Mean-field active stress model (implements the RDQ20-MF formulation). More...

#include <ActiveStressRegazzoni.h>

Inheritance diagram for ActiveStressRegazzoni:

Classes
class	Parameters
	Model parameters class. More...

Public Member Functions
	ActiveStressRegazzoni ()
	Constructor.

virtual std::unique_ptr< ActiveStressModelParameters >	get_parameters () const override
	Construct an instance of model parameters.

Public Member Functions inherited from ActiveStress
	ActiveStress (const unsigned int n_states_, const bool needs_fiber_stretch, const bool needs_fiber_stretch_rate)
	Constructor.

virtual	~ActiveStress ()=default
	Virtual destructor.

void	read_parameters (const ActiveStressParameters &params)
	Read model parameters from a parameter object.

void	distribute_parameters (const CmMod &cm_mod, const cmType &cm)
	Distribute model parameters to all parallel processes.

double	get_tension_fibers (const int idx) const
	Get the tension along fibers \(\eta_f \Tact\) at a given point.

double	get_tension_sheets (const int idx) const
	Get the tension along sheets \(\eta_s \Tact\) at a given point.

double	get_tension_sheet_normals (const int idx) const
	Get the tension along sheet normals \(\eta_n \Tact\) at a given point.

virtual void	init (const unsigned int tnNo)
	Initialize the model.

virtual void	advance_time_step (const double t, const double dt, const Vector< double > &calcium, const Vector< double > &fiber_stretch, const Vector< double > &fiber_stretch_rate)
	Advance in time.

bool	needs_fiber_stretch () const
	Whether this model uses the fiber stretch passed to advance_time_step. This flag can be used to determine whether fiber stretch computation can be skipped for efficiency.

bool	needs_fiber_stretch_rate () const
	Whether this model uses the fiber stretch rate passed to advance_time_step. This flag can be used to determine whether fiber stretch rate computation can be skipped for efficiency.

Static Public Attributes
static const std::string	label = "Regazzoni"
	Model label, used for factory registration and XML selection.

Protected Member Functions
virtual void	read_model_specific_parameters (const ActiveStressModelParameters &params) override
	Read model parameters from a parameter object.

virtual void	distribute_model_specific_parameters (const CmMod &cm_mod, const cmType &cm) override
	Distribute model parameters to all parallel processes.

virtual void	init_local (Vector< double > &state) const override
	Initialize the state vector for a single node.

virtual void	advance_time_step_local (const double t, const double dt, const double calcium, const double fiber_stretch, const double fiber_stretch_rate, Vector< double > &state) const override
	Advance in time for a single node.

virtual double	compute_active_tension_local (const Vector< double > &state, const double fiber_stretch) const override
	Compute the scalar active tension for a single node.

State vector layout
static constexpr unsigned int	n_ru_states = 16
	Number of regulatory-unit (RU) probability states (entries 0-15).

static constexpr unsigned int	n_xb_states = 4
	Number of crossbridge (XB) moment states (entries 16-19).

static constexpr unsigned int	n_state_variables = n_ru_states + n_xb_states
	Total number of state variables.

static constexpr unsigned int	ru_index (unsigned int TL, unsigned int TC, unsigned int TR, unsigned int CC)
	Flat index of the RU probability state P(TL, TC, TR, CC).

static constexpr unsigned int	xb_index (unsigned int i)
	Flat index of the XB moment state `i` (in [0, 3]), spanning [16, 19].

Additional Inherited Members
Public Attributes inherited from ActiveStress
const unsigned int	n_states
	Number of state variables for this model.

Protected Attributes inherited from ActiveStress
bool	needs_fiber_stretch_
	Backing store for needs_fiber_stretch.

bool	needs_fiber_stretch_rate_
	Backing store for needs_fiber_stretch_rate.

double	time
	Current time. Updated whenever calling advance_time_step.

Array< double >	states
	State variables for the model.

Vector< double >	active_tension
	Active tension at every node.

double	eta_f
	Active tension coefficient along the fiber direction.

double	eta_s
	Active tension coefficient along the sheet direction.

double	eta_n
	Active tension coefficient along the sheet-normal direction.

Detailed Description

Mean-field active stress model (implements the RDQ20-MF formulation).

This class implements the mean-field RDQ20-MF sarcomere model of cardiomyocyte force generation of Regazzoni, Dede', and Quarteroni (2020), described in [1] and validated against the authors' reference implementation [2]. The node-local state has 20 variables: 16 regulatory-unit (RU) probabilities (entries 0-15) describing the tropomyosin/troponin configuration of a triplet of neighbouring units, and 4 crossbridge (XB) moments (entries 16-19). The RU probabilities are advanced with an explicit forward-Euler substepping scheme — for every macro time step, a number of smaller sub-steps are taken to update the RU states — and the XB moments with one implicit-Euler step per time step; the active tension is then reconstructed from the XB first moments.

The returned scalar active tension is

\[ \Tact = a_\text{XB} \, (\mu_P^1 + \mu_N^1) \, \phi(SL)\;, \]

where \(\mu_P^1\) and \(\mu_N^1\) are the permissive and non-permissive first XB moments (state entries 17 and 19), \(\phi(SL)\) is the single-overlap fraction of the sarcomere at sarcomere length \(SL = SL_0 \, \fiberstretch\) (with \(\fiberstretch\) the fiber stretch), and \(a_\text{XB}\) is the tension upscaling factor. Because \(\mu_P^1 + \mu_N^1\) and \(\phi(SL)\) are dimensionless, \(a_\text{XB}\) sets the units of the returned active tension.

References:

Note: Although this model is governed by a system of ODEs, it inherits from ActiveStress rather than ActiveStressODE because it requires a customized time-stepping scheme to handle the stiffness of the model.

Todo:: Force-strain-rate feedback requires a stabilization strategy for robust use in coupled electromechanics. This will be addressed in a follow-up PR.

Constructor & Destructor Documentation

◆ ActiveStressRegazzoni()

ActiveStressRegazzoni::ActiveStressRegazzoni ( )

inline

Constructor.

Member Function Documentation

◆ advance_time_step_local()

void ActiveStressRegazzoni::advance_time_step_local	(	const double	t,
		const double	dt,
		const double	calcium,
		const double	fiber_stretch,
		const double	fiber_stretch_rate,
		Vector< double > &	state
	)		const

overrideprotectedvirtual

Advance in time for a single node.

Advances the RU probabilities (entries 0-15) with the forward-Euler substepping scheme and then the XB moments (entries 16-19) with one implicit-Euler step, using the calcium, fiber stretch and fiber-stretch rate at the node.

Implements ActiveStress.

◆ compute_active_tension_local()

double ActiveStressRegazzoni::compute_active_tension_local	(	const Vector< double > &	state,
		const double	fiber_stretch
	)		const

overrideprotectedvirtual

Compute the scalar active tension for a single node.

Evaluates \(\Tact\) as defined in the class description, using fiber_stretch to compute the sarcomere length \(SL = SL_0 \, \fiberstretch\). The returned value has the stress units of \(a_\text{XB}\).

Implements ActiveStress.

◆ distribute_model_specific_parameters()

void ActiveStressRegazzoni::distribute_model_specific_parameters	(	const CmMod &	cm_mod,
		const cmType &	cm
	)

overrideprotectedvirtual

Distribute model parameters to all parallel processes.

Implements ActiveStress.

◆ get_parameters()

virtual std::unique_ptr< ActiveStressModelParameters > ActiveStressRegazzoni::get_parameters ( ) const

inlineoverridevirtual

Construct an instance of model parameters.

Implements ActiveStress.

◆ init_local()

void ActiveStressRegazzoni::init_local ( Vector< double > & state ) const

overrideprotectedvirtual

Initialize the state vector for a single node.

Sets the state to (1, 0, ..., 0), i.e. all probability mass in the RU state P(0, 0, 0, 0) and all crossbridge moments equal to zero.

Parameters

[out] state State vector for a single node, to be initialized by this function.

Implements ActiveStress.

◆ read_model_specific_parameters()

void ActiveStressRegazzoni::read_model_specific_parameters ( const ActiveStressModelParameters & params )

overrideprotectedvirtual

Read model parameters from a parameter object.

Implements ActiveStress.

◆ ru_index()

static constexpr unsigned int ActiveStressRegazzoni::ru_index	(	unsigned int	TL,
		unsigned int	TC,
		unsigned int	TR,
		unsigned int	CC
	)

inlinestaticconstexpr

Flat index of the RU probability state P(TL, TC, TR, CC).

Each argument is 0 or 1 and denotes the state of, respectively, the left tropomyosin unit, the central tropomyosin unit, the right tropomyosin unit and the central troponin (calcium unbound/bound). The ordering matches the reference implementation's serialization (TL outermost, CC innermost) and spans [0, 15].

◆ xb_index()

static constexpr unsigned int ActiveStressRegazzoni::xb_index ( unsigned int i )

inlinestaticconstexpr

Flat index of the XB moment state i (in [0, 3]), spanning [16, 19].

Member Data Documentation

◆ label

const std::string ActiveStressRegazzoni::label = "Regazzoni"

inlinestatic

Model label, used for factory registration and XML selection.

◆ n_ru_states

constexpr unsigned int ActiveStressRegazzoni::n_ru_states = 16

staticconstexpr

Number of regulatory-unit (RU) probability states (entries 0-15).

◆ n_state_variables

constexpr unsigned int ActiveStressRegazzoni::n_state_variables = n_ru_states + n_xb_states

staticconstexpr

Total number of state variables.

◆ n_xb_states

constexpr unsigned int ActiveStressRegazzoni::n_xb_states = 4

staticconstexpr

Number of crossbridge (XB) moment states (entries 16-19).

The documentation for this class was generated from the following files:

solver/ActiveStressRegazzoni.h
solver/ActiveStressRegazzoni.cpp

Classes

Public Member Functions

Static Public Attributes

Protected Member Functions

State vector layout

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ActiveStressRegazzoni()

Member Function Documentation

◆ advance_time_step_local()

◆ compute_active_tension_local()

◆ distribute_model_specific_parameters()

◆ get_parameters()

◆ init_local()

◆ read_model_specific_parameters()

◆ ru_index()

◆ xb_index()

Member Data Documentation

◆ label

◆ n_ru_states

◆ n_state_variables

◆ n_xb_states