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Publications of Amanda Randles    :chronological  alphabetical  combined  bibtex listing:

Papers Published

  1. Gounley, J; Vardhan, M; Draeger, EW; Valero-Lara, P; Moore, SV; Randles, A, Propagation Pattern for Moment Representation of the Lattice Boltzmann Method, Ieee Transactions on Parallel and Distributed Systems, vol. 33 no. 3 (March, 2022), pp. 642-653 [doi]  [abs]
  2. Bazarin, RLM; Philippi, PC; Randles, A; Hegele, LA, Moments-based method for boundary conditions in the lattice Boltzmann framework: A comparative analysis for the lid driven cavity flow, Computers & Fluids, vol. 230 (November, 2021) [doi]  [abs]
  3. Herschlag, G; Lee, S; Vetter, JS; Randles, A, Analysis of GPU Data Access Patterns on Complex Geometries for the D3Q19 Lattice Boltzmann Algorithm, Ieee Transactions on Parallel and Distributed Systems, vol. 32 no. 10 (October, 2021), pp. 2400-2414 [doi]  [abs]
  4. Puleri, DF; Balogh, P; Randles, A, Computational models of cancer cell transport through the microcirculation., Biomechanics and Modeling in Mechanobiology, vol. 20 no. 4 (August, 2021), pp. 1209-1230 [doi]  [abs]
  5. Balogh, P; Gounley, J; Roychowdhury, S; Randles, A, A data-driven approach to modeling cancer cell mechanics during microcirculatory transport., Scientific Reports, vol. 11 no. 1 (July, 2021), pp. 15232 [doi]  [abs]
  6. Randles, A; Wirsching, H-G; Dean, JA; Cheng, Y-K; Emerson, S; Pattwell, SS; Holland, EC; Michor, F, Computational modelling of perivascular-niche dynamics for the optimization of treatment schedules for glioblastoma., Nature Biomedical Engineering, vol. 5 no. 4 (April, 2021), pp. 346-359 [doi]  [abs]
  7. Vardhan, M; Gounley, J; Chen, SJ; Chi, EC; Kahn, AM; Leopold, JA; Randles, A, Non-invasive characterization of complex coronary lesions., Scientific Reports, vol. 11 no. 1 (April, 2021), pp. 8145 [doi]  [abs]
  8. Feiger, B; Adebiyi, A; Randles, A, Multiscale modeling of blood flow to assess neurological complications in patients supported by venoarterial extracorporeal membrane oxygenation., Computers in Biology and Medicine, vol. 129 (February, 2021), pp. 104155 [doi]  [abs]
  9. Feiger, B; Lorenzana, E; Ranney, D; Bishawi, M; Doberne, J; Vekstein, A; Voigt, S; Hughes, C; Randles, A, Predicting aneurysmal degeneration of type B aortic dissection with computational fluid dynamics, Proceedings of the 12th Acm Conference on Bioinformatics, Computational Biology, and Health Informatics, Bcb 2021 (January, 2021), ISBN 9781450384506 [doi]  [abs]
  10. Bardhan, J; Leung, MA; Martin, E; Randles, A, DOE Computational Science Graduate Fellowship Research Showcase, Computing in Science & Engineering, vol. 23 no. 6 (January, 2021), pp. 5-8 [doi]
  11. Kaplan, M; Kneifel, C; Orlikowski, V; Dorff, J; Newton, M; Howard, A; Shinn, D; Bishawi, M; Chidyagwai, S; Balogh, P; Randles, A, Cloud Computing for COVID-19: Lessons Learned from Massively Parallel Models of Ventilator Splitting, Computing in Science & Engineering, vol. 22 no. 6 (November, 2020), pp. 37-47 [doi]  [abs]
  12. Pepona, M; Balogh, P; Puleri, DF; Hynes, WF; Robertson, C; Dubbin, K; Alvarado, J; Moya, ML; Randles, A, Investigating the Interaction Between Circulating Tumor Cells and Local Hydrodynamics via Experiment and Simulations., Cellular and Molecular Bioengineering, vol. 13 no. 5 (October, 2020), pp. 527-540 [doi]  [abs]
  13. Jang, LK; Alvarado, JA; Pepona, M; Wasson, EM; Nash, LD; Ortega, JM; Randles, A; Maitland, DJ; Moya, ML; Hynes, WF, Three-dimensional bioprinting of aneurysm-bearing tissue structure for endovascular deployment of embolization coils., Biofabrication, vol. 13 no. 1 (October, 2020) [doi]  [abs]
  14. Hynes, WF; Pepona, M; Robertson, C; Alvarado, J; Dubbin, K; Triplett, M; Adorno, JJ; Randles, A; Moya, ML, Examining metastatic behavior within 3D bioprinted vasculature for the validation of a 3D computational flow model., Science Advances, vol. 6 no. 35 (August, 2020), pp. eabb3308 [doi]  [abs]
  15. Cherian, J; Dabagh, M; Srinivasan, VM; Chen, S; Johnson, J; Wakhloo, A; Gupta, V; Macho, J; Randles, A; Kan, P, Balloon-Mounted Stents for Treatment of Refractory Flow Diverting Device Wall Malapposition., Operative Neurosurgery, vol. 19 no. 1 (July, 2020), pp. 37-42 [doi]  [abs]
  16. Ames, J; Puleri, DF; Balogh, P; Gounley, J; Draeger, EW; Randles, A, Multi-GPU Immersed Boundary Method Hemodynamics Simulations., Journal of Computational Science, vol. 44 (July, 2020) [doi]  [abs]
  17. Puleri, DF; Roychowdhury, S; Ames, J; Randles, A, Computational Framework to Evaluate the Hydrodynamics of Cell Scaffold Geometries., Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual International Conference, vol. 2020 (July, 2020), pp. 2299-2302, ISBN 9781728119908 [doi]  [abs]
  18. Roychowdhury, S; Gounley, J; Randles, A, Evaluating the Influence of Hemorheological Parameters on Circulating Tumor Cell Trajectory and Simulation Time, Proceedings of the Platform for Advanced Scientific Computing Conference, Pasc 2020 (June, 2020), ISBN 9781450379939 [doi]  [abs]
  19. Feiger, B; Gounley, J; Adler, D; Leopold, JA; Draeger, EW; Chaudhury, R; Ryan, J; Pathangey, G; Winarta, K; Frakes, D; Michor, F; Randles, A, Accelerating massively parallel hemodynamic models of coarctation of the aorta using neural networks., Scientific Reports, vol. 10 no. 1 (June, 2020), pp. 9508 [doi]  [abs]
  20. Feiger, B; Kochar, A; Gounley, J; Bonadonna, D; Daneshmand, M; Randles, A, Determining the impacts of venoarterial extracorporeal membrane oxygenation on cerebral oxygenation using a one-dimensional blood flow simulator., Journal of Biomechanics, vol. 104 (May, 2020), pp. 109707 [doi]  [abs]
  21. Shi, H; Ames, J; Randles, A, Harvis: an interactive virtual reality tool for hemodynamic modification and simulation, Journal of Computational Science, vol. 43 (May, 2020) [doi]  [abs]
  22. Dabagh, M; Gounley, J; Randles, A, Localization of Rolling and Firm-Adhesive Interactions Between Circulating Tumor Cells and the Microvasculature Wall., Cellular and Molecular Bioengineering, vol. 13 no. 2 (April, 2020), pp. 141-154 [doi]  [abs]
  23. Vardhan, M; Gounley, J; Hegele, L; Draeger, EW; Randles, A, Moment representation in the lattice Boltzmann method on massively parallel hardware, International Conference for High Performance Computing, Networking, Storage and Analysis, Sc (November, 2019), ISBN 9781450362290 [doi]  [abs]
  24. Ames, J; Rizzi, S; Insley, J; Patel, S; Hernández, B; Draeger, EW; Randles, A, Low-Overhead in Situ Visualization Using Halo Replay, 2019 Ieee 9th Symposium on Large Data Analysis and Visualization, Ldav 2019 (October, 2019), pp. 16-26, ISBN 9781728126050 [doi]  [abs]
  25. Herschlag, G; Gounley, J; Roychowdhury, S; Draeger, EW; Randles, A, Multi-physics simulations of particle tracking in arterial geometries with a scalable moving window algorithm, Proceedings Ieee International Conference on Cluster Computing, Iccc, vol. 2019-September (September, 2019), ISBN 9781728147345 [doi]  [abs]
  26. Lee, S; Gounley, J; Randles, A; Vetter, JS, Performance portability study for massively parallel computational fluid dynamics application on scalable heterogeneous architectures, Journal of Parallel and Distributed Computing, vol. 129 (July, 2019), pp. 1-13 [doi]  [abs]
  27. Dabagh, M; Nair, P; Gounley, J; Frakes, D; Gonzalez, LF; Randles, A, Hemodynamic and morphological characteristics of a growing cerebral aneurysm., Neurosurgical Focus, vol. 47 no. 1 (July, 2019), pp. E13 [doi]  [abs]
  28. Vardhan, M; Gounley, J; Chen, SJ; Kahn, AM; Leopold, JA; Randles, A, The importance of side branches in modeling 3D hemodynamics from angiograms for patients with coronary artery disease., Scientific Reports, vol. 9 no. 1 (June, 2019), pp. 8854 [doi]  [abs]
  29. Feiger, B; Vardhan, M; Gounley, J; Mortensen, M; Nair, P; Chaudhury, R; Frakes, D; Randles, A, Suitability of lattice Boltzmann inlet and outlet boundary conditions for simulating flow in image-derived vasculature., International Journal for Numerical Methods in Biomedical Engineering, vol. 35 no. 6 (June, 2019), pp. e3198 [doi]  [abs]
  30. Grigoryan, B; Paulsen, SJ; Corbett, DC; Sazer, DW; Fortin, CL; Zaita, AJ; Greenfield, PT; Calafat, NJ; Gounley, JP; Ta, AH; Johansson, F; Randles, A; Rosenkrantz, JE; Louis-Rosenberg, JD; Galie, PA; Stevens, KR; Miller, JS, Multivascular networks and functional intravascular topologies within biocompatible hydrogels., Science (New York, N.Y.), vol. 364 no. 6439 (May, 2019), pp. 458-464 [doi]  [abs]
  31. Vardhan, M; Das, A; Gouruev, J; Randles, A, Computational fluid modeling to understand the role of anatomy in bifurcation lesion disease, Proceedings 25th Ieee International Conference on High Performance Computing Workshops, Hipcw 2018 (February, 2019), pp. 56-64, ISBN 9781728101149 [doi]  [abs]
  32. Gounley, J; Vardhan, M; Randles, A, A Framework for Comparing Vascular Hemodynamics at Different Points in Time., Computer Physics Communications, vol. 235 (February, 2019), pp. 1-8 [doi]  [abs]
  33. Dabagh, M; Randles, A, Role of deformable cancer cells on wall shear stress-associated-VEGF secretion by endothelium in microvasculature., Plos One, vol. 14 no. 2 (January, 2019), pp. e0211418 [doi]  [abs]
  34. Gounley, J; Draeger, EW; Oppelstrup, T; Krauss, WD; Gunnels, JA; Chaudhury, R; Nair, P; Frakes, D; Leopold, JA; Randles, A, Computing the ankle-brachial index with parallel computational fluid dynamics., Journal of Biomechanics, vol. 82 (January, 2019), pp. 28-37 [doi]  [abs]
  35. Gounley, J; Draeger, EW; Randles, A, Immersed Boundary Method Halo Exchange in a Hemodynamics Application, Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 11536 LNCS (January, 2019), pp. 441-455, ISBN 9783030227333 [doi]  [abs]
  36. Hegele, LA; Scagliarini, A; Sbragaglia, M; Mattila, KK; Philippi, PC; Puleri, DF; Gounley, J; Randles, A, High-Reynolds-number turbulent cavity flow using the lattice Boltzmann method, Physical Review. E, vol. 98 no. 4 (October, 2018), American Physical Society (APS) [doi]  [abs]
  37. Herschlag, G; Lee, S; Vetter, JS; Randles, A, GPU data access on complex geometries for D3Q19 lattice boltzmann method, Proceedings 2018 Ieee 32nd International Parallel and Distributed Processing Symposium, Ipdps 2018 (August, 2018), pp. 825-834, IEEE, ISBN 9781538643686 [doi]  [abs]
  38. Rafat, M; Stone, HA; Auguste, DT; Dabagh, M; Randles, A; Heller, M; Rabinov, JD, Impact of diversity of morphological characteristics and Reynolds number on local hemodynamics in basilar aneurysms, Aiche Journal, vol. 64 no. 7 (July, 2018), pp. 2792-2802, WILEY [doi]  [abs]
  39. Randles, A; Frakes, DH; Leopold, JA, Computational Fluid Dynamics and Additive Manufacturing to Diagnose and Treat Cardiovascular Disease., Trends in Biotechnology, vol. 35 no. 11 (November, 2017), pp. 1049-1061 [doi]  [abs]
  40. Gounley, J; Vardhan, M; Randles, A, A computational framework to assess the influence of changes in vascular geometry on blood flow, Pasc 2017 Proceedings of the Platform for Advanced Scientific Computing Conference (June, 2017), ACM Press, ISBN 9781450350624 [doi]  [abs]
  41. Dabagh, M; Jalali, P; Butler, PJ; Randles, A; Tarbell, JM, Mechanotransmission in endothelial cells subjected to oscillatory and multi-directional shear flow., Journal of the Royal Society, Interface, vol. 14 no. 130 (May, 2017) [doi]  [abs]
  42. Gounley, J; Draeger, EW; Randles, A, Numerical simulation of a compound capsule in a constricted microchannel., Procedia Computer Science, vol. 108 (January, 2017), pp. 175-184 [doi]  [abs]
  43. Laurence, TA; Ly, S; Fong, E; Shusteff, M; Randles, A; Gounley, J; Draeger, E, Using stroboscopic flow imaging to validate large-scale computational fluid dynamics simulations, Progress in Biomedical Optics and Imaging Proceedings of Spie, vol. 10076 (January, 2017), SPIE, ISBN 9781510605930 [doi]  [abs]
  44. Gounley, J; Chaudhury, R; Vardhan, M; Driscoll, M; Pathangey, G; Winarta, K; Ryan, J; Frakes, D; Randles, A, Does the degree of coarctation of the aorta influence wall shear stress focal heterogeneity?, vol. 2016 no. 2016 (August, 2016), pp. 3429-3432, IEEE, ISBN 9781457702204 [doi]  [abs]
  45. Randles, A; Draeger, EW; Oppelstrup, T; Krauss, L; Gunnels, J, Massively Parallel Models of the Human Circulatory System, Http://Dl.Acm.Org/Citation.Cfm?Id=2807676, vol. 15-20-November-2015 (November, 2015), ACM, ISSN 2167-4329, ISBN 978-1-4503-3723-6 [citation.cfm], [doi]  [abs]
  46. Randles, A; Draeger, EW; Bailey, PE, Massively parallel simulations of hemodynamics in the primary large arteries of the human vasculature, Journal of Computational Science, vol. 9 (July, 2015), pp. 70-75, Elsevier BV, ISSN 1877-7503 [doi]  [abs]
  47. Whitley, HD; Scullard, CR; Benedict, LX; Castor, JI; Randles, A; Glosli, JN; Richards, DF; Desjarlais, MP; Graziani, FR, Lenard-Balescu calculations and classical molecular dynamics simulations of electrical and thermal conductivities of hydrogen plasmas, Contributions to Plasma Physics, vol. 55 no. 2-3 (February, 2015), pp. 192-202, WILEY, ISSN 0863-1042 [doi]  [abs]
  48. You, Y; Fu, H; Song, SL; Randles, A; Kerbyson, D; Marquez, A; Yang, G; Hoisie, A, Scaling Support Vector Machines on modern HPC platforms, Journal of Parallel and Distributed Computing, vol. 76 (January, 2015), pp. 16-31, Elsevier BV, ISSN 0743-7315 [doi]  [abs]
  49. Kale, V; Randles, A; Gropp, WD, Locality-optimized mixed static/dynamic scheduling for improving load balancing on SMPs, Acm International Conference Proceeding Series, vol. 09-12-September-2014 (September, 2014), pp. 115-116, ACM Press, ISBN 9781450328753 [doi]  [abs]
  50. Randles, A; Kaxiras, E, Parallel in time approximation of the lattice Boltzmann method for laminar flows, Journal of Computational Physics, vol. 270 (August, 2014), pp. 577-586, Elsevier BV, ISSN 0021-9991 [doi]  [abs]
  51. Randles, A; Rand, D; Lee, C; Morrisett, G; Pfister, H, Massively Parallel Model of Extended Memory Use In Evolutionary Game Dynamics (May, 2014), pp. 1217-1228, IEEE, ISBN 9781467360661 [doi]  [abs]
  52. Almendro, V; Cheng, Y-K; Randles, A; Itzkovitz, S; Marusyk, A; Ametller, E; Gonzalez-Farre, X; Muñoz, M; Russnes, HG; Helland, A; Rye, IH; Borresen-Dale, A-L; Maruyama, R; van Oudenaarden, A; Dowsett, M; Jones, RL; Reis-Filho, J; Gascon, P; Gönen, M; Michor, F; Polyak, K, Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity., Cell Reports, vol. 6 no. 3 (February, 2014), pp. 514-527, ISSN 2211-1247 [doi]  [abs]
  53. Randles, A; Draeger, E; Michor, F, Analysis of pressure gradient across aortic stenosis with massively parallel computational simulations, Computing in Cardiology, vol. 41 no. January (January, 2014), pp. 217-220, ISSN 2325-8861  [abs]
  54. Randles, A; Kaxiras, EK, A Spatio-Temporal Coupling Method to Reduce the Time-to-Solution of Cardiovascular Simulations, 2008 Ieee International Symposium on Parallel and Distributed Processing (January, 2014), pp. 593-602, ISBN 978-1-4799-3801-8 [doi]  [abs]
  55. Randles, A, MIC-SVM: Designing A Highly Efficient Support Vector Machine for Advanced Modern Multi-Core and Many-Core Architectures, 2008 Ieee International Symposium on Parallel and Distributed Processing (January, 2014), pp. 809-818, ISSN 1530-2075, ISBN 9780769552071 [doi]  [abs]
  56. Randles, A; Kale, V; Hammond, JR; Gropp, W; Kaxiras, E, Performance analysis of the lattice Boltzmann model beyond Navier-Stokes (October, 2013), pp. 1063-1074, IEEE, ISBN 9781467360661 [doi]  [abs]
  57. Keyes, DE; McInnes, LC; Woodward, C; Gropp, W; Myra, E; Pernice, M; Bell, J; Brown, J; Clo, A; Connors, J; Constantinescu, E; Estep, D; Evans, K; Farhat, C; Hakim, A; Hammond, G; Hansen, G; Hill, J; Isaac, T; Jiao, X; Jordan, K; Kaushik, D; Kaxiras, E; Koniges, A; Lee, K; Lott, A; Lu, Q; Magerlein, J; Maxwell, R; McCourt, M; Mehl, M; Pawlowski, R; Randles, AP; Reynolds, D; Rivière, B; Rüde, U; Scheibe, T; Shadid, J; Sheehan, B; Shephard, M; Siegel, A; Smith, B; Tang, X; Wilson, C; Wohlmuth, B, Multiphysics simulations: Challenges and opportunities, The International Journal of High Performance Computing Applications, vol. 27 no. 1 (February, 2013), pp. 4-83, SAGE Publications, ISSN 1094-3420 [doi]  [abs]
  58. Randles, AP, Massively parallel model of evolutionary game dynamics, Proceedings 2012 Sc Companion: High Performance Computing, Networking Storage and Analysis, Scc 2012 (December, 2012), pp. 1531, IEEE [doi]  [abs]
  59. Randles, A; Baecher, M; Pfister, H; Kaxiras, EK, A Lattice Boltzmann Simulation of Hemodynamics in a Patient-Speci c Aortic Coarctation Model, edited by Camara, O; Pop, M; Mansi, T; Sermesant, M; Young, A, Statistical Atlases and Computational Models of the Heart: Imaging and Modelling Challenges:, vol. 7746 (October, 2012), pp. 17-25, Springer Berlin Heidelberg [978-3-642-36961-2_3], [doi]  [abs]
  60. Borkin, MA; Gajos, KZ; Peters, A; Mitsouras, D; Melchionna, S; Rybicki, FJ; Feldman, CL; Pfister, H, Evaluation of artery visualizations for heart disease diagnosis., Ieee Transactions on Visualization and Computer Graphics, vol. 17 no. 12 (December, 2011), pp. 2479-2488, ISSN 1077-2626 [doi]  [abs]
  61. Randles, A; Zeger, L, Efficient Resource Allocation for Broadcasting Multi-Slot Messages With Random Access with Capture (October, 2011), IEEE [available here]
  62. Robson, B; Li, J; Dettinger, R; Peters, A; Boyer, SK, Drug discovery using very large numbers of patents. General strategy with extensive use of match and edit operations, Journal of Computer Aided Molecular Design, vol. 25 no. 5 (May, 2011), pp. 427-441, Springer Science and Business Media LLC, ISSN 0920-654X [doi]
  63. Randles, A; Melchionna, S; Kaxiras, E; Latt, J; Sircar, J; Bernaschi, M; Bisson, M; Succi, S, Multiscale simulation of cardiovascular flows on the IBM Bluegene/P: full heart-circulation system at red-blood cell resolution (November, 2010), ACM IEEE
  64. Randles, A; King, A; Budnik, T; McCarthy, P; Michaud, P; Mundy, M; Sexton, J; Stewart, G, Asynchronous task dispatch for high throughput computing for the eServer IBM Blue Gene Supercomputer, 2008 Ieee International Symposium on Parallel and Distributed Processing (April, 2008), IEEE, ISBN 978-1-4244-1693-6 [doi]  [abs]
  65. Jiang, K; Thorsen, O; Peters, A; Smith, B; Sosa, CP, An Efficient Parallel Implementation of the Hidden Markov Methods for Genomic Sequence-Search on a Massively Parallel System, Ieee Transactions on Parallel and Distributed Systems, vol. 19 no. 1 (January, 2008), pp. 15-23, Institute of Electrical and Electronics Engineers (IEEE), ISSN 1045-9219 [doi]
  66. Pang, Y-P; Mullins, TJ; Swartz, BA; McAllister, JS; Smith, BE; Archer, CJ; Musselman, RG; Peters, AE; Wallenfelt, BP; Pinnow, KW, EUDOC on the IBM Blue Gene/L system: Accelerating the transfer of drug discoveries from laboratory to patient, Ibm Journal of Research and Development, vol. 52 no. 1.2 (January, 2008), pp. 69-81, IBM, ISSN 0018-8646 [doi]
  67. Randles, A, Parallel Genomic Sequence-Search on a Massively Parallel System, edited by Thorsen, O; Jiang, K; Smith, B; Lin, H; Feng, W; Sosa, CP (May, 2007), ACM
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