Difference between revisions of "Example selectivity"
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Revision as of 19:45, 16 July 2017
Introduction
In this example, we show how to calculate selectivities and how to perform a degree of selectivity control analysis. We perform a calculation on a relatively simple chemokinetic network wherein a product A can be converted to product E or F. We wish to analyze which elementary reaction steps control the selectivity to E or F.
Input
In this example, the following input file is used:
&compounds
A; 0; 1
E; 0; 0
F; 0; 0
A*; 1; 0 ; 1
B*; 1; 0 ; 1
C*; 1; 0 ; 1
D*; 1; 0 ; 1
E*; 1; 0 ; 1
F*; 1; 0 ; 1
*; 1; 1.0
&reactions
# m^2 amu K sigma sticking J/mol
HK; {A} + {*} => {A*}; 1e-20; 1; 1; 1; 1; 80e3 ; 1
HK; {E} + {*} => {E*}; 1e-20; 1; 1; 1; 1; 80e3 ; 1
HK; {F} + {*} => {F*}; 1e-20; 1; 1; 1; 1; 80e3 ; 1
# vf vb Eaf Eab
AR; {A*} => {B*}; 1e13; 1e13; 90e3; 90e3 ;1
AR; {B*} => {C*}; 1e13; 1e13; 80e3; 90e3 ;1
AR; {B*} => {D*}; 1e13; 1e13; 70e3; 80e3 ;1
AR; {C*} => {E*}; 1e13; 1e13; 70e3; 120e3 ;1
AR; {D*} => {F*}; 1e13; 1e13; 70e3; 90e3 ;1
&settings
TYPE = SEQUENCERUN
PRESSURE = 1
REAGENTS = {A}
KEYCOMPONENT = {F}
EACT=1
ORDERS=1
DRC=1
TDRC=0
DEBUG=1
USETIMESTAMP=0
&runs
300; 1e6; 1e-10; 1e-10
350; 1e6; 1e-10; 1e-10
400; 1e6; 1e-10; 1e-10
450; 1e5; 1e-10; 1e-10
500; 1e4; 1e-10; 1e-10
550; 1e3; 1e-10; 1e-10
600; 1e2; 1e-10; 1e-10
650; 1e1; 1e-10; 1e-10
700; 1e1; 1e-10; 1e-10
750; 1e1; 1e-10; 1e-10
800; 1e0; 1e-10; 1e-10
850; 1e0; 1e-10; 1e-10
900; 1e0; 1e-10; 1e-10
950; 1e0; 1e-10; 1e-10
1000; 1e0; 1e-10; 1e-10
1100; 1e0; 1e-10; 1e-10
1200; 1e0; 1e-10; 1e-10
1300; 1e0; 1e-10; 1e-10
1400; 1e0; 1e-10; 1e-10
1500; 1e0; 1e-10; 1e-10
1600; 1e0; 1e-10; 1e-10
1700; 1e0; 1e-10; 1e-10
1800; 1e0; 1e-10; 1e-10
1900; 1e0; 1e-10; 1e-10
2000; 1e0; 1e-10; 1e-10
Running the calculation
The first step is to perform a regular calculation.
./mkmcxx -i input.mkm
Turn-over-frequencies as a function of temperature.
This results in the creation of a run folder wherein all the raw data is written. A plot of the turn-over frequencies is given on the right. We can easily see that there is a distinct selectivity pattern for E over F.
