Owen11Parameters.cpp

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#include "UnitCollection.hpp"
#include "Owen11Parameters.hpp"

std::string bib_info = "@article{Owen2011, \n author = {Owen, Markus R and Stamper, I Johanna and Muthana, Munitta and Richardson, Giles W and Dobson, Jon and Lewis, Claire E and Byrne, Helen M},"
        "\n journal = {Cancer research}, \n month = {apr}, \n number = {8}, \n pages = {2826--37},"
        "\n title = {{Mathematical modeling predicts synergistic antitumor effects of combining a macrophage-based, hypoxia-targeted gene therapy with chemotherapy.}},"
        "\n volume = {71}, \n year = {2011}}";

units::quantity<unit::pressure> mmHg(1.0*unit::mmHg);
units::quantity<unit::pressure> inlet_pressure(25.0 * unit::mmHg);
const boost::shared_ptr<ParameterInstance<unit::pressure> > Owen11Parameters::mpInletPressure =
        boost::shared_ptr<ParameterInstance<unit::pressure> >(new ParameterInstance<unit::pressure> (inlet_pressure,
                                                                                   "Owen11_InletPressure",
                                                                                   "Vessel network inlet pressure$",
                                                                                   "P_{in}",
                                                                                   bib_info));

units::quantity<unit::pressure> outlet_pressure(15.0 * unit::mmHg);
const boost::shared_ptr<ParameterInstance<unit::pressure> > Owen11Parameters::mpOutletPressure =
        boost::shared_ptr<ParameterInstance<unit::pressure> >(new ParameterInstance<unit::pressure> (outlet_pressure,
                                                                                   "Owen11_OutletPressure",
                                                                                   "Vessel network outlet pressure",
                                                                                   "P_{out}",
                                                                                   bib_info));
units::quantity<unit::length> cm (0.01*unit::metres);
units::quantity<unit::mass> g(1.e-3 *unit::kg);
units::quantity<unit::time> min(60.0*unit::seconds);
units::quantity<unit::dynamic_viscosity> plasma_visocity(0.72*g/(cm*min));
const boost::shared_ptr<ParameterInstance<unit::dynamic_viscosity> > Owen11Parameters::mpPlasmaViscosity =
        boost::shared_ptr<ParameterInstance<unit::dynamic_viscosity> >(new ParameterInstance<unit::dynamic_viscosity> (plasma_visocity,
                                                                                   "Owen11_PlasmaViscosity",
                                                                                   "Blood plasma viscosity",
                                                                                   "\\mu_{plasma}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::time> > Owen11Parameters::mpMinimumCellCyclePeriodNormal =
        boost::shared_ptr<ParameterInstance<unit::time> >(new ParameterInstance<unit::time> (3000.0*min,
                                                                                   "Owen11_MinCellCycleNormal",
                                                                                   "Minimum cell cycle period normal",
                                                                                   "T_{min}_{normal}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::time> > Owen11Parameters::mpMinimumCellCyclePeriodCancer =
        boost::shared_ptr<ParameterInstance<unit::time> >(new ParameterInstance<unit::time> (1600.0*min,
                                                                                   "Owen11_MinCellCycleCancer",
                                                                                   "Minimum cell cycle period cancer",
                                                                                   "T_{min}_{cancer}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::time> > Owen11Parameters::mpTimeToDeathDueToQuiescence =
        boost::shared_ptr<ParameterInstance<unit::time> >(new ParameterInstance<unit::time> (4000.0*min,
                                                                                   "Owen11_TimeDeathQuiescence",
                                                                                   "Time for death due to sustained quiescence",
                                                                                   "T_{death}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::pressure> > Owen11Parameters::mpOxygenPartialPressureAtHalfMaxCycleRateNormal =
        boost::shared_ptr<ParameterInstance<unit::pressure> >(new ParameterInstance<unit::pressure> (3.0*mmHg,
                                                                                   "Owen11_OxygenAtHalfMaxCycleRateNormal",
                                                                                   "Oxygen partial pressure at half max cell cycle rate normal",
                                                                                   "C_{\\phi}_{normal}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::pressure> > Owen11Parameters::mpOxygenPartialPressureAtHalfMaxCycleRateCancer =
        boost::shared_ptr<ParameterInstance<unit::pressure> >(new ParameterInstance<unit::pressure> (1.4*mmHg,
                                                                                   "Owen11_OxygenAtHalfMaxCycleRateCancer",
                                                                                   "Oxygen partial pressure at half max cell cycle rate cancer",
                                                                                   "C_{\\phi}_{cancer}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::pressure> > Owen11Parameters::mpOxygenPartialPressureAtQuiescence =
        boost::shared_ptr<ParameterInstance<unit::pressure> >(new ParameterInstance<unit::pressure> (8.9*mmHg,
                                                                                   "Owen11_OxygenAtQuiescence",
                                                                                   "Oxygen partial pressure at quiescence",
                                                                                   "C^{enter}_{quiesc}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::pressure> > Owen11Parameters::mpOxygenPartialPressureLeaveQuiescence =
        boost::shared_ptr<ParameterInstance<unit::pressure> >(new ParameterInstance<unit::pressure> (9.8*mmHg,
                                                                                   "Owen11_OxygenLeaveQuiescence",
                                                                                   "Oxygen partial pressure to leave quiescence",
                                                                                   "C^{leave}_{quiesc}",
                                                                                   bib_info));

units::quantity<unit::area> micron_sq(1.e-6*unit::metres*1.e-6*unit::metres);
units::quantity<unit::concentration> nano_molar(1.e-9 *unit::mole_per_metre_cubed);
units::quantity<unit::diffusivity_per_concentration> chemotactic_sensitivty(2.e4*micron_sq/(min*nano_molar));
const boost::shared_ptr<ParameterInstance<unit::diffusivity_per_concentration> > Owen11Parameters::mpChemotacticSensitivity =
        boost::shared_ptr<ParameterInstance<unit::diffusivity_per_concentration> >(new ParameterInstance<unit::diffusivity_per_concentration> (chemotactic_sensitivty,
                                                                                   "Owen11_ChemotacticSensitivity",
                                                                                   "Chemotactic sensitivity",
                                                                                   "\\Chi",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::diffusivity> > Owen11Parameters::mpCellMotilityNormal =
        boost::shared_ptr<ParameterInstance<unit::diffusivity> >(new ParameterInstance<unit::diffusivity> (0.0*micron_sq/min,
                                                                                   "Owen11_CellMotilityNormal",
                                                                                   "Maximum cell motility normal",
                                                                                   "D_{normal}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::diffusivity> > Owen11Parameters::mpCellMotilityCancer =
        boost::shared_ptr<ParameterInstance<unit::diffusivity> >(new ParameterInstance<unit::diffusivity> (0.5*micron_sq/min,
                                                                                   "Owen11_CellMotilityCancer",
                                                                                   "Maximum cell motility cancer",
                                                                                   "D_{cancer}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::diffusivity> > Owen11Parameters::mpCellMotilityEndothelial =
        boost::shared_ptr<ParameterInstance<unit::diffusivity> >(new ParameterInstance<unit::diffusivity> (1.0*micron_sq/min,
                                                                                   "Owen11_CellMotilityEndothelial",
                                                                                   "Maximum cell motility endothelial",
                                                                                   "D_{endo}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::membrane_permeability> > Owen11Parameters::mpVesselOxygenPermeability =
        boost::shared_ptr<ParameterInstance<unit::membrane_permeability> >(new ParameterInstance<unit::membrane_permeability> (6.0*cm/min,
                                                                                   "Owen11_VesselOxygenPermeability",
                                                                                   "Vessel permeability to oxygen",
                                                                                   "\\psi_{c}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::membrane_permeability> > Owen11Parameters::mpVesselVegfPermeability =
        boost::shared_ptr<ParameterInstance<unit::membrane_permeability> >(new ParameterInstance<unit::membrane_permeability> (1.e-5*cm/min,
                                                                                   "Owen11_VesselVegfPermeability",
                                                                                   "Vessel permeability to vegf",
                                                                                   "\\psi_{v}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::rate> > Owen11Parameters::mpCellOxygenConsumptionRate =
        boost::shared_ptr<ParameterInstance<unit::rate> >(new ParameterInstance<unit::rate> (13.0/min,
                                                                                   "Owen11_CellOxygenConsumptionRate",
                                                                                   "Cell oxygen consumption rate",
                                                                                   "k_c^{cell}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::rate> > Owen11Parameters::mpMaximumSproutingRate =
        boost::shared_ptr<ParameterInstance<unit::rate> >(new ParameterInstance<unit::rate> (0.00025/min,
                                                                                   "Owen11_MaximumSproutingRate",
                                                                                   "Maximum rate of sprouting",
                                                                                   "P^{max}_{sprout}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::concentration> > Owen11Parameters::mpVegfConventrationAtHalfMaxProbSprouting =
        boost::shared_ptr<ParameterInstance<unit::concentration> >(new ParameterInstance<unit::concentration> (0.5*nano_molar,
                                                                                   "Owen11_VegfConventrationAtHalfMaxProbSprouting",
                                                                                   "VEGF concentration at half maximal vessel sprouting probability",
                                                                                   "V_{sprout}",
                                                                                   bib_info));

units::quantity<unit::length> um(1.e-6*unit::metres);
const boost::shared_ptr<ParameterInstance<unit::length> > Owen11Parameters::mpSproutingExclusionRadius =
        boost::shared_ptr<ParameterInstance<unit::length> >(new ParameterInstance<unit::length> (80.0 * um,
                                                                                   "Owen11_SproutingExclusionRadius",
                                                                                   "Sprouting exclusion radius",
                                                                                   "R_{ex}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::time> > Owen11Parameters::mpMaxTimeWithLowWallShearStress =
        boost::shared_ptr<ParameterInstance<unit::time> >(new ParameterInstance<unit::time> (4000.0 * min,
                                                                                   "Owen11_MaxTimeWithLowWallShearStress",
                                                                                   "Maximum vessel survivial time with low wall shear stress",
                                                                                   "T_{prune}",
                                                                                   bib_info));

units::quantity<unit::force> dyne(g*cm/(unit::seconds*unit::seconds));
const boost::shared_ptr<ParameterInstance<unit::pressure> > Owen11Parameters::mpCriticalWallShearStress =
        boost::shared_ptr<ParameterInstance<unit::pressure> >(new ParameterInstance<unit::pressure> (8.0 * dyne/(cm*cm),
                                                                                   "Owen11_CriticalWallShearStress",
                                                                                   "Critical wall shear stress for vessel pruning",
                                                                                   "\\tau_{wall}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::time> > Owen11Parameters::mpMasterStepTime =
        boost::shared_ptr<ParameterInstance<unit::time> >(new ParameterInstance<unit::time> (30.0 * min,
                                                                                   "Owen11_MasterStepTime",
                                                                                   "Master step time",
                                                                                   "\\Delta t",
                                                                                   bib_info));

units::quantity<unit::time> day(60.0*60.0*24.0*unit::seconds);
const boost::shared_ptr<ParameterInstance<unit::time> > Owen11Parameters::mpSimulationDuration =
        boost::shared_ptr<ParameterInstance<unit::time> >(new ParameterInstance<unit::time> (200.0 * day,
                                                                                   "Owen11_SimulationDuration",
                                                                                   "Simulation duration",
                                                                                   "T_{final}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::length> > Owen11Parameters::mpLatticeSpacing =
        boost::shared_ptr<ParameterInstance<unit::length> >(new ParameterInstance<unit::length> (40.0*um,
                                                                                   "Owen11_LatticeSpacing",
                                                                                   "Lattice spacing",
                                                                                   "\\Delta x",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::diffusivity> > Owen11Parameters::mpOxygenDiffusivity =
        boost::shared_ptr<ParameterInstance<unit::diffusivity> >(new ParameterInstance<unit::diffusivity> (0.00145*cm*cm/min,
                                                                                   "Owen11_OxygenDiffusivity",
                                                                                   "Oxygen diffusivity ",
                                                                                   "D_{c}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::diffusivity> > Owen11Parameters::mpVegfDiffusivity =
        boost::shared_ptr<ParameterInstance<unit::diffusivity> >(new ParameterInstance<unit::diffusivity> (1.e-5*cm*cm/min,
                                                                                   "Owen11_VegfDiffusivity",
                                                                                   "Vegf diffusivity ",
                                                                                   "D_{v}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::rate> > Owen11Parameters::mpVegfDecayRate =
        boost::shared_ptr<ParameterInstance<unit::rate> >(new ParameterInstance<unit::rate> (0.01/min,
                                                                                   "Owen11_VegfDecayRate",
                                                                                   "Vegf decay rate ",
                                                                                   "\\delta_{v}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::dimensionless> > Owen11Parameters::mpInflowHaematocrit =
        boost::shared_ptr<ParameterInstance<unit::dimensionless> >(new ParameterInstance<unit::dimensionless> (0.45,
                                                                                   "Owen11_InflowHaematocrit",
                                                                                   "Inflow haematocrit",
                                                                                   "H_{in}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::rate> > Owen11Parameters::mpP53ProductionRateConstant =
        boost::shared_ptr<ParameterInstance<unit::rate> >(new ParameterInstance<unit::rate> (0.002/min,
                                                                                   "Owen11_P53ProductionRateConstant",
                                                                                   "Intracellular p53 production rate constant",
                                                                                   "k_7",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::rate> > Owen11Parameters::mpP53MaxDegradationRate =
        boost::shared_ptr<ParameterInstance<unit::rate> >(new ParameterInstance<unit::rate> (0.01/min,
                                                                                   "Owen11_P53MaxDegradationRate",
                                                                                   "Max p53 degradation rate",
                                                                                   "k_dash_7",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::pressure> > Owen11Parameters::mpOxygenTensionForHalfMaxP53Degradation =
        boost::shared_ptr<ParameterInstance<unit::pressure> >(new ParameterInstance<unit::pressure> (4.44*mmHg,
                                                                                   "Owen11_OxygenTensionForHalfMaxP53Degradation",
                                                                                   "Tissue oxygen tension for half-max p53 degradation",
                                                                                   "C_{p53}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::rate> > Owen11Parameters::mpCellVegfProductionRate =
        boost::shared_ptr<ParameterInstance<unit::rate> >(new ParameterInstance<unit::rate> (0.002/min,
                                                                                   "Owen11_CellVegfProductionRate",
                                                                                   "Basal VEGF production rate in cell",
                                                                                   "k_8",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::rate> > Owen11Parameters::mpMaxCellVegfProductionRate =
        boost::shared_ptr<ParameterInstance<unit::rate> >(new ParameterInstance<unit::rate> (0.01/min,
                                                                                   "Owen11_MaxCellVegfProductionRate",
                                                                                   "Max VEGF production rate in cell",
                                                                                   "k_8_dash",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::rate> > Owen11Parameters::mpP53EffectOnVegfProduction =
        boost::shared_ptr<ParameterInstance<unit::rate> >(new ParameterInstance<unit::rate> (-0.002/min,
                                                                                   "Owen11_P53EffectOnVegfProduction",
                                                                                   "Effect of P53 on VEGF production",
                                                                                   "k_8_dash_dash",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::dimensionless> > Owen11Parameters::mpVegfEffectOnVegfProduction =
        boost::shared_ptr<ParameterInstance<unit::dimensionless> >(new ParameterInstance<unit::dimensionless> (0.04,
                                                                                   "Owen11_VegfEffectOnVegfProduction",
                                                                                   "Effect of VEGF on VEGF production",
                                                                                   "j_5",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::pressure> > Owen11Parameters::mpOxygenTensionForHalfMaxVegfDegradation =
        boost::shared_ptr<ParameterInstance<unit::pressure> >(new ParameterInstance<unit::pressure> (4.44*mmHg,
                                                                                   "Owen11_OxygenTensionForHalfMaxVegfDegradation",
                                                                                   "Tissue oxygen tension for half-max vegf degradation",
                                                                                   "C_{VEGF}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::time> > Owen11Parameters::mpVesselRadiusUpdateTimestep =
        boost::shared_ptr<ParameterInstance<unit::time> >(new ParameterInstance<unit::time> (0.1*unit::seconds,
                                                                                   "Owen11_VesselRadiusUpdateTimestep",
                                                                                   "Vessel radius update timestep",
                                                                                   "\\epsilon_t",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::concentration_flow_rate> > Owen11Parameters::mpCellVegfSecretionRate =
        boost::shared_ptr<ParameterInstance<unit::concentration_flow_rate> >(new ParameterInstance<unit::concentration_flow_rate> (0.01*nano_molar/min,
                                                                                   "Owen11_CellVegfSecretionRate",
                                                                                   "Cell vegf secretion rate",
                                                                                   "k_v^{cell}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::length> > Owen11Parameters::mpMinimumRadius =
        boost::shared_ptr<ParameterInstance<unit::length> >(new ParameterInstance<unit::length> (1.e-6*unit::metres,
                                                                                   "Owen11_MinimumRadius",
                                                                                   "Minimum possible radius",
                                                                                   "R_{MIN}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::length> > Owen11Parameters::mpMaximumRadius =
        boost::shared_ptr<ParameterInstance<unit::length> >(new ParameterInstance<unit::length> (50.e-6*unit::metres,
                                                                                   "Owen11_MaximumRadius",
                                                                                   "Maximum possible radius",
                                                                                   "R_{MAX}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::flow_rate> > Owen11Parameters::mpReferenceFlowRateForMetabolicStimulus =
        boost::shared_ptr<ParameterInstance<unit::flow_rate> >(new ParameterInstance<unit::flow_rate> (4.e-5*cm*cm*cm/min,
                                                                                   "Owen11_ReferenceFlowRateForMetabolicStimulus",
                                                                                   "Reference flow rate for metabolic stimulus",
                                                                                   "Q_{ref}",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::rate> > Owen11Parameters::mpShrinkingTendency =
        boost::shared_ptr<ParameterInstance<unit::rate> >(new ParameterInstance<unit::rate> (1.7/unit::seconds,
                                                                                   "Owen11_ShrinkingTendency",
                                                                                   "Shrinking tendency",
                                                                                   "k_s",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::rate> > Owen11Parameters::mpSensitivityToIntravascularPressure =
        boost::shared_ptr<ParameterInstance<unit::rate> >(new ParameterInstance<unit::rate> (0.5/unit::seconds,
                                                                                   "Owen11_SensitivityToIntravascularPressure",
                                                                                   "Shrinking to intravascaulr pressure",
                                                                                   "k_p",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::rate> > Owen11Parameters::mpBasalMetabolicStimulus =
        boost::shared_ptr<ParameterInstance<unit::rate> >(new ParameterInstance<unit::rate> (1.7/unit::seconds,
                                                                                   "Owen11_BasalMetabolicStimulus",
                                                                                   "Basal metabolic stimulus",
                                                                                   "k^0_m",
                                                                                   bib_info));

const boost::shared_ptr<ParameterInstance<unit::pressure> > Owen11Parameters::mpReferencePartialPressure =
        boost::shared_ptr<ParameterInstance<unit::pressure> >(new ParameterInstance<unit::pressure> (20.0*mmHg,
                                                                                   "Owen11_ReferencePartialPressure",
                                                                                   "Reference partial pressure of inlet haematocrit vessels",
                                                                                   "C_{Ref}",
                                                                                   bib_info));