Publications of Amanda Randles

%% Papers Published   
@article{fds314522,
   Author = {Randles, A},
   Title = {Parallel Genomic Sequence-Search on a Massively Parallel
             System},
   Publisher = {ACM},
   Editor = {Thorsen, O and Jiang, K and Smith, B and Lin, H and Feng, W and Sosa,
             CP},
   Year = {2007},
   Month = {May},
   Key = {fds314522}
}

@article{fds314519,
   Author = {Jiang, K and Thorsen, O and Peters, A and Smith, B and Sosa,
             CP},
   Title = {An Efficient Parallel Implementation of the Hidden Markov
             Methods for Genomic Sequence-Search on a Massively Parallel
             System},
   Journal = {Ieee Transactions on Parallel and Distributed
             Systems},
   Volume = {19},
   Number = {1},
   Pages = {15-23},
   Publisher = {Institute of Electrical and Electronics Engineers
             (IEEE)},
   Year = {2008},
   Month = {January},
   ISSN = {1045-9219},
   Doi = {10.1109/tpds.2007.70712},
   Key = {fds314519}
}

@article{fds314520,
   Author = {Pang, Y-P and Mullins, TJ and Swartz, BA and McAllister, JS and Smith,
             BE and Archer, CJ and Musselman, RG and Peters, AE and Wallenfelt, BP and Pinnow, KW},
   Title = {EUDOC on the IBM Blue Gene/L system: Accelerating the
             transfer of drug discoveries from laboratory to
             patient},
   Journal = {Ibm Journal of Research and Development},
   Volume = {52},
   Number = {1.2},
   Pages = {69-81},
   Publisher = {IBM},
   Year = {2008},
   Month = {January},
   ISSN = {0018-8646},
   Doi = {10.1147/rd.521.0069},
   Key = {fds314520}
}

@article{fds340150,
   Author = {Peters, A and King, A and Budnik, T and McCarthy, P and Michaud, P and Mundy, M and Sexton, J and Stewart, G},
   Title = {Asynchronous task dispatch for high throughput computing for
             the eServer IBM Blue Gene® Supercomputer},
   Journal = {2008 Ieee International Symposium on Parallel and
             Distributed Processing},
   Publisher = {IEEE},
   Year = {2008},
   Month = {April},
   ISBN = {9781424416936},
   Doi = {10.1109/ipdps.2008.4536455},
   Key = {fds340150}
}

@article{fds314518,
   Author = {Randles, A and Melchionna, S and Kaxiras, E and Latt, J and Sircar, J and Bernaschi, M and Bisson, M and Succi, S},
   Title = {Multiscale simulation of cardiovascular flows on the IBM
             Bluegene/P: full heart-circulation system at red-blood cell
             resolution},
   Publisher = {ACM IEEE},
   Year = {2010},
   Month = {November},
   Key = {fds314518}
}

@article{fds314517,
   Author = {Robson, B and Li, J and Dettinger, R and Peters, A and Boyer,
             SK},
   Title = {Drug discovery using very large numbers of patents. General
             strategy with extensive use of match and edit
             operations},
   Journal = {Journal of Computer Aided Molecular Design},
   Volume = {25},
   Number = {5},
   Pages = {427-441},
   Publisher = {Springer Science and Business Media LLC},
   Year = {2011},
   Month = {May},
   ISSN = {0920-654X},
   Doi = {10.1007/s10822-011-9429-x},
   Key = {fds314517}
}

@article{fds314516,
   Author = {Randles, A and Zeger, L},
   Title = {Efficient Resource Allocation for Broadcasting Multi-Slot
             Messages With Random Access with Capture},
   Publisher = {IEEE},
   Year = {2011},
   Month = {October},
   url = {http://www.milcom.org/2011/},
   Key = {fds314516}
}

@article{fds314515,
   Author = {Borkin, MA and Gajos, KZ and Peters, A and Mitsouras, D and Melchionna,
             S and Rybicki, FJ and Feldman, CL and Pfister, H},
   Title = {Evaluation of artery visualizations for heart disease
             diagnosis.},
   Journal = {Ieee Transactions on Visualization and Computer
             Graphics},
   Volume = {17},
   Number = {12},
   Pages = {2479-2488},
   Year = {2011},
   Month = {December},
   ISSN = {1077-2626},
   Abstract = {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 disease. A key physical quantity of
             medical interest is endothelial shear stress (ESS). Low ESS
             has been associated with sites of lesion formation and rapid
             progression of disease in the coronary arteries. Having
             effective visualizations of a patient's ESS data is vital
             for the quick and thorough non-invasive evaluation by a
             cardiologist. We present a task taxonomy for hemodynamics
             based on a formative user study with domain experts. Based
             on the results of this study we developed HemoVis, an
             interactive visualization application for heart disease
             diagnosis that uses a novel 2D tree diagram representation
             of coronary artery trees. We present the results of a formal
             quantitative user study with domain experts that evaluates
             the effect of 2D versus 3D artery representations and of
             color maps on identifying regions of low ESS. We show
             statistically significant results demonstrating that our 2D
             visualizations are more accurate and efficient than 3D
             representations, and that a perceptually appropriate color
             map leads to fewer diagnostic mistakes than a rainbow color
             map.},
   Doi = {10.1109/tvcg.2011.192},
   Key = {fds314515}
}

@article{fds314505,
   Author = {Randles, AP},
   Title = {Massively parallel model of evolutionary game
             dynamics},
   Journal = {Proceedings 2012 Sc Companion: High Performance Computing,
             Networking Storage and Analysis, Scc 2012},
   Pages = {1531},
   Publisher = {IEEE},
   Year = {2012},
   Month = {December},
   Abstract = {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 strategies, requiring large
             populations of agents. We introduce a multi-level
             decomposition method that allows us to exploit both
             multi-node and thread-level parallel scaling while
             minimizing the communication overhead. We present the
             following contributions: (1) A production run modeling up to
             six memory steps for populations consisting of up to 1018
             agents, making this study one of the largest yet undertaken.
             (2) Results exhibiting near perfect weak scaling and 82%
             strong scaling efficiency up to 262,144 processors of the
             IBM Blue Gene/P supercomputer and 16,384 processors of the
             Blue Gene/Q. Our framework marks an important step in the
             study of game dynamics with potential applications in fields
             ranging from biology to economics and sociology. © 2012
             IEEE.},
   Doi = {10.1109/SC.Companion.2012.307},
   Key = {fds314505}
}

@article{fds314514,
   Author = {Keyes, DE and McInnes, LC and Woodward, C and Gropp, W and Myra, E and Pernice, M and Bell, J and Brown, J and Clo, A and Connors, J and Constantinescu, E and Estep, D and Evans, K and Farhat, C and Hakim, A and Hammond, G and Hansen, G and Hill, J and Isaac, T and Jiao, X and Jordan,
             K and Kaushik, D and Kaxiras, E and Koniges, A and Lee, K and Lott, A and Lu,
             Q and Magerlein, J and Maxwell, R and McCourt, M and Mehl, M and Pawlowski,
             R and Randles, AP and Reynolds, D and Rivière, B and Rüde, U and Scheibe,
             T and Shadid, J and Sheehan, B and Shephard, M and Siegel, A and Smith, B and Tang, X and Wilson, C and Wohlmuth, B},
   Title = {Multiphysics simulations: Challenges and
             opportunities},
   Journal = {The International Journal of High Performance Computing
             Applications},
   Volume = {27},
   Number = {1},
   Pages = {4-83},
   Publisher = {SAGE Publications},
   Year = {2013},
   Month = {February},
   ISSN = {1094-3420},
   Abstract = {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 multiphysics applications can be
             reduced, en route to their computational simulation, to a
             common algebraic coupling paradigm. Mathematical analysis of
             multiphysics coupling in this form is not always practical
             for realistic applications, but model problems
             representative of applications discussed herein can provide
             insight. A variety of software frameworks for multiphysics
             applications have been constructed and refined within
             disciplinary communities and executed on leading-edge
             computer systems. We examine several of these, expose some
             commonalities among them, and attempt to extrapolate best
             practices to future systems. From our study, we summarize
             challenges and forecast opportunities. © The Author(s)
             2012.},
   Doi = {10.1177/1094342012468181},
   Key = {fds314514}
}

@article{fds315888,
   Author = {Peters Randles and A and Bächer, M and Pfister, H and Kaxiras,
             E},
   Title = {A lattice Boltzmann simulation of hemodynamics in a
             patient-specific aortic coarctation model},
   Journal = {Lecture Notes in Computer Science (Including Subseries
             Lecture Notes in Artificial Intelligence and Lecture Notes
             in Bioinformatics)},
   Volume = {7746 LNCS},
   Pages = {17-25},
   Publisher = {Springer Berlin Heidelberg},
   Editor = {Camara, O and Manso, T and Pop, M and Rhode, K and Sermesant, M and Young,
             A},
   Year = {2013},
   Month = {April},
   url = {http://link.springer.com/chapter/10.1007/978-3-642-36961-2_3},
   Abstract = {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 Boltzmann method to resolve the
             characteristic fluid flow through the vessel. The inflow
             rates, as measured physiologically, are imposed providing
             accurate pulsatile flow. The simulation required a
             resolution of at least 20 microns to ensure a convergence of
             the pressure calculation. HARVEY, a large-scale parallel
             code, was run on the IBM Blue Gene/Q supercomputer to model
             the flow at this high resolution. We analyze and evaluate
             the strengths and weaknesses of our system. © 2013
             Springer-Verlag.},
   Doi = {10.1007/978-3-642-36961-2_3},
   Key = {fds315888}
}

@article{fds314526,
   Author = {Randles, AP and Kale, V and Hammond, J and Gropp, W and Kaxiras,
             E},
   Title = {Performance analysis of the lattice Boltzmann model beyond
             Navier-Stokes},
   Journal = {Proceedings Ieee 27th International Parallel and Distributed
             Processing Symposium, Ipdps 2013},
   Pages = {1063-1074},
   Publisher = {IEEE},
   Year = {2013},
   Month = {October},
   ISBN = {9781467360661},
   Abstract = {The lattice Boltzmann method is increasingly important in
             facilitating large-scale fluid dynamics simulations. To
             date, these simulations have been built on discretized
             velocity models of up to 27 neighbors. Recent work has shown
             that higher order approximations of the continuum Boltzmann
             equation enable not only recovery of the Navier-Stokes
             hydro-dynamics, but also simulations for a wider range of
             Knudsen numbers, which is especially important in micro- and
             nano-scale flows. These higher-order models have significant
             impact on both the communication and computational
             complexity of the application. We present a performance
             study of the higher-order models as compared to the
             traditional ones, on both the IBM Blue Gene/P and Blue
             Gene/Q architectures. We study the tradeoffs of many
             optimizations methods such as the use of deep halo level
             ghost cells that, alongside hybrid programming models,
             reduce the impact of extended models and enable efficient
             modeling of extreme regimes of computational fluid dynamics.
             © 2013 IEEE.},
   Doi = {10.1109/IPDPS.2013.109},
   Key = {fds314526}
}

@article{fds314512,
   Author = {Randles, AP and Rand, DG and Lee, C and Morrisett, G and Sircar, J and Nowak, MA and Pfister, H},
   Title = {Massively parallel model of extended memory use in
             evolutionary game dynamics},
   Journal = {Proceedings Ieee 27th International Parallel and Distributed
             Processing Symposium, Ipdps 2013},
   Pages = {1217-1228},
   Publisher = {IEEE},
   Year = {2013},
   Month = {October},
   ISBN = {9781467360661},
   Abstract = {To study the emergence of cooperative behavior, we have
             developed a scalable parallel framework for evolutionary
             game dynamics. This is a critical computational tool
             enabling large-scale agent simulation research. An important
             aspect is the amount of history, or memory steps, that each
             agent can keep. When six memory steps are taken into
             account, the strategy space spans 2 4096 potential
             strategies, requiring large populations of agents. We
             introduce a multi-level decomposition method that allows us
             to exploit both multi-node and thread-level parallel scaling
             while minimizing communication overhead. We present the
             results of a production run modeling up to six memory steps
             for populations consisting of up to 1018 agents, making this
             study one of the largest yet undertaken. The high rate of
             mutation within the population results in a non-trivial
             parallel implementation. The strong and weak scaling studies
             provide insight into parallel scalability and
             programmability trade-offs for large-scale simulations,
             while exhibiting near perfect weak and strong scaling on
             16,384 tasks on Blue Gene/Q. We further show 99% weak
             scaling up to 294,912 processors 82% strong scaling
             efficiency up to 262,144 processors of Blue Gene/P. Our
             framework marks an important step in the study of game
             dynamics with potential applications in fields ranging from
             biology to economics and sociology. © 2013
             IEEE.},
   Doi = {10.1109/IPDPS.2013.102},
   Key = {fds314512}
}

@article{fds314507,
   Author = {Randles, A and Draeger, E and Michor, F},
   Title = {Analysis of pressure gradient across aortic stenosis with
             massively parallel computational simulations},
   Journal = {Computing in Cardiology},
   Volume = {41},
   Number = {January},
   Pages = {217-220},
   Year = {2014},
   Month = {January},
   ISSN = {2325-8861},
   Abstract = {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-invasive method to measure the pressure
             gradient. With HARVEY, a massively parallel hemodynamics
             application, patient specific simulations can be conducted
             of large regions of the vasculature. The pressure across the
             stenosis is impacted by flow from nearby vessels. The
             purpose of this study was to study the impact of including
             these distal vessels in the simulation on the resulting
             pressure measurements. Computational fluid dynamic
             simulations were conducted in three subsets of one patient's
             vasculature. We demonstrate up to a 29% difference in
             calculated pressure gradient based on the number of vessels
             included in the simulation. These initial results are
             positive but need to be substantiated with further patient
             studies.},
   Key = {fds314507}
}

@article{fds344697,
   Author = {Randles, A and Kaxiras, E},
   Title = {A spatio-temporal coupling method to reduce the
             time-to-solution of cardiovascular simulations},
   Journal = {2008 Ieee International Symposium on Parallel and
             Distributed Processing},
   Pages = {593-602},
   Year = {2014},
   Month = {January},
   ISBN = {9780769552071},
   Abstract = {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 fully controllable accuracy and no
             decrease in stability. We discuss the coupling of spatial
             and temporal domain decompositions used in our
             implementation, and showcase the use of the method on a
             study of blood flow through the aorta. We observe an
             additional 40% reduction in overall wall clock time with no
             significant loss of accuracy, in agreement with a predictive
             performance model. © 2014 IEEE.},
   Doi = {10.1109/IPDPS.2014.68},
   Key = {fds344697}
}

@article{fds314525,
   Author = {You, Y and Song, SL and Fu, H and Marquez, A and Dehnavi, MM and Barker, K and Cameron, KW and Randles, AP and Yang, G},
   Title = {MIC-SVM: Designing a highly efficient support vector machine
             for advanced modern multi-core and many-core
             architectures},
   Journal = {2008 Ieee International Symposium on Parallel and
             Distributed Processing},
   Pages = {809-818},
   Year = {2014},
   Month = {January},
   ISBN = {9780769552071},
   ISSN = {1530-2075},
   Abstract = {Support Vector Machine (SVM) has 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 Performance Computing for
             power/performance prediction, auto-tuning, and runtime
             scheduling. However, even at the risk of losing prediction
             accuracy due to insufficient runtime information,
             researchers can only afford to apply offline model training
             to avoid significant runtime training overhead. Advanced
             multi- and many-core architectures offer massive parallelism
             with complex memory hierarchies which can make runtime
             training possible, but form a barrier to efficient parallel
             SVM design. To address the challenges above, we designed and
             implemented MIC-SVM, a highly efficient parallel SVM for x86
             based multi-core and many-core architectures, such as the
             Intel Ivy Bridge CPUs and Intel Xeon Phi co-processor (MIC).
             We propose various novel analysis methods and optimization
             techniques to fully utilize the multilevel parallelism
             provided by these architectures and serve as general
             optimization methods for other machine learning tools.
             MIC-SVM achieves 4.4-84x and 18-47x speedups against the
             popular LIBSVM, on MIC and Ivy Bridge CPUs respectively, for
             several real-world data-mining datasets. Even compared with
             GPUSVM, run on a top of the line NVIDIA k20x GPU, the
             performance of our MIC-SVM is competitive. We also conduct a
             cross-platform performance comparison analysis, focusing on
             Ivy Bridge CPUs, MIC and GPUs, and provide insights on how
             to select the most suitable advanced architectures for
             specific algorithms and input data patterns. © 2014
             IEEE.},
   Doi = {10.1109/IPDPS.2014.88},
   Key = {fds314525}
}

@article{fds314513,
   Author = {Almendro, V and Cheng, Y-K and Randles, A and Itzkovitz, S and Marusyk,
             A and Ametller, E and Gonzalez-Farre, X and Muñoz, M and Russnes, HG and Helland, A and Rye, IH and Borresen-Dale, A-L and Maruyama, R and van
             Oudenaarden, A and Dowsett, M and Jones, RL and Reis-Filho, J and Gascon, P and Gönen, M and Michor, F and Polyak,
             K},
   Title = {Inference of tumor evolution during chemotherapy by
             computational modeling and in situ analysis of genetic and
             phenotypic cellular diversity.},
   Journal = {Cell Reports},
   Volume = {6},
   Number = {3},
   Pages = {514-527},
   Year = {2014},
   Month = {February},
   ISSN = {2211-1247},
   Abstract = {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 distribution in breast
             tumors pre- and post-neoadjuvant chemotherapy. We found that
             intratumor genetic diversity was tumor-subtype specific, and
             it did not change during treatment in tumors with partial or
             no response. However, lower pretreatment genetic diversity
             was significantly associated with pathologic complete
             response. In contrast, phenotypic diversity was different
             between pre- and posttreatment samples. We also observed
             significant changes in the spatial distribution of cells
             with distinct genetic and phenotypic features. We used these
             experimental data to develop a stochastic computational
             model to infer tumor growth patterns and evolutionary
             dynamics. Our results highlight the importance of integrated
             analysis of genotypes and phenotypes of single cells in
             intact tissues to predict tumor evolution.},
   Doi = {10.1016/j.celrep.2013.12.041},
   Key = {fds314513}
}

@article{fds314511,
   Author = {Randles, A and Kaxiras, E},
   Title = {Parallel in time approximation of the lattice Boltzmann
             method for laminar flows},
   Journal = {Journal of Computational Physics},
   Volume = {270},
   Pages = {577-586},
   Publisher = {Elsevier BV},
   Year = {2014},
   Month = {August},
   ISSN = {0021-9991},
   Abstract = {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 number of grid points per core
             becomes too small. To overcome this fundamental strong
             scaling limit in space-parallel approaches, we present a
             novel time-parallel version of the lattice Boltzmann method
             using the parareal algorithm. This method is based on a
             predictor-corrector scheme combined with mesh refinement to
             enable the simulation of larger number of time steps. We
             present results of up to a 32× increase in speed for a
             model system consisting of a cylinder with conditions for
             laminar flow. The parallel gain obtainable is predicted with
             strong accuracy, providing a quantitative understanding of
             the potential impact of this method. © 2014 Elsevier
             Inc.},
   Doi = {10.1016/j.jcp.2014.04.006},
   Key = {fds314511}
}

@article{fds322671,
   Author = {Kale, V and Randles, A and Gropp, WD},
   Title = {Locality-optimized mixed static/dynamic scheduling for
             improving load balancing on SMPs},
   Journal = {Acm International Conference Proceeding Series},
   Volume = {09-12-September-2014},
   Pages = {115-116},
   Publisher = {ACM Press},
   Year = {2014},
   Month = {September},
   ISBN = {9781450328753},
   Abstract = {© ACM 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-grained,
             transient load imbalances. Here, we consider an alternate
             strategy for more general load imbalances where
             fine-grained, transient load imbalance may be coupled with
             coarse-grained load imbalance. Specifically, we implement a
             scheduling scheme in which we modify the data layout in
             mixed static/dynamic scheduling, and add an additional tuned
             constraint in the dequeue function of our scheduler. Through
             experimentation of an n-body particle simulation code on
             modern multi-core architectures, our technique gives a 19.4%
             performance gain over dynamic scheduling, and an overall
             48.6% performance gain over standard static
             scheduling.},
   Doi = {10.1145/2642769.2642788},
   Key = {fds322671}
}

@article{fds314509,
   Author = {Whitley, HD and Scullard, CR and Benedict, LX and Castor, JI and Randles, A and Glosli, JN and Richards, DF and Desjarlais, MP and Graziani, FR},
   Title = {Lenard-Balescu calculations and classical molecular dynamics
             simulations of electrical and thermal conductivities of
             hydrogen plasmas},
   Journal = {Contributions to Plasma Physics},
   Volume = {55},
   Number = {2-3},
   Pages = {192-202},
   Publisher = {WILEY},
   Year = {2015},
   Month = {January},
   ISSN = {0863-1042},
   Abstract = {© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. 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 approaches, classical Lenard-Balescu
             theory, we perform classical molecular dynamics simulations
             of hydrogen plasmas using 2-body quantum statistical
             potentials and compute both electrical and thermal
             conductivity from our particle trajectories using the Kubo
             approach. Our classical Lenard-Balescu results employing the
             identical statistical potentials agree well with the
             simulations. Comparison between quantum Lenard-Balescu and
             classical Lenard-Balescu for conductivities then allows us
             to both validate and critique the use of various statistical
             potentials for the prediction of plasma transport
             properties. These findings complement our earlier MD/kinetic
             theory work on temperature equilibration [1], and reach
             similar conclusions as to which forms of statistical
             potentials best reproduce true quantum behavior.},
   Doi = {10.1002/ctpp.201400066},
   Key = {fds314509}
}

@article{fds314510,
   Author = {You, Y and Fu, H and Song, SL and Randles, A and Kerbyson, D and Marquez,
             A and Yang, G and Hoisie, A},
   Title = {Scaling Support Vector Machines on modern HPC
             platforms},
   Journal = {Journal of Parallel and Distributed Computing},
   Volume = {76},
   Pages = {16-31},
   Publisher = {Elsevier BV},
   Year = {2015},
   Month = {January},
   ISSN = {0743-7315},
   Abstract = {© 2014 Elsevier Inc. All rights reserved. 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 Performance Computing for power/performance
             prediction, auto-tuning, and runtime scheduling. However,
             even at the risk of losing prediction accuracy due to
             insufficient runtime information, researchers can only
             afford to apply offline model training to avoid significant
             runtime training overhead. Advanced multi- and many-core
             architectures offer massive parallelism with complex memory
             hierarchies which can make runtime training possible, but
             form a barrier to efficient parallel SVM design. To address
             the challenges above, we designed and implemented MIC-SVM, a
             highly efficient parallel SVM for x86 based multi-core and
             many-core architectures, such as the Intel Ivy Bridge CPUs
             and Intel Xeon Phi co-processor (MIC). We propose various
             novel analysis methods and optimization techniques to fully
             utilize the multilevel parallelism provided by these
             architectures and serve as general optimization methods for
             other machine learning tools. MIC-SVM achieves 4.4-84× and
             18-47× speedups against the popular LIBSVM, on MIC and Ivy
             Bridge CPUs respectively, for several real-world data-mining
             datasets. Even compared with GPUSVM, running on the NVIDIA
             k20x GPU, the performance of our MIC-SVM is competitive. We
             also conduct a cross-platform performance comparison
             analysis, focusing on Ivy Bridge CPUs, MIC and GPUs, and
             provide insights on how to select the most suitable advanced
             architectures for specific algorithms and input data
             patterns.},
   Doi = {10.1016/j.jpdc.2014.09.005},
   Key = {fds314510}
}

@article{fds314508,
   Author = {Randles, A and Draeger, EW and Bailey, PE},
   Title = {Massively parallel simulations of hemodynamics in the
             primary large arteries of the human vasculature},
   Journal = {Journal of Computational Science},
   Volume = {9},
   Pages = {70-75},
   Publisher = {Elsevier BV},
   Year = {2015},
   Month = {July},
   ISSN = {1877-7503},
   Abstract = {© 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 local
             factors on global hemodynamics and to inform next generation
             drug delivery mechanisms. The HARVEY code successfully
             addresses key challenges that can hinder effective solution
             of image-based hemodynamics on contemporary supercomputers,
             such as limited memory capacity and bandwidth, flexible load
             balancing, and scalability. This work is the first
             demonstration of large fluid dynamics simulations of the
             aortofemoral region of the circulatory system at resolutions
             as small as 10. μm.},
   Doi = {10.1016/j.jocs.2015.04.003},
   Key = {fds314508}
}

@article{fds314524,
   Author = {Randles, A and Draeger, EW and Oppelstrup, T and Krauss, L and Gunnels,
             JA},
   Title = {Massively parallel models of the human circulatory
             system},
   Journal = {International Conference for High Performance Computing,
             Networking, Storage and Analysis, Sc},
   Volume = {15-20-November-2015},
   Publisher = {ACM Press},
   Year = {2015},
   Month = {November},
   ISBN = {9781450337236},
   ISSN = {2167-4329},
   url = {http://dl.acm.org/citation.cfm?id=2807676},
   Abstract = {© 2015 ACM. 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 the study of the influence
             of local factors on global hemodynamics. We present a new,
             highly scalable implementation of the lattice Boltzmann
             method which addresses key challenges such as multiscale
             coupling, limited memory capacity and bandwidth, and robust
             load balancing in complex geometries. We demonstrate the
             strong scaling of a three-dimensional, high-resolution
             simulation of hemodynamics in the systemic arterial tree on
             1,572,864 cores of Blue Gene/Q. Faster calculation of flow
             in full arterial networks enables unprecedented risk
             stratification on a perpatient basis. In pursuit of this
             goal, we have introduced computational advances that
             significantly reduce time-to-solution for biofluidic
             simulations.},
   Doi = {10.1145/2807591.2807676},
   Key = {fds314524}
}

@article{fds323711,
   Author = {Gounley, J and Chaudhury, R and Vardhan, M and Driscoll, M and Pathangey, G and Winarta, K and Ryan, J and Frakes, D and Randles,
             A},
   Title = {Does the degree of coarctation of the aorta influence wall
             shear stress focal heterogeneity?},
   Journal = {Conference Proceedings : ... Annual International Conference
             of the Ieee Engineering in Medicine and Biology Society.
             Ieee Engineering in Medicine and Biology Society. Annual
             Conference},
   Volume = {2016},
   Pages = {3429-3432},
   Year = {2016},
   Month = {August},
   ISBN = {9781457702204},
   Abstract = {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 the descending aorta. While
             it is known that coarctation of the aorta can influence
             indices of wall shear stress, it is unclear how the degree
             of narrowing influences resulting patterns. We hypothesized
             that the degree of coarctation would have a strong influence
             on focal heterogeneity of wall shear stress. To test this
             hypothesis, we modeled the fluid dynamics in a
             patient-specific aorta with varied degrees of coarctation.
             We first validated a massively parallel computational model
             against experimental results for the patient geometry and
             then evaluated local shear stress patterns for a range of
             degrees of coarctation. Wall shear stress patterns at two
             cross sectional slices prone to develop atherosclerotic
             plaques were evaluated. Levels at different focal regions
             were compared to the conventional measure of average
             circumferential shear stress to enable localized
             quantification of coarctation-induced shear stress
             alteration. We find that the coarctation degree causes
             highly heterogeneous changes in wall shear
             stress.},
   Doi = {10.1109/EMBC.2016.7591465},
   Key = {fds323711}
}

@article{fds328446,
   Author = {Gounley, J and Draeger, EW and Randles, A},
   Title = {Numerical simulation of a compound capsule in a constricted
             microchannel.},
   Journal = {Procedia Computer Science},
   Volume = {108},
   Pages = {175-184},
   Year = {2017},
   Month = {January},
   Abstract = {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 the potential to improve computational
             model fidelity. However, general simulations of compound
             capsules transiting a constricted microchannel have not been
             conducted and the influence of the compound capsule model on
             computational performance is not well known. In this study,
             we extend a parallel hemodynamics application to simulate
             the fluid-structure interaction between compound capsules
             and fluid. With this framework, we compare the deformation
             of simple and compound capsules in constricted
             microchannels, and explore how deformation depends on the
             capillary number and on the volume fraction of the inner
             membrane. The computational framework's parallel performance
             in this setting is evaluated and future development lessons
             are discussed.},
   Doi = {10.1016/j.procs.2017.05.209},
   Key = {fds328446}
}

@article{fds326839,
   Author = {Laurence, TA and Ly, S and Fong, E and Shusteff, M and Randles, A and Gounley, J and Draeger, E},
   Title = {Using stroboscopic flow imaging to validate large-scale
             computational fluid dynamics simulations},
   Journal = {Progress in Biomedical Optics and Imaging Proceedings of
             Spie},
   Volume = {10076},
   Publisher = {SPIE},
   Year = {2017},
   Month = {January},
   ISBN = {9781510605930},
   Abstract = {Copyright © 2017 SPIE. 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 computational fluid dynamics (CFD) simulations
             to understand and predict the dynamics of circulating tumor
             cells in clinically relevant environments. We use
             stroboscopic light sheet fluorescence imaging to track the
             paths and measure the velocities of fluorescent microspheres
             throughout a human aorta model. Performed over complex
             physiologicallyrealistic 3D geometries, large data sets are
             acquired with microscopic resolution over macroscopic
             distances.},
   Doi = {10.1117/12.2253319},
   Key = {fds326839}
}

@article{fds326715,
   Author = {Dabagh, M and Jalali, P and Butler, PJ and Randles, A and Tarbell,
             JM},
   Title = {Mechanotransmission in endothelial cells subjected to
             oscillatory and multi-directional shear flow.},
   Journal = {Journal of the Royal Society, Interface},
   Volume = {14},
   Number = {130},
   Year = {2017},
   Month = {May},
   Abstract = {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 disease localization. The
             objective of this study is to investigate computationally
             how the flow direction (reflected in WSS variation on the EC
             surface over time) influences the forces experienced by
             structural components of ECs that are believed to play
             important roles in mechanotransduction. A three-dimensional,
             multi-scale, multi-component, viscoelastic model of focally
             adhered ECs is developed, in which oscillatory WSS
             (reversing or non-reversing) parallel to the principal flow
             direction, or multi-directional oscillatory WSS with
             reversing axial and transverse components are applied over
             the EC surface. The computational model includes the
             glycocalyx layer, actin cortical layer, nucleus,
             cytoskeleton, focal adhesions (FAs), stress fibres and
             adherens junctions (ADJs). We show the distinct effects of
             atherogenic flow profiles (reversing unidirectional flow and
             reversing multi-directional flow) on subcellular structures
             relative to non-atherogenic flow (non-reversing flow).
             Reversing flow lowers stresses and strains due to
             viscoelastic effects, and multi-directional flow alters
             stress on the ADJs perpendicular to the axial flow
             direction. The simulations predict forces on integrins, ADJ
             filaments and other substructures in the range that activate
             mechanotransduction.},
   Doi = {10.1098/rsif.2017.0185},
   Key = {fds326715}
}

@article{fds328038,
   Author = {Gounley, J and Vardhan, M and Randles, A},
   Title = {A computational framework to assess the influence of changes
             in vascular geometry on blood flow},
   Journal = {Pasc 2017 Proceedings of the Platform for Advanced
             Scientific Computing Conference},
   Publisher = {ACM Press},
   Year = {2017},
   Month = {June},
   ISBN = {9781450350624},
   Abstract = {© 2017 Association for Computing Machinery. 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 a better understanding of the
             interplay between hemodynamic factors and changes in blood
             vessel geometry, there is an opportunity to improve clinical
             care by earlier identification of aneurysms or stenoses with
             significant potential for further development. Computational
             fluid dynamics has shown great promise for investigating
             this interplay and identifying the associated underlying
             mechanisms, by using patient-derived geometries and
             modifying them to represent potential evolution of the
             vascular disease. However, a general, extensible framework
             for comparing simulation results from different vascular
             geometries in a direct, quantitative manner does not
             currently exist. As a first step toward the development of
             such a framework, we present a method for quantifying the
             relationship between changes in vascular geometry and
             hemodynamic factors, such as wall shear stress. We apply
             this framework to study the correlation between wall shear
             stress and geometric changes in two opposite settings: When
             flow properties are associated with consequent changes in
             the vascular geometry, as in a thoracic aortic aneurysm, and
             when geometric changes alter the flow, as in a worsening
             aortic stenosis.},
   Doi = {10.1145/3093172.3093227},
   Key = {fds328038}
}

@article{fds329286,
   Author = {Randles, A and Frakes, DH and Leopold, JA},
   Title = {Computational Fluid Dynamics and Additive Manufacturing to
             Diagnose and Treat Cardiovascular Disease.},
   Journal = {Trends in Biotechnology},
   Volume = {35},
   Number = {11},
   Pages = {1049-1061},
   Year = {2017},
   Month = {November},
   Abstract = {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 enable the design and
             optimization of therapeutic devices and treatment
             strategies. The emerging synergy between large-scale
             simulations and 3D printing is having a two-fold benefit:
             first, 3D printing can be used to validate the complex
             simulations, and second, the flow models can be used to
             improve treatment planning for cardiovascular disease. In
             this review, we summarize and discuss recent methods and
             findings for leveraging advances in both additive
             manufacturing and patient-specific computational modeling,
             with an emphasis on new directions in these fields and
             remaining open questions.},
   Doi = {10.1016/j.tibtech.2017.08.008},
   Key = {fds329286}
}

@article{fds333543,
   Author = {Rafat, M and Stone, HA and Auguste, DT and Dabagh, M and Randles, A and Heller, M and Rabinov, JD},
   Title = {Impact of diversity of morphological characteristics and
             Reynolds number on local hemodynamics in basilar
             aneurysms},
   Journal = {Aiche Journal},
   Volume = {64},
   Number = {7},
   Pages = {2792-2802},
   Publisher = {WILEY},
   Year = {2018},
   Month = {July},
   Abstract = {© 2018 American Institute of Chemical Engineers
             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 rupture, which is critical for improved patient
             management. Existing aneurysm hemodynamics studies generally
             evaluate limited geometries or Reynolds numbers (Re), which
             are difficult to apply to a wide range of patient-specific
             cases. Association between hemodynamic characteristics and
             morphology is focused. Several two-dimensional (2D) and
             three-dimensional (3D) idealized and physiological
             geometries is assessed to characterize the hemodynamic
             landscape between flow patterns. The impact of morphology on
             velocity and wall shear stress (WSS) profiles were
             evaluated. Slight changes in aneurysm geometry is found or
             Re result in significant changes in the hemodynamic and WSS
             profiles. Our systematic mapping and nondimensional analysis
             qualitatively identify hemodynamic conditions that may
             predispose aneurysms to rupture. © 2018 American Institute
             of Chemical Engineers AIChE J, 64: 2792–2802,
             2018.},
   Doi = {10.1002/aic.16091},
   Key = {fds333543}
}

@article{fds337736,
   Author = {Herschlag, G and Lee, S and Vetter, JS and Randles,
             A},
   Title = {GPU data access on complex geometries for D3Q19 lattice
             boltzmann method},
   Journal = {Proceedings 2018 Ieee 32nd International Parallel and
             Distributed Processing Symposium, Ipdps 2018},
   Pages = {825-834},
   Publisher = {IEEE},
   Year = {2018},
   Month = {August},
   ISBN = {9781538643686},
   Abstract = {© 2018 IEEE. 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 lexicographically in the
             Structure of Array (SoA) layout. Although there are a
             variety of existing access patterns beyond the typical
             choices, no study has yet examined the relative efficacy
             between them. Here, we compare a suite of memory access
             schemes via empirical testing and performance modeling. We
             find strong evidence that semi-direct addressing is the
             superior addressing scheme for the majority of cases
             examined: Semi-direct addressing increases computational
             speed and often reduces memory consumption. For lattice
             layout, we find that the Collected Structure of Arrays
             (CSoA) layout outperforms the SoA layout. When compared to
             state-of-The-Art practices, our recommended addressing
             modifications lead to performance gains between 10-40%
             across different complex geometries, fluid volume fractions,
             and resolutions. The modifications also lead to a decrease
             in memory consumption by as much as 17%. Having discovered
             these improvements, we examine a highly resolved arterial
             geometry on a leadership class system. On this system we
             present the first near-optimal strong results for LBM with
             arterial geometries run on GPUS. We also demonstrate that
             the above recommendations remain valid for large scale, many
             device simulations, which leads to an increased
             computational speed and average memory usage reductions. To
             understand these observations, we employ performance
             modeling which reveals that semi-direct methods outperform
             indirect methods due to a reduced number of total
             loads/stores in memory, and that CSoA outperforms SoA and
             bundling due to improved caching behavior.},
   Doi = {10.1109/IPDPS.2018.00092},
   Key = {fds337736}
}

@article{fds339258,
   Author = {Hegele, LA and Scagliarini, A and Sbragaglia, M and Mattila, KK and Philippi, PC and Puleri, DF and Gounley, J and Randles,
             A},
   Title = {High-Reynolds-number turbulent cavity flow using the lattice
             Boltzmann method},
   Journal = {Physical Review. E},
   Volume = {98},
   Number = {4},
   Publisher = {American Physical Society (APS)},
   Year = {2018},
   Month = {October},
   Abstract = {© 2018 American Physical Society. 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 found to be stable up to the unprecedented Reynolds
             number Re=5×104 for this setup. Excellent agreement with
             energy balance equations, computational and experimental
             results are shown. We quantify rises in the production of
             turbulence and turbulent drag, and determine peak locations
             of turbulent production.},
   Doi = {10.1103/PhysRevE.98.043302},
   Key = {fds339258}
}

@article{fds341923,
   Author = {Dabagh, M and Randles, A},
   Title = {Role of deformable cancer cells on wall shear
             stress-associated-VEGF secretion by endothelium in
             microvasculature.},
   Journal = {Plos One},
   Volume = {14},
   Number = {2},
   Pages = {e0211418},
   Year = {2019},
   Month = {January},
   Abstract = {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. Endothelial cells
             lining large arteries have also been reported, in vitro and
             in vivo, to mediate VEGF expression significantly under
             exposure to high wall shear stress (WSS) > 0.6 Pa. The
             objective of the present study is to explore whether local
             hemodynamic conditions in the vicinity of a migrating
             deformable cancer cell can influence the function of
             endothelial cells to express VEGF within the
             microvasculature. A three-dimensional model of deformable
             cancer cells (DCCs) migrating within a capillary is
             developed by applying a massively parallel hemodynamics
             application to simulate the fluid-structure interaction
             between the DCC and fluid surrounding the DCC. We study how
             dynamic interactions between the DCC and its local
             microenvironment affect WSS exposed on endothelium, under
             physiological conditions of capillaries with different
             diameters and flow conditions. Moreover, we quantify the
             area of endothelium affected by the DCC. Our results show
             that the DCC alters local hemodynamics in its vicinity up to
             an area as large as 40 times the cancer cell lateral
             surface. In this area, endothelium experiences high WSS
             values in the range of 0.6-12 Pa. Endothelial cells exposed
             to this range of WSS have been reported to express VEGF.
             Furthermore, we demonstrate that stiffer cancer cells expose
             higher WSS on the endothelium. A strong impact of cell
             stiffness on its local microenvironment is observed in
             capillaries with diameters <16 μm. WSS-induced-VEGF by
             endothelium represents an important potential mechanism for
             cancer cell adhesion and metastasis in the microvasculature.
             This work serves as an important first step in understanding
             the mechanisms driving VEGF-expression by endothelium and
             identifying the underlying mechanisms of glycocalyx
             degradation by endothelium in microvasculature. The
             identification of angiogenesis factors involved in early
             stages of cancer cell-endothelium interactions and
             understanding their regulation will help, first to develop
             anti-angiogenic strategies applied to diagnostic studies and
             therapeutic interventions, second to predict accurately
             where different cancer cell types most likely adhere in
             microvasculature, and third to establish accurate criteria
             predisposing the cancer metastasis.},
   Doi = {10.1371/journal.pone.0211418},
   Key = {fds341923}
}

@article{fds339595,
   Author = {Gounley, J and Draeger, EW and Oppelstrup, T and Krauss, WD and Gunnels,
             JA and Chaudhury, R and Nair, P and Frakes, D and Leopold, JA and Randles,
             A},
   Title = {Computing the ankle-brachial index with parallel
             computational fluid dynamics.},
   Journal = {Journal of Biomechanics},
   Volume = {82},
   Pages = {28-37},
   Year = {2019},
   Month = {January},
   Abstract = {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 potentially determine the
             parameters that produce an ABI indicative of ischemia or
             other abnormalities in blood flow. However, 0- and 1-D
             computational methods are limited in describing a 3-D
             patient-derived geometry. Thus, we present a massively
             parallel framework for computational fluid dynamics (CFD)
             simulations in the full arterial system. Using the lattice
             Boltzmann method to solve the Navier-Stokes equations, we
             employ highly parallelized and scalable methods to generate
             the simulation domain and efficiently distribute the
             computational load among processors. For the first time, we
             compute an ABI with 3-D CFD. In this proof-of-concept study,
             we investigate the dependence of ABI on the presence of
             stenoses, or narrowed regions of the arteries, by directly
             modifying the arterial geometry. As a result, our framework
             enables the computation a hemodynamic factor characterizing
             flow at the scale of the full arterial system, in a manner
             that is extensible to patient-specific imaging data and
             holds potential for treatment planning.},
   Doi = {10.1016/j.jbiomech.2018.10.007},
   Key = {fds339595}
}

@article{fds344696,
   Author = {Gounley, J and Draeger, EW and Randles, A},
   Title = {Immersed Boundary Method Halo Exchange in a Hemodynamics
             Application},
   Journal = {Lecture Notes in Computer Science (Including Subseries
             Lecture Notes in Artificial Intelligence and Lecture Notes
             in Bioinformatics)},
   Volume = {11536 LNCS},
   Pages = {441-455},
   Year = {2019},
   Month = {January},
   ISBN = {9783030227333},
   Abstract = {© 2019, Springer Nature Switzerland AG. 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)
             algorithm, with separate solvers for Eulerian fluid and
             Lagrangian cell grids, plus a solver - e.g., immersed
             boundary method - for their interaction. Managing data
             motion in parallel FSI implementations is increasingly
             important, particularly for inhomogeneous systems like
             vascular geometries. In this study, we evaluate the
             influence of Eulerian and Lagrangian halo exchanges on
             efficiency and scalability of a partitioned FSI algorithm
             for blood flow. We describe an MPI+OpenMP implementation of
             the immersed boundary method coupled with lattice Boltzmann
             and finite element methods. We consider how communication
             and recomputation costs influence the optimization of halo
             exchanges with respect to three factors: immersed boundary
             interaction distance, cell suspension density, and relative
             fluid/cell solver costs.},
   Doi = {10.1007/978-3-030-22734-0_32},
   Key = {fds344696}
}

@article{fds337027,
   Author = {Gounley, J and Vardhan, M and Randles, A},
   Title = {A Framework for Comparing Vascular Hemodynamics at Different
             Points in Time.},
   Journal = {Computer Physics Communications},
   Volume = {235},
   Pages = {1-8},
   Year = {2019},
   Month = {February},
   Abstract = {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 basic research and the targeting of
             clinical care. One avenue for further analysis concerns the
             influence of time on the vascular geometries used in CFD
             simulations. The shape of blood vessels changes frequently,
             as in deformation within the cardiac cycle, and over long
             periods of time, such as the development of a stenotic
             plaque or an aneurysm. These changes in the vascular
             geometry will, in turn, influence flow within these blood
             vessels. By performing CFD simulations in geometries
             representing the blood vessels at different points in time,
             the interplay of these geometric changes with hemodynamics
             can be quantified. However, performing CFD simulations on
             different discrete grids leads to an additional challenge:
             how does one directly and quantitatively compare simulation
             results from different vascular geometries? In a previous
             study, we began to address this problem by proposing a
             method for the simplified case where the two geometries
             share a common centerline. In this companion paper, we
             generalize this method to address geometric changes which
             alter the vessel centerline. We demonstrate applications of
             this method to the study of wall shear stress in the left
             coronary artery. First, we compute the difference in wall
             shear stress between simulations using vascular geometries
             derived from patient imaging data at two points in the
             cardiac cycle. Second, we evaluate the relationship between
             changes in wall shear stress and the progressive development
             of a coronary aneurysm or stenosis.},
   Doi = {10.1016/j.cpc.2018.05.014},
   Key = {fds337027}
}

@article{fds342168,
   Author = {Vardhan, M and Das, A and Gouruev, J and Randles,
             A},
   Title = {Computational fluid modeling to understand the role of
             anatomy in bifurcation lesion disease},
   Journal = {Proceedings 25th Ieee International Conference on High
             Performance Computing Workshops, Hipcw 2018},
   Pages = {56-64},
   Year = {2019},
   Month = {February},
   ISBN = {9781728101149},
   Abstract = {© 2018 IEEE. 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
             characteristics of lesion and clinical diagnostic metrics.
             Methods: Geometric modifications along the bifurcation in a
             patient-derived left coronary artery were made to
             incorporate unique combination of anatomic features:
             curvature, length and occlusion severity. The resulting
             geometries were used to perform CFD simulations using
             physiological flow parameters. Three diagnostic metrics,
             resting gradient, instantaneous wave free ratio (iFR) and
             diastolic-systolic velocity ratio (DSVR), were computed from
             the simulations. Results: We report occlusion severity to be
             an independent predictor for lower resting gradient and iFR
             values, whereas lesion length and curvature did not yield
             dramatic changes in iFR and resting gradient. Our results
             suggest that DSVR is more sensitive to nuanced flow
             disturbances; however, it may be complex to derive direct
             correspondence to disease severity relative to resting
             gradient and iFR. Conclusion: Spatial lesion characteristics
             can be used to determine diseased bifurcation cases that may
             lead to interventional complications.},
   Doi = {10.1109/HiPCW.2018.8634225},
   Key = {fds342168}
}

@article{fds343372,
   Author = {Grigoryan, B and Paulsen, SJ and Corbett, DC and Sazer, DW and Fortin,
             CL and Zaita, AJ and Greenfield, PT and Calafat, NJ and Gounley, JP and Ta,
             AH and Johansson, F and Randles, A and Rosenkrantz, JE and Louis-Rosenberg, JD and Galie, PA and Stevens, KR and Miller,
             JS},
   Title = {Multivascular networks and functional intravascular
             topologies within biocompatible hydrogels.},
   Journal = {Science (New York, N.Y.)},
   Volume = {364},
   Number = {6439},
   Pages = {458-464},
   Year = {2019},
   Month = {May},
   Abstract = {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 multivascular design freedoms
             with photopolymerizable hydrogels by using food dye
             additives as biocompatible yet potent photoabsorbers for
             projection stereolithography. We demonstrate monolithic
             transparent hydrogels, produced in minutes, comprising
             efficient intravascular 3D fluid mixers and functional
             bicuspid valves. We further elaborate entangled vascular
             networks from space-filling mathematical topologies and
             explore the oxygenation and flow of human red blood cells
             during tidal ventilation and distension of a proximate
             airway. In addition, we deploy structured biodegradable
             hydrogel carriers in a rodent model of chronic liver injury
             to highlight the potential translational utility of this
             materials innovation.},
   Doi = {10.1126/science.aav9750},
   Key = {fds343372}
}

@article{fds342379,
   Author = {Feiger, B and Vardhan, M and Gounley, J and Mortensen, M and Nair, P and Chaudhury, R and Frakes, D and Randles, A},
   Title = {Suitability of lattice Boltzmann inlet and outlet boundary
             conditions for simulating flow in image-derived
             vasculature.},
   Journal = {International Journal for Numerical Methods in Biomedical
             Engineering},
   Volume = {35},
   Number = {6},
   Pages = {e3198},
   Year = {2019},
   Month = {June},
   Abstract = {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 LBM have been evaluated in
             idealized geometries, there have been no extensive
             comparisons in image-derived vasculature, where the
             geometries are highly complex. In this study, the Zou-He
             (ZH) and finite difference (FD) boundary conditions were
             evaluated in image-derived vascular geometries by comparing
             their stability, accuracy, and run times. The boundary
             conditions were compared in four arteries: a coarctation of
             the aorta, dissected aorta, femoral artery, and left
             coronary artery. The FD boundary condition was more stable
             than ZH in all four geometries. In general, simulations
             using the ZH and FD method showed similar convergence rates
             within each geometry. However, the ZH method proved to be
             slightly more accurate compared with experimental flow using
             three-dimensional printed vasculature. The total run times
             necessary for simulations using the ZH boundary condition
             were significantly higher as the ZH method required a larger
             relaxation time, grid resolution, and number of time steps
             for a simulation representing the same physiological time.
             Finally, a new inlet velocity profile algorithm is presented
             for complex inlet geometries. Overall, results indicated
             that the FD method should generally be used for large-scale
             blood flow simulations in image-derived vasculature
             geometries. This study can serve as a guide to researchers
             interested in using the LBM to simulate blood
             flow.},
   Doi = {10.1002/cnm.3198},
   Key = {fds342379}
}

@article{fds343753,
   Author = {Vardhan, M and Gounley, J and Chen, SJ and Kahn, AM and Leopold, JA and Randles, A},
   Title = {The importance of side branches in modeling 3D hemodynamics
             from angiograms for patients with coronary artery
             disease.},
   Journal = {Scientific Reports},
   Volume = {9},
   Number = {1},
   Pages = {8854},
   Year = {2019},
   Month = {June},
   Abstract = {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 in guiding percutaneous
             coronary interventions. The primary objective of this study
             is to build and validate a computational framework for
             accurate personalized 3-dimensional hemodynamic simulation
             across the complete coronary arterial tree and demonstrate
             the influence of side branches on coronary hemodynamics by
             comparing shear stress between coronary models with and
             without these included. The proposed novel computational
             framework based on biplane angiography enables significant
             arterial circulation analysis. This study shows that models
             that take into account flow through all side branches are
             required for precise computation of shear stress and
             pressure gradient whereas models that have only a subset of
             side branches are inadequate for biomechanical studies as
             they may overestimate volumetric outflow and shear stress.
             This study extends the ongoing computational efforts and
             demonstrates that models based on accurate coronary
             physiology can improve overall fidelity of biomechanical
             studies to compute hemodynamic risk-factors.},
   Doi = {10.1038/s41598-019-45342-5},
   Key = {fds343753}
}

@article{fds342167,
   Author = {Lee, S and Gounley, J and Randles, A and Vetter, JS},
   Title = {Performance portability study for massively parallel
             computational fluid dynamics application on scalable
             heterogeneous architectures},
   Journal = {Journal of Parallel and Distributed Computing},
   Volume = {129},
   Pages = {1-13},
   Year = {2019},
   Month = {July},
   Abstract = {© 2019 Elsevier Inc. 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 research
             community and targeting to platforms ideally suited to
             different vascular regions. In this work, we present a case
             study in performance portability that assesses (1) the ease
             of porting an MPI application optimized for one specific
             architecture to new platforms using variants of hybrid
             MPI+X programming models; (2) performance portability seen
             when simulating blood flow in three different vascular
             regions on diverse heterogeneous architectures; (3)
             model-based performance prediction for future architectures;
             and (4) performance scaling of the hybrid MPI+X
             programming on parallel heterogeneous systems. We discuss
             the lessons learned in porting HARVEY, a massively parallel
             CFD application, from traditional multicore CPUs to diverse
             heterogeneous architectures ranging from NVIDIA/AMD GPUs to
             Intel MICs and Altera FPGAs.},
   Doi = {10.1016/j.jpdc.2019.02.005},
   Key = {fds342167}
}

@article{fds345465,
   Author = {Dabagh, M and Nair, P and Gounley, J and Frakes, D and Gonzalez, LF and Randles, A},
   Title = {Hemodynamic and morphological characteristics of a growing
             cerebral aneurysm.},
   Journal = {Neurosurgical Focus},
   Volume = {47},
   Number = {1},
   Pages = {E13},
   Year = {2019},
   Month = {July},
   Abstract = {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 aneurysm growth, to present the key
             hemodynamic parameters essential for an accurate prediction
             of the growth, and to gain a deeper understanding of the
             underlying mechanisms. Patient-specific images of a growing
             cerebral aneurysm in 3 different growth stages acquired over
             a period of 40 months were segmented and reconstructed. A
             unique aspect of this patient-specific case study was that
             while one side of the aneurysm stayed stable, the other side
             continued to grow. This unique case enabled the authors to
             examine their aims in the same patient with parent and
             daughter arteries under the same inlet flow conditions.
             Pulsatile flow in the aneurysm models was simulated using
             computational fluid dynamics and was validated with in vitro
             experiments using particle image velocimetry measurements.
             The authors' detailed analysis of intrasaccular hemodynamics
             linked the growing regions of aneurysms to flow
             instabilities and complex vortex structures. Extremely low
             velocities were observed at or around the center of the
             unstable vortex structure, which matched well with the
             growing regions of the studied cerebral aneurysm.
             Furthermore, the authors observed that the aneurysm wall
             regions with a growth greater than 0.5 mm coincided with
             wall regions of lower (< 0.5 Pa) time-averaged wall shear
             stress (TAWSS), lower instantaneous (< 0.5 Pa) wall shear
             stress (WSS), and high (> 0.1) oscillatory shear index
             (OSI). To determine which set of parameters can best
             identify growing and nongrowing aneurysms, the authors
             performed statistical analysis for consecutive stages of the
             growing CA. The results demonstrated that the combination of
             TAWSS and the distance from the center of the vortical
             structure has the highest sensitivity and positive
             predictive value, and relatively high specificity and
             negative predictive value. These findings suggest that an
             unstable, recirculating flow structure within the aneurysm
             sac created in the region adjacent to the aneurysm wall with
             low TAWSS may be introduced as an accurate criterion to
             explain the hemodynamic conditions predisposing the aneurysm
             to growth. The authors' findings are based on one patient's
             data set, but the study lays out the justification for
             future large-scale verification. The authors' findings can
             assist clinicians in differentiating stable and growing
             aneurysms during preinterventional planning.},
   Doi = {10.3171/2019.4.FOCUS19195},
   Key = {fds345465}
}