#include <Diffusion.h>

Inheritance diagram for biogears::DiffusionCalculator:

Classes
struct	ConcentrationSet

struct	DiffusionCompartmentSet

struct	DiffusionMatrixSet

Public Member Functions
	~DiffusionCalculator ()=default

void	Initialize (SESubstanceManager &subMgr)

void	SetDiffusionState ()

void	CalculateLinearDiffusionMethods ()

void	CalculateNonLinearDiffusionMethods ()

std::vector< DiffusionCompartmentSet > &	GetDiffusionSets ()

std::vector< SESubstance * > &	GetFacilitatedDiffusionSubstances ()

std::vector< SESubstance * > &	GetInstantDiffusionSubstances ()

std::vector< SESubstance * > &	GetSimpleDiffusionSubstances ()

Public Member Functions inherited from biogears::Loggable
	Loggable ()

	Loggable (Logger *log)

virtual	~Loggable ()

virtual Logger *	GetLogger () const

Protected Member Functions
	DiffusionCalculator (BioGears &bg)

void	ClearConcentrations ()

void	CalculateActiveIonDiffusion (DiffusionCompartmentSet &cmptSet)
	Calculates the mass transport of ionic species Na, K, Ca, Cl against their electrochemical gradient using active pumps and cotransport. More...

void	CalculateMacromoleculeDiffusion (DiffusionCompartmentSet &cmptSet, const SESubstance &sub)

void	CalculatePassiveLymphDiffusion (SELiquidCompartment &source, SELiquidCompartment &target, const SESubstance &sub)

void	CalculateFacilitatedDiffusion (DiffusionCompartmentSet &cmptSet, const SESubstance &sub, double combinedCoefficient_g_Per_s)

void	CalculatePerfusionLimitedDiffusion (DiffusionCompartmentSet &cmptSet, const SESubstance &sub, double partitionCoeff)

Protected Member Functions inherited from biogears::Loggable
virtual void	Debug (const char msg, const char origin="") const

virtual void	Debug (const std::string &msg, const std::string &origin=empty) const

virtual void	Debug (std::ostream &msg, const std::string &origin=empty) const

virtual void	Info (const char msg, const char origin="") const

virtual void	Info (const std::string &msg, const std::string &origin=empty) const

virtual void	Info (std::ostream &msg, const std::string &origin=empty) const

virtual void	Warning (const char msg, const char origin="") const

virtual void	Warning (const std::string &msg, const std::string &origin=empty) const

virtual void	Warning (std::ostream &msg, const std::string &origin=empty) const

virtual void	Error (const char msg, const char origin="") const

virtual void	Error (const std::string msg, const std::string origin=empty) const

virtual void	Error (std::ostream &msg, const std::string &origin=empty) const

virtual void	Fatal (const char msg, const char origin="") const

virtual void	Fatal (const std::string &msg, const std::string &origin=empty) const

virtual void	Fatal (std::ostream &msg, const std::string &origin=empty) const

Static Protected Member Functions
static auto	make_unique (BioGears &bg) -> std::unique_ptr< DiffusionCalculator >

Protected Attributes
BioGears &	m_data

Protected Attributes inherited from biogears::Loggable
Logger *	m_Logger

Private Member Functions
void	DistributeMassbyVolumeWeighted (SELiquidCompartment &cmpt, const SESubstance &sub, double mass, const MassUnit &unit)

void	DistributeMassbyMassWeighted (SELiquidCompartment &cmpt, const SESubstance &sub, double mass, const MassUnit &unit)

double	SodiumPotassiumPump (double intraNa_mM, double extraNa_mM, double extraK_mM, double potential_V)

double	CalciumPump (double intraCa_M)

Private Attributes
double	m_dt_s

std::vector< SESubstance * >	m_SimpleDiffusionSubstances

std::vector< SESubstance * >	m_InstantDiffusionSubstances

std::vector< SESubstance * >	m_FacilitatedDiffusionSubstances

ConcentrationSet	m_InstantSubConcentrations

ConcentrationSet	m_SimpleSubConcentrations

DiffusionMatrixSet	m_InstantSubMatrices

DiffusionMatrixSet	m_SimpleSubMatrices

std::vector< DiffusionCompartmentSet >	m_DiffusionSets

Eigen::VectorXd	m_PermeabilityCoefficients

Eigen::VectorXd	m_TissueMasses_g

Eigen::VectorXd	m_VolumeRatiosVascularExtra

Eigen::VectorXd	m_VolumeRatiosExtraIntra

Friends
class	BioGears

class	BioGearsEngineTest

Additional Inherited Members
Static Public Attributes inherited from biogears::Loggable
static const std::string	empty

static const char *	empty_cStr

Constructor & Destructor Documentation

biogears::DiffusionCalculator::DiffusionCalculator ( BioGears & bg )

protected

biogears::DiffusionCalculator::~DiffusionCalculator ( )

default

Member Function Documentation

double biogears::DiffusionCalculator::CalciumPump ( double intraCa_M )

private

void biogears::DiffusionCalculator::CalculateActiveIonDiffusion ( DiffusionCompartmentSet & cmptSet )

protected

Calculates the mass transport of ionic species Na, K, Ca, Cl against their electrochemical gradient using active pumps and cotransport.

Parameters

tissue	tissue compartment
vascular	vascular space adjoining tissue compartment
extra	extracellular space in tissue compartment
intra	intracellular space in tissue compartment
timestep_s	the time step

This active transport moves ions to maintain their resting intracellular and extracellular concentrations using the cell membrane potential and active transport. The current experience by each ion is calculated by comparing its nernst potential to the membrane potential. Active pumps are then called which have been tuned to drive ionic current to maintain homeostatic concentrations. Since this method replaces diffusion for Na, Ca, K, and Cl, transport from the extracellular space to the vascular space is also handled here and balancing of the ions is also performed.

\ [lindblad] 1996model

void biogears::DiffusionCalculator::CalculateFacilitatedDiffusion	(	DiffusionCompartmentSet &	cmptSet,
		const SESubstance &	sub,
		double	combinedCoefficient_g_Per_s
	)

protected

void biogears::DiffusionCalculator::CalculateLinearDiffusionMethods ( )

void biogears::DiffusionCalculator::CalculateMacromoleculeDiffusion	(	DiffusionCompartmentSet &	cmptSet,
		const SESubstance &	sub
	)

protected

void biogears::DiffusionCalculator::CalculateNonLinearDiffusionMethods ( )

Todo:: Define relationship between tissue mass and membrane area.

void biogears::DiffusionCalculator::CalculatePassiveLymphDiffusion	(	SELiquidCompartment &	source,
		SELiquidCompartment &	target,
		const SESubstance &	sub
	)

protected

void biogears::DiffusionCalculator::CalculatePerfusionLimitedDiffusion	(	DiffusionCompartmentSet &	cmptSet,
		const SESubstance &	sub,
		double	partitionCoeff
	)

protected

void biogears::DiffusionCalculator::ClearConcentrations ( )

protected

void biogears::DiffusionCalculator::DistributeMassbyMassWeighted	(	SELiquidCompartment &	cmpt,
		const SESubstance &	sub,
		double	mass,
		const MassUnit &	unit
	)

private

void biogears::DiffusionCalculator::DistributeMassbyVolumeWeighted	(	SELiquidCompartment &	cmpt,
		const SESubstance &	sub,
		double	mass,
		const MassUnit &	unit
	)

private

std::vector<DiffusionCompartmentSet>& biogears::DiffusionCalculator::GetDiffusionSets ( )

inline

std::vector<SESubstance*>& biogears::DiffusionCalculator::GetFacilitatedDiffusionSubstances ( )

inline

std::vector<SESubstance*>& biogears::DiffusionCalculator::GetInstantDiffusionSubstances ( )

inline

std::vector<SESubstance*>& biogears::DiffusionCalculator::GetSimpleDiffusionSubstances ( )

inline

void biogears::DiffusionCalculator::Initialize ( SESubstanceManager & subMgr )

auto biogears::DiffusionCalculator::make_unique ( BioGears & bg ) -> std::unique_ptr<DiffusionCalculator>

staticprotected

void biogears::DiffusionCalculator::SetDiffusionState ( )

double biogears::DiffusionCalculator::SodiumPotassiumPump	(	double	intraNa_mM,
		double	extraNa_mM,
		double	extraK_mM,
		double	potential_V
	)

private

Friends And Related Function Documentation

friend class BioGears

friend

friend class BioGearsEngineTest

friend

Member Data Documentation

BioGears& biogears::DiffusionCalculator::m_data

protected

std::vector<DiffusionCompartmentSet> biogears::DiffusionCalculator::m_DiffusionSets

private

double biogears::DiffusionCalculator::m_dt_s

private

std::vector<SESubstance*> biogears::DiffusionCalculator::m_FacilitatedDiffusionSubstances

private

std::vector<SESubstance*> biogears::DiffusionCalculator::m_InstantDiffusionSubstances

private

ConcentrationSet biogears::DiffusionCalculator::m_InstantSubConcentrations

private

DiffusionMatrixSet biogears::DiffusionCalculator::m_InstantSubMatrices

private

Eigen::VectorXd biogears::DiffusionCalculator::m_PermeabilityCoefficients

private

std::vector<SESubstance*> biogears::DiffusionCalculator::m_SimpleDiffusionSubstances

private

ConcentrationSet biogears::DiffusionCalculator::m_SimpleSubConcentrations

private

DiffusionMatrixSet biogears::DiffusionCalculator::m_SimpleSubMatrices

private

Eigen::VectorXd biogears::DiffusionCalculator::m_TissueMasses_g

private

Eigen::VectorXd biogears::DiffusionCalculator::m_VolumeRatiosExtraIntra

private

Eigen::VectorXd biogears::DiffusionCalculator::m_VolumeRatiosVascularExtra

private

Classes

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation