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== Why is a reactor? ==
{{Template:Nanouanl}}


=== Introduction ===
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<p style="text-align: center;">
<img alt="" src="http://openwetware.org/images/7/73/UANLReactor1.png" style="width: 475px; height: 402px;" /></p>
<p>
&nbsp;</p>
<p>
&nbsp;</p>
<p>
<strong><span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Theory</span></span></strong></p>
<p>
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">To describe the dynamic behavior of a Semi-Continuous Tank Reactor (SCTR) mass, component and energy balance equations must be developed. This requires an understanding of the functional expressions that describe chemical reaction. A reaction will create new components while simultaneously reducing reactant concentrations. The reaction may give off heat or my require energy to proceed.</span></span></p>
<p>
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">To develop a realistic SCTR model the change of individual species (or components) with respect to time must be considered. This is because individual components can appear / disappear because of reaction (remember that the overall mass of reactants and products will always stay the same). If there are N components, N &ndash; 1 component balances and an overall mass balance expression are required. Alternatively a component balance may be written for each species.</span></span></p>
<p>
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">In certain SCTR&acute;s (generally small vessels) the wall dynamics can have a significant effect on the thermal control and stability of a SCTR. If this is the case then an energy balance expression should be developed describing the rate of change of wall temperature with respect to time, assuming that the wall temperature is the same at any point.</span></span></p>
<p>
&nbsp;</p>
<p>
<strong><span style="font-size:14px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Idea</span></span></strong></p>
<p>
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">For an ideal approach, the CCMV capsid could be considered as reactor with an accumulation of the product inside the capsid. An analysis of a reactor is a common in chemical engineering. The reactor proposed is a complete opposite type from tubular plug-flow and stirred batch reactors, or a continuous stirred tank reactor and can be very useful when studying the behavior of a gas, liquid or solid.</span></span></p>
<p>
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">The reactor&#39;s behavior is modeled by a Semi-Continuous Tank Reactor, assuming perfect mixing in the container.</span></span></p>


For an ideal approach, the CCMV capsid could be considered as reactor with an accumulation of the product inside the capsid. An analysis of a reactor is a common in chemical engineering. The reactor proposed is a complete opposite type from tubular plug-flow and stirred batch reactors, or a continuous stirred tank reactor and can be very useful when studying the behavior of a gas, liquid or solid.  
<h2>
<span style="font-size:16px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><span class="mw-headline">Why is this a reactor? </span></span></span></h2>
<h3>
<span style="font-size:14px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><span class="mw-headline">Introduction </span></span></span></h3>
<p>
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">For an ideal approach, the CCMV capsid could be considered as reactor with an accumulation of the product inside the capsid. An analysis of a reactor is a common in chemical engineering. The reactor proposed is a complete opposite type from tubular plug-flow and stirred batch reactors, or a continuous stirred tank reactor and can be very useful when studying the behavior of a gas, liquid or solid.</span></span></p>
<p>
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">The reactor&#39;s behavior is modeled by a Semi-Continuous Tank Reactor, assuming perfect mixing in the container.</span></span></p>
<h4>
<span style="font-size:14px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><span class="mw-headline">Enzymatic Reaction</span></span></span></h4>
<p>
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">The general reaction scheme is described as follows:</span></span></p>


The reactor's behavior is modeled by a Semi-Continuous Tank Reactor, assuming perfect mixing in the container.<sup>1</sup>
\begin{equation}
E + S \leftrightarrow ES \rightarrow E^0 + P
\end{equation}


====Enzymatic Reaction====
<p>
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">With a reaction rate of:</span></span></p>


The general reaction scheme is described as follows:
\begin{equation}
\frac{d[ES]}{dt}=k_1[E][S]-k_{-1}[ES]-k_2[ES]
\end{equation}


<math>E + S \leftrightarrow ES \rightarrow E^0 + P</math>
<p>
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">This equation is affected by the constants k<sub>1</sub> , k<sub>-1</sub> and k<sub>2</sub>.</span></span></p>
<p>
&nbsp;</p>
<p>
<strong><span style="font-size:14px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Mass balance</span></span></strong></p>
<p>
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">Material balances are important, as a first step in devising a new process (or analyzing an existing one). They are almost always a prerequisite for all calculations for process engineering problems. The concept of mass balance is based on the physical principle that matter cannot be either created nor destroyed, only transformed. The law of mass transformation balances describe the mass of the inputs of the process with the output, as waste, products or emissions. This whole process is accounting for the material used in a reaction. Applying a mass balance to our system we obtained: </span></span></p>
<p style="text-align: center;">
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">ACCUMULATION = INPUT + APPEARANCE BY REACTION - DISAPPEARANCE BY REACTION </span></span></p>
<p>
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">where </span></span></p>
<p>
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">Input =F<sub>0,&nbsp;</sub>Appearance =V(r<sub>P</sub>), Disappearance =V(-r<sub>S</sub>) and Accumulation = \(\frac{d[P]}{dt}\)</span></span></p>  


With a reaction rate of:
\begin{equation}
\frac{d[P]}{dt}=F_0+V(r_P)-V(-r_S)
\end{equation}


<math>\frac{d[ES]}{dt}=k_1[E][S]-k_{-1}[ES]-k_2[ES]</math> . . . '''1.1'''
<p>
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">The inlet flow was determined by diffusion. A mass balance, applied to a spherical envelope is described as:</span></span></p>


This equation is affected by the constants k<sub>1</sub> , k<sub>-1</sub> and k<sub>2</sub>.
\begin{equation}
\frac{d}{dr}(r^2N_{Ar})=0
\end{equation}


====Mass balance====
<p>
Material balances are important, as a first step in devising a new process (or analyzing an existing one). They are almost always a prerequisite for all calculations for process engineering problems. The concept of mass balance is based on the physical principle that matter cannot be either created nor destroyed, only transformed. The law of mass transformation balances describe the mass of the inputs of the process with the output, as waste, products or emissions. This whole process is accounting for the material used in a reaction.
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">where N<sub>Ar</sub> represents molar flux. When N<sub>Br</sub>=0 we obtain</span></span></p>


Applying a mass balance to our system we obtained:
\begin{equation}
\frac{d}{dr}(r^2\frac{cD_{AB}}{1-x_A}\frac{dx_A}{dr})=0
\end{equation}


'''ACCUMULATION = INPUT + APPEARANCE BY REACTION - DISAPPEARANCE BY REACTION
<p>
'''
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">At a constant temperature the product (cD<sub>AB</sub>) is equally constant and x<sub>A</sub>=1-x<sub>B</sub>, the equation can be integrated into the following expression:</span></span></p>


where
\begin{equation}  
 
F_A=4\pi r_1^2N_{Ar}|_{r=r1}=
Input = F<sub>0</sub>
 
Appearance = V(r<sub>P</sub>)
 
Disappearance = V(-r<sub>S</sub>)
 
Accumulation = <math>\tfrac{d[P]}{dt}</math>
 
<math>\frac{d[P]}{dt}=F_0+V(r_P)-V(-r_S)</math> . . . '''1.2'''
 
The inlet flow was determined by diffusion. A mass balance, applied to a spherical envelope is described as:
 
<math>\frac{d}{dr}(r^2N_{Ar})=0</math> . . . '''1.3'''
 
where N<sub>Ar</sub> represents molar flux. When N<sub>Br</sub>=0 we obtain
 
<math>\frac{d}{dr}(r^2\frac{cD_{AB}}{1-x_A}\frac{dx_A}{dr})=0</math> . . . '''1.4'''
 
At a constant temperature the product (cD<sub>AB</sub>) is equally constant and x<sub>A</sub>=1-x<sub>B</sub>, the equation can be integrated into the following expression<sup>2</sup>:
 
<math>F_A=4\pi r_1^2N_{Ar}|_{r=r1}=
\frac{4\pi cD_{AB}}{1/r_1-1/r_2}
\frac{4\pi cD_{AB}}{1/r_1-1/r_2}
\ln\frac{x_{B2}}{x_{B1}}
\ln\frac{x_{B2}}{x_{B1}}
</math> . . . '''1.5'''
\end{equation}


where ''x'' are the fractions, ''c'' is the concentration and ''r'' are the respective radius.  
<p>
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">where &#39;&#39;x&#39;&#39; are the fractions, &#39;&#39;c&#39;&#39; is the concentration and &#39;&#39;r&#39;&#39; are the respective radius. </span></span></p>


This equation defines the nanoreactor inflow.
<p>
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">This equation defines the nanoreactor inflow.<br />
<br />
We neglect the possibility of an outflow of species because:</span></span></p>
<ul>
<li>
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">The gradient of concentration of S tends to stay inside the capsid</span></span></li>
<li>
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">The positive charge in the outside of the VLP made a repulsion of the specie S</span></span></li>
<li>
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">An evident agglomeration of specie P will increase it size and remain inside</span></span></li>
</ul>
<p>
&nbsp;</p>
<p>
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;"><strong><span style="font-size: 14px;">Diffusion coefficient</span></strong><br />
For S and P being ionic silver and reduced silver respectively. The ionic silver diffusion coefficient in solution is described by Nerst&#39;s equation (1888):</span></span></p>


We neglect the possibility of an outflow of species because:<sup>3</sup>
\begin{equation}
*The gradient of concentration of S tends to stay inside the capsid
D_{AB}°=
*The positive charge in the outside of the VLP made a repulsion of the specie S
*An evident agglomeration of specie P will increase it size and remain inside
 
====Diffusion coefficient====
For S and P being ionic silver and reduced silver respectively.
The ionic silver diffusion coefficient in solution is described by Nerst's equation (1888)<sup>4</sup>:
 
<math>D_{AB}°=
\frac{RT}{F^2}
\frac{RT}{F^2}
\frac{\lambda^o_+\lambda^o_-}{\lambda^o_++\lambda^o_-}
\frac{\lambda^o_+\lambda^o_-}{\lambda^o_++\lambda^o_-}
\frac{|Z_-|+|Z_+|}{|Z_+Z_-|}
\frac{|Z_-|+|Z_+|}{|Z_+Z_-|}
</math> . . . '''1.6'''
\end{equation}


where
<p>
where</p>
<ul>
<li>
<em>F</em> = Faraday&#39;s constant [A&middot;s/g<sub>eq</sub>]</li>
<li>
<em>D<sub>AB</sub>&deg;</em> = Diffusion coefficient at infinite dilution [m<sup>2</sup>/s]</li>
<li>
<em>&lambda;<sub>+</sub>&deg;</em>= Cationic conductivity at infinite dilution</li>
<li>
<em>&lambda;<sub>-</sub>&deg; </em>= Anionic conductivity at infinite dilution</li>
<li>
<em>Z<sup>+</sup></em>= Cation valence</li>
<li>
<em>Z<sup>-</sup> </em>= Anionic valence</li>
<li>
<em>T</em> = Absolute temperature [K]</li>
</ul>
<p>
&nbsp;</p>
<p>
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><span style="font-size:14px;"><strong>Boiling temperature</strong></span><br />
Via Joback&#39;s method, we estimate the normal boiling temperature:</span></span></p>
\begin{equation}
T_b=\mathbf{198} + \sum_{k} N_k(tbk)
\end{equation}


*''F'' = Faraday's constant [A·s/g<sub>eq</sub>]
<p>
*''D<sub>AB</sub>°'' = Diffusion coefficient at infinite dilution [m<sup>2</sup>/s]
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">in which &#39;&#39;N<sub>k</sub>&#39;&#39; is the number of times that the contribution group is present in the compound.</span></span></p>
*''λ<sub>+</sub>°'' = Cationic conductivity at infinite dilution
*''λ<sub>-</sub>°'' = Anionic conductivity at infinite dilution
*''Z<sup>+</sup>'' = Cation valence
*''Z<sup>-</sup>'' = Anionic valence
*''T'' = Absolute temperature [K]


====Boiling temperature====
<p>
Via Joback's method, we estimate the normal boiling temperature:<sup>5</sup>
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><strong><span style="font-size: 14px;">Critical temperature</span></strong><br />
<span style="font-size: 12px;">Using a similar approach, also by Joback, we estimate the critical temperature:</span></span></p>


<math>T_b=\mathbf{198} + \sum_{k} N_k(tbk)</math> . . . '''1.7'''
\begin{equation}
 
T_c=T_b\Bigg[
in which ''N<sub>k</sub>'' is the number of times that the contribution group is present in the compound.
 
====Critical temperature====
Using a similar approach, also by Joback, we estimate the critical temperature:<sup>5</sup>
 
<math>T_c=T_b\Bigg[
\mathbf{0.584}+\mathbf{0.965}
\mathbf{0.584}+\mathbf{0.965}
\bigg\{\sum_{k} N_k(tck) \bigg\} -
\bigg\{\sum_{k} N_k(tck) \bigg\} -
\bigg\{\sum_{k} N_k(tck) \bigg\}^2
\bigg\{\sum_{k} N_k(tck) \bigg\}^2
\Bigg]^{-1}
\Bigg]^{-1}
</math> . . . '''1.8'''
\end{equation}


Joback's Method Contributions (Table C1. Prausnitz)
<p>
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Table 1. Joback&#39;s Method Contribution</span></span></p>
<p style="text-align: center;">
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/1/11/UANLReactortable1.PNG" /></span></span></p>
<p>
<span style="font-size:14px;"><strong><span style="font-family: trebuchet ms,helvetica,sans-serif;">Conductivity</span></strong></span></p>
<p>
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">The conductivity of the compound is determined by the Sastri method:</span></span><math></math></p>


{|border="2" class="wikitable" style="text-align:center;"
\begin{equation}
! align="left"| Contribution Group
\lambda_L=\lambda_ba^m
! ''tbk'', '''K'''
\end{equation}
! ''tck'', '''K'''
! align="left"| Contribution Group
! ''tbk'', '''K'''
! ''tck'', '''K'''
! align="left"| Contribution Group
! ''tbk'', '''K'''
! ''tck'', '''K'''
! align="left"| Contribution Group
! ''tbk'', '''K'''
! ''tck'', '''K'''
|-
|CH<sub>3</sub>
|23.58
|0.0141
|CH<sub>2</sub><sub>(ss)</sub>
|27.15
|0.01
|ACOH
|76.34
|0.0240
|NH
|50.17
|0.0295
|-
|CH<sub>2</sub>
|22.88
|0.0181
|CH<sub>(ss)</sub>
|21.78
|0.0122
|O
|22.42
|0.0168
|NH<sub>(ss)</sub>
|52.82
|0.0130
|-
|CH
|21.74
|0.0164
|C<sub>(ss)</sub>
|21.32
|0.0042
|O<sub>(ss)</sub>
|31.22
|0.0098
|N
|11.74
|0.0169
|-
|C
|18.25
|0.0067
|=CH<sub>(ds)</sub>
|26.73
|0.0082
|C=O
|76.75
|0.0380
|=N-<sub>(ds)</sub>
|74.60
|0.0255
|-
|=CH<sub>2</sub>
|18.18
|0.0113
|=C<sub>(ds)</sub>
|31.01
|0.0143
|C=O<sub>(ds)</sub>
|94.97
|0.0284
|=NH
|X
|X
|-
|=CH
|24.96
|0.0129
|F
| -0.03
|0.0111
|CH=O
|72.20
|0.0379
|CN
|125.66
|0.0496
|-
|=C
|24.14
|0.0117
|Cl
|38.13
|0.0105
|COOH
|169.09
|0.0791
|NO<sub>2</sub>
|152.54
|0.0437
|-
|=C=
|26.15
|0.0026
|Br
|66.86
|0.0133
|COO
|81.10
|0.0481
|SH
|63.56
|0.0031
|-
|≡CH
|9.20
|0.0027
|I
|93.84
|0.0068
|=O
| -10
|0.0143
|S
|68.78
|0.0119
|-
|≡C
|27.38
|0.0020
|OH
|92.88
|0.0741
|NH<sub>2</sub>
|73.23
|0.0243
|S<sub>(ss)</sub>
|52.10
|0.0019
|}
<sub>(ss) indicates a group in a nonaromatic ring, (ds) indicates a group in an aromatic ring, X indicates a non-available parameter</sub>


====Conductivity====
<p>
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">where *&#39;&#39;&lambda;<sub>L</sub>&#39;&#39; = thermic conductivity of the liquid [ W/(m&middot;K)] *&#39;&#39;&lambda;<sub>b</sub>&#39;&#39; = thermic conductivity at normal boiling point [ W/(m&middot;K)] *&#39;&#39;T<sub>br</sub>&#39;&#39; = &#39;&#39;T<sub>b</sub>/T<sub>c</sub>&#39;&#39; = normal boiling reduced temperature *&#39;&#39;T<sub>r</sub>&#39;&#39; = &#39;&#39;T/T<sub>c</sub>&#39;&#39; = reduced temperature *&#39;&#39;T<sub>c</sub>&#39;&#39; = critical temperature [K]</span></span></p>


<p>
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">and</span></span></p>


The conductivity of the compound is determined by the Sastri method:<sup>5</sup>
\begin{equation}
m=1-\bigg(\frac{1-T_r}{1-T_{br}}\bigg)^n
\end{equation}


<math>\bold{\lambda_L=\lambda_ba^m}</math> . . . '''1.9'''
<p>
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">with
a = 0.16 and n = 0.2 for the compound.</span></span></p>


where
<p>
*''λ<sub>L</sub>'' = thermic conductivity of the liquid [ W/(m·K)]
<span style="font-size:14px;">Table 2. Sastri&#39;s Contributions</span></p>
*''λ<sub>b</sub>'' = thermic conductivity at normal boiling point [ W/(m·K)]
<p style="text-align: center;">
*''T<sub>br</sub>'' = ''T<sub>b</sub>/T<sub>c</sub>'' = normal boiling reduced temperature
<img alt="" src="http://openwetware.org/images/6/68/UANLReactortable2.PNG" style="width: 840px; height: 411px;" /></p>
*''T<sub>r</sub>'' = ''T/T<sub>c</sub>'' = reduced temperature
<p style="text-align: justify;">
*''T<sub>c</sub>'' = critical temperature [K]
<strong><span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 14px;">Euler Method </span></span></strong></p>
<p style="text-align: justify;">
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">Every time we propose a Matter Balance is quietly easy to assume a Steady-State, but in real life we could spec some disturbances in the out-flux stream caused by the Accumulation. The Accumulation of substance inside the reactor is highly common and when the capsid of the CCMV simulates a reactor it is not an exception. In this case an agglomeration of Silver Nano-particles of different sizes will be notorious and it is described by solving the differential equations of concentration of product in function of time, presented in the Mass Balance previously described. A common method to approach the change within time is by the numeric method of Euler. Suppose that we want to approximate the solution of the initial value problem:</span></span></p>


and


<math>m=1-\bigg(\frac{1-T_r}{1-T_{br}}\bigg)^n</math> . . . '''1.10'''


with
\(y'(t) = f(t,y(t)), \qquad \qquad y(t_0)=y_0\)
a = 0.16 and n = 0.2 for the compound


<p>
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Choose a value <span class="texhtml"><i>h</i></span> for the size of every step and set <span class="texhtml"><i>t</i><sub><i>n</i></sub> = <i>t</i><sub>0</sub> + <i>n</i><i>h</i></span>. Now, one step of the Euler method from <span class="texhtml"><i>t</i><sub><i>n</i></sub></span> to <span class="texhtml"><i>t</i><sub><i>n</i> + 1</sub> = <i>t</i><sub><i>n</i></sub> + <i>h</i></span> is </span></span></p>


Sastri's Contributions (Table 10.5. Prausnitz)                        
\(y_{n+1} = y_n + hf(t_n,y_n)\)


{|border="2" class="wikitable" style="text-align:center;"
<p>
! align="left"| Hydrocarbon Groups
The value of <img alt="\bold y_n" class="tex" src="http://openwetware.org/images/math/2/d/4/2d412236ddab9fd085d86d331fc41efd.png" /> is an approximation of the solution to the ODE at time <img alt="\bold t_n" class="tex" src="http://openwetware.org/images/math/2/0/c/20c21da56097aa97a9ad83c743109920.png" />: <img alt="y_n \approx y(t_n)" class="tex" src="http://openwetware.org/images/math/8/7/b/87bcb4988b614d2564dfa184f3a422c0.png" />. The Euler method is explicit, i.e. the solution <img alt="\bold y_{n+1}" class="tex" src="http://openwetware.org/images/math/3/a/6/3a6394ef8d7be438136b4ddb094e7d02.png" /> is an explicit function of <img alt="\bold y_i" class="tex" src="http://openwetware.org/images/math/c/5/4/c54efad69ef8398a457edc184511a782.png" /> for <img alt="i \leq n" class="tex" src="http://openwetware.org/images/math/0/6/4/064c678d55189edf8539d54cb383f358.png" />.</p>
! ''Δλ<sub>b</sub>''
! align="left"| Non-Hydrocarbon Groups
! ''Δλ<sub>b</sub>''
! align="left"| Non-Hydrocarbon Groups
! ''Δλ<sub>b</sub>''
|-
|CH<sub>3</sub>
|0.0545
|O
|0.0100
|N<sub>(ring)</sub>
|0.0135
|-
|CH<sub>2</sub>
|0.0008
|OH<sup>2</sup>
|0.0830
|CN
|0.0645
|-
|CH
| -0.0600
|OH<sup>3</sup>
|0.0680
|NO<sub>2</sub>
|0.0700
|-
|C
| -0.1230
|CO<sub>(ketone)</sub>
|0.0175
|S
|0.0100
|-
|=CH<sub>2</sub>
|0.0545
|CHO<sub>(aldehyde)</sub>
|0.0730
|F<sup>4</sup>
|0.0568
|-
|=CH
|0.0020
|COO<sub>(ester)</sub>
|0.0070
|F<sup>5</sup>
|0.0510
|-
|=C
| -0.0630
|COOH<sub>(acid)</sub>
|0.0650
|Cl
|0.0550
|-
|=C=
|0.1200
|NH<sub>2</sub>
|0.0880
|Br
|0.0415
|-
|Ring<sup>1</sup>
|0.1130
|NH
|0.0065
|I
|0.0245
|-
|
|
|NH<sub>(ring)</sub>
|0.0450
|H<sup>6</sup>
|0.0675
|-
|
|
|N
| -0.0605
|3 member ring
|0.1500
|-
|
|
|
|
|Ring<sup>7</sup><sub>(other)</sub>
|0.1100
|-
|}
<sup>1</sup><sub>In polycyclic compounds, all rings are treated as separated rings, <sup>2</sup>In aliphatic primary alcohols and phenols with no branch chains, <sup>3</sup>In all alcohols except as described in<sup>2</sup>, <sup>4</sup>In perfluoro carbons, <sup>5</sup>In all cases except as described in <sup>4</sup>, <sup>6</sup>This contribution is used for methane, formic acid, and formates, <sup>7</sup>In polycyclic non-hydrocarbon compounds, all rings are considered as non-hydrocarbon rings</sub>


==== Euler Method ====
<p>
Every time we propose a Matter Balance is quietly easy to assume a Steady-State, but in real life we could spec some disturbances in the out-flux stream caused by the Accumulation. The Accumulation of substance inside the reactor is highly common and when the capsid of the CCMV simulates a reactor it is not an exception. In this case an agglomeration of Silver Nano-particles of different sizes will be notorious and it is described by solving the differential equations of concentration of product in function of time, presented in the Mass Balance previously described.
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">While the Euler method integrates a first-order ODE, any ODE of order <em>N</em> can be represented as a first-order ODE: to treat the equation:</span></span></p>


A common method to approach the change within time is by the numeric method of Euler.<sup>6</sup>
\(y^{(N)}(t) = f(t, y(t), y'(t), \ldots, y^{(N-1)}(t)\)


Suppose that we want to approximate the solution of the initial value problem
<p>
<span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">we introduce auxiliary variables <img alt="z_1(t)=y(t), z_2(t)=y'(t),\ldots, z_N(t)=y^{(N-1)}(t)" class="tex" height="18" src="http://openwetware.org/images/math/f/6/f/f6f962f62d0359b6b4acdc15835bcc12.png" width="298" /> and obtain the equivalent equation</span></span></p>


<math>y'(t) = f(t,y(t)), \qquad \qquad y(t_0)=y_0 </math>
\begin{equation}
 
\mathbf{z}'(t)
Choose a value <math>h</math> for the size of every step and set <math>t_n = t_0 + nh</math>. Now, one step of the Euler method from <math>t_n</math> to <math>t_{n+1} = t_n + h</math> is
  = \begin{pmatrix} z_1'(t)\\ \vdots\\ z_{N-1}'(t)\\ z_N'(t) \end{pmatrix}
 
  = \begin{pmatrix} y'(t)\\ \vdots\\ y^{(N-1)}(t)\\ y^{(N)}(t) \end{pmatrix}
<math>\bold y_{n+1} = y_n + hf(t_n,y_n)</math>
  = \begin{pmatrix} z_2(t)\\ \vdots\\ z_N(t)\\ f(t,z_1(t),\ldots,z_N(t)) \end{pmatrix}
 
\end{equation}
The value of <math>\bold y_n</math> is an approximation of the solution to the ODE at time <math>\bold t_n</math>: <math>y_n \approx y(t_n)</math>. The Euler method is explicit, i.e. the solution <math>\bold y_{n+1}</math> is an explicit function of <math>\bold y_i</math> for <math>i \leq n</math>.
 
While the Euler method integrates a first-order ODE, any ODE of order ''N'' can be represented as a first-order ODE:
to treat the equation
 
<math> y^{(N)}(t) = f(t, y(t), y'(t), \ldots, y^{(N-1)}(t)) </math>,


we introduce auxiliary variables <math>z_1(t)=y(t), z_2(t)=y'(t),\ldots, z_N(t)=y^{(N-1)}(t)</math> and obtain
<p>
the equivalent equation
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">This is a first-order system in the variable <img alt="\mathbf{z}(t)" class="tex" src="http://openwetware.org/images/math/3/5/f/35f48cc203de93ed9cb8f7f095824943.png" /> and can be handled by Euler&#39;s method or, in fact, by any other scheme for first-order systems.</span></span></p>
<p>
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Applying the method to our system, the differential equation are</span></span></p>


<math> \mathbf{z}'(t)
\begin{equation}\frac{dC_E}{dt}=-k_1C_EC_S+k_{-1}C_{ES}+k_2C_{ES}\end{equation}
  = \begin{pmatrix} z_1'(t)\\ \vdots\\ z_{N-1}'(t)\\ z_N'(t) \end{pmatrix}
\begin{equation}\frac{dC_S}{dt}=-k_1C_EC_S+\frac{F_S}{V_{reactor}}\end{equation}
  = \begin{pmatrix} y'(t)\\ \vdots\\ y^{(N-1)}(t)\\ y^{(N)}(t) \end{pmatrix}
\begin{equation}\frac{dC_{ES}}{dt}=k_1C_EC_S-k_{-1}C_{ES}-k_2C_{ES}\end{equation}
  = \begin{pmatrix} z_2(t)\\ \vdots\\ z_N(t)\\ f(t,z_1(t),\ldots,z_N(t)) \end{pmatrix} </math>
\begin{equation}\frac{dC_P}{dt}=k_2C_{ES}\end{equation}


This is a first-order system in the variable <math>\mathbf{z}(t)</math> and can be handled by Euler's method or, in fact, by any other scheme for first-order systems.
<p>
<strong><span style="font-size:16px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">RESULTS</span></span></strong></p>
<p>
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">For a <img alt="\bold k_1=1x10^7M^{-1}s^{-1}, k_{-1}=200s^{-1}" class="tex" height="16" src="http://openwetware.org/images/math/4/4/b/44bfa2eee3eb22cd70da118e5bd36c9d.png" width="206" /> and <img alt="\bold k_2=100s^{-1}" class="tex" height="17" src="http://openwetware.org/images/math/2/a/4/2a482255e383194d015e64611209e531.png" width="83" /> with <img alt="C_{Eo}=5.44x10^{-4} \frac {mol}{L}" class="tex" height="25" src="http://openwetware.org/images/math/a/7/f/a7fbf944891ea0b8505bc79880e02372.png" width="111" /> and <img alt="C_{So}=1.0x10^{-4} \frac {mol}{L} " class="tex" height="25" src="http://openwetware.org/images/math/5/6/3/5639d7021a88d1160cb0566dd02be0b5.png" width="104" /></span></span></p>
<p>
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Considering a volume of capsid and enzyme <img alt="\bold V_{capsid}=3.05x10^{-21}Lts, \bold V_{enzyme}=1.41x10^{-23}Lts" class="tex" height="19" src="http://openwetware.org/images/math/2/9/3/2931f720a329d6f8a887db0996c34735.png" width="338" /> respectively we obtained:</span></span></p>


===References===


#Fogler H. Scott, Elements of Chemical Reaction Engineering 4th Edition, Pretince Hall 2006, pages 37-45
<p>
#Bird R. B, Stewart W.E. & Lightfoot E.N., Fenómenos de Trasporte, Reverté Ediciones SA de CV 2006, pages 17-9 – 17-11.
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">A tendency analysis of graphs was made for each figure.</span></span></p>
#Geankoplis, Christie John, Procesos de transporte y principios de procesos de separación, 4th Edition. Continental 2006, pages 449-451
<ul>
#Anthony L. Hines & Robert N. Maddox, Mass Transfer Fundamentals and Applications, Prentince Hall PTR 1985, pages 34-35
<li>
#Poling, Prausnitz & O’Connel, The Properties of Gases and Liquids, 5th Edition. McGrawl-Hill 2001, pages 2.26,10.45-10.46, C.2-C.4
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 1: It is a fact that a continuous inflow flux of substrate within time is represented; this fact will lead an accumulation of material inside the reactor.</span></span></li>
#Hoffman, Joe D., Numerical Methods for Engineers and Scientists, 2th Edition. Marcel Decker, Inc. 2001, pages 355-359
</ul>
<p style="text-align: center;">
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/4/4b/Reactorfig1.1.jpg" style="width: 498px; height: 310px;" /></span></span></p>
<p style="text-align: center;">
<span style="font-size:11px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 1.- Substrate concentration within time</span></span></p>
<ul>
<li>
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 2: It could be appreciated a decrement in concentration of pure enzyme because the matter agglomeration effect, which leads an increment of enzyme-substrate concentration inside the capsid, making more possible to find this last state of enzyme within time.</span></span></li>
</ul>
<p style="text-align: center;">
<span _fck_bookmark="1" style="display: none;">&nbsp;</span><span _fck_bookmark="1" style="display: none;"> </span><span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/d/de/Reactorfig1.2.jpg" style="width: 498px; height: 310px;" /></span></span></p>
<p style="text-align: center;">
<span style="font-size:11px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 2.-&nbsp; Enzyme and Enzyme-Substrate&nbsp; concentrations within time</span></span></p>
<ul>
<li>
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 3: It is easily noticed that production of silver nanoparticles rise proportional with the inlet flux considering that all flux react forming the complex enzyme-substrate.</span></span></li>
</ul>
<p style="text-align: center;">
<span _fck_bookmark="1" style="display: none;">&nbsp;</span><span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/3/3c/Reactorfig3.1.jpg" /><span _fck_bookmark="1" style="display: none;">&nbsp;</span></span></span></p>
<p style="text-align: center;">
<span style="font-size:11px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 3.- Product concentration within time</span></span></p>
<ul>
<li>
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 4: It describes the real percentage of volume required to &ldquo;Figure 1&rdquo; reach equilibrium. For a set time of 1.5 ms it requires 1061% of available volume.</span></span></li>
</ul>
<p style="text-align: center;">
<span _fck_bookmark="1" style="display: none;">&nbsp;</span><span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/1/18/Reactorfig4.1.jpg" style="width: 512px; height: 310px;" /><span _fck_bookmark="1" style="display: none;">&nbsp;</span></span></span></p>
<p style="text-align: center;">
<span style="font-size:11px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 4.- Percentage of occupied volume in reactor within time</span></span></p>
<p>
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">A second analysis for the real reactor volume will be made, representing the theoretical maximum value.</span></span></p>
<p>
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">In figures 5, 7 and 8 the same behavior as the previous figures 1, 3 and 4, respectively, analysis are appreciated. In figure 6 a constant relative concentration for enzyme and the complex enzyme-substrate, demonstrating that our system is an appropriate media for the reduction reaction of ionic silver. This phenomenon is explained by the approach of non-declined enzymatic activity for the available small volume (3053nm<sup>3</sup>).</span></span></p>
<p style="text-align: center;">
<br />
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/e/e6/Reactorfig2.1.jpg" /></span></span></p>
<p style="text-align: center;">
<span style="font-size:11px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 5.- Substrate concentration within time at 100%volume capacity</span></span></p>
<p style="text-align: center;">
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/8/83/Reactorfig2.2.jpg" style="width: 498px; height: 310px;" /></span></span></p>
<p style="text-align: center;">
<span style="font-size:11px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 6.-&nbsp; Enzyme and Enzyme-Substrate&nbsp; concentrations within time at 100% volume capacity</span></span></p>
<p style="text-align: center;">
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/f/f7/Reactorfig4.2.jpg" /></span></span></p>
<p style="text-align: center;">
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 7.- Product concentration within time at 100%volume capacity</span></span></p>
<p style="text-align: center;">
<span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/d/de/Reactorfig3.2.jpg" style="width: 498px; height: 310px;" /></span></span></p>
<p style="text-align: center;">
<span style="font-size:11px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 8.- Percentage of occupied volume in reactor within time at 100% volume capacity</span></span></p>
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<html> <!-- MathJax (LaTeX for the web) --> <script type="text/x-mathjax-config"> MathJax.Hub.Config({tex2jax: {inlineMath: [['$','$'], ['\\(','\\)']]}}); MathJax.Hub.Config({ TeX: { equationNumbers: { autoNumber: "AMS" } } }); </script> <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> <head> <title>HTML Editor Sample Page</title> </head> <body> <p style="text-align: center;"> <img alt="" src="http://openwetware.org/images/7/73/UANLReactor1.png" style="width: 475px; height: 402px;" /></p> <p> &nbsp;</p> <p> &nbsp;</p> <p> <strong><span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Theory</span></span></strong></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">To describe the dynamic behavior of a Semi-Continuous Tank Reactor (SCTR) mass, component and energy balance equations must be developed. This requires an understanding of the functional expressions that describe chemical reaction. A reaction will create new components while simultaneously reducing reactant concentrations. The reaction may give off heat or my require energy to proceed.</span></span></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">To develop a realistic SCTR model the change of individual species (or components) with respect to time must be considered. This is because individual components can appear / disappear because of reaction (remember that the overall mass of reactants and products will always stay the same). If there are N components, N &ndash; 1 component balances and an overall mass balance expression are required. Alternatively a component balance may be written for each species.</span></span></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">In certain SCTR&acute;s (generally small vessels) the wall dynamics can have a significant effect on the thermal control and stability of a SCTR. If this is the case then an energy balance expression should be developed describing the rate of change of wall temperature with respect to time, assuming that the wall temperature is the same at any point.</span></span></p> <p> &nbsp;</p> <p> <strong><span style="font-size:14px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Idea</span></span></strong></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">For an ideal approach, the CCMV capsid could be considered as reactor with an accumulation of the product inside the capsid. An analysis of a reactor is a common in chemical engineering. The reactor proposed is a complete opposite type from tubular plug-flow and stirred batch reactors, or a continuous stirred tank reactor and can be very useful when studying the behavior of a gas, liquid or solid.</span></span></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">The reactor&#39;s behavior is modeled by a Semi-Continuous Tank Reactor, assuming perfect mixing in the container.</span></span></p> <h2> <span style="font-size:16px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><span class="mw-headline">Why is this a reactor? </span></span></span></h2> <h3> <span style="font-size:14px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><span class="mw-headline">Introduction </span></span></span></h3> <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">For an ideal approach, the CCMV capsid could be considered as reactor with an accumulation of the product inside the capsid. An analysis of a reactor is a common in chemical engineering. The reactor proposed is a complete opposite type from tubular plug-flow and stirred batch reactors, or a continuous stirred tank reactor and can be very useful when studying the behavior of a gas, liquid or solid.</span></span></p> <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">The reactor&#39;s behavior is modeled by a Semi-Continuous Tank Reactor, assuming perfect mixing in the container.</span></span></p> <h4> <span style="font-size:14px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><span class="mw-headline">Enzymatic Reaction</span></span></span></h4> <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">The general reaction scheme is described as follows:</span></span></p> \begin{equation} E + S \leftrightarrow ES \rightarrow E^0 + P \end{equation} <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">With a reaction rate of:</span></span></p> \begin{equation} \frac{d[ES]}{dt}=k_1[E][S]-k_{-1}[ES]-k_2[ES] \end{equation} <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">This equation is affected by the constants k<sub>1</sub> , k<sub>-1</sub> and k<sub>2</sub>.</span></span></p> <p> &nbsp;</p> <p> <strong><span style="font-size:14px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Mass balance</span></span></strong></p> <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">Material balances are important, as a first step in devising a new process (or analyzing an existing one). They are almost always a prerequisite for all calculations for process engineering problems. The concept of mass balance is based on the physical principle that matter cannot be either created nor destroyed, only transformed. The law of mass transformation balances describe the mass of the inputs of the process with the output, as waste, products or emissions. This whole process is accounting for the material used in a reaction. Applying a mass balance to our system we obtained: </span></span></p> <p style="text-align: center;"> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">ACCUMULATION = INPUT + APPEARANCE BY REACTION - DISAPPEARANCE BY REACTION </span></span></p> <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">where </span></span></p> <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">Input =F<sub>0,&nbsp;</sub>Appearance =V(r<sub>P</sub>), Disappearance =V(-r<sub>S</sub>) and Accumulation = \(\frac{d[P]}{dt}\)</span></span></p> \begin{equation} \frac{d[P]}{dt}=F_0+V(r_P)-V(-r_S) \end{equation} <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">The inlet flow was determined by diffusion. A mass balance, applied to a spherical envelope is described as:</span></span></p> \begin{equation} \frac{d}{dr}(r^2N_{Ar})=0 \end{equation} <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">where N<sub>Ar</sub> represents molar flux. When N<sub>Br</sub>=0 we obtain</span></span></p> \begin{equation} \frac{d}{dr}(r^2\frac{cD_{AB}}{1-x_A}\frac{dx_A}{dr})=0 \end{equation} <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">At a constant temperature the product (cD<sub>AB</sub>) is equally constant and x<sub>A</sub>=1-x<sub>B</sub>, the equation can be integrated into the following expression:</span></span></p> \begin{equation} F_A=4\pi r_1^2N_{Ar}|_{r=r1}= \frac{4\pi cD_{AB}}{1/r_1-1/r_2} \ln\frac{x_{B2}}{x_{B1}} \end{equation} <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">where &#39;&#39;x&#39;&#39; are the fractions, &#39;&#39;c&#39;&#39; is the concentration and &#39;&#39;r&#39;&#39; are the respective radius. </span></span></p> <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">This equation defines the nanoreactor inflow.<br /> <br /> We neglect the possibility of an outflow of species because:</span></span></p> <ul> <li> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">The gradient of concentration of S tends to stay inside the capsid</span></span></li> <li> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">The positive charge in the outside of the VLP made a repulsion of the specie S</span></span></li> <li> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">An evident agglomeration of specie P will increase it size and remain inside</span></span></li> </ul> <p> &nbsp;</p> <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;"><strong><span style="font-size: 14px;">Diffusion coefficient</span></strong><br /> For S and P being ionic silver and reduced silver respectively. The ionic silver diffusion coefficient in solution is described by Nerst&#39;s equation (1888):</span></span></p> \begin{equation} D_{AB}°= \frac{RT}{F^2} \frac{\lambda^o_+\lambda^o_-}{\lambda^o_++\lambda^o_-} \frac{|Z_-|+|Z_+|}{|Z_+Z_-|} \end{equation} <p> where</p> <ul> <li> <em>F</em> = Faraday&#39;s constant [A&middot;s/g<sub>eq</sub>]</li> <li> <em>D<sub>AB</sub>&deg;</em> = Diffusion coefficient at infinite dilution [m<sup>2</sup>/s]</li> <li> <em>&lambda;<sub>+</sub>&deg;</em>= Cationic conductivity at infinite dilution</li> <li> <em>&lambda;<sub>-</sub>&deg; </em>= Anionic conductivity at infinite dilution</li> <li> <em>Z<sup>+</sup></em>= Cation valence</li> <li> <em>Z<sup>-</sup> </em>= Anionic valence</li> <li> <em>T</em> = Absolute temperature [K]</li> </ul> <p> &nbsp;</p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><span style="font-size:14px;"><strong>Boiling temperature</strong></span><br /> Via Joback&#39;s method, we estimate the normal boiling temperature:</span></span></p> \begin{equation} T_b=\mathbf{198} + \sum_{k} N_k(tbk) \end{equation} <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">in which &#39;&#39;N<sub>k</sub>&#39;&#39; is the number of times that the contribution group is present in the compound.</span></span></p> <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><strong><span style="font-size: 14px;">Critical temperature</span></strong><br /> <span style="font-size: 12px;">Using a similar approach, also by Joback, we estimate the critical temperature:</span></span></p> \begin{equation} T_c=T_b\Bigg[ \mathbf{0.584}+\mathbf{0.965} \bigg\{\sum_{k} N_k(tck) \bigg\} - \bigg\{\sum_{k} N_k(tck) \bigg\}^2 \Bigg]^{-1} \end{equation} <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Table 1. Joback&#39;s Method Contribution</span></span></p> <p style="text-align: center;"> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/1/11/UANLReactortable1.PNG" /></span></span></p> <p> <span style="font-size:14px;"><strong><span style="font-family: trebuchet ms,helvetica,sans-serif;">Conductivity</span></strong></span></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">The conductivity of the compound is determined by the Sastri method:</span></span><math></math></p> \begin{equation} \lambda_L=\lambda_ba^m \end{equation} <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">where *&#39;&#39;&lambda;<sub>L</sub>&#39;&#39; = thermic conductivity of the liquid [ W/(m&middot;K)] *&#39;&#39;&lambda;<sub>b</sub>&#39;&#39; = thermic conductivity at normal boiling point [ W/(m&middot;K)] *&#39;&#39;T<sub>br</sub>&#39;&#39; = &#39;&#39;T<sub>b</sub>/T<sub>c</sub>&#39;&#39; = normal boiling reduced temperature *&#39;&#39;T<sub>r</sub>&#39;&#39; = &#39;&#39;T/T<sub>c</sub>&#39;&#39; = reduced temperature *&#39;&#39;T<sub>c</sub>&#39;&#39; = critical temperature [K]</span></span></p> <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">and</span></span></p> \begin{equation} m=1-\bigg(\frac{1-T_r}{1-T_{br}}\bigg)^n \end{equation} <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">with a = 0.16 and n = 0.2 for the compound.</span></span></p> <p> <span style="font-size:14px;">Table 2. Sastri&#39;s Contributions</span></p> <p style="text-align: center;"> <img alt="" src="http://openwetware.org/images/6/68/UANLReactortable2.PNG" style="width: 840px; height: 411px;" /></p> <p style="text-align: justify;"> <strong><span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 14px;">Euler Method </span></span></strong></p> <p style="text-align: justify;"> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">Every time we propose a Matter Balance is quietly easy to assume a Steady-State, but in real life we could spec some disturbances in the out-flux stream caused by the Accumulation. The Accumulation of substance inside the reactor is highly common and when the capsid of the CCMV simulates a reactor it is not an exception. In this case an agglomeration of Silver Nano-particles of different sizes will be notorious and it is described by solving the differential equations of concentration of product in function of time, presented in the Mass Balance previously described. A common method to approach the change within time is by the numeric method of Euler. Suppose that we want to approximate the solution of the initial value problem:</span></span></p> \(y'(t) = f(t,y(t)), \qquad \qquad y(t_0)=y_0\) <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Choose a value <span class="texhtml"><i>h</i></span> for the size of every step and set <span class="texhtml"><i>t</i><sub><i>n</i></sub> = <i>t</i><sub>0</sub> + <i>n</i><i>h</i></span>. Now, one step of the Euler method from <span class="texhtml"><i>t</i><sub><i>n</i></sub></span> to <span class="texhtml"><i>t</i><sub><i>n</i> + 1</sub> = <i>t</i><sub><i>n</i></sub> + <i>h</i></span> is </span></span></p> \(y_{n+1} = y_n + hf(t_n,y_n)\) <p> The value of <img alt="\bold y_n" class="tex" src="http://openwetware.org/images/math/2/d/4/2d412236ddab9fd085d86d331fc41efd.png" /> is an approximation of the solution to the ODE at time <img alt="\bold t_n" class="tex" src="http://openwetware.org/images/math/2/0/c/20c21da56097aa97a9ad83c743109920.png" />: <img alt="y_n \approx y(t_n)" class="tex" src="http://openwetware.org/images/math/8/7/b/87bcb4988b614d2564dfa184f3a422c0.png" />. The Euler method is explicit, i.e. the solution <img alt="\bold y_{n+1}" class="tex" src="http://openwetware.org/images/math/3/a/6/3a6394ef8d7be438136b4ddb094e7d02.png" /> is an explicit function of <img alt="\bold y_i" class="tex" src="http://openwetware.org/images/math/c/5/4/c54efad69ef8398a457edc184511a782.png" /> for <img alt="i \leq n" class="tex" src="http://openwetware.org/images/math/0/6/4/064c678d55189edf8539d54cb383f358.png" />.</p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">While the Euler method integrates a first-order ODE, any ODE of order <em>N</em> can be represented as a first-order ODE: to treat the equation:</span></span></p> \(y^{(N)}(t) = f(t, y(t), y'(t), \ldots, y^{(N-1)}(t)\) <p> <span style="font-family:trebuchet ms,helvetica,sans-serif;"><span style="font-size: 12px;">we introduce auxiliary variables <img alt="z_1(t)=y(t), z_2(t)=y'(t),\ldots, z_N(t)=y^{(N-1)}(t)" class="tex" height="18" src="http://openwetware.org/images/math/f/6/f/f6f962f62d0359b6b4acdc15835bcc12.png" width="298" /> and obtain the equivalent equation</span></span></p> \begin{equation} \mathbf{z}'(t) = \begin{pmatrix} z_1'(t)\\ \vdots\\ z_{N-1}'(t)\\ z_N'(t) \end{pmatrix} = \begin{pmatrix} y'(t)\\ \vdots\\ y^{(N-1)}(t)\\ y^{(N)}(t) \end{pmatrix} = \begin{pmatrix} z_2(t)\\ \vdots\\ z_N(t)\\ f(t,z_1(t),\ldots,z_N(t)) \end{pmatrix} \end{equation} <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">This is a first-order system in the variable <img alt="\mathbf{z}(t)" class="tex" src="http://openwetware.org/images/math/3/5/f/35f48cc203de93ed9cb8f7f095824943.png" /> and can be handled by Euler&#39;s method or, in fact, by any other scheme for first-order systems.</span></span></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Applying the method to our system, the differential equation are</span></span></p> \begin{equation}\frac{dC_E}{dt}=-k_1C_EC_S+k_{-1}C_{ES}+k_2C_{ES}\end{equation} \begin{equation}\frac{dC_S}{dt}=-k_1C_EC_S+\frac{F_S}{V_{reactor}}\end{equation} \begin{equation}\frac{dC_{ES}}{dt}=k_1C_EC_S-k_{-1}C_{ES}-k_2C_{ES}\end{equation} \begin{equation}\frac{dC_P}{dt}=k_2C_{ES}\end{equation} <p> <strong><span style="font-size:16px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">RESULTS</span></span></strong></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">For a <img alt="\bold k_1=1x10^7M^{-1}s^{-1}, k_{-1}=200s^{-1}" class="tex" height="16" src="http://openwetware.org/images/math/4/4/b/44bfa2eee3eb22cd70da118e5bd36c9d.png" width="206" /> and <img alt="\bold k_2=100s^{-1}" class="tex" height="17" src="http://openwetware.org/images/math/2/a/4/2a482255e383194d015e64611209e531.png" width="83" /> with <img alt="C_{Eo}=5.44x10^{-4} \frac {mol}{L}" class="tex" height="25" src="http://openwetware.org/images/math/a/7/f/a7fbf944891ea0b8505bc79880e02372.png" width="111" /> and <img alt="C_{So}=1.0x10^{-4} \frac {mol}{L} " class="tex" height="25" src="http://openwetware.org/images/math/5/6/3/5639d7021a88d1160cb0566dd02be0b5.png" width="104" /></span></span></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Considering a volume of capsid and enzyme <img alt="\bold V_{capsid}=3.05x10^{-21}Lts, \bold V_{enzyme}=1.41x10^{-23}Lts" class="tex" height="19" src="http://openwetware.org/images/math/2/9/3/2931f720a329d6f8a887db0996c34735.png" width="338" /> respectively we obtained:</span></span></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">A tendency analysis of graphs was made for each figure.</span></span></p> <ul> <li> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 1: It is a fact that a continuous inflow flux of substrate within time is represented; this fact will lead an accumulation of material inside the reactor.</span></span></li> </ul> <p style="text-align: center;"> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/4/4b/Reactorfig1.1.jpg" style="width: 498px; height: 310px;" /></span></span></p> <p style="text-align: center;"> <span style="font-size:11px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 1.- Substrate concentration within time</span></span></p> <ul> <li> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 2: It could be appreciated a decrement in concentration of pure enzyme because the matter agglomeration effect, which leads an increment of enzyme-substrate concentration inside the capsid, making more possible to find this last state of enzyme within time.</span></span></li> </ul> <p style="text-align: center;"> <span _fck_bookmark="1" style="display: none;">&nbsp;</span><span _fck_bookmark="1" style="display: none;"> </span><span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/d/de/Reactorfig1.2.jpg" style="width: 498px; height: 310px;" /></span></span></p> <p style="text-align: center;"> <span style="font-size:11px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 2.-&nbsp; Enzyme and Enzyme-Substrate&nbsp; concentrations within time</span></span></p> <ul> <li> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 3: It is easily noticed that production of silver nanoparticles rise proportional with the inlet flux considering that all flux react forming the complex enzyme-substrate.</span></span></li> </ul> <p style="text-align: center;"> <span _fck_bookmark="1" style="display: none;">&nbsp;</span><span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/3/3c/Reactorfig3.1.jpg" /><span _fck_bookmark="1" style="display: none;">&nbsp;</span></span></span></p> <p style="text-align: center;"> <span style="font-size:11px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 3.- Product concentration within time</span></span></p> <ul> <li> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 4: It describes the real percentage of volume required to &ldquo;Figure 1&rdquo; reach equilibrium. For a set time of 1.5 ms it requires 1061% of available volume.</span></span></li> </ul> <p style="text-align: center;"> <span _fck_bookmark="1" style="display: none;">&nbsp;</span><span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/1/18/Reactorfig4.1.jpg" style="width: 512px; height: 310px;" /><span _fck_bookmark="1" style="display: none;">&nbsp;</span></span></span></p> <p style="text-align: center;"> <span style="font-size:11px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 4.- Percentage of occupied volume in reactor within time</span></span></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">A second analysis for the real reactor volume will be made, representing the theoretical maximum value.</span></span></p> <p> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">In figures 5, 7 and 8 the same behavior as the previous figures 1, 3 and 4, respectively, analysis are appreciated. In figure 6 a constant relative concentration for enzyme and the complex enzyme-substrate, demonstrating that our system is an appropriate media for the reduction reaction of ionic silver. This phenomenon is explained by the approach of non-declined enzymatic activity for the available small volume (3053nm<sup>3</sup>).</span></span></p> <p style="text-align: center;"> <br /> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/e/e6/Reactorfig2.1.jpg" /></span></span></p> <p style="text-align: center;"> <span style="font-size:11px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 5.- Substrate concentration within time at 100%volume capacity</span></span></p> <p style="text-align: center;"> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/8/83/Reactorfig2.2.jpg" style="width: 498px; height: 310px;" /></span></span></p> <p style="text-align: center;"> <span style="font-size:11px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 6.-&nbsp; Enzyme and Enzyme-Substrate&nbsp; concentrations within time at 100% volume capacity</span></span></p> <p style="text-align: center;"> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/f/f7/Reactorfig4.2.jpg" /></span></span></p> <p style="text-align: center;"> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 7.- Product concentration within time at 100%volume capacity</span></span></p> <p style="text-align: center;"> <span style="font-size:12px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;"><img alt="" src="http://openwetware.org/images/d/de/Reactorfig3.2.jpg" style="width: 498px; height: 310px;" /></span></span></p> <p style="text-align: center;"> <span style="font-size:11px;"><span style="font-family: trebuchet ms,helvetica,sans-serif;">Figure 8.- Percentage of occupied volume in reactor within time at 100% volume capacity</span></span></p> </body> </html>