arXiv subjects

Jeffrey A. Weiss

Publications and source records attributed to Jeffrey A. Weiss.

11 recordsLinked to original sources

arXiv2026

FUSE: A Partitioned Field-Exchange Framework for Coupling Physics Simulations in FEBio

Computational biomechanics increasingly requires models that combine mechanics, transport, chemistry, and biological regulation across different spatial and temporal scales. The FEBio simulation software provides extensive open-source capabilities for modeling these processes using monolithic approaches. However, assembling independently developed physics models into reproducible coupled workflows remains challenging. Existing approaches often require custom scripts or external software pipelines, which can limit model reuse and complicate development. We present FUSE, the FEBio Unified Simulation and Exchange framework, a partitioned coupling plugin that enables separately defined FEBio models to communicate through structured field exchange. FUSE is designed for problems that are best solved independently, particularly when fast mechanical responses influence slower biological or chemical evolution. The framework uses a time-decoupled strategy in which a primary model advances on the longer time scale, while one or more secondary models are repeatedly initialized, supplied with updated fields, solved over shorter time horizons, with results returned to the primary model. Field exchange utilizes existing FEBio data maps, output fields, and user-specified filters, allowing coupled workflows to be constructed without modifying the underlying solvers. The framework was able to reproduce reference coupled solutions while handling bidirectional transfer, spatial field mapping, and filtered exchange of model variables. Example applications demonstrated coupling between mechanical loading and chemical degradation in injured cartilage and interaction between biological tissue formation and mechanical feedback during bone healing. By separating coupling logic from physics implementation, FUSE provides a practical mechanism for building maintainable multiphysics workflows within FEBio.

cs.CE↗

arXiv2026

A geometric feature tracking approach for noninvasive patient specific estimation of leaflet strain from 3D images of heart valves

Valvular heart disease is prevalent and a major contributor to heart failure. Valve leaflet strain is a promising metric for evaluating the mechanics underlying the initiation and progression of valvular pathology. However, generalizable methods for noninvasively quantifying valvular strain from clinically acquired patient images remain limited. To address this limitation, we developed a geometric feature-tracking framework to quantify in vivo leaflet strain from 3DE images. The method integrates a cohort-derived geometric reference atlas to establish geometric correspondence and introduces a novel distance-weighted coherent point drift algorithm for non-rigid registration. We evaluated performance against a finite element benchmark model and compared the approach with conventional point-based tracking methods. The framework was applied to pediatric and adult patient datasets (N = 31) across variable valve morphologies. The proposed method demonstrated greater accuracy in quantifying anatomical alignment and leaflet strain than conventional point-based approaches. Validation against the finite element benchmark confirmed improved strain estimation. The framework achieved reliable inter-phase tracking of valve deformation across diverse morphologies in pediatric and adult patients. Analysis identified a consistent distribution pattern of the 1st principal strain associated with leaflet billow (prolapse). This feature-tracking framework provides a generalizable method for noninvasive quantification of atrioventricular valve leaflet strain from clinical 3DE images. Characterization of biomechanical strain patterns may improve prognostic assessment and support longitudinal evaluation of valvular heart disease. Further investigation of the biomechanical signatures of heart valve disease has the potential to enhance prognostic assessment and longitudinal evaluation of valvular heart disease.

q-bio.QM↗

arXiv2026

An open-source computational framework for immersed fluid-structure interaction modeling using FEBio and MFEM

Fluid-structure interaction (FSI) simulation of biological systems presents significant computational challenges, particularly for applications involving large structural deformations and contact mechanics, such as heart valve dynamics. Traditional ALE methods encounter fundamental difficulties with such problems due to mesh distortion, motivating immersed techniques. This work presents a novel open-source immersed FSI framework that strategically couples two mature finite element libraries: MFEM, a GPU-ready and scalable library with state-of-the-art parallel performance developed at LLNL, and FEBio, a nonlinear finite element solver with sophisticated solid mechanics capabilities designed for biomechanics applications developed at the University of Utah and Columbia University. This coupling creates a unique synergy wherein the fluid solver leverages MFEM's distributed-memory parallelization and pathway to GPU acceleration, while the immersed solid exploits FEBio's comprehensive suite of hyperelastic and viscoelastic constitutive models and advanced solid mechanics modeling targeted for biomechanics applications. FSI coupling is achieved using a fictitious domain methodology with variational multiscale stabilization for enhanced accuracy on under-resolved grids expected with unfitted meshes used in immersed FSI. A fully implicit, monolithic scheme provides robust coupling for strongly coupled FSI characteristic of cardiovascular applications. The framework's modular architecture facilitates straightforward extension to additional physics and element technologies. Several test problems are considered to demonstrate the capabilities of the proposed framework, including a 3D semilunar heart valve simulation. This platform addresses a critical need for open-source immersed FSI software combining advanced biomechanics modeling with high-performance computing infrastructure.

q-bio.QM↗

arXiv2026

Effect of Right Ventricular Outflow Tract Material Properties on Simulated Transcatheter Pulmonary Placement

Finite element (FE) simulations emulating transcatheter pulmonary valve (TPV) system deployment in patient-specific right ventricular outflow tracts (RVOT) assume material properties for the RVOT and adjacent tissues. Sensitivity of the deployment to variation in RVOT material properties is unknown. Moreover, the effect of a transannular patch stiffness and location on simulated TPV deployment has not been explored. A sensitivity analysis on the material properties of a patient-specific RVOT during TPV deployment, modeled as an uncoupled HGO material, was conducted using FEBioUncertainSCI. Further, the effects of a transannular patch during TPV deployment were analyzed by considering two patch locations and four patch stiffnesses. Visualization of results and quantification were performed using custom metrics implemented in SlicerHeart and FEBio. Sensitivity analysis revealed that the shear modulus of the ground matrix (c), fiber modulus (k1), and fiber mean orientation angle (gamma) had the greatest effect on 95th %ile stress, whereas only c had the greatest effect on 95th %ile Lagrangian strain. First-order sensitivity indices contributed the greatest to the total-order sensitivity indices. Simulations using a transannular patch revealed that peak stress and strain were dependent on patch location. As stiffness of the patch increased, greater stress was observed at the interface connecting the patch to the RVOT, and stress in the patch itself increased while strain decreased. The total enclosed volume by the TPV device remained unchanged across all simulated patch cases. This study highlights that while uncertainties in tissue material properties and patch locations may influence functional outcomes, FE simulations provide a reliable framework for evaluating these outcomes in TPVR.

physics.med-ph↗

arXiv2025

Integrated Open-Source Framework for Simulation of Transcatheter Pulmonary Valves in Native Right Ventricular Outflow Tracts

Background - Pulmonary insufficiency is a consequence of transannular patch repair in Tetralogy of Fallot (ToF), leading to late morbidity and mortality. Transcatheter native outflow tract pulmonary valve replacement (TPVR) has become common, but assessment of patient candidacy and selection of the optimal device remains challenging. We demonstrate an integrated open-source workflow for simulation of TPVR in image-derived models to inform device selection. Methods - Machine learning-based segmentation of CT scans was implemented to define the right ventricular outflow tract (RVOT). A custom workflow for device positioning and pre-compression was implemented in SlicerHeart. Resulting geometries were exported to FEBio for simulation. Visualization of results and quantification were performed using custom metrics implemented in SlicerHeart and FEBio. Results - RVOT model creation and device placement could be completed in under 1 minute. Virtual device placement using FE simulations visually mimicked actual device placement and allowed quantification of vessel strain, stress, and contact area. Regions of higher strain and stress were observed at the proximal and distal end locations of the TPVs where the devices impinge the RVOT wall. No other consistent trends were observed across simulations. The observed variability in mechanical metrics across RVOTS, stents, and locations in the RVOT highlights that no single device performs optimally in all anatomies, thereby reinforcing the need for simulation-based patient-specific assessment. Conclusions - This study demonstrates the feasibility of a novel open-source workflow for the rapid simulation of TPVR which with further refinement may inform assessment of patient candidacy and optimal device selection.

q-bio.TO↗

arXiv2025

Simulation of Transcatheter Therapies for Atrioventricular Valve Regurgitation in an Open-Source Finite Element Simulation Framework

Purpose: Transcatheter edge-to-edge repair (TEER) and annuloplasty devices are increasingly used to treat mitral valve regurgitation, yet their mechanical effects and interactions remain poorly understood. This study aimed to establish an open-source finite element modeling (FEM) framework for simulating patient-specific mitral valve repairs and to evaluate how TEER, annuloplasty, and combined strategies influence leaflet coaptation and valve mechanics. Methods: Four G4 MitraClip geometries were modeled and deployed in FEBio to capture leaflet grasp and subsequent clip-leaflet motion under physiologic pressurization. CardioBand annuloplasty was simulated by reducing annular circumference via displacement-controlled boundary conditions, and Mitralign suture annuloplasty was modeled using discrete nodal constraints. Simulations were performed for prolapse and dilated annulus cases. Valve competence (regurgitant orifice area, ROA), coaptation/contact area (CA), and leaflet stress and strain distributions were quantified. Results: In prolapse, TEER restored coaptation but increased leaflet stresses, whereas band and suture annuloplasty produced distinct valve morphologies with lower stress distributions. In dilation, TEER alone left residual regurgitation, while annuloplasty improved closure. Combined TEER & band annuloplasty minimized ROA, maximized CA, and reduced stresses relative to TEER alone, though stresses remained higher than annuloplasty alone. Conclusion: This study establishes a reproducible, open-source FEM framework for simulating transcatheter TEER and annuloplasty repairs, with the potential to be extended beyond the mitral valve. By quantifying the mechanical trade-offs of TEER, suture annuloplasty, band annuloplasty, and their combinations, this methodology highlights the potential of virtual repair to guide patient selection and optimize surgical planning.

physics.med-ph↗

arXiv2025

ADEPT: A Noninvasive Method for Determining Elastic Parameters of Valve Tissue

Computer simulation of "virtual interventions" may inform optimal valve repair for a given patient prior to intervention. However, the paucity of noninvasive methods to determine in vivo mechanical parameters of valves limits the accuracy of computer prediction and their clinical application. To address this, we propose ADEPT: A noninvasive method for Determining Elastic Parameters of valve Tissue. In this work, we demonstrated its application to the tricuspid valve of a child. We first tracked valve displacements from open to closed frames within a 3D echocardiogram time sequence using image registration. Physics-informed neural networks were subsequently applied to estimate the nonlinear mechanical properties from first principles and reference displacements. The simulated model using these patient-specific parameters closely aligned with the reference image segmentation, achieving a mean symmetric distance of less than 1 mm. Our approach doubled the accuracy of the simulated model compared to the generic parameters reported in the literature.

q-bio.QM↗

arXiv2024

Effect of Parametric Variation of Chordae Tendineae Structure on Simulated Atrioventricular Valve Closure

Many approaches have been used to model chordae tendineae geometries in finite element simulations of atrioventricular heart valves. Unfortunately, current "functional" chordae tendineae geometries lack fidelity that would be helpful when informing clinical decisions. The objectives of this work are (i) to improve synthetic chordae tendineae geometry fidelity to consider branching and (ii) to define how the chordae tendineae geometry affects finite element simulations of valve closure. In this work, we develop an open-source method to construct synthetic chordae tendineae geometries in the SlicerHeart Extension of 3D Slicer. The generated geometries are then used in FEBio finite element simulations of atrioventricular valve function to evaluate how variations in chordae tendineae geometry influence valve behavior. Effects are evaluated using functional and mechanical metrics. Our findings demonstrated that altering the chordae tendineae geometry of a stereotypical mitral valve led to changes in clinically relevant valve metrics and valve mechanics. Specifically, cross sectional area had the most influence over valve closure metrics, followed by chordae tendineae density, length, radius and branches. We then used this information to showcase the flexibility of our new workflow by altering the chordae tendineae geometry of two additional geometries (mitral valve with annular dilation and tricuspid valve) to improve finite element predictions. This study presents a flexible, open-source method for generating synthetic chordae tendineae with realistic branching structures. Further, we establish relationships between the chordae tendineae geometry and valve functional/mechanical metrics. This research contribution helps enrich our open-source workflow and brings the finite element simulations closer to use in a patient-specific clinical setting.

physics.med-ph↗

arXiv2024

FEBio FINESSE: An open-source finite element simulation approach to estimate in vivo heart valve strains using shape enforcement

Finite element simulations are an enticing tool to evaluate heart valve function in healthy and diseased patients; however, patient-specific simulations derived from 3D echocardiography are hampered by several technical challenges. In this work, we present an open-source method to enforce matching between finite element simulations and in vivo image-derived heart valve geometry in the absence of patient-specific material properties, leaflet thickness, and chordae tendineae structures. We evaluate FEBio Finite Element Simulations with Shape Enforcement (FINESSE) using three synthetic test cases covering a wide range of model complexity. Our results suggest that FINESSE can be used to not only enforce finite element simulations to match an image-derived surface, but to also estimate the first principal leaflet strains within +/- 0.03 strain. Key FINESSE considerations include: (i) appropriately defining the user-defined penalty, (ii) omitting the leaflet commissures to improve simulation convergence, and (iii) emulating the chordae tendineae behavior via prescribed leaflet free edge motion or a chordae emulating force. We then use FINESSE to estimate the in vivo valve behavior and leaflet strains for three pediatric patients. In all three cases, FINESSE successfully matched the target surface with median errors similar to or less than the smallest voxel dimension. Further analysis revealed valve-specific findings, such as the tricuspid valve leaflet strains of a 2-day old patient with HLHS being larger than those of two 13-year old patients. The development of this open source pipeline will enable future studies to begin linking in vivo leaflet mechanics with patient outcomes

physics.med-ph↗

arXiv2023

The effects of leaflet material properties on the simulated function of regurgitant mitral valves

Advances in three-dimensional imaging provide the ability to construct and analyze finite element (FE) models to evaluate the biomechanical behavior and function of atrioventricular valves. However, while obtaining patient-specific valve geometry is now possible, non-invasive measurement of patient-specific leaflet material properties remains nearly impossible. Both valve geometry and tissue properties play a significant role in governing valve dynamics, leading to the central question of whether clinically relevant insights can be attained from FE analysis of atrioventricular valves without precise knowledge of tissue properties. As such we investigated 1) the influence of tissue extensibility and 2) the effects of constitutive model parameters and leaflet thickness on simulated valve function and mechanics. We compared metrics of valve function (e.g., leaflet coaptation and regurgitant orifice area) and mechanics (e.g., stress and strain) across one normal and three regurgitant mitral valve (MV) models with common mechanisms of regurgitation (annular dilation, leaflet prolapse, leaflet tethering) of both moderate and severe degree. We developed a novel fully-automated approach to accurately quantify regurgitant orifice areas of complex valve geometries. We found that the relative ordering of the mechanical and functional metrics was maintained across a group of valves using material properties up to 15% softer than the representative adult mitral constitutive model. Our findings suggest that FE simulations can be used to qualitatively compare how differences and alterations in valve structure affect relative atrioventricular valve function even in populations where material properties are not precisely known.

physics.med-ph↗

arXiv2022

A Computational Framework for Atrioventricular Valve Modeling using Open-Source Software

Atrioventricular valve regurgitation is a significant cause of morbidity and mortality in patients with acquired and congenital cardiac valve disease. Image-derived computational modeling of atrioventricular valves has advanced substantially over the last decade and holds particular promise to inform valve repair in small and heterogeneous populations which are less likely to be optimized through empiric clinical application. While an abundance of computational biomechanics studies have investigated mitral and tricuspid valve disease in adults, few studies have investigated application to vulnerable pediatric and congenital heart populations. Further, to date, investigators have primarily relied upon a series of commercial applications that are neither designed for image-derived modeling of cardiac valves, nor freely available to facilitate transparent and reproducible valve science. To address this deficiency, we aimed to build an open-source computational framework for the image-derived biomechanical analysis of atrioventricular valves. In the present work, we integrated an open-source valve modeling platform, SlicerHeart, and an open-source biomechanics finite element modeling software, FEBio, to facilitate image-derived atrioventricular valve model creation and finite element analysis. We present a detailed verification and sensitivity analysis to demonstrate the fidelity of this modeling in application to 3D echocardiography-derived pediatric mitral and tricuspid valve models. Our analyses achieved excellent agreement with those reported in the literature. As such, this evolving computational framework offers a promising initial foundation for future development and investigation of valve mechanics, in particular collaborative efforts targeting the development of improved repairs for children with congenital heart disease.

q-bio.TO↗