Tabulated Value for g

t = [0 42];
initialcon = [0.637 0.0253 0.0249 0.0172 0.0491 0.241 4.84e-3 2.48e-4];  %should have 8
[t,y] = ode15s(@dSdT, t, initialcon, @dSdTplot); %function, time frame, initial condition
figure
plot(t, y)
title('Changing Concentration of Components Over Time')
xlabel('Time (h)') 
ylabel('Concentration (g/L)') 
legend({'Cellulose','Cellobiose', 'Glucose', 'Xylan', 'Xylobiose', 'Xylose', 'HMF', 'Furfural'},'Location','e')
grid


function [ f ] = dSdT(t,y)
c = y(1);
g2 = y(2);
g = y(3);
xn = y(4);
x2 = y(5);
x = y(6);

dCdt = -(r1) - (r2); 
dG2dt = ((342.30/342.28)*(r1)) - (r3);
dGdt = ((180.16/162.14) * (r2)) + ((360.31/342.30) * (r3));
dXNdt = -(r4) - (r5);
dX2dt = ((282.24/264.22) * (r4)) - (r6);
dXdt = ((150.13/132.11) * (r5)) + ((300.226/282.24) * (r6));
dHdt = kh*g; %ADD MASS CHANGE
dFdt = kf*x;  %ADD MASS CHANGE

f = [dCdt; dG2dt; dGdt; dXNdt; dX2dt; dXdt; dHdt; dFdt]; %dWdt

end

This is my code that I have set up for changing concetratons using ode15s. The file works absolutely fine (as I have no posted all the values of the file that are used to derive r1, r2 etc).

My question is how can I extract the data values of g (glucose)? I want to create a separate graph, preferentially on excel, where I can compare the concentration profile of glucose at different temperatures. I have taken the semi colon away from the g = y(3) term but all the values are posted as g= 0.5 g=0.45 g=0.4 etc so I cannot use this in excel. If someone could point me in the right direction for extracting this data I would be very grateful

Will

[Star Strider]

I can’t run your code.

When I attempted to, I got:

Undefined function or variable 'r1'.

This is not defined in ‘dSdT’ (or anywhere else that I can see), and not passed as an additional parameter in the ‘dSdT’ argument list.

[Will Seccombe]

Like I said I didn't include the full code as I didn't think it was needed but here it is

t = [0 42];
initialcon = [0.637 0.0253 0.0249 0.0172 0.0491 0.241 4.84e-3 2.48e-4];  %should have 8
[t,y] = ode15s(@dSdT, t, initialcon, @dSdTplot); %function, time frame, initial condition
figure
plot(t, y)
title('Changing Concentration of Components Over Time')
xlabel('Time (h)') 
ylabel('Concentration (g/L)') 
legend({'Cellulose','Cellobiose', 'Glucose', 'Xylan', 'Xylobiose', 'Xylose', 'HMF', 'Furfural'},'Location','e')
grid


function [ f ] = dSdT(t,y)
c = y(1);
g2 = y(2);
g = y(3);
xn = y(4);
x2 = y(5);
x = y(6);


k1r = 22.3; %kg system /g protein h-1 %obnamia 2014
k2r = 7.18; %kg system /g protein h-1 %obnamia 2014
k3r = 285.5; %g substrate /g protein h-1 %obnamia 2014
k4r = 4.41; %kg system /g protein h-1 %https://www.researchgate.net/publication/328309323_Novel_Kinetic_Models_of_Xylan_Dissolution_and_Degradation_during_Ethanol_Based_Auto-Catalyzed_Organosolv_Pretreatment_of_Bamboo
k5r = 7.2; %kg system /g protein h-1 %https://pdf.sciencedirectassets.com/271363/1-s2.0-S0008621500X02832/1-s2.0-S0008621500854841/main.pdf?x-amz-security-token=AgoJb3JpZ2luX2VjEEwaCXVzLWVhc3QtMSJHMEUCIQCC00Y2%2BxNSUCaouLIs1VflYYTxIB0Ii6H4JqSdwGXylgIgOnHrZIANajeoM7AVNeu1vLjj5ZbJeNqp%2Bc0gcWKTmTYq4wMI9f%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FARACGgwwNTkwMDM1NDY4NjUiDHIuyFhlWXghZwmNlyq3AwAMg1OrzmTMpFOJIweL0%2FaTDCErbLGNr6jPripmWnyDP%2FQXteQ74iUtuT8COeR6kDAjAT7EjzmXocivSmufxaYxFk94yS3D82Vci0bFd7tDfu5Z4Y4cqN5AhEfztvu6zdZFjpGUhtlEX53vISWAUUB5s51olXkF3zP1bUReDNoGAZ7PH3DrxCjX9pZsd8dYvJHoczqvm2VyNibTF0wvtIUDdKQRgwcDURhA0YqMUrfW4ec4EHpLmR85NgOLjR3FXFDnMjxbnnQ629K0KI2ERT66fsQB6rJ2qxWLVJ%2BQ6tGfF6vcLOc3zbU%2FteXVBsD0SfmbuhYx20XgRaU2%2FAF6oNc%2Fl7qvkJIz%2B%2BGnHGLegxbyHW02A7ywcglKy4BFwUVbPc8G8c9CnLJryhOMJSDUq%2BuhxRV2S7%2Fi5zY82xuNABhvB40gVytVnbZjadnmtSfp8bGeJe94mKeRNfnIT1m%2Fjf%2B1SzqDyjCup1mC9ftMWDk%2BGIBn2V76ui%2FkjIIMTcIcZofkfWIEqP%2FAwBDmOVKNyc3BhtjSwLWL1ylMII6DvuPmMpVCBOpWOwaSa33ViQdx0AAp1UeRZ9cwwPzp5AU6tAEpCwaCuBBTZk9Mu2t%2FiEII9ILNXZ1GZfxYKLSzOKdZxQf6BxtrPxBrHBMRZbbbolDB0DBXUEfpgpmjvHBSny9HHNrR6UBwJk%2F%2F1INJeQ57aBHRu%2BTbIj4jwSJ46d7xYh%2BwfReNfoNZC1HWBvUDgtjlUw9%2FAtizdD7aYqdKNUir4gQ64OZiunCCOVlrk7YVoA%2FIEZA5HnCPf2vksKt8cEC5GVEPLKsc4tRDYYWT2nZP2xObQJM%3D&AWSAccessKeyId=ASIAQ3PHCVTYZWP54XFZ&Expires=1553632955&Signature=bVIBr%2FxbeWlU4aiw27zjsMjjiv0%3D&hash=7702c7e19eac9a6628afaf4900fe353b33ba72e08e7c1481bd284218d91d07bd&host=68042c943591013ac2b2430a89b270f6af2c76d8dfd086a07176afe7c76c2c61&pii=S0008621500854841&tid=spdf-9f5699fb-b56d-4d3b-a304-6fc30d44a8f2&sid=542a214b7904d343144ac42-8f8ebd30566cgxrqb&type=client
k6r = 150; %g substrate /g protein h-1 %https://link.springer.com/article/10.1007/s11705-010-1010-y
kh = 8.28e-8;   %hmf rate constant %reference on google sheets
kf = 3.96e-4;  %furfural rate constant %reference on google sheets

K1ig2 = 0.015;  %in g protein / kg substrate %obnamia 2014
K1ig = 0.1;     %in g protein / kg substrate %obnamia 2014
K1ix = 0.1;     %in g protein / kg substrate %obnamia 2014
K2ig2 = 132;    %in g protein / kg substrate %obnamia 2014
K2ig = 0.04;    %in g protein / kg substrate %obnamia 2014
K2ix = 0.2;      %in g protein / kg substrate %obnamia 2014
K3ig = 3.9;     %in g protein / kg substrate %obnamia 2014
K3ix = 201;     %in g protein / kg substrate %obnamia 2014
K4ix2 = 0.48;      %in g protein / kg substrate %https://aem.asm.org/content/aem/71/9/5318.full.pdf
K4ix = 14.1;    %https://aem.asm.org/content/aem/51/4/746.full.pdf
K4ig = 6;   %https://www.researchgate.net/publication/46037545_Production_of_cellulases_and_xylanases_under_catabolic_repression_conditions_from_mutant_PR-22_of_Cellulomonas_flavigena
K5ix = 14.1; %https://aem.asm.org/content/aem/51/4/746.full.pdf
K5ig = 6; % https://www.researchgate.net/publication/46037545_Production_of_cellulases_and_xylanases_under_catabolic_repression_conditions_from_mutant_PR-22_of_Cellulomonas_flavigena
K6ix = 2.89; %https://www.microbiologyresearch.org/docserver/fulltext/micro/135/2/mic-135-2-293.pdf?expires=1553629132&id=id&accname=sgid026735&checksum=992991FB9A3B6F10DAD4C52021775443
K6ig = 1.02; %https://www.brenda-enzymes.org/enzyme.php?ecno=3.2.1.37#Ki%20VALUE%20[mM]

K3M = 24.3; %in g protein / kg substrate %obnamia 2014
K6M = 24.3; %assumed the same due to no data %http://foodb.ca/compounds/FDB001135

E1f = 1;    %assume all enzymes free initially
E2f = 1;    %assume all enzymes free initially
E3f = 1;    %assume all enzymes free initially
E4f = 1;        %assume all enzymes free initially
K1ad = 0.4; %g/g %obnamia 2014
K2ad = 0.1; %g/g %obnamia 2014
K3ad = 0.573; %g/g % using average MW=35000 from https://onlinelibrary.wiley.com/doi/pdf/10.1002/polc.5070110119 and value from https://jb.asm.org/content/jb/184/9/2399.full.pdf 
K4ad = 2.3e-5;      %http://www.jbc.org/content/early/2012/08/22/jbc.M112.391532.full.pdf
E1max = 0.2; % g protein/ g cellulose %obnamia 2014
E2max = 0.2; % g protein/ g cellbiose %obnamia 2014
E3max = 0.2;      %assuming the same for all enzymes
E4max = 0.2;      %assuming the same for all enzymes

W0 = 67550; %in g/kg form 
C0 = 0.637; %in g/kg form
XN0 = 0.0172; %in g/kg form
a = 1; %obnamia 2014
b = 1; %assumed

Rc = a * (c/C0);
Rx = b * (xn/XN0);

E1b = (E1max * K1ad * E1f * c)/(1 + (K1ad * E1f));
E2b = (E2max * K2ad * E2f * c)/(1 + (K2ad * E2f));
E3b = (E1max * K3ad * E3f * c)/(1 + (K3ad * E3f));
E4b = (E1max * K4ad * E4f * c)/(1 + (K4ad * E4f));

r1 = (k1r * E1b * Rc * c)/(1 + (g2/K1ig2) + (g/K1ig) + (x/K1ix));
r2 = (k2r * (E1b+E2b) * Rc * c)/(1 + (g2/K2ig2) + (g/K2ig) + (x/K2ix));
r3 = (k3r * E2f * g2)/( K3M * (1 + (g/K3ig) + (x/K3ix) + g2));
r4 = (k4r * E3b * Rx * xn)/(1 + (x2/K4ix2) + (x/K4ix) + (g/K4ig));
r5 = (k5r * (E3b+E4b) * Rx * xn)/(1 + (x/K5ix) + (g/K5ig));
r6 = (k6r * E4f * x2)/( (K6M * ( 1+ (x/K6ix) + (g/K6ig))) + x2);

dCdt = -(r1) - (r2); 
dG2dt = ((342.30/342.28)*(r1)) - (r3);
dGdt = ((180.16/162.14) * (r2)) + ((360.31/342.30) * (r3));
dXNdt = -(r4) - (r5);
dX2dt = ((282.24/264.22) * (r4)) - (r6);
dXdt = ((150.13/132.11) * (r5)) + ((300.226/282.24) * (r6));
dHdt = kh*g; %ADD MASS CHANGE
dFdt = kf*x;  %ADD MASS CHANGE

f = [dCdt; dG2dt; dGdt; dXNdt; dX2dt; dXdt; dHdt; dFdt]; %dWdt

end

Answer 1

[Star Strider]

The [G] value appears to be the third value (row) in the ‘f’ vector, and so is the third column in ‘y’.

To plot it, try this:

figure
plot(t, y(:,3))
grid

If that gives you the result you want, then you know that ‘y(:,3)’ is [G].

[Will Seccombe]

I am trying to get a table of the concentration values aganst time to put into excel not plot the concentration profile of just glucose. How do I obtain the data points for g used in the graph?

[Star Strider]

Using a table is likely easiest:

GlucoseTable = table(t, y(:,3), 'VariableNames',{'Time','Glucose'})

then use the writetable (link) function to save it to your Excel file.