All Publications

  • Digital twinning of cardiac electrophysiology for congenital heart disease. bioRxiv : the preprint server for biology Salvador, M., Kong, F., Peirlinck, M., Parker, D. W., Chubb, H., Dubin, A. M., Marsden, A. L. 2023


    In recent years, blending mechanistic knowledge with machine learning has had a major impact in digital healthcare. In this work, we introduce a computational pipeline to build certified digital replicas of cardiac electrophysiology in pediatric patients with congenital heart disease. We construct the patient-specific geometry by means of semi-automatic segmentation and meshing tools. We generate a dataset of electrophysiology simulations covering cell-to-organ level model parameters and utilizing rigorous mathematical models based on differential equations. We previously proposed Branched Latent Neural Maps (BLNMs) as an accurate and efficient means to recapitulate complex physical processes in a neural network. Here, we employ BLNMs to encode the parametrized temporal dynamics of in silico 12-lead electrocardiograms (ECGs). BLNMs act as a geometry-specific surrogate model of cardiac function for fast and robust parameter estimation to match clinical ECGs in pediatric patients. Identifiability and trustworthiness of calibrated model parameters are assessed by sensitivity analysis and uncertainty quantification.

    View details for DOI 10.1101/2023.11.27.568942

    View details for PubMedID 38076810

    View details for PubMedCentralID PMC10705388

  • 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


    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

  • 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


    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

  • 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


    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

  • Neural Network Vessel Lumen Regression for Automated Lumen Cross-Section Segmentation in Cardiovascular Image-Based Modeling. Cardiovascular engineering and technology Maher, G. n., Parker, D. n., Wilson, N. n., Marsden, A. n. 2020


    We accelerate a pathline-based cardiovascular model building method by training machine learning models to directly predict vessel lumen surface points from computed tomography (CT) and magnetic resonance (MR) medical image data.We formulate vessel lumen detection as a regression task using a polar coordiantes representation.Neural networks trained with our regression formulation allow predictions to be made with significantly higher accuracy than existing methods that identify the vessel lumen through binary pixel classification. The regression formulation enables machine learning models to be trained end-to-end for vessel lumen detection without post-processing steps that reduce accuracy.By employing our models in a pathline-based cardiovascular model building pipeline we substantially reduce the manual segmentation effort required to build accurate cardiovascular models, and reduce the overall time required to perform patient-specific cardiovascular simulations. While our method is applied here for cardiovascular model building it is generally applicable to segmentation of tree-like and tubular structures from image data.

    View details for DOI 10.1007/s13239-020-00497-5

    View details for PubMedID 33179176

  • Integrated Image-Based Computational Fluid Dynamics Modeling Software as an Instructional Tool. Journal of biomechanical engineering Stevens Boster, K. n., Dong, M. n., Oakes, J. n., Bellini, C. n., Rayz, V. n., LaDisa, J. n., Parker, D. n., Wilson, N. n., Shadden, S. C., Marsden, A. n., Goergen, C. n. 2020


    Computational modeling of cardiovascular flows is becoming increasingly important in a range of biomedical applications, and understanding the fundamentals of computational modeling is important for engineering students. In addition to their purpose as research tools, integrated image-based computational fluid dynamics platforms can be used to teach the fundamental principles involved in computational modeling and generate interest in studying cardiovascular disease. We report the results of a study performed at five institutions designed to investigate the effectiveness of an integrated modeling platform as an instructional tool and describe "best practices" for using an integrated modeling platform in the classroom. Use of an integrated modeling platform as an instructional tool in nontraditional educational settings (workshops, study abroad programs, in outreach) is also discussed. Results of the study show statistically significant improvements in understanding after using the integrated modeling platform, suggesting such platforms can be effective tools for teaching fundamental cardiovascular computational modeling principles.

    View details for DOI 10.1115/1.4047479

    View details for PubMedID 32529203

  • Engineering controllable bidirectional molecular motors based on myosin NATURE NANOTECHNOLOGY Chen, L., Nakamura, M., Schindler, T. D., Parker, D., Bryant, Z. 2012; 7 (4): 252-256


    Cytoskeletal motors drive the transport of organelles and molecular cargoes within cells and have potential applications in molecular detection and diagnostic devices. Engineering molecular motors with controllable properties will allow selective perturbation of mechanical processes in living cells and provide optimized device components for tasks such as molecular sorting and directed assembly. Biological motors have previously been modified by introducing activation/deactivation switches that respond to metal ions and other signals. Here, we show that myosin motors can be engineered to reversibly change their direction of motion in response to a calcium signal. Building on previous protein engineering studies and guided by a structural model for the redirected power stroke of myosin VI, we have constructed bidirectional myosins through the rigid recombination of structural modules. The performance of the motors was confirmed using gliding filament assays and single fluorophore tracking. Our strategy, in which external signals trigger changes in the geometry and mechanics of myosin lever arms, should make it possible to achieve spatiotemporal control over a range of motor properties including processivity, stride size and branchpoint turning.

    View details for DOI 10.1038/NNANO.2012.19

    View details for Web of Science ID 000302578300012

    View details for PubMedID 22343382

    View details for PubMedCentralID PMC3332125

  • Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics CELLULAR AND MOLECULAR BIOENGINEERING Parker, D., Bryant, Z., Delp, S. L. 2009; 2 (3): 366-374


    Experimental and computational approaches are needed to uncover the mechanisms by which molecular motors convert chemical energy into mechanical work. In this article, we describe methods and software to generate structurally realistic models of molecular motor conformations compatible with experimental data from different sources. Coarse-grained models of molecular structures are constructed by combining groups of atoms into a system of rigid bodies connected by joints. Contacts between rigid bodies enforce excluded volume constraints, and spring potentials model system elasticity. This simplified representation allows the conformations of complex molecular motors to be simulated interactively, providing a tool for hypothesis building and quantitative comparisons between models and experiments. In an example calculation, we have used the software to construct atomically detailed models of the myosin V molecular motor bound to its actin track. The software is available at

    View details for DOI 10.1007/s12195-009-0084-4

    View details for Web of Science ID 000270168900010

    View details for PubMedCentralID PMC2860290

  • Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics. Cellular and molecular bioengineering Parker, D., Bryant, Z., Delp, S. L. 2009; 2 (3): 366-374


    Experimental and computational approaches are needed to uncover the mechanisms by which molecular motors convert chemical energy into mechanical work. In this article, we describe methods and software to generate structurally realistic models of molecular motor conformations compatible with experimental data from different sources. Coarse-grained models of molecular structures are constructed by combining groups of atoms into a system of rigid bodies connected by joints. Contacts between rigid bodies enforce excluded volume constraints, and spring potentials model system elasticity. This simplified representation allows the conformations of complex molecular motors to be simulated interactively, providing a tool for hypothesis building and quantitative comparisons between models and experiments. In an example calculation, we have used the software to construct atomically detailed models of the myosin V molecular motor bound to its actin track. The software is available at

    View details for DOI 10.1007/s12195-009-0084-4

    View details for PubMedID 20428469

    View details for PubMedCentralID PMC2860290

  • Morphometry-based impedance boundary conditions for patient-specific modeling of blood flow in pulmonary arteries ANNALS OF BIOMEDICAL ENGINEERING Spilker, R. L., Feinstein, J. A., Parker, D. W., Reddy, V. M., Taylor, C. A. 2007; 35 (4): 546-559


    Patient-specific computational models could aid in planning interventions to relieve pulmonary arterial stenoses common in many forms of congenital heart disease. We describe a new approach to simulate blood flow in subject-specific models of the pulmonary arteries that consists of a numerical model of the proximal pulmonary arteries created from three-dimensional medical imaging data with terminal impedance boundary conditions derived from linear wave propagation theory applied to morphometric models of distal vessels. A tuning method, employing numerical solution methods for nonlinear systems of equations, was developed to modify the distal vasculature to match measured pressure and flow distribution data. One-dimensional blood flow equations were solved with a finite element method in image-based pulmonary arterial models using prescribed inlet flow and morphometry-based impedance at the outlets. Application of these methods in a pilot study of the effect of removal of unilateral pulmonary arterial stenosis induced in a pig showed good agreement with experimental measurements for flow redistribution and main pulmonary arterial pressure. Next, these methods were applied to a patient with repaired tetralogy of Fallot and predicted insignificant hemodynamic improvement with relief of the stenosis. This method of coupling image-based and morphometry-based models could enable increased fidelity in pulmonary hemodynamic simulation.

    View details for DOI 10.1007/s10439-006-9240-3

    View details for PubMedID 17294117

  • Extending the absorbing boundary method to fit dwell-time distributions of molecular motors with complex kinetic pathways PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Liao, J., Spudich, J. A., Parker, D., Delp, S. L. 2007; 104 (9): 3171-3176


    Dwell-time distributions, waiting-time distributions, and distributions of pause durations are widely reported for molecular motors based on single-molecule biophysical experiments. These distributions provide important information concerning the functional mechanisms of enzymes and their underlying kinetic and mechanical processes. We have extended the absorbing boundary method to simulate dwell-time distributions of complex kinetic schemes, which include cyclic, branching, and reverse transitions typically observed in molecular motors. This extended absorbing boundary method allows global fitting of dwell-time distributions for enzymes subject to different experimental conditions. We applied the extended absorbing boundary method to experimental dwell-time distributions of single-headed myosin V, and were able to use a single kinetic scheme to fit dwell-time distributions observed under different ligand concentrations and different directions of optical trap forces. The ability to use a single kinetic scheme to fit dwell-time distributions arising from a variety of experimental conditions is important for identifying a mechanochemical model of a molecular motor. This efficient method can be used to study dwell-time distributions for a broad class of molecular motors, including kinesin, RNA polymerase, helicase, F(1) ATPase, and to examine conformational dynamics of other enzymes such as ion channels.

    View details for DOI 10.1073/pnas.0611519104

    View details for Web of Science ID 000244661400029

    View details for PubMedID 17360624

    View details for PubMedCentralID PMC1805548

  • Mechanobiology of mandibular distraction osteogenesis: finite element analyses with a rat model JOURNAL OF ORTHOPAEDIC RESEARCH Loboa, E. G., Fang, T. D., Parker, D. W., Warren, S. M., Fong, K. D., Longaker, M. T., Carter, D. R. 2005; 23 (3): 663-670


    Three-dimensional finite element (FE) analyses were performed to characterize the local mechanical environment created within the tissue regenerate during mandibular distraction osteogenesis (DO) in a rat model. Finite element models were created from three-dimensional computed tomography image data of rat hemi-mandibles at four different time points during an optimal distraction osteogenesis protocol (i.e., most successful protocol for bone formation): end latency (post-operative day (POD) 5), distraction day 2 (POD 7), distraction day 5 (POD 10), and distraction day 8 (POD 13). A 0.25 mm distraction was simulated and the resulting hydrostatic stresses and maximum principal tensile strains were determined within the tissue regenerate. When compared to previous histological findings, finite element analyses showed that tensile strains up to 13% corresponded to regions of new bone formation and regions of periosteal hydrostatic pressure with magnitudes less than 17 kPa corresponded to locations of cartilage formation. Tensile strains within the center of the gap were much higher, leading us to conclude that tissue damage would occur there if the tissue was not compliant enough to withstand such high strains, and that this damage would trigger formation of new mesenchymal tissue. These data were consistent with histological evidence showing mesenchymal tissue present in the center of the gap throughout distraction. Finite element analyses performed at different time points during distraction were instrumental in determining the changes in hydrostatic stress and tensile strain fields throughout distraction, providing a mechanical environment rationale for the different levels of bone formation in end latency, and distraction day 2, 5, and 8 specimens.

    View details for DOI 10.1016/j.orthres.2004.09.010

    View details for Web of Science ID 000229375000022

    View details for PubMedID 15885489

  • Time-resolved three-dimensional phase-contrast MRI 10th Annual Meeting of the International-Society-for-Magnetic-Resonance-in-Medicine (ISMRM) Markl, M., Chan, F. P., Alley, M. T., Wedding, K. L., Draney, M. T., Elkins, C. J., Parker, D. W., Wicker, R., Taylor, C. A., Herfkens, R. J., Pelc, N. J. JOHN WILEY & SONS INC. 2003: 499–506


    To demonstrate the feasibility of a four-dimensional phase contrast (PC) technique that permits spatial and temporal coverage of an entire three-dimensional volume, to quantitatively validate its accuracy against an established time resolved two-dimensional PC technique to explore advantages of the approach with regard to the four-dimensional nature of the data.Time-resolved, three-dimensional anatomical images were generated simultaneously with registered three-directional velocity vector fields. Improvements compared to prior methods include retrospectively gated and respiratory compensated image acquisition, interleaved flow encoding with freely selectable velocity encoding (venc) along each spatial direction, and flexible trade-off between temporal resolution and total acquisition time.The implementation was validated against established two-dimensional PC techniques using a well-defined phantom, and successfully applied in volunteer and patient examinations. Human studies were performed after contrast administration in order to compensate for loss of in-flow enhancement in the four-dimensional approach.Advantages of the four-dimensional approach include the complete spatial and temporal coverage of the cardiovascular region of interest and the ability to obtain high spatial resolution in all three dimensions with higher signal-to-noise ratio compared to two-dimensional methods at the same resolution. In addition, the four-dimensional nature of the data offers a variety of image processing options, such as magnitude and velocity multi-planar reformation, three-directional vector field plots, and velocity profiles mapped onto selected planes of interest.

    View details for DOI 10.1002/jmri.10272

    View details for Web of Science ID 000182453200016

    View details for PubMedID 12655592

  • Quantification of wall shear stress in large blood vessels using lagrangian interpolation functions with cine phase-contrast magnetic resonance imaging ANNALS OF BIOMEDICAL ENGINEERING Cheng, C. P., Parker, D., Taylor, C. A. 2002; 30 (8): 1020-1032


    Arterial wall shear stress is hypothesized to be an important factor in the localization of atherosclerosis. Current methods to compute wall shear stress from magnetic resonance imaging (MRI) data do not account for flow profiles characteristic of pulsatile flow in noncircular vessel lumens. We describe a method to quantify wall shear stress in large blood vessels by differentiating velocity interpolation functions defined using cine phase-contrast MRI data on a band of elements in the neighborhood of the vessel wall. Validation was performed with software phantoms and an in vitro flow phantom. At an image resolution corresponding to in vivo imaging data of the human abdominal aorta, time-averaged, spatially averaged wall shear stress for steady and pulsatile flow were determined to be within 16% and 23% of the analytic solution, respectively. These errors were reduced to 5% and 8% with doubling in image resolution. For the pulsatile software phantom, the oscillation in shear stress was predicted to within 5%. The mean absolute error of circumferentially resolved shear stress for the nonaxisymmetric phantom decreased from 28% to 15% with a doubling in image resolution. The irregularly shaped phantom and in vitro investigation demonstrated convergence of the calculated values with increased image resolution. We quantified the shear stress at the supraceliac and infrarenal regions of a human abdominal aorta to be 3.4 and 2.3 dyn/cm2, respectively.

    View details for DOI 10.1114/1.1511239

    View details for Web of Science ID 000179121200004

    View details for PubMedID 12449763

  • In vivo quantification of blood flow and wall shear stress in the human abdominal aorta during lower limb exercise ANNALS OF BIOMEDICAL ENGINEERING Taylor, C. A., Cheng, C. P., Espinosa, L. A., Tang, B. T., Parker, D., Herfkens, R. J. 2002; 30 (3): 402-408


    Magnetic resonance (MR) imaging techniques and a custom MR-compatible exercise bicycle were used to measure, in vivo, the effects of exercise on hemodynamic conditions in the abdominal aorta of eleven young, healthy subjects. Heart rate increased from 73 +/- 6.2 beats/min at rest to 110 +/- 8.8 beats/min during exercise (p<0.0001). The total blood flow through the abdominal aorta increased from 2.9 +/- 0.6 L/min at rest to 7.2 +/- 1.4 L/min during exercise (p <0.0005) while blood flow to the digestive and renal circulations decreased from 2.1 +/- 0.5 L/min at rest to 1.6 +/- 0.7 L/min during exercise (p<0.01). Infrarenal blood flow increased from 0.9 +/- 0.4 L/min at rest to 5.6 +/- 1.1 L/min during exercise (p<0.0005). Wall shear stress increased in the supraceliac aorta from 3.5 +/- 0.8 dyn/cm2 at rest to 6.2 +/- 0.5 dyn/cm2 during exercise (p<0.0005) and increased in the infrarenal aorta from 1.3 +/- 0.8 dyn/cm2 at rest to 5.2 +/- 1.3 dyn/cm2 during exercise (p<0.0005).

    View details for DOI 10.1114/1.1476016

    View details for Web of Science ID 000175849500012

    View details for PubMedID 12051624

  • Predictive medicine: computational techniques in therapeutic decision-making. Computer aided surgery Taylor, C. A., Draney, M. T., Ku, J. P., Parker, D., Steele, B. N., Wang, K., Zarins, C. K. 1999; 4 (5): 231-247


    The current paradigm for surgery planning for the treatment of cardiovascular disease relies exclusively on diagnostic imaging data to define the present state of the patient, empirical data to evaluate the efficacy of prior treatments for similar patients, and the judgement of the surgeon to decide on a preferred treatment. The individual variability and inherent complexity of human biological systems is such that diagnostic imaging and empirical data alone are insufficient to predict the outcome of a given treatment for an individual patient. We propose a new paradigm of predictive medicine in which the physician utilizes computational tools to construct and evaluate a combined anatomic/physiologic model to predict the outcome of alternative treatment plans for an individual patient. The predictive medicine paradigm is implemented in a software system developed for Simulation-Based Medical Planning. This system provides an integrated set of tools to test hypotheses regarding the effect of alternate treatment plans on blood flow in the cardiovascular system of an individual patient. It combines an Internet-based user interface developed using Java and VRML, image segmentation, geometric solid modeling, automatic finite element mesh generation, computational fluid dynamics, and scientific visualization techniques. This system is applied to the evaluation of alternate, patient-specific treatments for a case of lower extremity occlusive cardiovascular disease.

    View details for PubMedID 10581521

  • Image based geometric modeling of the human vasculature in computational hemodynamics ASME Summer Bioengineering Meeting Parker, D., Wang, K., Taylor, C. ASME. 1999
  • Imaged based 3D solid model construction of human arteries for blood flow simulations Parker, D., Taylor, C. A., Wang, K., Chang, H. K., Zhang, Y. T. IEEE. 1998: 998–1001
  • Level set methods and MR image segmentation for geometric modeling in computational hemodynamics Wang, K. C., Taylor, C. A., Hsiau, Z., Parker, D., Dutton, R. W., Chang, H. K., Zhang, Y. T. IEEE. 1998: 3079–82