Team:ITB Indonesia/Modeling/Difussion
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- | + | <h1>Diffusion</h1> | |
+ | <p>First thing to do is calculate how much aflatoxin would enter the cell every time. Aflatoxin diffused into cell through simple diffusion mechanism, it means that aflatoxin difusion is drived by concentration gradient.<br /> | ||
+ | Assumption :</p> | ||
+ | <ul> | ||
+ | <li>Aflatoxin homogenely diffused into cell</li> | ||
+ | </ul> | ||
+ | <p><img src="difussion_clip_image002.png" alt="" width="214" height="35" /><br /> | ||
+ | Parameters of the equation :</p> | ||
+ | <table border="1" cellspacing="0" cellpadding="0"> | ||
+ | <tr> | ||
+ | <td width="73" valign="top"><br /> | ||
+ | <strong>Variable</strong></td> | ||
+ | <td width="302" valign="top"><p><strong>Definition</strong></p></td> | ||
+ | <td width="113" valign="top"><p><strong>Value</strong></p></td> | ||
+ | <td width="127" valign="top"><p><strong>Source</strong></p></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td width="73" valign="top"><p>P</p></td> | ||
+ | <td width="302" valign="top"><p>Permeability aflatoxin-membrane E. coli</p></td> | ||
+ | <td width="113" valign="top"><p>1,01 x 10-4 cm/s</p></td> | ||
+ | <td width="127" valign="top"><p>Calculated (See Sect 1)</p></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td width="73" valign="top"><p>A</p></td> | ||
+ | <td width="302" valign="top"><p>E. coli membrane cell area</p></td> | ||
+ | <td width="113" valign="top"><p>Changing with time</p></td> | ||
+ | <td width="127" valign="top"><p>Calculated (see Sect 2)</p></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td width="73" valign="top"><p><img src="difussion_clip_image004.png" alt="" width="18" height="19" /></p></td> | ||
+ | <td width="302" valign="top"><p>Concentration gradient between inner and outer side of the cell</p></td> | ||
+ | <td width="113" valign="top"><p>-</p></td> | ||
+ | <td width="127" valign="top"><p>Depends on case</p></td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | <h3><strong>I. Permeability aflatoxin-membrane</strong></h3> | ||
+ | <p> | ||
+ | Permeability value between solute and solvent can be described through this equation :<br /> | ||
+ | <img src="difussion_clip_image006.png" alt="" width="59" height="34" /></p> | ||
+ | <table border="1" cellspacing="0" cellpadding="0"> | ||
+ | <tr> | ||
+ | <td width="73" valign="top"><br /> | ||
+ | <strong>Variable</strong></td> | ||
+ | <td width="302" valign="top"><p><strong>Definition</strong></p></td> | ||
+ | <td width="113" valign="top"><p><strong>Value</strong></p></td> | ||
+ | <td width="127" valign="top"><p><strong>Source</strong></p></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td width="73" valign="top"><p>D</p></td> | ||
+ | <td width="302" valign="top"><p>Diffusivity constant of aflatoxin-membrane E. coli</p></td> | ||
+ | <td width="113" valign="top"><p>2,05 x 10-9 cm2/s</p></td> | ||
+ | <td width="127" valign="top"><p>Calculated (see below)</p></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td width="73" valign="top"><p>K</p></td> | ||
+ | <td width="302" valign="top"><p>Partition constant of aflatoxin-membrane E. coli</p></td> | ||
+ | <td width="113" valign="top"><p>0,64</p></td> | ||
+ | <td width="127" valign="top"><p>[9]</p></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td width="73" valign="top"><p>d</p></td> | ||
+ | <td width="302" valign="top"><p>E. coli membrane thickness</p></td> | ||
+ | <td width="113" valign="top"><p>13 nm</p></td> | ||
+ | <td width="127" valign="top"><p>[2]</p></td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | <p>To determine the value of diffusivity constant, we use Stoke-Einstein equation<br /> | ||
+ | <img src="difussion_clip_image008.png" alt="" width="62" height="38" /><br /> | ||
+ | where the radii value of solute (r) can be determined with the help of molecular weight<br /> | ||
+ | <img src="difussion_clip_image010.png" alt="" width="109" height="42" /> <br /> | ||
+ | So, to simplify our equation, we try to find the correlation between diffusivity constant and solute molecular weight. It can be done through dividing two sets of case (diffusion of protein with well-known molecular weight and diffusion of aflatoxin) and the result is<br /> | ||
+ | <img src="difussion_clip_image012.png" alt="" width="88" height="38" /></p> | ||
+ | <table border="1" cellspacing="0" cellpadding="0"> | ||
+ | <tr> | ||
+ | <td width="73" valign="top"><br /> | ||
+ | <strong>Variable</strong></td> | ||
+ | <td width="302" valign="top"><p><strong>Definition</strong></p></td> | ||
+ | <td width="113" valign="top"><p><strong>Value</strong></p></td> | ||
+ | <td width="127" valign="top"><p><strong>Source</strong></p></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td width="73" valign="top"><p>ρ</p></td> | ||
+ | <td width="302" valign="top"><p>Aflatoxin density</p></td> | ||
+ | <td width="113" valign="top"><p>1,64 g/cm3</p></td> | ||
+ | <td width="127" valign="top"><p>[7]</p></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td width="73" valign="top"><p>MW</p></td> | ||
+ | <td width="302" valign="top"><p>Aflatoxin molecular weight</p></td> | ||
+ | <td width="113" valign="top"><p>312,3</p></td> | ||
+ | <td width="127" valign="top"><p>[8]</p></td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | <h3><strong>II. Aflatoxin membrane cell area</strong></h3> | ||
+ | <p> | ||
+ | To simulate the effect of cell growth to diffusion phenomena, we modify the diffusion equation. Membrane cell area will be increased along with cell number, and it affected by cell growth.<br /> | ||
+ | We simplify this problem by assuming cell growth is like growing sphere. When the cell number doubled, it can be stated that the membrane cell area and cell volume doubled too.<br /> | ||
+ | <img src="difussion_clip_image014.jpg" alt="" width="424" height="145" /><br /> | ||
+ | Cell membrane area can be evaluated every time by this equation :<br /> | ||
+ | <img src="difussion_clip_image016.png" alt="" width="59" height="19" /> <br /> | ||
+ | where the value of A0 represents membrane cell area of one E. coli cell and n is cell number at certain time. The value of n can be determined with cell growth kinetic :<br /> | ||
+ | <img src="difussion_clip_image018.png" alt="" width="127" height="19" /> <br /> | ||
+ | So, the equation’s final form to evaluate cell membrane area every time become :<br /> | ||
+ | <img src="difussion_clip_image020.png" alt="" width="150" height="19" /> <br /> | ||
+ | With the same principle, we can evaluate cell volume every time :<br /> | ||
+ | <img src="difussion_clip_image022.png" alt="" width="145" height="19" /><br /> | ||
+ | To gather the value of A0 dan V0, we use the data that bacteria has area to volume ratio 3:1 [4]. Cell density and wet cell mass of E. coli can be known from literature</p> | ||
+ | <table border="1" cellspacing="0" cellpadding="0"> | ||
+ | <tr> | ||
+ | <td width="205" valign="top"><br /> | ||
+ | <strong>Variable</strong></td> | ||
+ | <td width="205" valign="top"><p align="center"><strong>Value</strong></p></td> | ||
+ | <td width="205" valign="top"><p align="center"><strong>Source</strong></p></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td width="205" valign="top"><p align="center">Cell density</p></td> | ||
+ | <td width="205" valign="top"><p align="center">1,105 g/ml</p></td> | ||
+ | <td width="205" valign="top"><p align="center">[5]</p></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td width="205" valign="top"><p align="center">Wet cell mass</p></td> | ||
+ | <td width="205" valign="top"><p align="center">10-12 g</p></td> | ||
+ | <td width="205" valign="top"><p align="center">[6]</p></td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | <p>So the value of A0 and V0 is :</p> | ||
+ | <div align="center"> | ||
+ | <table border="1" cellspacing="0" cellpadding="0"> | ||
+ | <tr> | ||
+ | <td width="205" valign="top"><br /> | ||
+ | <strong>Variable</strong></td> | ||
+ | <td width="205" valign="top"><p align="center"><strong>Value</strong></p></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td width="205" valign="top"><p align="center">A0</p></td> | ||
+ | <td width="205" valign="top"><p align="center">2,715 x 10-18 m3</p></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td width="205" valign="top"><p align="center">V0</p></td> | ||
+ | <td width="205" valign="top"><p align="center">9,05 x 10-19 m3</p></td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
</div> | </div> | ||
</div> | </div> |
Revision as of 09:53, 26 September 2013
Please Add Title Here!
Diffusion
First thing to do is calculate how much aflatoxin would enter the cell every time. Aflatoxin diffused into cell through simple diffusion mechanism, it means that aflatoxin difusion is drived by concentration gradient.
Assumption :
- Aflatoxin homogenely diffused into cell
Parameters of the equation :
Variable |
Definition |
Value |
Source |
P |
Permeability aflatoxin-membrane E. coli |
1,01 x 10-4 cm/s |
Calculated (See Sect 1) |
A |
E. coli membrane cell area |
Changing with time |
Calculated (see Sect 2) |
Concentration gradient between inner and outer side of the cell |
- |
Depends on case |
I. Permeability aflatoxin-membrane
Permeability value between solute and solvent can be described through this equation :
Variable |
Definition |
Value |
Source |
D |
Diffusivity constant of aflatoxin-membrane E. coli |
2,05 x 10-9 cm2/s |
Calculated (see below) |
K |
Partition constant of aflatoxin-membrane E. coli |
0,64 |
[9] |
d |
E. coli membrane thickness |
13 nm |
[2] |
To determine the value of diffusivity constant, we use Stoke-Einstein equation
where the radii value of solute (r) can be determined with the help of molecular weight
So, to simplify our equation, we try to find the correlation between diffusivity constant and solute molecular weight. It can be done through dividing two sets of case (diffusion of protein with well-known molecular weight and diffusion of aflatoxin) and the result is
Variable |
Definition |
Value |
Source |
ρ |
Aflatoxin density |
1,64 g/cm3 |
[7] |
MW |
Aflatoxin molecular weight |
312,3 |
[8] |
II. Aflatoxin membrane cell area
To simulate the effect of cell growth to diffusion phenomena, we modify the diffusion equation. Membrane cell area will be increased along with cell number, and it affected by cell growth.
We simplify this problem by assuming cell growth is like growing sphere. When the cell number doubled, it can be stated that the membrane cell area and cell volume doubled too.
Cell membrane area can be evaluated every time by this equation :
where the value of A0 represents membrane cell area of one E. coli cell and n is cell number at certain time. The value of n can be determined with cell growth kinetic :
So, the equation’s final form to evaluate cell membrane area every time become :
With the same principle, we can evaluate cell volume every time :
To gather the value of A0 dan V0, we use the data that bacteria has area to volume ratio 3:1 [4]. Cell density and wet cell mass of E. coli can be known from literature
Variable |
Value |
Source |
Cell density |
1,105 g/ml |
[5] |
Wet cell mass |
10-12 g |
[6] |
So the value of A0 and V0 is :
Variable |
Value |
A0 |
2,715 x 10-18 m3 |
V0 |
9,05 x 10-19 m3 |