</sup> g) / (1 ml) = 2.18 nM</center> |
− | <p><font face="Times New Roman" size="4pt">There are 362 GFP-nanobody per each magnetosome, the molarity of GFP-nanobody is:</p></font> | + | <p><font face="Times New Roman" size="4pt">There are 362 GFP-nanobody per each magnetosome, so the molarity of GFP-nanobody is:</p></font> |
− | <Center>Molarity of GFP-nanobody = 2.18 | + | <Center>Molarity of GFP-nanobody = 2.18 nM × 362 = 7.78 × 10<sup>-7</sup> M</Center> |
− | <p><font face="Times New Roman" size="4pt">After that, a software called Simbiology is used in MATLAB | + | <p><font face="Times New Roman" size="4pt">After that, a software called Simbiology is used in MATLAB to model and stimulate the dynamics of the association and dissociation between the molecules. By constructing a model about the mathematical relationship between molecules, reaction process can be stimulated.</p></font> |
Revision as of 15:28, 18 September 2015