A Plugin Framework for Extending the Simulation Capabilities of FEBio

Plugin-based interoperability and ecosystem management for the MolSSI Driver Interface Project

The MolSSI Driver Interface (MDI) Project is an effort to simplify and standardize the process of enabling tight interoperability between independently developed code bases and is supported by numerous software packages across the domain of chemical physics. It enables a wide variety of use cases, including quantum mechanics/molecular mechanics, advanced sampling, path integral molecular dynamics, machine learning, ab initio molecular dynamics, etc. We describe two major developments within the MDI Project that provide novel solutions to key interoperability challenges. The first of these is the development of the MDI Plugin System, which allows MDI-supporting libraries to be used as highly modular plugins, with MDI enforcing a standardized application programming interface across plugins. Codes can use these plugins without linking against them during their build process, and end-users can select which plugin(s) they wish to use at runtime. The MDI Plugin System features a sophisticated callback system that allows codes to interact with plugins on a highly granular level and represents a significant advancement toward increased modularity among scientific codes. The second major development is MDI Mechanic, an ecosystem management tool that utilizes Docker containerization to simplify the process of developing, validating, maintaining, and deploying MDI-supporting codes. Additionally, MDI Mechanic provides a framework for launching MDI simulations in which each interoperating code is executed within a separate computational environment. This eliminates the need to compile multiple production codes within a single computational environment, reducing opportunities for dependency conflicts and lowering the barrier to entry for users of MDI-enabled codes.

The need for speed - Does the force-velocity property significantly alter strain distributions within skeletal muscle?

Skeletal muscles are complex structures with nonlinear constitutive properties. This complexity often requires finite element (FE) modeling to better understand muscle behavior and response to activation, especially the fiber strain distributions that can be difficult to measure in vivo. However, many FE muscle models designed to study fiber strain do not include force-velocity behavior. To investigate force-velocity property impact on strain distributions within skeletal muscle, we modified a muscle constitutive model with active and passive force-length properties to include force-velocity properties. We implemented the new constitutive model as a plugin for the FE software FEBio and applied it to four geometries: 1) a single element, 2) a multiple-element model representing a single fiber, 3) a model of tapering fibers, and 4) a model representing the bicep femoris long head (BFLH) morphology. Maximum fiber velocity and boundary conditions of the finite element models were varied to test their influence on fiber strain distribution. We found that force-velocity properties in the constitutive model behaved as expected for the single element and multi-element conditions. In the tapered fiber models, fiber strain distributions were impacted by changes in maximum fiber velocity; the range of strains increased with maximum fiber velocity, which was most noted in isometric contraction simulations. In the BFLH model, maximum fiber velocity had minimal impact on strain distributions, even in the context of sprinting. Taken together, the combination of muscle model geometry, activation, and displacement parameters play a critical part in determining the magnitude of impact of force-velocity on strain distribution.

Surgical Patching in Congenital Heart Disease: The Role of Imaging and Modelling

In congenital heart disease, patches are not tailored to patient-specific anatomies, leading to shape mismatch with likely functional implications. The design of patches through imaging and modelling may be beneficial, as it could improve clinical outcomes and reduce the costs associated with redo procedures. Whilst attention has been paid to the material of the patches used in congenital surgery, this review outlines the current knowledge on this subject and isolated experimental work that uses modelling and imaging-derived information (including 3D printing) to inform the design of the surgical patch.

Spatial Configurations of 3D Extracellular Matrix Collagen Density and Anisotropy Simultaneously Guide Angiogenesis

Extracellular matrix (ECM) collagen density and fibril anisotropy are thought to affect the development of new vasculatures during pathologic and homeostatic angiogenesis. Computational simulation is emerging as a tool to investigate the role of matrix structural configurations on cell guidance. However, prior computational models have only considered the orientation of collagen as a model input. Recent experimental evidence indicates that cell guidance is simultaneously influenced by the direction and intensity of alignment (i.e., degree of anisotropy) as well as the local collagen density. The objective of this study was to explore the role of ECM collagen anisotropy and density during sprouting angiogenesis through simulation in the AngioFE and FEBio modeling frameworks. AngioFE is a plugin for FEBio (Finite Elements for Biomechanics) that simulates cell-matrix interactions during sprouting angiogenesis. We extended AngioFE to represent ECM collagen as deformable 3D ellipsoidal fibril distributions (EFDs). The rate and direction of microvessel growth were modified to depend simultaneously on the ECM collagen anisotropy (orientation and degree of anisotropy) and density. The sensitivity of growing neovessels to these stimuli was adjusted so that AngioFE could reproduce the growth and guidance observed in experiments where microvessels were cultured in collagen gels of varying anisotropy and density. We then compared outcomes from simulations using EFDs to simulations that used AngioFE's prior vector field representation of collagen anisotropy. We found that EFD simulations were more accurate than vector field simulations in predicting experimentally observed microvessel guidance. Predictive simulations demonstrated the ability of anisotropy gradients to recruit microvessels across short and long distances relevant to wound healing. Further, simulations predicted that collagen alignment could enable microvessels to overcome dense tissue interfaces such as tumor-associated collagen structures (TACS) found in desmoplasia and tumor-stroma interfaces. This approach can be generalized to other mechanobiological relationships during cell guidance phenomena in computational settings.

Deformation of Gels with Spherical Auxetic Inclusions

Auxetic metamaterials possess unnatural properties, such as a negative Poisson’s ratio, which offers interesting features when combined with traditional materials. This paper describes the deformation behavior of a gel consisting of spherical auxetic inclusions when embedded in a conventional matrix. The auxetic inclusions and conventional matrix were modeled as spherical objects with a controlled pore shape. The auxetic particle had a reentrant honeycomb, and the conventional phase contained honeycomb-shaped pores. The deformation behavior was simulated using various existing models based on continuum mechanics. For the continuum mechanics models—the simplest of which are the Mori–Tanaka theory and self-consistent field mechanics models—the auxetic particle was homogenized as a solid element with Young’s modulus and Poisson’s ratio and compared with the common composite gel filled with rigid spheres. The finite element analysis simulations using these models were performed for two cases: (1) a detailed model of one particle and its surroundings in which the structure included the design of both the reentrant and conventional honeycombs; and (2) a multiparticle face-centered cubic lattice where both the classic matrix and auxetic particle were homogenized. Our results suggest that auxetic inclusion-filled gels provide an unsurpassed balance of low density and enhanced stiffness.

Texas TriValve 1.0 : a reverse‑engineered, open model of the human tricuspid valve

Nearly 1.6 million Americans suffer from a leaking tricuspid heart valve. To make matters worse, current valve repair options are far from optimal leading to recurrence of leakage in up to 30% of patients. We submit that a critical step toward improving outcomes is to better understand the "forgotten" valve. High-fidelity computer models may help in this endeavour. However, the existing models are limited by averaged or idealized geometries, material properties, and boundary conditions. In our current work, we overcome the limitations of existing models by (reverse) engineering the tricuspid valve from a beating human heart in an organ preservation system. The resulting finite-element model faithfully captures the kinematics and kinetics of the native tricuspid valve as validated against echocardiographic data and others' previous work. To showcase the value of our model, we also use it to simulate disease-induced and repair-induced changes to valve geometry and mechanics. Specifically, we simulate and compare the effectiveness of tricuspid valve repair via surgical annuloplasty and via transcatheter edge-to-edge repair. Importantly, our model is openly available for others to use. Thus, our model will allow us and others to perform virtual experiments on the healthy, diseased, and repaired tricuspid valve to better understand the valve itself and to optimize tricuspid valve repair for better patient outcomes.

SlicerHeart: An open-source computing platform for cardiac image analysis and modeling

Cardiovascular disease is a significant cause of morbidity and mortality in the developed world. 3D imaging of the heart's structure is critical to the understanding and treatment of cardiovascular disease. However, open-source tools for image analysis of cardiac images, particularly 3D echocardiographic (3DE) data, are limited. We describe the rationale, development, implementation, and application of SlicerHeart, a cardiac-focused toolkit for image analysis built upon 3D Slicer, an open-source image computing platform. We designed and implemented multiple Python scripted modules within 3D Slicer to import, register, and view 3DE data, including new code to volume render and crop 3DE. In addition, we developed dedicated workflows for the modeling and quantitative analysis of multi-modality image-derived heart models, including heart valves. Finally, we created and integrated new functionality to facilitate the planning of cardiac interventions and surgery. We demonstrate application of SlicerHeart to a diverse range of cardiovascular modeling and simulation including volume rendering of 3DE images, mitral valve modeling, transcatheter device modeling, and planning of complex surgical intervention such as cardiac baffle creation. SlicerHeart is an evolving open-source image processing platform based on 3D Slicer initiated to support the investigation and treatment of congenital heart disease. The technology in SlicerHeart provides a robust foundation for 3D image-based investigation in cardiovascular medicine.

Three-Dimensional Anisotropic Hyperelastic Constitutive Model Describing the Mechanical Response of Human and Mouse Cervix

The mechanical function of the uterine cervix is critical for a healthy pregnancy. During pregnancy, the cervix undergoes significant softening to allow for a successful delivery. Abnormal cervical remodeling is suspected to contribute to preterm birth. Material constitutive models describing known biological shifts in pregnancy are essential to predict the mechanical integrity of the cervix. In this work, the material response of human cervical tissue under spherical indentation and uniaxial tensile tests loaded along different anatomical directions is experimentally measured. A deep-learning segmentation tool is applied to capture the tissue deformation during the uniaxial tensile tests. A 3-dimensional, equilibrium anisotropic continuous fiber constitutive model is formulated, considering collagen fiber directionality, fiber bundle dispersion, and the entropic nature of wavy cross-linked collagen molecules. Additionally, the universality of the material model is demonstrated by characterizing previously published mouse cervix mechanical data. Overall, the proposed material model captures the tension-compression asymmetric material responses and the remodeling characteristics of both human and mouse cervical tissue. The pregnant (PG) human cervix (mean locking stretch ζ=2.4, mean initial stiffness ξ=12 kPa, mean bulk modulus κ=0.26 kPa, mean dispersion b=1.0) is more compliant compared with the nonpregnant (NP) cervix (mean ζ=1.3, mean ξ=32 kPa, mean κ=1.4 kPa, mean b=1.4). Creating a validated material model, which describes the role of collagen fiber directionality, dispersion, and crosslinking, enables tissue-level biomechanical simulations to determine which material and anatomical factors drive the cervix to open prematurely. STATEMENT OF SIGNIFICANCE: In this study, we report a 3D anisotropic hyperelastic constitutive model based on Langevin statistic mechanics and successfully describe the material behavior of both human and mouse cervical tissue using this model. This model bridges the connection between the extracellular matrix (ECM) microstructure remodeling and the macro mechanical properties change of the cervix during pregnancy via microstructure-associated material parameters. This is the first model, to our knowledge, to connect the the entropic nature of wavy cross-linked collagen molecules with the mechanical behavior of the cervix. Inspired by microstructure, this model provides a foundation to understand further the relationship between abnormal cervical ECM remodeling and preterm birth. Furthermore, with a relatively simple form, the proposed model can be applied to other fibrous tissues in the future.

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.

Right ventricular myocardial mechanics: Multi-modal deformation, microstructure, modeling, and comparison to the left ventricle

The right ventricular myocardium, much like the rest of the right side of the heart, has been consistently understudied. Presently, little is known about its mechanics, its microstructure, and its constitutive behavior. In this work, we set out to provide the first data on the mechanics of the mature right ventricular myocardium in both simple shear and uniaxial loading and to compare these data to the mechanics of the left ventricular myocardium. To this end, we tested ovine tissue samples of the right and left ventricle under a comprehensive mechanical testing protocol that consisted of six simple shear modes and three tension/compression modes. After mechanical testing, we conducted a histology-based microstructural analysis on each right ventricular sample that yielded high resolution fiber distribution maps across the entire samples. Equipped with this detailed mechanical and histological data, we employed an inverse finite element framework to determine the optimal form and parameters for microstructure-based constitutive models. The results of our study show that right ventricular myocardium is less stiff then the left ventricular myocardium in the fiber direction, but similarly exhibits non-linear, anisotropic, and tension/compression asymmetric behavior with direction-dependent Poynting effect. In addition, we found that right ventricular myocardial fibers change angles transmurally and are dispersed within the sheet plane and normal to it. Through our inverse finite element analysis, we found that the Holzapfel model successfully fits these data, even when selectively informed by rudimentary microstructural information. And, we found that the inclusion of higher-fidelity microstructural data improved the Holzapfel model's predictive ability. Looking forward, this investigation is a critical step towards understanding the fundamental mechanical behavior of right ventricular myocardium and lays the groundwork for future whole-organ mechanical simulations.

Tools for computational analysis of moving boundary problems in cellular mechanobiology

A cell's ability to change shape is one of the most fundamental biological processes and is essential for maintaining healthy organisms. When the ability to control shape goes awry, it often results in a diseased system. As such, it is important to understand the mechanisms that allow a cell to sense and respond to its environment so as to maintain cellular shape homeostasis. Because of the inherent complexity of the system, computational models that are based on sound theoretical understanding of the biochemistry and biomechanics and that use experimentally measured parameters are an essential tool. These models involve an inherent feedback, whereby shape is determined by the action of regulatory signals whose spatial distribution depends on the shape. To carry out computational simulations of these moving boundary problems requires special computational techniques. A variety of alternative approaches, depending on the type and scale of question being asked, have been used to simulate various biological processes, including cell motility, division, mechanosensation, and cell engulfment. In general, these models consider the forces that act on the system (both internally generated, or externally imposed) and the mechanical properties of the cell that resist these forces. Moving forward, making these techniques more accessible to the non-expert will help improve interdisciplinary research thereby providing new insight into important biological processes that affect human health. This article is categorized under: Cancer > Cancer>Computational Models Cancer > Cancer>Molecular and Cellular Physiology.

Scaffold Architecture and Matrix Strain Modulate Mesenchymal Cell and Microvascular Growth and Development in a Time Dependent Manner

BACKGROUND

Volumetric tissue-engineered constructs are limited in development due to the dependence on well-formed vascular networks. Scaffold pore size and the mechanical properties of the matrix dictates cell attachment, proliferation and successive tissue morphogenesis. We hypothesize scaffold pore architecture also controls stromal-vessel interactions during morphogenesis.

METHODS

The interaction between mesenchymal stem cells (MSCs) seeded on hydroxyapatite scaffolds of 450, 340, and 250 μm pores and microvascular fragments (MVFs) seeded within 20 mg/mL fibrin hydrogels that were cast into the cell-seeded scaffolds, was assessed in vitro over 21 days and compared to the fibrin hydrogels without scaffold but containing both MSCs and MVFs. mRNA sequencing was performed across all groups and a computational mechanics model was developed to validate architecture effects on predicting vascularization driven by stiffer matrix behavior at scaffold surfaces compared to the pore interior.

RESULTS

Lectin staining of decalcified scaffolds showed continued vessel growth, branching and network formation at 14 days. The fibrin gel provides no resistance to spread-out capillary networks formation, with greater vessel loops within the 450 μm pores and vessels bridging across 250 μm pores. Vessel growth in the scaffolds was observed to be stimulated by hypoxia and successive angiogenic signaling. Fibrin gels showed linear fold increase in VEGF expression and no change in BMP2. Within scaffolds, there was multiple fold increase in VEGF between days 7 and 14 and early multiple fold increases in BMP2 between days 3 and 7, relative to fibrin. There was evidence of yap/taz based hippo signaling and mechanotransduction in the scaffold groups. The vessel growth models determined by computational modeling matched the trends observed experimentally.

CONCLUSION

The differing nature of hypoxia signaling between scaffold systems and mechano-transduction sensing matrix mechanics were primarily responsible for differences in osteogenic cell and microvessel growth. The computational model implicated scaffold architecture in dictating branching morphology and strain in the hydrogel within pores in dictating vessel lengths.