Scholars@Duke
Amanda Randles

Amanda Randles

Alfred Winborne and Victoria Stover Mordecai Associate Professor of Biomedical Sciences
Biomedical Engineering
amanda.randles@duke.edu
Box 90281, Durham, NC 27708
Wilkinson Building, Room No. 325, 534 Research Drive, Durham, NC 27708

Selected Publications

Modeling the effect of patient size on cerebral perfusion during veno-arterial extracorporeal membrane oxygenation.

Journal Article Perfusion · October 2024 INTRODUCTION: A well-known complication of veno-arterial extracorporeal membrane oxygenation (VA ECMO) is differential hypoxia, in which poorly-oxygenated blood ejected from the left ventricle mixes with and displaces well-oxygenated blood from the circuit ... Full text Link to item Cite

Establishing the longitudinal hemodynamic mapping framework for wearable-driven coronary digital twins.

Journal Article NPJ digital medicine · September 2024 Understanding the evolving nature of coronary hemodynamics is crucial for early disease detection and monitoring progression. We require digital twins that mimic a patient's circulatory system by integrating continuous physiological data and computing hemo ... Full text Open Access Cite

Surgical Modulation of Pulmonary Artery Shear Stress: A Patient-Specific CFD Analysis of the Norwood Procedure.

Journal Article Cardiovasc Eng Technol · August 2024 PURPOSR: This study created 3D CFD models of the Norwood procedure for hypoplastic left heart syndrome (HLHS) using standard angiography and echocardiogram data to investigate the impact of shunt characteristics on pulmonary artery (PA) hemodynamics. Lever ... Full text Link to item Cite

Diagnostic Performance of Coronary Angiography Derived Computational Fractional Flow Reserve.

Journal Article J Am Heart Assoc · July 2, 2024 BACKGROUND: Computational fluid dynamics can compute fractional flow reserve (FFR) accurately. However, existing models are limited by either the intravascular hemodynamic phenomarkers that can be captured or the fidelity of geometries that can be modeled. ... Full text Open Access Link to item Cite

Optimizing Temporal Waveform Analysis: A Novel Pipeline for Efficient Characterization of Left Coronary Artery Velocity Profiles.

Journal Article ArXiv · February 15, 2024 Continuously measured arterial blood velocity can provide insight into physiological parameters and potential disease states. The efficient and effective description of the temporal profiles of arterial velocity is crucial for both clinical practice and re ... Link to item Cite

Investigating the Influence of Heterogeneity Within Cell Types on Microvessel Network Transport.

Journal Article Cellular and molecular bioengineering · December 2023 BackgroundCurrent research on the biophysics of circulating tumor cells often overlooks the heterogeneity of cell populations, focusing instead on average cellular properties. This study aims to address the gap by considering the diversity of cell ... Full text Open Access Cite

Performance Evaluation of Heterogeneous GPU Programming Frameworks for Hemodynamic Simulations

Conference ACM International Conference Proceeding Series · November 12, 2023 Preparing for the deployment of large scientific and engineering codes on upcoming exascale systems with GPU-dense nodes is made challenging by the unprecedented diversity of device architectures and heterogeneous programming models. In this work, we evalu ... Full text Open Access Cite

Moment Representation of Regularized Lattice Boltzmann Methods on NVIDIA and AMD GPUs

Conference ACM International Conference Proceeding Series · November 12, 2023 The lattice Boltzmann method is a highly scalable Navier-Stokes solver that has been applied to flow problems in a wide array of domains. However, the method is bandwidth-bound on modern GPU accelerators and has a large memory footprint. In this paper, we ... Full text Cite

Cloud Computing to Enable Wearable-Driven Longitudinal Hemodynamic Maps.

Conference International Conference for High Performance Computing, Networking, Storage and Analysis : [proceedings]. SC (Conference : Supercomputing) · November 2023 Tracking hemodynamic responses to treatment and stimuli over long periods remains a grand challenge. Moving from established single-heartbeat technology to longitudinal profiles would require continuous data describing how the patient's state evolves, new ... Full text Cite

Enhancing Adaptive Physics Refinement Simulations Through the Addition of Realistic Red Blood Cell Counts.

Conference International Conference for High Performance Computing, Networking, Storage and Analysis : [proceedings]. SC (Conference : Supercomputing) · November 2023 Simulations of cancer cell transport require accurately modeling mm-scale and longer trajectories through a circulatory system containing trillions of deformable red blood cells, whose intercellular interactions require submicron fidelity. Using a hybrid C ... Full text Cite

Low-Cost Post Hoc Reconstruction of HPC Simulations at Full Resolution

Journal Article 2023 IEEE 13th Symposium on Large Data Analysis and Visualization (LDAV) · October 23, 2023 Full text Open Access Cite

Establishing metrics to quantify spatial similarity in spherical and red blood cell distributions

Journal Article Journal of Computational Science · July 1, 2023 As computational power increases and systems with millions of red blood cells can be simulated, it is important to note that varying spatial distributions of cells may affect simulation outcomes. Since a single simulation may not represent the ensemble beh ... Full text Cite

Establishing massively parallel models to examine the influence of cell heterogeneity on tumor growth

Journal Article Journal of Computational Science · July 1, 2023 Parallel 3D cellular automaton models of tumor growth can efficiently capture emergent morphology. We extended a 2D growth model to 3D to examine the influence of symmetric division in heterogeneous tumors on growth dynamics. As extending to 3D severely in ... Full text Cite

The Role of Immersion for Improving Extended Reality Analysis of Personalized Flow Simulations.

Journal Article Cardiovascular engineering and technology · April 2023 PurposeComputational models of flow in patient-derived arterial geometries have become a key paradigm of biomedical research. These fluid models are often challenging to visualize due to high spatial heterogeneity and visual complexity. Virtual im ... Full text Cite

Effect of constitutive law on the erythrocyte membrane response to large strains.

Journal Article Computers & mathematics with applications (Oxford, England : 1987) · February 2023 Three constitutive laws, that is the Skalak, neo-Hookean and Yeoh laws, commonly employed for describing the erythrocyte membrane mechanics are theoretically analyzed and numerically investigated to assess their accuracy for capturing erythrocyte deformati ... Full text Cite

Optimizing Cloud Computing Resource Usage for Hemodynamic Simulation

Conference Proceedings - 2023 IEEE International Parallel and Distributed Processing Symposium, IPDPS 2023 · January 1, 2023 Cloud computing resources are becoming an increasingly attractive option for simulation workflows but require users to assess a wider variety of hardware options and associated costs than required by traditional in-house hardware or fixed allocations at le ... Full text Cite

Distributed Acceleration of Adhesive Dynamics Simulations.

Conference Proceedings of 2022 29th European MPI Users' Group Meeting (EuroMPI/USA'2022) : September 26-28, 2022, Chattanooga, TN. European MPI Users' Group Meeting (29th : 2022 : Chattanooga, Tenn.) · September 2022 Cell adhesion plays a critical role in processes ranging from leukocyte migration to cancer cell transport during metastasis. Adhesive cell interactions can occur over large distances in microvessel networks with cells traveling over distances much greater ... Full text Cite

High Performance Adaptive Physics Refinement to Enable Large-Scale Tracking of Cancer Cell Trajectory.

Conference Proceedings. IEEE International Conference on Cluster Computing · September 2022 The ability to track simulated cancer cells through the circulatory system, important for developing a mechanistic understanding of metastatic spread, pushes the limits of today's supercomputers by requiring the simulation of large fluid volumes at cellula ... Full text Cite

The role of adhesive receptor patterns on cell transport in complex microvessels.

Journal Article Biomechanics and modeling in mechanobiology · August 2022 Cell transport is governed by the interaction of fluid dynamic forces and biochemical factors such as adhesion receptor expression and concentration. Although the effect of endothelial receptor density is well understood, it is not clear how the spacing an ... Full text Cite

Propagation pattern for moment representation of the lattice Boltzmann method.

Journal Article IEEE transactions on parallel and distributed systems : a publication of the IEEE Computer Society · March 2022 A propagation pattern for the moment representation of the regularized lattice Boltzmann method (LBM) in three dimensions is presented. Using effectively lossless compression, the simulation state is stored as a set of moments of the lattice Boltzmann dist ... Full text Cite

Characterization of hemodynamics in anomalous aortic origin of coronary arteries using patient-specific modeling.

Journal Article J Biomech · February 2022 The anomalous aortic origin of coronary arteries (AAOCA) is a congenital disease that can lead to sudden cardiac death (SCD) during strenuous physical activity. Despite AAOCA being the second leading cause of SCD among young athletes, the mechanism behind ... Full text Link to item Cite

Evaluation of U-Net Based Architectures for Automatic Aortic Dissection Segmentation

Journal Article ACM Transactions on Computing for Healthcare · January 1, 2022 Segmentation and reconstruction of arteries is important for a variety of medical and engineering fields, such as surgical planning and physiological modeling. However, manual methods can be laborious and subject to a high degree of human variability. In t ... Full text Cite

Patient- and Ventilator-Specific Modeling to Drive the Use and Development of 3D Printed Devices for Rapid Ventilator Splitting During the COVID-19 Pandemic

Conference Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) · January 1, 2022 In the early days of the COVID-19 pandemic, there was a pressing need for an expansion of the ventilator capacity in response to the COVID19 pandemic. Reserved for dire situations, ventilator splitting is complex, and has previously been limited to patient ... Full text Cite

Developing a Scalable Cellular Automaton Model of 3D Tumor Growth

Conference Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) · January 1, 2022 Parallel three-dimensional (3D) cellular automaton models of tumor growth can efficiently model tumor morphology over many length and time scales. Here, we extended an existing two-dimensional (2D) model of tumor growth to study how tumor morphology could ... Full text Cite

Establishing Metrics to Quantify Underlying Structure in Vascular Red Blood Cell Distributions

Conference Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) · January 1, 2022 Simulations of the microvasculature can elucidate the effects of various blood flow parameters on micro-scale cellular and fluid phenomena. At this scale, the non-Newtonian behavior of blood requires the use of explicit cell models, which are necessary for ... Full text Cite

Analysis identifying minimal governing parameters for clinically accurate in silico fractional flow reserve.

Journal Article Frontiers in medical technology · January 2022 BackgroundPersonalized hemodynamic models can accurately compute fractional flow reserve (FFR) from coronary angiograms and clinical measurements (FFR baseline ), but obtaining patient-specific data could be challenging and sometimes not feasi ... Full text Cite

The role of extended reality for planning coronary artery bypass graft surgery

Conference Proceedings - 2022 IEEE Visualization Conference - Short Papers, VIS 2022 · January 1, 2022 Immersive visual displays are becoming more common in the diagnostic imaging and pre-procedural planning of complex cardiology revascularization surgeries. One such procedure is coronary artery bypass grafting (CABG) surgery, which is a gold standard treat ... Full text Cite

DEVELOPING A DIGITAL TWIN FOR SINGLE-CELL MECHANICAL PHENOTYPING MICROFLUIDIC DEVICES

Conference MicroTAS 2022 - 26th International Conference on Miniaturized Systems for Chemistry and Life Sciences · January 1, 2022 Microfluidics can be used to characterize individual cells in a population based on their mechanical traits. In this work, we digitally replicate the microfluidic device developed by Li et al. [1] and perform simulations of a representative AP-1060 cell. W ... Cite

Evaluation of intracoronary hemodynamics identifies perturbations in vorticity

Journal Article Frontiers in Systems Biology · January 1, 2022 Background and objective: Coronary artery disease (CAD) is highly prevalent and associated with adverse events. Challenges have emerged in the treatment of intermediate coronary artery stenoses. These lesions are often interrogated with fractional flow res ... Full text Open Access Cite

Moments-based method for boundary conditions in the lattice Boltzmann framework: A comparative analysis for the lid driven cavity flow

Journal Article Computers and Fluids · November 15, 2021 Dealing with boundary conditions (BC) was ever considered a puzzling question in the lattice Boltzmann (LB) method. The most popular BC models are based on Ad-Hoc rules and, although these BC models were shown to be suitable for low-order LB equations, the ... Full text Cite

An Interpretable Machine Learning Model to Classify Coronary Bifurcation Lesions.

Journal Article Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · November 2021 Coronary bifurcation lesions are a leading cause of Coronary Artery Disease (CAD). Despite its prevalence, coronary bifurcation lesions remain difficult to treat due to our incomplete understanding of how various features of lesion anatomy synergistically ... Full text Cite

Global Sensitivity Analysis For Clinically Validated 1D Models of Fractional Flow Reserve.

Journal Article Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · November 2021 Computation of Fractional Flow Reserve (FFR) through computational fluid dynamics (CFD) is used to guide intervention and often uses a number of clinically-derived metrics, but these patient-specific data could be costly and difficult to obtain. Understand ... Full text Cite

Analysis of GPU Data Access Patterns on Complex Geometries for the D3Q19 Lattice Boltzmann Algorithm

Journal Article IEEE Transactions on Parallel and Distributed Systems · October 1, 2021 GPU performance of the lattice Boltzmann method (LBM) depends heavily on memory access patterns. When implemented with GPUs on complex domains, typically, geometric data is accessed indirectly and lattice data is accessed lexicographically. Although there ... Full text Cite

Computational models of cancer cell transport through the microcirculation.

Journal Article Biomechanics and modeling in mechanobiology · August 2021 The transport of cancerous cells through the microcirculation during metastatic spread encompasses several interdependent steps that are not fully understood. Computational models which resolve the cellular-scale dynamics of complex microcirculatory flows ... Full text Cite

A data-driven approach to modeling cancer cell mechanics during microcirculatory transport.

Journal Article Scientific reports · July 2021 In order to understand the effect of cellular level features on the transport of circulating cancer cells in the microcirculation, there has been an increasing reliance on high-resolution in silico models. Accurate simulation of cancer cells flowing with b ... Full text Cite

Non-invasive characterization of complex coronary lesions.

Journal Article Scientific reports · April 2021 Conventional invasive diagnostic imaging techniques do not adequately resolve complex Type B and C coronary lesions, which present unique challenges, require personalized treatment and result in worsened patient outcomes. These lesions are often excluded f ... Full text Cite

Computational modelling of perivascular-niche dynamics for the optimization of treatment schedules for glioblastoma.

Journal Article Nature biomedical engineering · April 2021 Glioblastoma stem-like cells dynamically transition between a chemoradiation-resistant state and a chemoradiation-sensitive state. However, physical barriers in the tumour microenvironment restrict the delivery of chemotherapy to tumour compartments that a ... Full text Cite

Application of physics-based flow models in cardiovascular medicine: Current practices and challenges.

Journal Article Biophysics reviews · March 2021 Personalized physics-based flow models are becoming increasingly important in cardiovascular medicine. They are a powerful complement to traditional methods of clinical decision-making and offer a wealth of physiological information beyond conventional ana ... Full text Cite

Multiscale modeling of blood flow to assess neurological complications in patients supported by venoarterial extracorporeal membrane oxygenation.

Journal Article Computers in biology and medicine · February 2021 Computational blood flow models in large arteries elucidate valuable relationships between cardiovascular diseases and hemodynamics, leading to improvements in treatment planning and clinical decision making. One such application with potential to benefit ... Full text Cite

Predicting aneurysmal degeneration of type B aortic dissection with computational fluid dynamics

Conference Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2021 · January 18, 2021 Stanford Type B aortic dissection (TBAD) is a deadly cardiovascular disease with mortality rates as high as 50% in complicated cases. Patients with TBAD are often medically managed, but in ∼20-40% of cases, patients experience aneurysmal degeneration in th ... Full text Cite

DOE Computational Science Graduate Fellowship Research Showcase

Journal Article Computing in Science and Engineering · January 1, 2021 Full text Cite

Cloud Computing for COVID-19: Lessons Learned From Massively Parallel Models of Ventilator Splitting.

Journal Article Computing in science & engineering · November 2020 A patient-specific airflow simulation was developed to help address the pressing need for an expansion of the ventilator capacity in response to the COVID-19 pandemic. The computational model provides guidance regarding how to split a ventilator between tw ... Full text Cite

Three-dimensional bioprinting of aneurysm-bearing tissue structure for endovascular deployment of embolization coils.

Journal Article Biofabrication · October 2020 Various types of embolization devices have been developed for the treatment of cerebral aneurysms. However, it is challenging to properly evaluate device performance and train medical personnel for device deployment without the aid of functionally relevant ... Full text Cite

Investigating the Interaction Between Circulating Tumor Cells and Local Hydrodynamics via Experiment and Simulations.

Journal Article Cellular and molecular bioengineering · October 2020 IntroductionThe biological and mechanical properties of circulating tumor cells (CTCs) in combination with the hemodynamics affect the preference of metastatic sites in the vasculature. Despite the extensive literature on the effects of biological ... Full text Cite

Rapid Ventilator Splitting During COVID-19 Pandemic Using 3D Printed Devices and Numerical Modeling of 200 Million Patient Specific Air Flow Scenarios.

Journal Article Res Sq · August 12, 2020 There has been a pressing need for an expansion of the ventilator capacity in response to the recent COVID19 pandemic. To address this need, we present a system to enable rapid and efficacious splitting between two or more patients with varying lung compli ... Full text Link to item Cite

Examining metastatic behavior within 3D bioprinted vasculature for the validation of a 3D computational flow model.

Journal Article Science advances · August 2020 Understanding the dynamics of circulating tumor cell (CTC) behavior within the vasculature has remained an elusive goal in cancer biology. To elucidate the contribution of hydrodynamics in determining sites of CTC vascular colonization, the physical forces ... Full text Cite

Balloon-Mounted Stents for Treatment of Refractory Flow Diverting Device Wall Malapposition.

Journal Article Operative neurosurgery (Hagerstown, Md.) · July 2020 BackgroundAs indications for flow diversion (FD) have expanded, new challenges in deployment of flow diverting devices (FDDs) have been encountered. We present 4 cases with aneurysms in which deployment of FDDs were complicated by device malapposi ... Full text Cite

Multi-GPU Immersed Boundary Method Hemodynamics Simulations.

Journal Article Journal of computational science · July 2020 Large-scale simulations of blood flow that resolve the 3D deformation of each comprising cell are increasingly popular owing to algorithmic developments in conjunction with advances in compute capability. Among different approaches for modeling cell-resolv ... Full text Cite

Computational Framework to Evaluate the Hydrodynamics of Cell Scaffold Geometries.

Conference Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · July 2020 The fluid dynamics of microporous materials are important to many biomedical processes such as cell deposition in scaffold materials, tissue engineering, and bioreactors. Microporous scaffolds are frequently composed of suspensions of beads that have varyi ... Full text Cite

Evaluating the Influence of Hemorheological Parameters on Circulating Tumor Cell Trajectory and Simulation Time

Conference Proceedings of the Platform for Advanced Scientific Computing Conference, PASC 2020 · June 29, 2020 Extravasation of circulating tumor cells (CTCs) occurs primarily in the microvasculature, where flow and cell interactions significantly affect the blood rheology. Capturing cell trajectory at this scale requires the coupling of several interaction models, ... Full text Cite

Accelerating massively parallel hemodynamic models of coarctation of the aorta using neural networks.

Journal Article Scientific reports · June 2020 Comorbidities such as anemia or hypertension and physiological factors related to exertion can influence a patient's hemodynamics and increase the severity of many cardiovascular diseases. Observing and quantifying associations between these factors and he ... Full text Cite

Determining the impacts of venoarterial extracorporeal membrane oxygenation on cerebral oxygenation using a one-dimensional blood flow simulator.

Journal Article Journal of biomechanics · May 2020 Venoarterial extracorporeal membrane oxygenation (VA-ECMO) is a mechanical system that provides rapid and short-term support for patients with cardiac failure. In many patients, pulmonary function is also impaired, resulting in poorly-oxygenated cardiac ou ... Full text Cite

Harvis: an interactive virtual reality tool for hemodynamic modification and simulation

Journal Article Journal of Computational Science · May 1, 2020 Cardiovascular disease (CVD) affects more than 90 million adults in the United States. In recent years, computational hemodynamic models have helped improve our understanding of CVD progression; however, such research workflows can be challenging and unint ... Full text Cite

Localization of Rolling and Firm-Adhesive Interactions Between Circulating Tumor Cells and the Microvasculature Wall.

Journal Article Cellular and molecular bioengineering · April 2020 IntroductionThe adhesion of tumor cells to vessel wall is a critical stage in cancer metastasis. Firm adhesion of cancer cells is usually followed by their extravasation through the endothelium. Despite previous studies identifying the influential ... Full text Cite

Moment representation in the lattice Boltzmann method on massively parallel hardware

Conference International Conference for High Performance Computing, Networking, Storage and Analysis, SC · November 17, 2019 The widely-used lattice Boltzmann method (LBM) for computational fluid dynamics is highly scalable, but also significantly memory bandwidth-bound on current architectures. This paper presents a new regularized LBM implementation that reduces the memory foo ... Full text Cite

Low-Overhead in Situ Visualization Using Halo Replay

Conference 2019 IEEE 9th Symposium on Large Data Analysis and Visualization, LDAV 2019 · October 1, 2019 In situ visualization and analysis is of increasing importance as the compute and I/O gap further widens with the advance to exascale capable computing. Yet, in situ methods impose resource constraints leading to the difficult task of balancing simulation ... Full text Cite

Multi-physics simulations of particle tracking in arterial geometries with a scalable moving window algorithm

Conference Proceedings - IEEE International Conference on Cluster Computing, ICCC · September 1, 2019 In arterial systems, cancer cell trajectories determine metastatic cancer locations; similarly, particle trajectories determine drug delivery distribution. Predicting trajectories is challenging, as the dynamics are affected by local interactions with red ... Full text Cite

Projection of Temperature-Related Myocardial Infarction in Augsburg, Germany: Moving on From the Paris Agreement on Climate Change.

Journal Article Deutsches Arzteblatt international · August 2019 BackgroundSubstantial efforts are required to limit global warming to under 2 °C, with 1.5 °C as the target (Paris Agreement goal). We set out to project future temperature-related myocardial infarction (MI) events in Augsburg, Germany, at increas ... Full text Cite

Performance portability study for massively parallel computational fluid dynamics application on scalable heterogeneous architectures

Journal Article Journal of Parallel and Distributed Computing · July 1, 2019 Patient-specific hemodynamic simulations have the potential to greatly improve both the diagnosis and treatment of a variety of vascular diseases. Portability will enable wider adoption of computational fluid dynamics (CFD) applications in the biomedical r ... Full text Cite

Hemodynamic and morphological characteristics of a growing cerebral aneurysm.

Journal Article Neurosurg Focus · July 1, 2019 The growth of cerebral aneurysms is linked to local hemodynamic conditions, but the driving mechanisms of the growth are poorly understood. The goal of this study was to examine the association between intraaneurysmal hemodynamic features and areas of aneu ... Full text Link to item Cite

Suitability of lattice Boltzmann inlet and outlet boundary conditions for simulating flow in image-derived vasculature.

Journal Article International journal for numerical methods in biomedical engineering · June 2019 The lattice Boltzmann method (LBM) is a popular alternative to solving the Navier-Stokes equations for modeling blood flow. When simulating flow using the LBM, several choices for inlet and outlet boundary conditions exist. While boundary conditions in the ... Full text Cite

The importance of side branches in modeling 3D hemodynamics from angiograms for patients with coronary artery disease.

Journal Article Scientific reports · June 2019 Genesis of atherosclerotic lesions in the human arterial system is critically influenced by the fluid mechanics. Applying computational fluid dynamic tools based on accurate coronary physiology derived from conventional biplane angiogram data may be useful ... Full text Cite

Multivascular networks and functional intravascular topologies within biocompatible hydrogels.

Journal Article Science (New York, N.Y.) · May 2019 Solid organs transport fluids through distinct vascular networks that are biophysically and biochemically entangled, creating complex three-dimensional (3D) transport regimes that have remained difficult to produce and study. We establish intravascular and ... Full text Cite

Temporal variations in the triggering of myocardial infarction by air temperature in Augsburg, Germany, 1987-2014.

Journal Article European heart journal · May 2019 AimsThe association between air temperature and mortality has been shown to vary over time, but evidence of temporal changes in the risk of myocardial infarction (MI) is lacking. We aimed to estimate the temporal variations in the association betw ... Full text Cite

A Framework for Comparing Vascular Hemodynamics at Different Points in Time.

Journal Article Computer physics communications · February 2019 Computational simulations of blood flow contribute to our understanding of the interplay between vascular geometry and hemodynamics. With an improved understanding of this interplay from computational fluid dynamics (CFD), there is potential to improve bas ... Full text Cite

Computing the ankle-brachial index with parallel computational fluid dynamics.

Journal Article Journal of biomechanics · January 2019 The ankle-brachial index (ABI), a ratio of arterial blood pressure in the ankles and upper arms, is used to diagnose and monitor circulatory conditions such as coarctation of the aorta and peripheral artery disease. Computational simulations of the ABI can ... Full text Cite

Role of deformable cancer cells on wall shear stress-associated-VEGF secretion by endothelium in microvasculature.

Journal Article PloS one · January 2019 Endothelial surface layer (glycocalyx) is the major physiological regulator of tumor cell adhesion to endothelium. Cancer cells express vascular endothelial growth factor (VEGF) which increases the permeability of a microvessel wall by degrading glycocalyx ... Full text Cite

Immersed Boundary Method Halo Exchange in a Hemodynamics Application

Conference Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) · January 1, 2019 In recent years, highly parallelized simulations of blood flow resolving individual blood cells have been demonstrated. Simulating such dense suspensions of deformable particles in flow often involves a partitioned fluid-structure interaction (FSI) algorit ... Full text Cite

High-Reynolds-number turbulent cavity flow using the lattice Boltzmann method

Journal Article Physical Review E · October 4, 2018 We present a boundary condition scheme for the lattice Boltzmann method that has significantly improved stability for modeling turbulent flows while maintaining excellent parallel scalability. Simulations of a three-dimensional lid-driven cavity flow are f ... Full text Cite

GPU data access on complex geometries for D3Q19 lattice boltzmann method

Conference Proceedings - 2018 IEEE 32nd International Parallel and Distributed Processing Symposium, IPDPS 2018 · August 3, 2018 GPU performance of the lattice Boltzmann method (LBM) depends heavily on memory access patterns. When LBM is advanced with GPUS on complex computational domains, geometric data is typically accessed indirectly, and lattice data is typically accessed lexico ... Full text Cite

Computational fluid modeling to understand the role of anatomy in bifurcation lesion disease

Conference Proceedings - 25th IEEE International Conference on High Performance Computing Workshops, HiPCW 2018 · July 2, 2018 Background: Treatment of bifurcation lesion disease is complex with limited studies that describe the influence of lesion anatomy on clinical outcomes. Hypothesis: Computational simulations can be used to understand the interplay between morphological char ... Full text Cite

Impact of diversity of morphological characteristics and Reynolds number on local hemodynamics in basilar aneurysms

Journal Article AIChE Journal · July 1, 2018 Morphological and hemodynamic parameters have been suggested to affect the rupture of cerebral aneurysms, but detailed mechanisms of rupture are poorly understood. The purpose of our study is to determine criteria for predicting the risk of aneurysm ruptur ... Full text Cite

Computational Fluid Dynamics and Additive Manufacturing to Diagnose and Treat Cardiovascular Disease.

Journal Article Trends in biotechnology · November 2017 Noninvasive engineering models are now being used for diagnosing and planning the treatment of cardiovascular disease. Techniques in computational modeling and additive manufacturing have matured concurrently, and results from simulations can inform and en ... Full text Cite

A computational framework to assess the influence of changes in vascular geometry on blood flow

Conference PASC 2017 - Proceedings of the Platform for Advanced Scientific Computing Conference · June 26, 2017 Many vascular abnormalities, such as aneurysms or stenoses, develop gradually over time. In the early stages of their development, they require monitoring but do not pose sufficient risk to the patient for a clinician to recommend invasive treatment. With ... Full text Cite

Mechanotransmission in endothelial cells subjected to oscillatory and multi-directional shear flow.

Journal Article Journal of the Royal Society, Interface · May 2017 Local haemodynamics are linked to the non-uniform distribution of atherosclerosic lesions in arteries. Low and oscillatory (reversing in the axial flow direction) wall shear stress (WSS) induce inflammatory responses in endothelial cells (ECs) mediating di ... Full text Cite

Using stroboscopic flow imaging to validate large-scale computational fluid dynamics simulations

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2017 The utility and accuracy of computational modeling often requires direct validation against experimental measurements. The work presented here is motivated by taking a combined experimental and computational approach to determine the ability of large-scale ... Full text Cite

Numerical simulation of a compound capsule in a constricted microchannel.

Conference Procedia computer science · January 2017 Simulations of the passage of eukaryotic cells through a constricted channel aid in studying the properties of cancer cells and their transport in the bloodstream. Compound capsules, which explicitly model the outer cell membrane and nuclear lamina, have t ... Full text Cite

Does the degree of coarctation of the aorta influence wall shear stress focal heterogeneity?

Conference · October 13, 2016 The development of atherosclerosis in the aorta is associated with low and oscillatory wall shear stress for normal patients. Moreover, localized differences in wall shear stress heterogeneity have been correlated with the presence of complex plaques in th ... Open Access Link to item Cite

Massively Parallel Models of the Human Circulatory System

Conference http://dl.acm.org/citation.cfm?id=2807676 · November 16, 2015 The potential impact of blood flow simulations on the diagnosis and treatment of patients suffering from vascular disease is tremendous. Empowering models of the full arterial tree can provide insight into diseases such as arterial hypertension and enables ... Full text Link to item Cite

Massively parallel simulations of hemodynamics in the primary large arteries of the human vasculature.

Journal Article Journal of computational science · July 2015 We present a computational model of three-dimensional and unsteady hemodynamics within the primary large arteries in the human on 1,572,864 cores of the IBM Blue Gene/Q. Models of large regions of the circulatory system are needed to study the impact of lo ... Full text Cite

Lenard-Balescu calculations and classical molecular dynamics simulations of electrical and thermal conductivities of hydrogen plasmas

Journal Article Contributions to Plasma Physics · February 1, 2015 We present a discussion of kinetic theory treatments of linear electrical and thermal transport in hydrogen plasmas, for a regime of interest to inertial confinement fusion applications. In order to assess the accuracy of one of the more involved of these ... Full text Cite

Scaling Support Vector Machines on modern HPC platforms

Journal Article Journal of Parallel and Distributed Computing · January 1, 2015 Support Vector Machines (SVM) have been widely used in data-mining and Big Data applications as modern commercial databases start to attach an increasing importance to the analytic capabilities. In recent years, SVM was adapted to the field of High Perform ... Full text Cite

Analysis of pressure gradient across aortic stenosis with massively parallel computational simulations

Conference http://ieeexplore.ieee.org/document/7043018/ · September 10, 2014 Coarctation of the aorta (CoA) is one of the most common congenital heart defects in the United States, and despite treatment, patients have a decrease in life expectancy. Computational fluid dynamics simulations can provide the physician with a non-invasi ... Link to item Cite

Locality-optimized mixed static/dynamic scheduling for improving load balancing on SMPs

Conference ACM International Conference Proceeding Series · September 9, 2014 Application performance can be degraded significantly due to node-local load imbalances during application execution. Prior work suggested using a mixed static/dynamic scheduling approach for handling this problem, specifically in the context of fine-grain ... Full text Cite

Parallel in time approximation of the lattice Boltzmann method for laminar flows

Journal Article Journal of Computational Physics · August 1, 2014 Fluid dynamics simulations using grid-based methods, such as the lattice Boltzmann equation, can benefit from parallel-in-space computation. However, for a fixed-size simulation of this type, the efficiency of larger processor counts will saturate when the ... Full text Cite

Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity.

Journal Article Cell reports · February 2014 Cancer therapy exerts a strong selection pressure that shapes tumor evolution, yet our knowledge of how tumors change during treatment is limited. Here, we report the analysis of cellular heterogeneity for genetic and phenotypic features and their spatial ... Full text Cite

A spatio-temporal coupling method to reduce the time-to-solution of cardiovascular simulations

Other Proceedings of the International Parallel and Distributed Processing Symposium, IPDPS · January 1, 2014 We present a new parallel-in-time method designed to reduce the overall time-to-solution of a patient-specific cardiovascular flow simulation. Using a modified Para real algorithm, our approach extends strong scalability beyond spatial parallelism with ful ... Full text Open Access Cite

Analysis of pressure gradient across aortic stenosis with massively parallel computational simulations

Journal Article Computing in Cardiology · January 1, 2014 Coarctation of the aorta (CoA) is one of the most common congenital heart defects in the United States, and despite treatment, patients have a decrease in life expectancy. Computational fluid dynamics simulations can provide the physician with a non-invasi ... Cite

Multiphysics simulations: Challenges and opportunities

Journal Article International Journal of High Performance Computing Applications · February 1, 2013 We consider multiphysics applications from algorithmic and architectural perspectives, where "algorithmic" includes both mathematical analysis and computational complexity, and "architectural" includes both software and hardware environments. Many diverse ... Full text Cite

Massively parallel model of evolutionary game dynamics

Journal Article Proceedings - 2012 SC Companion: High Performance Computing, Networking Storage and Analysis, SCC 2012 · December 1, 2012 To study the emergence of cooperative behavior, we have developed a scalable parallel framework. An important aspect is the amount of history that each agent can keep. When six memory steps are taken into account, the strategy space spans 24096 potential s ... Full text Cite

A Lattice Boltzmann Simulation of Hemodynamics in a Patient-Speci c Aortic Coarctation Model

Journal Article Statistical Atlases and Computational Models of the Heart: Imaging and Modelling Challenges: · October 5, 2012 In this paper, we propose a system to determine the pressure gradient at rest in the aorta. We developed a technique to efficiently initialize a regular simulation grid from a patient-specific aortic triangulated model. On this grid we employ the lattice B ... Full text Link to item Cite

Evaluation of artery visualizations for heart disease diagnosis.

Journal Article IEEE transactions on visualization and computer graphics · December 2011 Heart disease is the number one killer in the United States, and finding indicators of the disease at an early stage is critical for treatment and prevention. In this paper we evaluate visualization techniques that enable the diagnosis of coronary artery d ... Full text Cite

Efficient methods for broadcasting multi-slot messages with random access with capture

Conference 2011 - MILCOM 2011 Military Communications Conference · November 2011 Full text Cite

Drug discovery using very large numbers of patents: general strategy with extensive use of match and edit operations.

Journal Article Journal of computer-aided molecular design · May 2011 A patent data base of 6.7 million compounds generated by a very high performance computer (Blue Gene) requires new techniques for exploitation when extensive use of chemical similarity is involved. Such exploitation includes the taxonomic classification of ... Full text Cite

Poster reception---Optimizing EUDOC for the IBM eServer Blue Gene supercomputer

Conference Proceedings of the 2006 ACM/IEEE conference on Supercomputing - SC '06 · 2006 Full text Cite