https://staging.physiomeproject.org/workspace/178 en-us https://staging.physiomeproject.org/workspace/178/@@file/b2146c6c6b06de44ace1035d9cbcd1d68d199808 Added ?SaveDefinitions -> True? to ?Manipulate? blocks so that CDF export works. Randall Britten 2013-12-05 https://staging.physiomeproject.org/workspace/178/@@file/e9152114cef924356e3de8388fda9a4b62312857 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. Randall Britten 2013-12-05 https://staging.physiomeproject.org/workspace/178/@@file/d5ee1c73f701f6fa278542d2ed7eb0adefc1b459 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. Randall Britten 2013-12-05 https://staging.physiomeproject.org/workspace/178/@@file/27d3423b2b1906f3deeaa8b1e680bcc936503fe5 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. Randall Britten 2013-12-04 https://staging.physiomeproject.org/workspace/178/@@file/036973299d99e8b16951be71961cfa46c526be18 Cool! Got parametric plot and cursor interaction combined with contour plot. Randall Britten 2013-12-04 https://staging.physiomeproject.org/workspace/178/@@file/16aeb5f2bab21e5e8f455ed8587f4e0ec3f057f9 Got cursor to determine initial conditions :-) Randall Britten 2013-12-04 https://staging.physiomeproject.org/workspace/178/@@file/e0573b63951643705784862975918d28bbf6e971 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. Randall Britten 2013-12-04 https://staging.physiomeproject.org/workspace/178/@@file/9c96ab8b0692285a17e8ca678ddf3863fe2dc4d6 Extracted the ODE numerical solve call to make Manipulate block cleaner. Also, showing final values of pH and HCO3. Randall Britten 2013-12-02 https://staging.physiomeproject.org/workspace/178/@@file/4974e16c7aecd08cc0dba0e42f06dd530aa5a7b8 Allow time range of ODE solution to be adjusted. Randall Britten 2013-12-02 https://staging.physiomeproject.org/workspace/178/@@file/2653eaa51ed0bd5e017f09c9ab5eb6ef244c691e Manipulate now shows ODE results allowing for initial pH and initial CO2 level to be adjusted. Randall Britten 2013-12-02 https://staging.physiomeproject.org/workspace/178/@@file/cafd543bf16066ca9f7cf7fedca65030ad04f46e 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. Randall Britten 2013-12-02 https://staging.physiomeproject.org/workspace/178/@@file/2b59edd002f0721d39e738789ddbbe9529b4de3e 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. Randall Britten 2013-09-13 https://staging.physiomeproject.org/workspace/178/@@file/7304f0d67d73cdb6489a08d8de649e29d42971f6 Simplified calculation of initial HCO3. Randall Britten 2013-09-13 https://staging.physiomeproject.org/workspace/178/@@file/50e3114fd363d10b5b77daad447c7c82d1d65561 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. Randall Britten 2013-09-13 https://staging.physiomeproject.org/workspace/178/@@file/494e3dc94373433a0bf3fdc7c37aaf20b64d095c 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! Randall Britten 2013-09-13 https://staging.physiomeproject.org/workspace/178/@@file/731411e3536157b0905b93c3ba526dde603b4b20 Corrected conversion between partial pressure and concentration: based on solubility, not ideal gas law since we are modelling the solution. Seems obvious. Randall Britten 2013-09-13 https://staging.physiomeproject.org/workspace/178/@@file/0d40d8be0318a1f0645059f932f2f1424398f8cf Mathematica Davenport plot using contours of pCO2 as a function of pH and [HCO3-]. Randall Britten 2013-09-13 https://staging.physiomeproject.org/workspace/178/@@file/bce14624c36bb41f33dea5b2ae7e725be9cd3cfe Backout changeset f90bdc4dcf7f06125137b0272f5cb6a7d4b973ad Randall Britten 2013-09-13 https://staging.physiomeproject.org/workspace/178/@@file/88933857fe4e38c4de28aae14a7140c602d3b19a Mathematica Davenport plot using contours of pCO2 as a function of pH and [HCO3-]. Randall Britten 2013-09-13 https://staging.physiomeproject.org/workspace/178/@@file/f005ef715944cfc7f4035a7a7d5cad7f8a1da2a5 Turns out that you have to use the reciprocal as the multiplier! Randall Britten 2013-09-11 https://staging.physiomeproject.org/workspace/178/@@file/a8e77a8940455c1250de09e50fdb1ab6bffb85d2 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. Randall Britten 2013-09-11 https://staging.physiomeproject.org/workspace/178/@@file/2320d7dee569a63f5be4e47ea0b81fe1eaa0c151 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. Randall Britten 2013-09-11 https://staging.physiomeproject.org/workspace/178/@@file/e1501746c35cafc2cfc25f935e022ef65fe8a492 Including pH in model, setting initial pH to 7.4, which I think is physiologically realistic. Other parameters still seem far from physiological though. Randall Britten 2013-09-10 https://staging.physiomeproject.org/workspace/178/@@file/570f21971b7fca13184af0019fce2b3c677b1266 Added an H+ ion source (i.e. a proton source). Randall Britten 2013-07-15 https://staging.physiomeproject.org/workspace/178/@@file/030ab6f6440c2795b9c7b0115f73ca1888f008d4 Added a CO2 (Carbon dioxide) source and sync term. Randall Britten 2013-07-15 https://staging.physiomeproject.org/workspace/178/@@file/3de98843f02c6e130b6c607fdb35e2edca2a57e6 Original versions from Peter Hunter. Randall Britten 2013-07-15