Boyce E. Griffith

An adaptive, formally second order accurate version of the immersed boundary method

Like many problems in biofluid mechanics, cardiac mechanics can be modeled as the dynamic interaction of a viscous incompressible fluid (the blood) and a (visco-)elastic structure (the muscular walls and the valves of the heart). The immersed boundary method is a mathematical formulation and numerical approach to such problems that was originally introduced to study blood flow through heart valves, and extensions of this work have yielded a three-dimensional model of the heart and great vessels. In the present work, we introduce a new adaptive version of the immersed boundary method. This adaptive scheme employs the same hierarchical structured grid approach (but a different numerical scheme) as the two-dimensional adaptive immersed boundary method of Roma et al. [A multilevel self adaptive version of the immersed boundary method, Ph.D. Thesis, Courant Institute of Mathematical Sciences, New York University, 1996; An adaptive version of the immersed boundary method, J. Comput. Phys. 153 (2) (1999) 509–534] and is based on a formally second order accurate (i.e., second order accurate for problems with sufficiently smooth solutions) version of the immersed boundary method that we have recently described [B.E. Griffith, C.S. Peskin, On the order of accuracy of the immersed boundary method: higher order convergence rates for sufficiently smooth problems, J. Comput. Phys. 208 (1) (2005) 75–105]. Actual second order convergence rates are obtained for both the uniform and adaptive methods by considering the interaction of a viscous incompressible flow and an anisotropic incompressible viscoelastic shell. We also present initial results from the application of this methodology to the three-dimensional simulation of blood flow in the heart and great vessels. The results obtained by the adaptive method show good qualitative agreement with simulation results obtained by earlier non-adaptive versions of the method, but the flow in the vicinity of the model heart valves indicates that the new methodology provides enhanced boundary layer resolution. Differences are also observed in the flow about the mitral valve leaflets.

Immersed boundary model of aortic heart valve dynamics with physiological driving and loading conditions

The immersed boundary (IB) method is a mathematical and numerical framework for problems of fluid–structure interaction, treating the particular case in which an elastic structure is immersed in a viscous incompressible fluid. The IB approach to such problems is to describe the elasticity of the immersed structure in Lagrangian form, and to describe the momentum, viscosity, and incompressibility of the coupled fluid–structure system in Eulerian form. Interaction between Lagrangian and Eulerian variables is mediated by integral equations with Dirac delta function kernels. The IB method provides a unified formulation for fluid–structure interaction models involving both thin elastic boundaries and also thick viscoelastic bodies. In this work, we describe the application of an adaptive, staggered-grid version of the IB method to the three-dimensional simulation of the fluid dynamics of the aortic heart valve. Our model describes the thin leaflets of the aortic valve as immersed elastic boundaries, and describes the wall of the aortic root as a thick, semi-rigid elastic structure. A physiological left-ventricular pressure waveform is used to drive flow through the model valve, and dynamic pressure loading conditions are provided by a reduced (zero-dimensional) circulation model that has been fit to clinical data. We use this model and method to simulate aortic valve dynamics over multiple cardiac cycles. The model is shown to approach rapidly a periodic steady state in which physiological cardiac output is obtained at physiological pressures. These realistic flow rates are not specified in the model, however. Instead, they emerge from the fluid–structure interaction simulation.

SIMULATING THE FLUID DYNAMICS OF NATURAL AND PROSTHETIC HEART VALVES USING THE IMMERSED BOUNDARY METHOD

The immersed boundary method is both a general mathematical framework and a particular numerical approach to problems of fluid-structure interaction. In the present work, we describe the application of the immersed boundary method to the simulation of the fluid dynamics of heart valves, including a model of a natural aortic valve and a model of a chorded prosthetic mitral valve. Each valve is mounted in a semi-rigid flow chamber. In the case of the mitral valve, the flow chamber is a circular pipe, and in the case of the aortic valve, the flow chamber is a model of the aortic root. The model valves and flow chambers are immersed in a viscous incompressible fluid, and realistic fluid boundary conditions are prescribed at the upstream and downstream ends of the chambers. To connect the immersed boundary models to the boundaries of the fluid domain, we introduce a novel modification of the standard immersed boundary scheme. In particular, near the outer boundaries of the fluid domain, we modify the construction of the regularized delta function which mediates fluid-structure coupling in the immersed boundary method, whereas in the interior of the fluid domain, we employ a standard four-point delta function which is frequently used with the immersed boundary method. The standard delta function is used wherever possible, and the modified delta function continuously transitions to the standard delta function away from the outer boundaries of the fluid domain. Three-dimensional computational results are presented to demonstrate the capabilities of our immersed boundary approach to simulating the fluid dynamics of heart valves.

An accurate and efficient method for the incompressible Navier-Stokes equations using the projection method as a preconditioner

The projection method is a widely used fractional-step algorithm for solving the incompressible Navier-Stokes equations. Despite numerous improvements to the methodology, however, imposing physical boundary conditions with projection-based fluid solvers remains difficult, and obtaining high-order accuracy may not be possible for some choices of boundary conditions. In this work, we present an unsplit, linearly-implicit discretization of the incompressible Navier-Stokes equations on a staggered grid along with an efficient solution method for the resulting system of linear equations. Since our scheme is not a fractional-step algorithm, it is straightforward to specify general physical boundary conditions accurately; however, this capability comes at the price of having to solve the time-dependent incompressible Stokes equations at each timestep. To solve this linear system efficiently, we employ a Krylov subspace method preconditioned by the projection method. In our implementation, the subdomain solvers required by the projection preconditioner employ the conjugate gradient method with geometric multigrid preconditioning. The accuracy of the scheme is demonstrated for several problems, including forced and unforced analytic test cases and lid-driven cavity flows. These tests consider a variety of physical boundary conditions with Reynolds numbers ranging from 1 to 30000. The effectiveness of the projection preconditioner is compared to an alternative preconditioning strategy based on an approximation to the Schur complement for the time-dependent incompressible Stokes operator. The projection method is found to be a more efficient preconditioner in most cases considered in the present work.

Staggered schemes for fluctuating hydrodynamics

We develop numerical schemes for solving the isothermal compressible and incompressible equations of fluctuating hydrodynamics on a grid with staggered momenta. We develop a second-order accurate spatial discretization of the diffusive, advective, and stochastic fluxes that satisfies a discrete fluctuation-dissipation balance and construct temporal discretizations that are at least second-order accurate in time deterministically and in a weak sense. Specifically, the methods reproduce the correct equilibrium covariances of the fluctuating fields to the third (compressible) and second (incompressible) orders in the time step, as we verify numerically. We apply our techniques to model recent experimental measurements of giant fluctuations in diffusively mixing fluids in a microgravity environment [A. Vailati et al., Nat. Comm., 2 (2011), 290]. Numerical results for the static spectrum of nonequilibrium concentration fluctuations are in excellent agreement between the compressible and incompressible simulati...

Structure-based finite strain modelling of the human left ventricle in diastole

Finite strain analyses of the left ventricle provide important information on heart function and have the potential to provide insights into the biomechanics of myocardial contractility in health and disease. Systolic dysfunction is the most common cause of heart failure; however, abnormalities of diastolic function also contribute to heart failure, and are associated with conditions including left ventricular hypertrophy and diabetes. The clinical significance of diastolic abnormalities is less well understood than systolic dysfunction, and specific treatments are presently lacking. To obtain qualitative and quantitative information on heart function in diastole, we develop a three-dimensional computational model of the human left ventricle that is derived from noninvasive imaging data. This anatomically realistic model has a rule-based fibre structure and a structure-based constitutive model. We investigate the sensitivity of this comprehensive model to small changes in the constitutive parameters and to changes in the fibre distribution. We make extensive comparisons between this model and similar models that employ different constitutive models, and we demonstrate qualitative and quantitative differences in stress and strain distributions for the different constitutive models. We also provide an initial validation of our model through comparisons to experimental data on stress and strain distributions in the left ventricle.

Emerging Trends in Heart Valve Engineering: Part I. Solutions for Future

As the first section of a multi-part review series, this section provides an overview of the ongoing research and development aimed at fabricating novel heart valve replacements beyond what is currently available for patients. Here we discuss heart valve replacement options that involve a biological component or process for creation, either in vitro or in vivo (tissue-engineered heart valves), and heart valves that are fabricated from polymeric material that are considered permanent inert materials that may suffice for adults where growth is not required. Polymeric materials provide opportunities for cost-effective heart valves that can be more easily manufactured and can be easily integrated with artificial heart and ventricular assist device technologies. Tissue engineered heart valves show promise as a regenerative patient specific model that could be the future of all valve replacement. Because tissue-engineered heart valves depend on cells for their creation, understanding how cells sense and respond to chemical and physical stimuli in their microenvironment is critical and therefore, is also reviewed.

A modified Holzapfel-Ogden law for a residually stressed finite strain model of the human left ventricle in diastole

In this work, we introduce a modified Holzapfel-Ogden hyperelastic constitutive model for ventricular myocardium that accounts for residual stresses, and we investigate the effects of residual stresses in diastole using a magnetic resonance imaging–derived model of the human left ventricle (LV). We adopt an invariant-based constitutive modelling approach and treat the left ventricular myocardium as a non-homogeneous, fibre-reinforced, incompressible material. Because in vivo images provide the configuration of the LV in a loaded state even in diastole, an inverse analysis is used to determine the corresponding unloaded reference configuration. The residual stress in this unloaded state is estimated by two different methods. One is based on three-dimensional strain measurements in a local region of the canine LV, and the other uses the opening angle method for a cylindrical tube. We find that including residual stress in the model changes the stress distributions across the myocardium and that whereas both methods yield qualitatively similar changes, there are quantitative differences between the two approaches. Although the effects of residual stresses are relatively small in diastole, the model can be extended to explore the full impact of residual stress on LV mechanical behaviour for the whole cardiac cycle as more experimental data become available. In addition, although not considered here, residual stresses may also play a larger role in models that account for tissue growth and remodelling.

Inertial Coupling Method for particles in an incompressible fluctuating fluid

Abstract We develop an inertial coupling method for modeling the dynamics of point-like “blob” particles immersed in an incompressible fluid, generalizing previous work for compressible fluids (Balboa Usabiaga et al., 2013 [42]). The coupling consistently includes excess (positive or negative) inertia of the particles relative to the displaced fluid, and accounts for thermal fluctuations in the fluid momentum equation. The coupling between the fluid and the blob is based on a no-slip constraint equating the particle velocity with the local average of the fluid velocity, and conserves momentum and energy. We demonstrate that the formulation obeys a fluctuation–dissipation balance, owing to the non-dissipative nature of the no-slip coupling. We develop a spatio-temporal discretization that preserves, as best as possible, these properties of the continuum formulation. In the spatial discretization, the local averaging and spreading operations are accomplished using compact kernels commonly used in immersed boundary methods. We find that the special properties of these kernels allow the blob to provide an effective model of a particle; specifically, the volume, mass, and hydrodynamic properties of the blob are remarkably grid-independent. We develop a second-order semi-implicit temporal integrator that maintains discrete fluctuation–dissipation balance, and is not limited in stability by viscosity. Furthermore, the temporal scheme requires only constant-coefficient Poisson and Helmholtz linear solvers, enabling a very efficient and simple FFT-based implementation on GPUs. We numerically investigate the performance of the method on several standard test problems. In the deterministic setting, we find the blob to be a remarkably robust approximation to a rigid sphere, at both low and high Reynolds numbers. In the stochastic setting, we study in detail the short and long-time behavior of the velocity autocorrelation function and observe agreement with all of the known behavior for rigid sphere immersed in a fluctuating fluid. The proposed inertial coupling method provides a low-cost coarse-grained (minimal resolution) model of particulate flows over a wide range of time-scales ranging from Brownian to convection-driven motion.

Temporal integrators for fluctuating hydrodynamics

Including the effect of thermal fluctuations in traditional computational fluid dynamics requires developing numerical techniques for solving the stochastic partial differential equations of fluctuating hydrodynamics. These Langevin equations possess a special fluctuation-dissipation structure that needs to be preserved by spatio-temporal discretizations in order for the computed solution to reproduce the correct long-time behavior. In particular, numerical solutions should approximate the Gibbs-Boltzmann equilibrium distribution, and ideally this will hold even for large time step sizes. We describe finite-volume spatial discretizations for the fluctuating Burgers and fluctuating incompressible Navier-Stokes equations that obey a discrete fluctuation-dissipation balance principle just like the continuum equations. We develop implicit-explicit predictor-corrector temporal integrators for the resulting stochastic method-of-lines discretization. These stochastic Runge-Kutta schemes treat diffusion implicitly and advection explicitly, are weakly second-order accurate for additive noise for small time steps, and give a good approximation to the equilibrium distribution even for very strong fluctuations. Numerical results demonstrate that a midpoint predictor-corrector scheme is very robust over a broad range of time step sizes.