| 2013-12-05 |
Randall Britten |
Added ?SaveDefinitions -> True? to ?Manipulate? blocks so that CDF export works.
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| 2013-12-05 |
Randall Britten |
Seem to have successfully resolved all units issues now, and also worked around the quirks in the Mathematica 3D plotting functions. Works quite nicely now.
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| 2013-12-05 |
Randall Britten |
Attempting to clean up issues with units and unit conversions by more disciplined use of units suffixes in variable names. Some progress made so far. Still having issues showing trajectory relative to 3D plot.
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| 2013-12-04 |
Randall Britten |
Working nicely now. Shows contour plot, 3D plot and individual time series of each reactant/product (i.e. reaction species), as well as final value.
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| 2013-12-04 |
Randall Britten |
Cool! Got parametric plot and cursor interaction combined with contour plot.
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| 2013-12-04 |
Randall Britten |
Got cursor to determine initial conditions :-)
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| 2013-12-04 |
Randall Britten |
Attempts to get parametric plot of trajectory of point in {H, HCO3, CO2} space. Partially working. Haven?t succeeded yet in setting initial conditions based on cursor position.
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| 2013-12-02 |
Randall Britten |
Extracted the ODE numerical solve call to make Manipulate block cleaner.
Also, showing final values of pH and HCO3.
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| 2013-12-02 |
Randall Britten |
Allow time range of ODE solution to be adjusted.
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| 2013-12-02 |
Randall Britten |
Manipulate now shows ODE results allowing for initial pH and initial CO2 level to be adjusted.
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| 2013-12-02 |
Randall Britten |
Added 3D plot.
Also, made ODE numerical solve parameterised by initial conditions, which is work towards being able to pick IV?s from Manipulate UI and see solution interactively.
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| 2013-09-13 |
Randall Britten |
Initial value for HCO3 is now calculated from given initial pH and initial CO2 partial pressure, in the same way as in the Mathematica document. The system now remains at equilibrium :-)
Also, using kf = K kb, with kb=1 and K calculated from given pK = 6.1, which is apparently the accepted value in the textbooks.
Also, now actually using the initial values for CO2 concentration that was calculated from given partial pressure.
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| 2013-09-13 |
Randall Britten |
Simplified calculation of initial HCO3.
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| 2013-09-13 |
Randall Britten |
Finally, got ODE to match Davenport plot nicely.
Using kb = 1, and deriving kf from K derived from textbook pK = 6.1, then deriving initialHCO3.
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| 2013-09-13 |
Randall Britten |
Updated Mathematica to explore what equilibrium the textbook value of pK=6.1 gives compared to using the initial values read off Peter's slides.
Change pK = pKbyInitial to pK = pKfromTextbook to see the difference: textbook value does not match initial conditions on slide being at equilibrium, and ODE runs to a pH of around 4.5!
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| 2013-09-13 |
Randall Britten |
Corrected conversion between partial pressure and concentration: based on solubility, not ideal gas law since we are modelling the solution. Seems obvious.
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| 2013-09-13 |
Randall Britten |
Mathematica Davenport plot using contours of pCO2 as a function of pH and [HCO3-].
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| 2013-09-13 |
Randall Britten |
Backout changeset f90bdc4dcf7f06125137b0272f5cb6a7d4b973ad
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| 2013-09-13 |
Randall Britten |
Mathematica Davenport plot using contours of pCO2 as a function of pH and [HCO3-].
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| 2013-09-11 |
Randall Britten |
Turns out that you have to use the reciprocal as the multiplier!
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| 2013-09-11 |
Randall Britten |
Although this runs, it is not producing numerically sensible results yet.
Current state is partly a debugging state, and so the PhysicalConstants.cellml model isn't being used yet.
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| 2013-09-11 |
Randall Britten |
First attempt at introducing partial pressure as units for CO2 concentration. Still seem to be some problems with units and scaling, and a minor problem with encapsulation that should be easy to fix.
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| 2013-09-10 |
Randall Britten |
Including pH in model, setting initial pH to 7.4, which I think is physiologically realistic. Other parameters still seem far from physiological though.
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| 2013-07-15 |
Randall Britten |
Added an H+ ion source (i.e. a proton source).
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| 2013-07-15 |
Randall Britten |
Added a CO2 (Carbon dioxide) source and sync term.
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| 2013-07-15 |
Randall Britten |
Original versions from Peter Hunter.
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