All Publications


  • Virtual shape-editing of patient-specific vascular models using Regularized Kelvinlets. IEEE transactions on bio-medical engineering Pham, J., Kong, F., James, D. L., Marsden, A. L. 2024; PP

    Abstract

    OBJECTIVE: Cardiovascular diseases, and the interventions performed to treat them, can lead to changes in the shape of patient vasculatures and their hemodynamics. Computational modeling and simulations of patient-specific vascular networks are increasingly used to quantify these hemodynamic changes, but they require modifying the shapes of the models. Existing methods to modify these shapes include editing 2D lumen contours prescribed along vessel centerlines and deforming meshes with geometry-based approaches. However, these methods can require extensive by-hand prescription of the desired shapes and often do not work robustly across a range of vascular anatomies. To overcome these limitations, we develop techniques to modify vascular models using physics-based principles that can automatically generate smooth deformations and readily apply them across different vascular anatomies.METHODS: We adapt Regularized Kelvinlets, analytical solutions to linear elastostatics, to perform elastic shape-editing of vascular models. The Kelvinlets are packaged into three methods that allow us to artificially create aneurysms, stenoses, and tortuosity.RESULTS: Our methods are able to generate such geometric changes across a wide range of vascular anatomies. We demonstrate their capabilities by creating sets of aneurysms, stenoses, and tortuosities with varying shapes and sizes on multiple patient-specific models.CONCLUSION: Our Kelvinlet-based deformers allow us to edit the shape of vascular models, regardless of their anatomical locations, and parametrically vary the size of the geometric changes.SIGNIFICANCE: These methods will enable researchers to more easily perform virtual-surgery-like deformations, computationally explore the impact of vascular shape on patient hemodynamics, and generate synthetic geometries for data-driven research.

    View details for DOI 10.1109/TBME.2024.3355307

    View details for PubMedID 38300772

  • Rapid model-guided design of organ-scale synthetic vasculature for biomanufacturing. ArXiv Sexton, Z. A., Hudson, A. R., Herrmann, J. E., Shiwarski, D. J., Pham, J., Szafron, J. M., Wu, S. M., Skylar-Scott, M., Feinberg, A. W., Marsden, A. 2023

    Abstract

    Our ability to produce human-scale bio-manufactured organs is critically limited by the need for vascularization and perfusion. For tissues of variable size and shape, including arbitrarily complex geometries, designing and printing vasculature capable of adequate perfusion has posed a major hurdle. Here, we introduce a model-driven design pipeline combining accelerated optimization methods for fast synthetic vascular tree generation and computational hemodynamics models. We demonstrate rapid generation, simulation, and 3D printing of synthetic vasculature in complex geometries, from small tissue constructs to organ scale networks. We introduce key algorithmic advances that all together accelerate synthetic vascular generation by more than 230 -fold compared to standard methods and enable their use in arbitrarily complex shapes through localized implicit functions. Furthermore, we provide techniques for joining vascular trees into watertight networks suitable for hemodynamic CFD and 3D fabrication. We demonstrate that organ-scale vascular network models can be generated in silico within minutes and can be used to perfuse engineered and anatomic models including a bioreactor, annulus, bi-ventricular heart, and gyrus. We further show that this flexible pipeline can be applied to two common modes of bioprinting with free-form reversible embedding of suspended hydrogels and writing into soft matter. Our synthetic vascular tree generation pipeline enables rapid, scalable vascular model generation and fluid analysis for bio-manufactured tissues necessary for future scale up and production.

    View details for PubMedID 37645046

    View details for PubMedCentralID PMC10462165

  • svMorph: Interactive Geometry-Editing Tools for Virtual Patient-Specific Vascular Anatomies. Journal of biomechanical engineering Pham, J., Wyetzner, S., Pfaller, M., Parker, D., James, D., Marsden, A. 2022

    Abstract

    We propose svMorph, a framework for interactive virtual sculpting of patient-specific vascular anatomic models. Our framework includes three tools for the creation of tortuosity, aneurysms, and stenoses in tubular vascular geometries. These shape edits are performed via geometric operations on the surface mesh and vessel centerline curves of the input model. The tortuosity tool also uses the physics-based Oriented Particles method, coupled with linear blend skinning, to achieve smooth, elastic-like deformations. Our tools can be applied separately or in combination to produce simulation-suitable morphed models. They are also compatible with popular vascular modeling software, such as SimVascular. To illustrate our tools, we morph several image-based, patient-specific models to create a range of shape changes and simulate the resulting hemodynamics via three-dimensional, computational fluid dynamics. We also demonstrate the ability to quickly estimate the hemodynamic effects of the shape changes via automated generation of associated zero-dimensional lumped-parameter models.

    View details for DOI 10.1115/1.4056055

    View details for PubMedID 36282508

  • Framework for patient-specific simulation of hemodynamics in heart failure with counterpulsation support. Frontiers in cardiovascular medicine Arduini, M., Pham, J., Marsden, A. L., Chen, I. Y., Ennis, D. B., Dual, S. A. 2022; 9: 895291

    Abstract

    Despite being responsible for half of heart failure-related hospitalizations, heart failure with preserved ejection fraction (HFpEF) has limited evidence-based treatment options. Currently, a substantial clinical issue is that the disease etiology is very heterogenous with no patient-specific treatment options. Modeling can provide a framework for evaluating alternative treatment strategies. Counterpulsation strategies have the capacity to improve left ventricular diastolic filling by reducing systolic blood pressure and augmenting the diastolic pressure that drives coronary perfusion. Here, we propose a framework for testing the effectiveness of a soft robotic extra-aortic counterpulsation strategy using a patient-specific closed-loop hemodynamic lumped parameter model of a patient with HFpEF. The soft robotic device prototype was characterized experimentally in a physiologically pressurized (50-150 mmHg) soft silicone vessel and modeled as a combination of a pressure source and a capacitance. The patient-specific model was created using open-source software and validated against hemodynamics obtained by imaging of a patient (male, 87 years, HR = 60 bpm) with HFpEF. The impact of actuation timing on the flows and pressures as well as systolic function was analyzed. Good agreement between the patient-specific model and patient data was achieved with relative errors below 5% in all categories except for the diastolic aortic root pressure and the end systolic volume. The most effective reduction in systolic pressure compared to baseline (147 vs. 141 mmHg) was achieved when actuating 350 ms before systole. In this case, flow splits were preserved, and cardiac output was increased (5.17 vs. 5.34 L/min), resulting in increased blood flow to the coronaries (0.15 vs. 0.16 L/min). Both arterial elastance (0.77 vs. 0.74 mmHg/mL) and stroke work (11.8 vs. 10.6 kJ) were decreased compared to baseline, however left atrial pressure increased (11.2 vs. 11.5 mmHg). A higher actuation pressure is associated with higher systolic pressure reduction and slightly higher coronary flow. The soft robotic device prototype achieves reduced systolic pressure, reduced stroke work, slightly increased coronary perfusion, but increased left atrial pressures in HFpEF patients. In future work, the framework could include additional physiological mechanisms, a larger patient cohort with HFpEF, and testing against clinically used devices.

    View details for DOI 10.3389/fcvm.2022.895291

    View details for PubMedID 35979018

    View details for PubMedCentralID PMC9376255

  • Automated generation of 0D and 1D reduced-order models of patient-specific blood flow. International journal for numerical methods in biomedical engineering Pfaller, M. R., Pham, J., Verma, A., Pegolotti, L., Wilson, N. M., Parker, D. W., Yang, W., Marsden, A. L. 2022: e3639

    Abstract

    Three-dimensional (3D) cardiovascular fluid dynamics simulations typically require hours to days of computing time on a high-performance computing cluster. One-dimensional (1D) and lumped-parameter zero-dimensional (0D) models show great promise for accurately predicting blood bulk flow and pressure waveforms with only a fraction of the cost. They can also accelerate uncertainty quantification, optimization, and design parameterization studies. Despite several prior studies generating 1D and 0D models and comparing them to 3D solutions, these were typically limited to either 1D or 0D and a singular category of vascular anatomies. This work proposes a fully automated and openly available framework to generate and simulate 1D and 0D models from 3D patient-specific geometries, automatically detecting vessel junctions and stenosis segments. Our only input is the 3D geometry; we do not use any prior knowledge from 3D simulations. All computational tools presented in this work are implemented in the open-source software platform SimVascular. We demonstrate the reduced-order approximation quality against rigid-wall 3D solutions in a comprehensive comparison with N=72 publicly available models from various anatomies, vessel types, and disease conditions. Relative average approximation errors of flows and pressures typically ranged from 1% to 10% for both 1D and 0D models, measured at the outlets of terminal vessel branches. In general, 0D model errors were only slightly higher than 1D model errors despite requiring only a third of the 1D runtime. Automatically generated ROMs can significantly speed up model development and shift the computational load from high-performance machines to personal computers. This article is protected by copyright. All rights reserved.

    View details for DOI 10.1002/cnm.3639

    View details for PubMedID 35875875

  • Elucidating tricuspid Doppler signal interpolation and its implication for assessing pulmonary hypertension PULMONARY CIRCULATION Dual, S. A., Verdonk, C., Amsallem, M., Pham, J., Obasohan, C., Nataf, P., McElhinney, D. B., Arunamata, A., Kuznetsova, T., Zamanian, R., Feinstein, J. A., Marsden, A., Haddad, F. 2022; 12 (3): e12125

    Abstract

    Doppler echocardiography plays a central role in the assessment of pulmonary hypertension (PAH). We aim to improve quality assessment of systolic pulmonary arterial pressure (SPAP) by applying a cubic polynomial interpolation to digitized tricuspid regurgitation (TR) waveforms. Patients with PAH and advanced lung disease were divided into three cohorts: a derivation cohort (n = 44), a validation cohort (n = 71), an outlier cohort (n = 26), and a non-PAH cohort (n = 44). We digitized TR waveforms and analyzed normalized duration, skewness, kurtosis, and first and second derivatives of pressure. Cubic polynomial interpolation was applied to three physiology-driven phases: the isovolumic phase, ejection phase, and "shoulder" point phase. Coefficients of determination and a Bland-Altman analysis was used to assess bias between methods. The cubic polynomial interpolation of the TR waveform correlated strongly with expert read right ventricular systolic pressure (RVSP) with R 2 > 0.910 in the validation cohort. The biases when compared to invasive SPAP measured within 24 h were 6.03 [4.33; 7.73], -2.94 [1.47; 4.41], and -3.11 [-4.52; -1.71] mmHg, for isovolumic, ejection, and shoulder point interpolations, respectively. In the outlier cohort with more than 30% difference between echocardiographic estimates and invasive SPAP, cubic polynomial interpolation significantly reduced underestimation of RVSP. Cubic polynomial interpolation of the TR waveform based on isovolumic or early ejection phase may improve RVSP estimates.

    View details for DOI 10.1002/pul2.12125

    View details for Web of Science ID 000843054900001

    View details for PubMedID 36016669

    View details for PubMedCentralID PMC9395694

  • On the Periodicity of Cardiovascular Fluid Dynamics Simulations. Annals of biomedical engineering Pfaller, M. R., Pham, J., Wilson, N. M., Parker, D. W., Marsden, A. L. 2021

    Abstract

    Three-dimensional cardiovascular fluid dynamics simulations typically require computation of several cardiac cycles before they reach a periodic solution, rendering them computationally expensive. Furthermore, there is currently no standardized method to determine whether a simulation has yet reached that periodic state. In this work, we propose the use of an asymptotic error measurement to quantify the difference between simulation results and their ideal periodic state using open-loop lumped-parameter modeling. We further show that initial conditions are crucial in reducing computational time and develop an automated framework to generate appropriate initial conditions from a one-dimensional model of blood flow. We demonstrate the performance of our initialization method using six patient-specific models from the Vascular Model Repository. In our examples, our initialization protocol achieves periodic convergence within one or two cardiac cycles, leading to a significant reduction in computational cost compared to standard methods. All computational tools used in this work are implemented in the open-source software platform SimVascular. Automatically generated initial conditions have the potential to significantly reduce computation time in cardiovascular fluid dynamics simulations.

    View details for DOI 10.1007/s10439-021-02796-x

    View details for PubMedID 34169398