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Computer modeling and simulation is a powerful tool for assessing the performance of medical devices such as bioprosthetic heart valves (BHVs) that promises to accelerate device design and regulation. This study describes work to develop dynamic computer models of BHVs in the aortic test section of an experimental pulse-duplicator platform that is used in academia, industry, and regulatory agencies to assess BHV performance. These computational models are based on a hyperelastic finite element extension of the immersed boundary method for fluid–structure interaction (FSI). We focus on porcine tissue and bovine pericardial BHVs, which are commonly used in surgical valve replacement. We compare our numerical simulations to experimental data from two similar pulse duplicators, including a commercial ViVitro system and a custom platform related to the ViVitro pulse duplicator. Excellent agreement is demonstrated between the computational and experimental results for bulk flow rates, pressures, valve open areas, and the timing of valve opening and closure in conditions commonly used to assess BHV performance. In addition, reasonable agreement is demonstrated for quantitative measures of leaflet kinematics under these same conditions. This work represents a step towards the experimental validation of this FSI modeling platform for evaluating BHVs. Electronic supplementary material The online version of this article (10.1007/s10439-020-02466-4) contains supplementary material, which is available to authorized users. more...

Fluid–structure interaction is ubiquitous in nature and occurs at all biological scales. Immersed methods provide mathematical and computational frameworks for modeling fluid–structure systems. These methods, which typically use an Eulerian description of the fluid and a Lagrangian description of the structure, can treat thin immersed boundaries and volumetric bodies, and they can model structures that are flexible or rigid or that move with prescribed deformational kinematics. Immersed formulations do not require body-fitted discretizations and thereby avoid the frequent grid regeneration that can otherwise be required for models involving large deformations and displacements. This article reviews immersed methods for both elastic structures and structures with prescribed kinematics. It considers formulations using integral operators to connect the Eulerian and Lagrangian frames and methods that directly apply jump conditions along fluid–structure interfaces. Benchmark problems demonstrate the effectiveness of these methods, and selected applications at Reynolds numbers up to approximately 20,000 highlight their impact in biological and biomedical modeling and simulation. more...

This paper presents a one-sided immersed boundary (IB) method using kernel functions constructed via a moving least squares (MLS) method. The resulting kernels effectively couple structural degrees of freedom to fluid variables on only one side of the fluid-structure interface. This reduces spurious feedback forcing and internal flows that are typically observed in IB models that use isotropic kernel functions to couple the structure to fluid degrees of freedom on both sides of the interface. The method developed here extends the original MLS methodology introduced by Vanella and Balaras (J Comput Phys, 2009). Prior IB/MLS methods have used isotropic kernel functions that coupled fluid variables on both sides of the boundary to the interfacial degrees of freedom. The original IB/MLS approach converts the cubic spline weights typically employed in MLS reconstruction into an IB kernel function that satisfies particular discrete moment conditions. This paper shows that the same approach can be used to construct one-sided kernel functions (kernel functions are referred to as generating functions in the MLS literature). We also examine the performance of the new approach for a family of kernel functions introduced by Peskin. It is demonstrated that the one-sided MLS construction tends to generate non-monotone interpolation kernels with large over- and undershoots. We present two simple weight shifting strategies to construct generating functions that are positive and monotone, which enhances the stability of the resulting IB methodology. Benchmark cases are used to test the order of accuracy and verify the one-sided IB/MLS simulations in both two and three spatial dimensions. This new IB/MLS method is also used to simulate flow over the Ahmed car model, which highlights the applicability of this methodology for modeling complex engineering flows., Comment: In Press, Journal of Computational Physics (2021) more...

An immersed interface-lattice Boltzmann method (II-LBM) is developed for modeling fluid-structure systems. The key element of this approach is the determination of the jump conditions that are satisfied by the distribution functions within the framework of the lattice Boltzmann method where forces are imposed along a surface immersed in an incompressible fluid. In this initial II-LBM, the discontinuity related to the normal portion of the interfacial force is sharply resolved by imposing the relevant jump conditions using an approach that is analogous to imposing the corresponding pressure discontinuity in the incompressible Navier-Stokes equations. We show that the jump conditions for the distribution functions are the same in both single-relaxation-time and multi-relaxation-time LBM formulations. Tangential forces are treated using the immersed boundary-lattice Boltzmann method (IB-LBM). In our implementation, a level set approach is used to impose jump conditions for rigid-body models. For flexible boundary models, we describe the moving interface by interpolating the positions of marker points that move with the fluid. The II-LBM is compared to a direct forcing IB-LBM for rigid-body fluid-structure interaction, and a classical IB-LBM for cases involving elastic interfaces. Higher order accuracy is observed with the II-LBM as compared to the IB-LBM for selected benchmark problems. Because the jump conditions of the distribution function also satisfy the continuity of the velocity field across the interface, the error in the velocity field is much smaller for the II-LBM than the IB-LBM. The II-LBM is also demonstrated to provide superior volume conservation when simulating flexible boundaries. more...

Fluid-structure systems occur in a range of scientific and engineering applications. The immersed boundary(IB) method is a widely recognized and effective modeling paradigm for simulating fluid-structure interaction(FSI) in such systems, but a difficulty of the IB formulation is that the pressure and viscous stress are generally discontinuous at the interface. The conventional IB method regularizes these discontinuities, which typically yields low-order accuracy at these interfaces. The immersed interface method(IIM) is an IB-like approach to FSI that sharply imposes stress jump conditions, enabling higher-order accuracy, but prior applications of the IIM have been largely restricted to methods that rely on smooth representations of the interface geometry. This paper introduces an IIM that uses only a C0 representation of the interface,such as those provided by standard nodal Lagrangian FE methods. Verification examples for models with prescribed motion demonstrate that the method sharply resolves stress discontinuities along the IB while avoiding the need for analytic information of the interface geometry. We demonstrate that only the lowest-order jump conditions for the pressure and velocity gradient are required to realize global 2nd-order accuracy. Specifically,we show 2nd-order global convergence rate along with nearly 2nd-order local convergence in the Eulerian velocity, and between 1st-and 2nd-order global convergence rates along with 1st-order local convergence for the Eulerian pressure. We also show 2nd-order local convergence in the interfacial displacement and velocity along with 1st-order local convergence in the fluid traction. As a demonstration of the method's ability to tackle complex geometries,this approach is also used to simulate flow in an anatomical model of the inferior vena cava., Added a non-axisymmetric example (flow within eccentric rotating cylinder in Sec. 4.3) - Added a more in-depth analysis and comparison with a body-fitted approach for the application in Sec. 4.7 more...

High-order numerical methods for solving elliptic equations over arbitrary domains typically require specialized machinery, such as high-quality conforming grids for finite elements method, and quadrature rules for boundary integral methods. These tools make it difficult to apply these techniques to higher dimensions. In contrast, fixed Cartesian grid methods, such as the immersed boundary (IB) method, are easy to apply and generalize, but typically are low-order accurate. In this study, we introduce the Smooth Forcing Extension (SFE) method, a fixed Cartesian grid technique that builds on the insights of the IB method, and allows one to obtain arbitrary orders of accuracy. Our approach relies on a novel Fourier continuation method to compute extensions of the inhomogeneous terms to any desired regularity. This is combined with the highly accurate Non-Uniform Fast Fourier Transform for interpolation operations to yield a fast and robust method. Numerical tests confirm that the technique performs precisely as expected on one-dimensional test problems. In higher dimensions, the performance is even better, in some cases yielding sub-geometric convergence. We also demonstrate how this technique can be applied to solving parabolic problems and for computing the eigenvalues of elliptic operators on general domains, in the process illustrating its stability and amenability to generalization. more...

The immersed boundary–finite element method (IBFE) is an approach to describing the dynamics of an elastic structure immersed in an incompressible viscous fluid. In this formulation, there are generally discontinuities in the pressure and viscous stress at fluid–structure interfaces. The standard immersed boundary approach, which connects the Lagrangian and Eulerian variables via integral transforms with regularized Dirac delta function kernels, smooths out these discontinuities, which generally leads to low order accuracy. This paper describes an approach to accurately resolve pressure discontinuities for these types of formulations, in which the solid may undergo large deformations. Our strategy is to decompose the physical pressure field into a sum of two pressure–like fields, one defined on the entire computational domain, which includes both the fluid and solid subregions, and one defined only on the solid subregion. Each of these fields is continuous on its domain of definition, which enables high accuracy via standard discretization methods without sacrificing sharp resolution of the pressure discontinuity. Numerical tests demonstrate that this method improves rates of convergence for displacements, velocities, stresses, and pressures as compared to the conventional IBFE method. Further, it produces much smaller errors at reasonable numbers of degrees of freedom. The performance of this method is tested on several cases with analytic solutions, a nontrivial benchmark problem of incompressible solid mechanics, and an example involving a thick, actively contracting torus. more...

We develop a fluid-structure interaction (FSI) model of the mitral valve (MV) that uses an anatomically\ud and physiologically realistic description of the MV leaflets and chordae tendineae. Three different\ud chordae models — complex, “pseudo-fibre”, and simplified chordae — are compared to determine how\ud different chordae representations affect the dynamics of the MV. The leaflets and chordae are modelled as\ud fibre-reinforced hyperelastic materials, and FSI is modelled using an immersed boundary-finite element\ud (IB/FE) method. The MV model is first verified under static boundary conditions against the commercial\ud FE software ABAQUS, and then used to simulate MV dynamics under physiological pressure conditions.\ud Interesting flow patterns and vortex formulation are observed in all three cases. To quantify the highly\ud complex system behaviour resulting from FSI, an energy budget analysis of the coupled MV FSI model\ud is performed. Results show that the complex and pseudo-fibre chordae models yield good valve closure\ud during systole, but that the simplified chordae model leads to poorer leaflet coaptation and an unrealistic\ud bulge in the anterior leaflet belly. An energy budget analysis shows that the MV models with complex\ud and pseudo-fibre chordae have similar energy distribution patterns, but the MV model with the simplified\ud chordae consumes more energy, especially during valve closing and opening. We find that the complex\ud chordae and pseudo-fibre chordae have similar impact on the overall MV function, but that the simplified\ud chordae representation is less accurate. Because a pseudo-fibre chordal structure is easier to construct\ud and less computationally intensive, it may be a good candidate for modelling MV dynamics or interaction\ud between the MV and heart in patient-specific applications. more...

The immersed boundary method is a mathematical framework for modeling fluid-structure interaction. This formulation describes the momentum, viscosity, and incompressibility of the fluid-structure system in Eulerian form, and it uses Lagrangian coordinates to describe the structural deformations, stresses, and resultant forces. Integral transforms with Dirac delta function kernels connect the Eulerian and Lagrangian frames. The fluid and the structure are both typically treated as incompressible materials. Upon discretization, however, the incompressibility of the structure is only maintained approximately. To obtain an immersed method for incompressible hyperelastic structures that is robust under large structural deformations, we introduce a volumetric energy in the solid region that stabilizes the formulation and improves the accuracy of the numerical scheme. This formulation augments the discrete Lagrange multiplier for the incompressibility constraint, thereby improving the original method's accuracy. This volumetric energy is incorporated by decomposing the strain energy into isochoric and dilatational components, as in standard solid mechanics formulations of nearly incompressible elasticity. We study the performance of the stabilized method using several quasi-static solid mechanics benchmarks, a dynamic fluid-structure interaction benchmark, and a detailed three-dimensional model of esophageal transport. The accuracy achieved by the stabilized immersed formulation is comparable to that of a stabilized finite element method for incompressible elasticity using similar numbers of structural degrees of freedom., Comment: Extensive revisions more...

Detailed models of the biomechanics of the heart are important both for developing improved interventions for patients with heart disease and also for patient risk stratification and treatment planning. For instance, stress distributions in the heart affect cardiac remodelling, but such distributions are not presently accessible in patients. Biomechanical models of the heart offer detailed three-dimensional deformation, stress and strain fields that can supplement conventional clinical data. In this work, we introduce dynamic computational models of the human left ventricle (LV) that are derived from clinical imaging data obtained from a healthy subject and from a patient with a myocardial infarction (MI). Both models incorporate a detailed invariant-based orthotropic description of the passive elasticity of the ventricular myocardium along with a detailed biophysical model of active tension generation in the ventricular muscle. These constitutive models are employed within a dynamic simulation framework that accounts for the inertia of the ventricular muscle and the blood that is based on an immersed boundary (IB) method with a finite element description of the structural mechanics. The geometry of the models is based on data obtained non-invasively by cardiac magnetic resonance (CMR). CMR imaging data are also used to estimate the parameters of the passive and active constitutive models, which are determined so that the simulated end-diastolic and end-systolic volumes agree with the corresponding volumes determined from the CMR imaging studies. Using these models, we simulate LV dynamics from end-diastole to end-systole. The results of our simulations are shown to be in good agreement with subject-specific CMR-derived strain measurements and also with earlier clinical studies on human LV strain distributions. more...

Simulating the electric field-driven motion of rigid or deformable bodies in fluid media requires the solution of coupled equations of electrodynamics and hydrodynamics. In this work, we present a numerical method for treating such equations of electrohydrodynamics in an immersed body framework. In our approach, the electric field and fluid equations are solved on an Eulerian grid, and the immersed structures are modeled by meshless collections of Lagrangian nodes that move freely through the background Eulerian grid. Fluid-structure interaction is handled by an efficient distributed Lagrange multiplier approach, whereas the body force induced by the electric field is calculated using the Maxwell stress tensor. In addition, we adopt an adaptive mesh refinement (AMR) approach to discretizing the equations that permits us to resolve localized electric field gradients and fluid boundary layers with relatively low computational cost. Using this framework, we address a broad range of problems, including the dielectrophoretic motion of particles in microfluidic channels, three-dimensional nanowire assembly, and the effects of rotating electric fields to orient particles and to separate cells using their dielectric properties in a lab-on-a-chip device. We also simulate the phenomenon of electrolocation, whereby an animal uses distortions of a self-generated electric field to locate objects. Specifically, we perform simulations of a black ghost knifefish that tracks and captures prey using electrolocation. Although the proposed tracking algorithm is not intended to correspond to the physiological tracking mechanisms used by the real knifefish, extensions of this algorithm could be used to develop artificial ''electrosense'' for underwater vehicles. To our knowledge, these dynamic simulations of electrolocation are the first of their kind. more...

We analyze the stability and convergence of first-order accurate and second-order accurate timestepping schemes for the Navier--Stokes equations with variable viscosity. These schemes are characterized by a mixed implicit/explicit treatment of the viscous term, in which a numerical parameter, $\lambda$, determines the degree of splitting between the implicit and explicit contributions. The reason for this splitting is that it avoids the need to solve computationally expensive linear systems that may change at each timestep. Provided the parameter $\lambda$ is within a permissible range, we prove that the first-order accurate and second-order accurate schemes are convergent. We show further that the efficiency of the second-order accurate scheme depends on how $\lambda$ is chosen within the permissible range, and we discuss choices that work well in practice. We use parameters motivated by this analysis to simulate internal gravity waves, which arise in stratified fluids with variable density. We examine h... more...

Many problems of interest in biological fluid mechanics involve interactions between fluids and solids that require the coupled solution of momentum equations for both the fluid and the solid. In this work, we develop a mathematical framework and an adaptive numerical method for such fluid-structure interaction (FSI) problems in which the structure may be rigid, deforming, or elastic. We employ an immersed boundary (IB) formulation of the problem that permits us to avoid body conforming discretizations and to use fast Cartesian grid solvers. Rigidity and deformational kinematic constraints are imposed using a formulation based on distributed Lagrange multipliers, and a conventional IB method is used to describe the elasticity of the immersed body. We use Cartesian grid adaptive mesh refinement (AMR) to discretize the equations of motion and thereby obtain a solution methodology that efficiently captures thin boundary layers at fluid-solid interfaces as well as flow structures shed from such interfaces. This adaptive methodology is validated for several benchmark problems in two and three spatial dimensions. In addition, we use this scheme to simulate free swimming, including the maneuvering of a two-dimensional model eel and a three-dimensional model of the weakly electric black ghost knifefish. more...

Understanding the interaction between the valves and walls of the heart is important in assessing and subsequently treating heart dysfunction. This study presents an integrated model of the mitral valve (MV) coupled to the left ventricle (LV), with the geometry derived from in vivo clinical magnetic resonance images. Numerical simulations using this coupled MV-LV model are developed using an immersed boundary/finite element method. The model incorporates detailed valvular features, left ventricular contraction, nonlinear soft tissue mechanics, and fluid-mediated interactions between the MV and LV wall. We use the model to simulate cardiac function from diastole to systole. Numerically predicted LV pump function agrees well with in vivo data of the imaged healthy volunteer, including the peak aortic flow rate, the systolic ejection duration, and the LV ejection fraction. In vivo MV dynamics are qualitatively captured. We further demonstrate that the diastolic filling pressure increases significantly with impaired myocardial active relaxation to maintain a normal cardiac output. This is consistent with clinical observations. The coupled model has the potential to advance our fundamental knowledge of mechanisms underlying MV-LV interaction, and help in risk stratification and optimisation of therapies for heart diseases. more...

The Immersed Boundary (IB) method is a mathematical framework for constructing robust numerical methods to study fluid-structure interaction in problems involving an elastic structure immersed in a viscous fluid. The IB formulation uses an Eulerian representation of the fluid and a Lagrangian representation of the structure. The Lagrangian and Eulerian frames are coupled by integral transforms with delta function kernels. The discretized IB equations use approximations to these transforms with regularized delta function kernels to interpolate the fluid velocity to the structure, and to spread structural forces to the fluid. It is well-known that the conventional IB method can suffer from poor volume conservation since the interpolated Lagrangian velocity field is not generally divergence-free, and so this can cause spurious volume changes. In practice, the lack of volume conservation is especially pronounced for cases where there are large pressure differences across thin structural boundaries. The aim of this paper is to greatly reduce the volume error of the IB method by introducing velocity-interpolation and force-spreading schemes with the properties that the interpolated velocity field in which the structure moves is at least C1 and satisfies a continuous divergence-free condition, and that the force-spreading operator is the adjoint of the velocity-interpolation operator. We confirm through numerical experiments in two and three spatial dimensions that this new IB method is able to achieve substantial improvement in volume conservation compared to other existing IB methods, at the expense of a modest increase in the computational cost. Further, the new method provides smoother Lagrangian forces (tractions) than traditional IB methods. The method presented here is restricted to periodic computational domains. Its generalization to non-periodic domains is important future work., 49 pages, 13 figures more...

We present a general variable viscosity and variable density immersed boundary method that is first-order accurate in the variable density case and, for problems possessing sufficient regularity, second-order accurate in the constant density case. The viscosity and density are considered material properties and are defined by a dynamically updated tesselation. Empirical convergence rates are reported for a test problem of a two-dimensional viscoelastic shell with spatially varying material properties. The reduction to first-order accuracy in the variable density case can be avoided by using an iterative scheme, although this approach may not be efficient enough for practical use. In our time-stepping scheme, both the inertial and viscous terms are split into two parts: a constant-coefficient part that is treated implicitly, and a variable-coefficient part that is treated explicitly. This splitting allows the resulting equations to be solved efficiently using fast constant-coefficient linear solvers, and i... more...

In this work, we extend our previous esophageal transport model using an immersed boundary (IB) method with discrete fiber-based structures, to one using a continuum mechanics-based model that is approximated based on finite elements (IB-FE). To deal with the leakage of flow when the Lagrangian mesh becomes coarser than the fluid mesh, we employ adaptive interaction quadrature points for Lagrangian-Eulerian interaction equations based on a previous work. In particular, we introduce a new anisotropic adaptive interaction quadrature rule. The new rule permits us to vary the interaction quadrature points not only at each time-step and element but also at different orientations per element. For the material model, we extend our previous fiber-based model to a continuum-based model. We first study a case in which a three-dimensional short tube is dilated. Results match very well with those from the implicit FE method. We remark that in our IB-FE case, the three-dimensional tube undergoes a very large deformation and the Lagrangian mesh-size becomes about 6 times of Eulerian mesh-size. To validate the method in handling fiber-matrix material models, we perform a second study on dilating a long fiber-reinforced tube. Errors are small when we compare numerical solutions with analytical solutions. The technique is then applied to the problem of esophageal transport. We present three cases that differ in the material model and muscle fiber architecture. The overall transport features are consistent with those from the previous model. We remark that the continuum-based model can handle more realistic and complicated material behavior. This is demonstrated in our third case with spatially varying fiber architecture. We find this unique muscle fiber architecture could generate a so-called pressure transition zone. This suggests an important role of muscle fiber architecture in esophageal transport., 47 pages, 17 figures more...

Many problems involving the interaction of an elastic structure and a viscous fluid can be solved by the immersed boundary (IB) method. In the IB approach to such problems, the elastic forces generated by the immersed structure are applied to the surrounding fluid, and the motion of the immersed structure is determined by the local motion of the fluid. Recently, the IB method has been extended to treat more general elasticity models that include both positional and rotational degrees of freedom. For such models, force and torque must both be applied to the fluid. The positional degrees of freedom of the immersed structure move according to the local linear velocity of the fluid, whereas the rotational degrees of freedom move according to the local angular velocity. This paper introduces a spatially adaptive, formally second-order accurate version of this generalized immersed boundary method. We use this adaptive scheme to simulate the dynamics of an elastic ring immersed in fluid. To describe the elasticity of the ring, we use an unconstrained version of Kirchhoff rod theory. We demonstrate empirically that our numerical scheme yields essentially second-order convergence rates when applied to such problems. We also study dynamical instabilities of such fluid-structure systems, and we compare numerical results produced by our method to classical analytic results from elastic rod theory. more...

The immersed boundary (IB) method is an approach to problems of fluid-structure interaction in which an elastic structure is immersed in a viscous incompressible fluid. The IB formulation of such problems uses a Lagrangian description of the structure and an Eulerian description of the fluid. It is well known that some versions of the IB method can suffer from poor volume conservation. Methods have been introduced to improve the volume-conservation properties of the IB method, but they either have been fairly specialized, or have used complex, nonstandard Eulerian finite-difference discretizations. In this paper, we use quasi-static and dynamic benchmark problems to investigate the effect of the choice of Eulerian discretization on the volume-conservation properties of a formally second-order accurate IB method. We consider both collocated and staggered-grid discretization methods. For the tests considered herein, the staggered-grid IB scheme generally yields at least a modest improvement in volume conservation when compared to cell-centered methods, and in many cases considered in this work, the spurious volume changes exhibited by the staggered-grid IB method are more than an order of magnitude smaller than those of the collocated schemes. We also compare the performance of cell-centered schemes that use either exact or approximate projection methods. We find that the volume-conservation properties of approximate projection IB methods depend strongly on the formulation of the projection method. When used with the IB method, we find that pressure-free approximate projection methods can yield extremely poor volume conservation, whereas pressure-increment approximate projection methods yield volume conservation that is nearly identical to that of a cell-centered exact projection method. more...

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. more...

We develop a rigid multiblob method for numerically solving the mobility problem for suspensions of passive and active rigid particles of complex shape in Stokes flow in unconfined, partially confined, and fully confined geometries. As in a number of existing methods, we discretize rigid bodies using a collection of minimally-resolved spherical blobs constrained to move as a rigid body, to arrive at a potentially large linear system of equations for the unknown Lagrange multipliers and rigid-body motions. Here we develop a block-diagonal preconditioner for this linear system and show that a standard Krylov solver converges in a modest number of iterations that is essentially independent of the number of particles. For unbounded suspensions and suspensions sedimented against a single no-slip boundary, we rely on existing analytical expressions for the Rotne-Prager tensor combined with a fast multipole method or a direct summation on a Graphical Processing Unit to obtain an simple yet efficient and scalable implementation. For fully confined domains, such as periodic suspensions or suspensions confined in slit and square channels, we extend a recently-developed rigid-body immersed boundary method to suspensions of freely-moving passive or active rigid particles at zero Reynolds number. We demonstrate that the iterative solver for the coupled fluid and rigid body equations converges in a bounded number of iterations regardless of the system size. We optimize a number of parameters in the iterative solvers and apply our method to a variety of benchmark problems to carefully assess the accuracy of the rigid multiblob approach as a function of the resolution. We also model the dynamics of colloidal particles studied in recent experiments, such as passive boomerangs in a slit channel, as well as a pair of non-Brownian active nanorods sedimented against a wall., Under revision in CAMCOS, Nov 2016 more...

The immersed boundary method is an approach to fluid-structure interaction that uses a Lagrangian\ud description of the structural deformations, stresses, and forces along with an Eulerian description of the\ud momentum, viscosity, and incompressibility of the fluid-structure system. The original immersed boundary\ud methods described immersed elastic structures using systems of flexible fibers, and even now, most\ud immersed boundary methods still require Lagrangian meshes that are finer than the Eulerian grid. This\ud work introduces a coupling scheme for the immersed boundary method to link the Lagrangian and Eulerian\ud variables that facilitates independent spatial discretizations for the structure and background grid. This\ud approach employs a finite element discretization of the structure while retaining a finite difference scheme\ud for the Eulerian variables. We apply this method to benchmark problems involving elastic, rigid, and actively\ud contracting structures, including an idealized model of the left ventricle of the heart. Our tests include cases\ud in which, for a fixed Eulerian grid spacing, coarser Lagrangian structural meshes yield discretization errors\ud that are as much as several orders of magnitude smaller than errors obtained using finer structural meshes.\ud The Lagrangian-Eulerian coupling approach developed in this work enables the effective use of these coarse\ud structural meshes with the immersed boundary method. This work also contrasts two different weak forms\ud of the equations, one of which is demonstrated to be more effective for the coarse structural discretizations\ud facilitated by our coupling approach. more...

We develop an immersed boundary (IB) method for modeling flows around fixed or moving rigid bodies that is suitable for a broad range of Reynolds numbers, including steady Stokes flow. The spatio-temporal discretization of the fluid equations is based on a standard staggered-grid approach. Fluid-body interaction is handled using Peskin's IB method; however, unlike existing IB approaches to such problems, we do not rely on penalty or fractional-step formulations. Instead, we use an unsplit scheme that ensures the no-slip constraint is enforced exactly in terms of the Lagrangian velocity field evaluated at the IB markers. Fractional-step approaches, by contrast, can impose such constraints only approximately. Imposing these constraints exactly requires the solution of a large linear system that includes the fluid velocity and pressure as well as Lagrange multiplier forces that impose the motion of the body. To solve this system efficiently, we develop a preconditioner for the constrained IB formulation that is based on an analytical approximation to the Schur complement. This approach is enabled by the near translational and rotational invariance of Peskin's IB method. We demonstrate that only a few cycles of a geometric multigrid method for the fluid equations are required in each application of the preconditioner, and we demonstrate robust convergence of the overall Krylov solver despite the approximations made in the preconditioner. We apply the method to a number of test problems at zero and finite Reynolds numbers, and we demonstrate first-order convergence of the method to several analytical solutions and benchmark computations., Submitted to CAMCOS more...

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. more...

© 2015 Elsevier Inc. Esophageal transport is a physiological process that mechanically transports an ingested food bolus from the pharynx to the stomach via the esophagus, a multi-layered muscular tube. This process involves interactions between the bolus, the esophagus, and the neurally coordinated activation of the esophageal muscles. In this work, we use an immersed boundary (IB) approach to simulate peristaltic transport in the esophagus. The bolus is treated as a viscous fluid that is actively transported by the muscular esophagus, and the esophagus is modeled as an actively contracting, fiber-reinforced tube. Before considering the full model of the esophagus, however, we first consider a standard benchmark problem of flow past a cylinder. Next a simplified version of our model is verified by comparison to an analytic solution to the tube dilation problem. Finally, three different complex models of the multi-layered esophagus, which differ in their activation patterns and the layouts of the mucosal layers, are extensively tested. To our knowledge, these simulations are the first of their kind to incorporate the bolus, the multi-layered esophagus tube, and muscle activation into an integrated model. Consistent with experimental observations, our simulations capture the pressure peak generated by the muscle activation pulse that travels along the bolus tail. These fully resolved simulations provide new insights into roles of the mucosal layers during bolus transport. In addition, the information on pressure and the kinematics of the esophageal wall resulting from the coordination of muscle activation is provided, which may help relate clinical data from manometry and ultrasound images to the underlying esophageal motor function. more...

The immersed boundary method is both a mathematical formulation and a numerical scheme for problems involving the interaction of a viscous incompressible fluid and a (visco-)elastic structure. In [M.-C. Lai, Simulations of the flow past an array of circular cylinders as a test of the immersed boundary method, Ph.D. thesis, Courant Institute of Mathematical Sciences, New York University, 1998; M.-C. Lai, C.S. Peskin, An immersed boundary method with formal second-order accuracy and reduced numerical viscosity, J. Comput. Phys. 160 (2000) 705-719], Lai and Peskin introduced a formally second order accurate immersed boundary method, but the convergence properties of their algorithm have only been examined computationally for problems with nonsmooth solutions. Consequently, in practice only first order convergence rates have been observed. In the present work, we describe a new formally second order accurate immersed boundary method and demonstrate its performance for a prototypical fluid-structure interaction problem, involving an immersed viscoelastic shell of finite thickness, studied over a broad range of Reynolds numbers. We consider two sets of material properties for the viscoelastic structure, including a case where the material properties of the coupled system are discontinuous at the fluid-structure interface. For both sets of material properties, the true solutions appear to possess sufficient smoothness for the method to converge at a second order rate for fully resolved computations. more...

The goal of our work is to predict the patterns of blood flow in a model of the human heart using the Immersed Boundary method. In this method, fluid is moved by forces associated with the deformation of flexible boundaries which are immersed in, and interacting with, the fluid. In the present work the boundary is comprised of the muscular walls and valve leaflets of the heart. The method benefits by having an anatomically correct model of the heart. This report describes the construction of a model based on CT data from a particular individual, opening up the possibility of simulating interventions in an individual for clinical purposes. more...

The immersed boundary (IB) method is an approach to fluid-structure interaction that uses Lagrangian variables to describe the structure and Eulerian variables to describe the fluid. Explicit time stepping schemes for the IB method require solvers only for Eulerian equations, for which fast Cartesian grid solution methods are available. Such methods are relatively straightforward to develop and are widely used in practice but often require very small time steps to maintain stability. Implicit-time IB methods permit the stable use of large time steps, but efficient implementations of such methods require significantly more complex solvers that effectively treat both Lagrangian and Eulerian variables simultaneously. Several different approaches to solving the coupled Lagrangian-Eulerian equations have been proposed, but a complete understanding of this problem is still emerging. This paper presents a geometric multigrid method for an implicit-time discretization of the IB equations. This multigrid scheme uses a generalization of box relaxation that is shown to handle problems in which the physical stiffness of the structure is very large. Numerical examples are provided to illustrate the effectiveness and efficiency of the algorithms described herein. These tests show that using multigrid as a preconditioner for a Krylov method yields improvements in both robustness and efficiency as compared to using multigrid as a solver. They also demonstrate that with a time step 100--1000 times larger than that permitted by an explicit IB method, the multigrid-preconditioned implicit IB method is approximately 50--200 times more efficient than the explicit method. more...

Finite stress and strain analyses of the heart provide insight into the biomechanics of myocardial function and dysfunction. Herein, we describe progress toward dynamic patient-specific models of the left ventricle using an immersed boundary (IB) method with a finite element (FE) structural mechanics model. We use a structure-based hyperelastic strain-energy function to describe the passive mechanics of the ventricular myocardium, a realistic anatomical geometry reconstructed from clinical magnetic resonance images of a healthy human heart, and a rule-based fiber architecture. Numerical predictions of this IB/FE model are compared with results obtained by a commercial FE solver. We demonstrate that the IB/FE model yields results that are in good agreement with those of the conventional FE model under diastolic loading conditions, and the predictions of the LV model using either numerical method are shown to be consistent with previous computational and experimental data. These results are among the first to analyze the stress and strain predictions of IB models of ventricular mechanics, and they serve both to verify the IB/FE simulation framework and to validate the IB/FE model. Moreover, this work represents an important step toward using such models for fully dynamic fluid–structure interaction simulations of the heart. © 2014 The Authors. International Journal for Numerical Methods in Engineering published by John Wiley & Sons, Ltd. more...

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). 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, A. Donev was supported in part by the Air Force Office of Scientific Research under grant number FA9550-12-1-0356. B. Griffith acknowledges research support from the National Science Foundation un-der awards OCI 1047734 and DMS 1016554. R. Delgado-Buscalioni and F. Balboa acknowledge funding from the Spanish government FIS2010-22047-C05 and from the Comunidad de Madrid MODELICO-CM (S2009/ESP-1691). Collaboration between A. Donev and R. Delgado-Buscalioni was fostered at the Kavli Institute for Theoretical Physics in Santa Barbara, California, and supported in part by the National Science Foundation under Grant No. NSF PHY05-51164 more...

We describe an immersed boundary method for problems of fluid-solute-structure interaction. The numerical scheme employs linearly implicit timestepping, allowing for the stable use of timesteps that are substantially larger than those permitted by an explicit method, and local mesh refinement, making it feasible to resolve the steep gradients associated with the space charge layers as well as the chemical potential, which is used in our formulation to control the permeability of the membrane to the (possibly charged) solute. Low Reynolds number fluid dynamics are described by the time-dependent incompressible Stokes equations, which are solved by a cell-centered approximate projection method. The dynamics of the chemical species are governed by the advection-electrodiffusion equations, and our semi-implicit treatment of these equations results in a linear system which we solve by GMRES preconditioned via a fast adaptive composite-grid (FAC) solver. Numerical examples demonstrate the capabilities of this methodology, as well as its convergence properties. more...

The immersed boundary method is both a general mathematical framework and a particular numerical approach to problems of fluid-structure interaction. In this paper, we describe the application of the immersed boundary method to the simulation of cardiovascular fluid dynamics, focusing on the fluid dynamics of the aortic heart valve (the valve which prevents the backflow of blood from the aorta into the left ventricle of the heart) and aortic root (the initial portion of the aorta, which attaches to the heart). The aortic valve and root are modeled as a system of elastic fibers, and the blood is modeled as a viscous incompressible fluid. Three-dimensional simulation results obtained using a parallel and adaptive version of the immersed boundary method are presented. These results demonstrate that it is feasible to perform three-dimensional immersed boundary simulations of cardiovascular fluid dynamics in which realistic cardiac output is obtained at realistic pressures. more...