arXiv subjects

Matthew A. Jolley

Publications and source records attributed to Matthew A. Jolley.

17 recordsLinked to original sources

arXiv2026

SDFStent: Real-time interactive virtual stenting via SDF deformation fields

Stenting is among the most common transcatheter interventions for congenital heart disease (CHD). Patient-specific computational fluid dynamics (CFD) simulations can predict hemodynamic outcomes of intervention scenarios but require post-operative vascular geometries that reflect stent-induced shape changes, which existing tools either model inadequately or require extensive time or manual effort to generate. We present SDFStent, a signed distance function (SDF) based mesh deformation method for virtual stenting that operates in real time, maintains mesh integrity, and preserves junction geometry. The stent is modeled as a pipe surface composed of piecewise-capsule SDFs joined by a smooth-minimum operator. Mesh vertices near the expanding SDF surface are displaced along the SDF gradient with a compactly supported fall-off function and an alpha blending mask. SDFStent was benchmarked against three existing approaches and validated on three tetralogy of Fallot (ToF) patients and three coarctation of the aorta (CoA) patients using rigid-wall steady-state CFD simulations against clinical catheterization measurements. Against a prescribed diameter of 6.0 mm, the method produced a mean stented diameter of 5.92 $\pm$ 0.08 mm in 1.5 s, over 100$\times$ faster than the best stenting-specific comparator. All output meshes were watertight and self-intersection-free. CFD-simulated post-operative pressure drops agreed with clinical measurements within 4 mmHg (mean error 2 mmHg). SDFStent produces simulation-ready post-stent models that match prescribed stent dimensions at interactive speeds, from pre-operative anatomy and catheterization data alone. The implementation is open-source and available in 3D Slicer. Its scriptable architecture enables automated generation of large synthetic cohorts for data-driven surrogate modeling.

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 Repair on Dynamic Patient-Specific Left Atrioventricular Valve Models

Purpose: To develop and evaluate a dynamic, image-derived patient-specific physical simulation platform for the assessment of left atrioventricular valve (LAVV) repair strategies in pediatric patients with repaired atrioventricular canal defects. Methods: 3D transesophageal echocardiographic images of two patients with regurgitant LAVVs were identified from an institutional database. Custom code in SlicerHeart was used to segment leaflets, define the annulus, and generate patient-specific valve molds. Silicone valve models were fabricated and tested in a pulse duplicator under simulated physiological conditions. Five unrepaired valves were analyzed for manufacturing consistency, and multiple surgical repair techniques were compared for two patient-specific models. Results: Manufacturing variability was low in annular metrics (CV for annular circumference: 2.1; commissural distance: 4.1; annulus height: 14.7) but higher in leaflet closure metrics (billow height: 11.1%; billow volume: 18.9%; tenting height: 45.9%; tenting volume: 73.5%). In Patient 1, cleft closure and an Alfieri stitch both eliminated the regurgitant orifice area, but the Alfieri stitch resulted in elevated mean pressure gradient (17 mmHg vs. 4-9 mmHg for other repairs) and deteriorated with repeated loading. In Patient 2, no repair eliminated regurgitation entirely; however, combining an 11 mm patch augmentation with commissuroplasty reduced regurgitant area to 0.147 cm2, the smallest observed among tested strategies. Conclusion: This study demonstrates the feasibility of a dynamic physical simulation platform for preclinical LAVV repair evaluation. This proof-of-concept work highlights the platform potential for refining repair strategies before clinical application, which may be particularly relevant in small and heterogeneous populations with congenital heart disease.

physics.med-ph↗

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

Geodesic-based Predictive Shape Modeling of the Right Ventricle in Patients with Hypoplastic Left Heart Syndrome

Hypoplastic left heart syndrome (HLHS) is characterized by severe underdevelopment of left ventricle requiring staged surgical reconstruction (stages) to allow the right ventricle (RV) alone to support the circulation. In this setting changes in RV size and shape over time reflect adaptations to single-ventricle physiology, dysfunction of the associated tricuspid valve (TV), and are associated with circulatory failure. As such, an accurate prediction of the RV shape of a patient would inform understanding of both RV and TV failure, as well as clinical prognosis and associated decision making. We present a geodesic-based predictive shape modeling framework applied a cohort of RVs obtained from 15 HLHS patients at three individual time points. Reasonable predictions on stage 1 RV shapes can generated using pre-stage 1 RV shapes and two predictors from prior clinical and demographic measures. Our results demonstrate the future potential for a data-driven method to predict how the morphology of the RV of an individual patient will change in size and shape over time. Future studies will seek to expand the training sample size and integrate more comprehensive demographic and morphological data into the proposed predictive model.

physics.med-ph↗

arXiv2025

Towards Patient-Specific Surgical Planning for Bicuspid Aortic Valve Repair: Fully Automated Segmentation of the Aortic Valve in 4D CT

The bicuspid aortic valve (BAV) is the most prevalent congenital heart defect and may require surgery for complications such as stenosis, regurgitation, and aortopathy. BAV repair surgery is effective but challenging due to the heterogeneity of BAV morphology. Multiple imaging modalities can be employed to assist the quantitative assessment of BAVs for surgical planning. Contrast-enhanced 4D computed tomography (CT) produces volumetric temporal sequences with excellent contrast and spatial resolution. Segmentation of the aortic cusps and root in these images is an essential step in creating patient specific models for visualization and quantification. While deep learning-based methods are capable of fully automated segmentation, no BAV-specific model exists. Among valve segmentation studies, there has been limited quantitative assessment of the clinical usability of the segmentation results. In this work, we developed a fully automated multi-label BAV segmentation pipeline based on nnU-Net. The predicted segmentations were used to carry out surgically relevant morphological measurements including geometric cusp height, commissural angle and annulus diameter, and the results were compared against manual segmentation. Automated segmentation achieved average Dice scores of over 0.7 and symmetric mean distance below 0.7 mm for all three aortic cusps and the root wall. Clinically relevant benchmarks showed good consistency between manual and predicted segmentations. Overall, fully automated BAV segmentation of 3D frames in 4D CT can produce clinically usable measurements for surgical risk stratification, but the temporal consistency of segmentations needs to be improved.

eess.IV↗

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

Identifying heterogeneous micromechanical properties of biological tissues via physics-informed neural networks

The heterogeneous micromechanical properties of biological tissues have profound implications across diverse medical and engineering domains. However, identifying full-field heterogeneous elastic properties of soft materials using traditional engineering approaches is fundamentally challenging due to difficulties in estimating local stress fields. Recently, there has been a growing interest in using data-driven models to learn full-field mechanical responses such as displacement and strain from experimental or synthetic data. However, research studies on inferring full-field elastic properties of materials, a more challenging problem, are scarce, particularly for large deformation, hyperelastic materials. Here, we propose a physics-informed machine learning approach to identify the elasticity map in nonlinear, large deformation hyperelastic materials. We evaluate the prediction accuracies and computational efficiency of physics-informed neural networks (PINNs) by inferring the heterogeneous elasticity maps across three materials with structural complexity that closely resemble real tissue patterns, such as brain tissue and tricuspid valve tissue. We further applied our improved architecture to three additional examples of breast cancer tissue and extended our analysis to three hyperelastic constitutive models: Neo-Hookean, Mooney Rivlin, and Gent. Our selected network architecture consistently produced highly accurate estimations of heterogeneous elasticity maps, even when there was up to 10% noise present in the training data.

math.NA↗

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

Effective Data Sampling Strategies and Boundary Condition Constraints of Physics-Informed Neural Networks for Identifying Material Properties in Solid Mechanics

Material identification is critical for understanding the relationship between mechanical properties and the associated mechanical functions. However, material identification is a challenging task, especially when the characteristic of the material is highly nonlinear in nature, as is common in biological tissue. In this work, we identify unknown material properties in continuum solid mechanics via physics-informed neural networks (PINNs). To improve the accuracy and efficiency of PINNs, we developed efficient strategies to nonuniformly sample observational data. We also investigated different approaches to enforce Dirichlet boundary conditions as soft or hard constraints. Finally, we apply the proposed methods to a diverse set of time-dependent and time-independent solid mechanic examples that span linear elastic and hyperelastic material space. The estimated material parameters achieve relative errors of less than 1%. As such, this work is relevant to diverse applications, including optimizing structural integrity and developing novel materials.

cond-mat.mtrl-sci↗

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↗

arXiv2019

Interactive-Automatic Segmentation and Modelling of the Mitral Valve

Mitral valve regurgitation is the most common valvular disease, affecting 10% of the population over 75 years old. Left untreated, patients with mitral valve regurgitation can suffer declining cardiac health until cardiac failure and death. Mitral valve repair is generally preferred over valve replacement. However, there is a direct correlation between the volume of cases performed and surgical outcomes, therefore there is a demand for the ability of surgeons to practice repairs on patient specific models in advance of surgery. This work demonstrates a semi-automated segmentation method to enable fast and accurate modelling of the mitral valve that captures patient-specific valve geometry. This modelling approach utilizes 3D active contours in a user-in-the-loop system which segments first the atrial blood pool, then the mitral leaflets. In a group of 15 mitral valve repair patients, valve segmentation and modelling attains an overall accuracy (mean absolute surface distance) of 1.40+-0.26 mm, and an accuracy of 1.01+-0.13 mm when only comparing the extracted leaflet surface proximal to the ultrasound probe. Thus this image-based segmentation tool has the potential to improve the workflow for extracting patient-specific mitral valve geometry for 3D modelling of the valve.

eess.IV↗