Solute transport across a contact interface in deformable porous media

A multiphasic model for determination of mouse ascending thoracic aorta mass transport properties with and without aneurysm

Thoracic aortic aneurysms (TAAs) are associated with aortic wall remodeling that affects transmural transport or the movement of fluid and solute across the wall. In previous work, we used a Fbln4E57K/E57K (MU) mouse model to investigate transmural transport changes as a function of aneurysm severity. We compared wild-type (WT), MU with no aneurysm (MU-NA), MU with aneurysm (MU-A), and MU with an additional genetic mutation that led to increased aneurysm penetrance (MU-XA). We found that all aneurysmal aortas (MU-A and MU-XA) had lower fluid flux compared to WT. Non-aneurysmal aortas (MU-NA) had higher 4 kDa FITC-dextran solute flux than WT, but aneurysmal MU-A and MU-XA aortas had solute fluxes similar to WT. Our experimental results could not isolate competing factors, such as changes in aortic geometry and solid material properties among these mouse models, to determine how intrinsic transport properties change with aneurysm severity. The objective of this study is to use biphasic and multiphasic models to identify changes in transport material properties. Our biphasic model indicates that hydraulic permeability is significantly decreased in the severe aneurysm model (MU-XA) compared to non-aneurysmal aortas (MU-NA). Our multiphasic model shows that effective solute diffusivity is increased in MU-NA aortas compared to all others. Our findings reveal changes in intrinsic transport properties that depend on aneurysm severity and are important for understanding the movement of fluids and solutes that may play a role in the diagnosis, progression, or treatment of TAA.

A multiphasic model for determination of water and solute transport across the arterial wall: effects of elastic fiber defects

Transport of solute across the arterial wall is a process driven by both convection and diffusion. In disease, the elastic fibers in the arterial wall are disrupted and lead to altered fluid and mass transport kinetics. A computational mixture model was used to numerically match previously published data of fluid and solute permeation experiments in groups of mouse arteries with genetic (knockout of fibulin-5) or chemical (treatment with elastase) disruption of elastic fibers. A biphasic model of fluid permeation indicated the governing property to be the hydraulic permeability, which was estimated to be 1.52×10^-9, 1.01×10^-8, and 1.07×10^-8 mm⁴/μN.s for control, knockout, and elastase groups, respectively. A multiphasic model incorporating solute transport was used to estimate effective diffusivities that were dependent on molecular weight, consistent with expected transport behaviors in multiphasic biological tissues. The effective diffusivity for the 4 kDA FITC-dextran solute, but not the 70 or 150 kDa FITC-dextran solutes, was dependent on elastic fiber structure, with increasing values from control to knockout to elastase groups, suggesting that elastic fiber disruption affects transport of lower molecular weight solutes. The model used here sets the groundwork for future work investigating transport through the arterial wall.

A Finite Element Algorithm for Large Deformation Biphasic Frictional Contact Between Porous-Permeable Hydrated Soft Tissues

The frictional response of porous and permeable hydrated biological tissues such as articular cartilage is significantly dependent on interstitial fluid pressurization. To model this response, it is common to represent such tissues as biphasic materials, consisting of a binary mixture of a porous solid matrix and an interstitial fluid. However, no computational algorithms currently exist in either commercial or open-source software that can model frictional contact between such materials. Therefore, this study formulates and implements a finite element algorithm for large deformation biphasic frictional contact in the open-source finite element software FEBio. This algorithm relies on a local form of a biphasic friction model that has been previously validated against experiments, and implements the model into our recently-developed surface-to-surface (STS) contact algorithm. Contact constraints, including those specific to pressurized porous media, are enforced with the penalty method regularized with an active-passive augmented Lagrangian scheme. Numerical difficulties specific to challenging finite deformation biphasic contact problems are overcome with novel smoothing schemes for fluid pressures and Lagrange multipliers. Implementation accuracy is verified against semi-analytical solutions for biphasic frictional contact, with extensive validation performed using canonical cartilage friction experiments from prior literature. Essential details of the formulation are provided in this paper, and the source code of this biphasic frictional contact algorithm is made available to the general public.

Finite Element Framework for Computational Fluid Dynamics in FEBio

The mechanics of biological fluids is an important topic in biomechanics, often requiring the use of computational tools to analyze problems with realistic geometries and material properties. This study describes the formulation and implementation of a finite element framework for computational fluid dynamics (CFD) in FEBio, a free software designed to meet the computational needs of the biomechanics and biophysics communities. This formulation models nearly incompressible flow with a compressible isothermal formulation that uses a physically realistic value for the fluid bulk modulus. It employs fluid velocity and dilatation as essential variables: The virtual work integral enforces the balance of linear momentum and the kinematic constraint between fluid velocity and dilatation, while fluid density varies with dilatation as prescribed by the axiom of mass balance. Using this approach, equal-order interpolations may be used for both essential variables over each element, contrary to traditional mixed formulations that must explicitly satisfy the inf-sup condition. The formulation accommodates Newtonian and non-Newtonian viscous responses as well as inviscid fluids. The efficiency of numerical solutions is enhanced using Broyden's quasi-Newton method. The results of finite element simulations were verified using well-documented benchmark problems as well as comparisons with other free and commercial codes. These analyses demonstrated that the novel formulation introduced in FEBio could successfully reproduce the results of other codes. The analogy between this CFD formulation and standard finite element formulations for solid mechanics makes it suitable for future extension to fluid-structure interactions (FSIs).

A Formulation for Fluid Structure-Interactions in FEBio Using Mixture Theory

Many physiological systems involve strong interactions between fluids and solids, posing a signicant challenge when modeling biomechanics. The objective of this study was to implement a fluid-structure interaction (FSI) solver in the free, open-source finite element code FEBio (febio.org), that combined the existing solid mechanics and rigid body dynamics solver with a recently-developed computational fluid dynamics (CFD) solver. A novel Galerkin-based finite element FSI formulation was introduced based on mixture theory, where the FSI domain was described as a mixture of fluid and solid constituents that have distinct motions. The mesh was defined on the solid domain, specialized to have zero mass, negligible stiffness and zero frictional interactions with the fluid, whereas the fluid was modeled as isothermal and compressible. The mixture framework provided the foundation for evaluating material time derivatives in a material frame for the solid and in a spatial frame for the fluid. Similar to our recently reported CFD solver, our FSI formulation did not require stabilization methods to achieve good convergence, producing a compact set of equations and code implementation. The code was successfully verified against benchmark problems and an analytical solution for squeeze-film lubrication. It was validated against experimental measurements of the flow rate in a peristaltic pump, and illustrated using non-Newtonian blood flow through a bifurcated carotid artery with a thick arterial wall. The successful formulation and implementation of this FSI solver enhances the multiphysics modeling capabilities in FEBio relevant to the biomechanics and biophysics communities.

A Plugin Framework for Extending the Simulation Capabilities of FEBio

The FEBio software suite is a set of software tools for nonlinear finite element analysis in biomechanics and biophysics. FEBio employs mixture theory to account for the multiconstituent nature of biological materials, integrating the field equations for irreversible thermodynamics, solid mechanics, fluid mechanics, mass transport with reactive species, and electrokinetics. This communication describes the development and application of a new "plugin" framework for FEBio. Plugins are dynamically linked libraries that allow users to add new features and to couple FEBio with other domain-specific software applications without modifying the source code directly. The governing equations and simulation capabilities of FEBio are reviewed. The implementation, structure, use, and application of the plugin framework are detailed. Several example plugins are described in detail to illustrate how plugins enrich, extend, and leverage existing capabilities in FEBio, including applications to deformable image registration, constitutive modeling of biological tissues, coupling to an external software package that simulates angiogenesis using a discrete computational model, and a nonlinear reaction-diffusion solver. The plugin feature facilitates dissemination of new simulation methods, reproduction of published results, and coupling of FEBio with other domain-specific simulation approaches such as compartmental modeling, agent-based modeling, and rigid-body dynamics. We anticipate that the new plugin framework will greatly expand the range of applications for the FEBio software suite and thus its impact.

Finite Element Formulation of Multiphasic Shell Elements for Cell Mechanics Analyses in FEBio

With the recent implementation of multiphasic materials in the open-source finite element (FE) software FEBio (febio.org), 3D models of cells embedded within the tissue may now be analyzed, accounting for porous solid matrix deformation, transport of interstitial fluid and solutes, membrane potential, and reactions. The cell membrane is a critical component in cell models, which selectively regulates the transport of fluid and solutes in the presence of large concentration and electric potential gradients, while also facilitating the transport of various proteins. The cell membrane is much thinner than the cell; therefore, in an FE environment, shell elements formulated as 2D surfaces in 3D space would be preferred for modeling the cell membrane, for the convenience of mesh generation from image-based data, especially for convoluted membranes. However, multiphasic shell elements are yet to be developed in the FE literature and commercial FE software. This study presents a novel formulation of multiphasic shell elements and its implementation in FEBio. The shell model includes front- and back-face nodal degrees of freedom for the solid displacement, effective fluid pressure and effective solute concentrations, and a linear interpolation of these variables across the shell thickness. This formulation was verified against classical models of cell physiology and validated against reported experimental measurements in chondrocytes. This implementation of passive transport of fluid and solutes across multiphasic membranes makes it possible to model the biomechanics of isolated cells or cells embedded in their extracellular matrix, accounting for solvent and solute transport.

FEBio: History and Advances

The principal goal of the FEBio project is to provide an advanced finite element tool for the biomechanics and biophysics communities that allows researchers to model mechanics, transport, and electrokinetic phenomena for biological systems accurately and efficiently. In addition, because FEBio is geared toward the research community, the code is designed such that new features can be added easily, thus making it an ideal tool for testing novel computational methods. Finally, because the success of a code is determined by its user base, integral goals of the FEBio project have been to offer support and outreach to our community; to provide mechanisms for dissemination of results, models, and data; and to encourage interaction between users. This review presents the history of the FEBio project, from its initial developments through its current funding period. We also present a glimpse into the future of FEBio.

Toward patient-specific articular contact mechanics

The mechanics of contacting cartilage layers is fundamentally important to understanding the development, homeostasis and pathology of diarthrodial joints. Because of the highly nonlinear nature of both the materials and the contact problem itself, numerical methods such as the finite element method are typically incorporated to obtain solutions. Over the course of five decades, we have moved from an initial qualitative understanding of articular cartilage material behavior to the ability to perform complex, three-dimensional contact analysis, including multiphasic material representations. This history includes the development of analytical and computational contact analysis methods that now provide the ability to perform highly nonlinear analyses. Numerical implementations of contact analysis based on the finite element method are rapidly advancing and will soon enable patient-specific analysis of joint contact mechanics using models based on medical image data. In addition to contact stress on the articular surfaces, these techniques can predict variations in strain and strain through the cartilage layers, providing the basis to predict damage and failure. This opens up exciting areas for future research and application to patient-specific diagnosis and treatment planning applied to a variety of pathologies that affect joint function and cartilage homeostasis.

Subject-specific analysis of joint contact mechanics: application to the study of osteoarthritis and surgical planning

Advances in computational mechanics, constitutive modeling, and techniques for subject-specific modeling have opened the door to patient-specific simulation of the relationships between joint mechanics and osteoarthritis (OA), as well as patient-specific preoperative planning. This article reviews the application of computational biomechanics to the simulation of joint contact mechanics as relevant to the study of OA. This review begins with background regarding OA and the mechanical causes of OA in the context of simulations of joint mechanics. The broad range of technical considerations in creating validated subject-specific whole joint models is discussed. The types of computational models available for the study of joint mechanics are reviewed. The types of constitutive models that are available for articular cartilage are reviewed, with special attention to choosing an appropriate constitutive model for the application at hand. Issues related to model generation are discussed, including acquisition of model geometry from volumetric image data and specific considerations for acquisition of computed tomography and magnetic resonance imaging data. Approaches to model validation are reviewed. The areas of parametric analysis, factorial design, and probabilistic analysis are reviewed in the context of simulations of joint contact mechanics. Following the review of technical considerations, the article details insights that have been obtained from computational models of joint mechanics for normal joints; patient populations; the study of specific aspects of joint mechanics relevant to OA, such as congruency and instability; and preoperative planning. Finally, future directions for research and application are summarized.