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Andrew Kuprat

Andrew Kuprat

Computational Biology
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-18
Richland, WA 99352

PNNL Publications


  • Corley RA, S Kabilan, AP Kuprat, JP Carson, RE Jacob, KR Minard, JG Teeguarden, C Timchalk, S Pipavath, RW Glenny, and DR Einstein. 2015. "COMPARATIVE RISKS OF ALDEHYDE CONSTITUENTS IN CIGARETTE SMOKE USING TRANSIENT COMPUTATIONAL FLUID DYNAMICS/PHYSIOLOGICALLY BASED PHARMACOKINETIC MODELS OF THE RAT AND HUMAN RESPIRATORY TRACTS." Toxicological Sciences 146(1):65-88.  doi:10.1093/toxsci/kfv071
  • Jung HB, KC Carroll, S Kabilan, DJ Heldebrant, DW Hoyt, L Zhong, T Varga, SA Stephens, L Adams, A Bonneville, AP Kuprat, and CA Fernandez. 2015. "Stimuli-Responsive/Rheoreversible Hydraulic Fracturing Fluids as a Greener Alternative to Support Geothermal and Fossil Energy Production." Green Chemistry 17(5):2799-2812.  doi:10.1039/c4gc01917b
  • Shao H, S Kabilan, SA Stephens, N Suresh, ANR Beck, T Varga, PF Martin, AP Kuprat, HB Jung, W Um, A Bonneville, DJ Heldebrant, KC Carroll, J Moore, and CA Fernandez. 2015. "Environmentally Friendly, Rheoreversible, Hydraulic-fracturing Fluids for Enhanced Geothermal Systems." Geothermics 58:22-31.  doi:10.1016/j.geothermics.2015.07.010
  • Thomas M, K Kleese van Dam, MJ Marshall, AP Kuprat, JP Carson, CS Lansing, ZC Guillen, EA Miller, I Lanekoff, and J Laskin. 2015. "Towards adaptive, streaming analysis of x-ray tomography data." Synchrotron Radiation News 28(2):10-14.  doi:10.1080/08940886.2015.1013414


  • Jung HB, S Kabilan, JP Carson, AP Kuprat, W Um, PF Martin, ME Dahl, TA Kafentzis, T Varga, SA Stephens, BW Arey, KC Carroll, A Bonneville, and CA Fernandez. 2014. "Wellbore cement fracture evolution at the cement-basalt caprock interface during geologic carbon sequestration." Applied Geochemistry 47:1-16.  doi:10.1016/j.apgeochem.2014.04.010
  • Thomas M, MJ Marshall, EA Miller, AP Kuprat, K Kleese van Dam, and JP Carson. 2014. "3D Imaging of Microbial Biofilms: Integration of Synchrotron Imaging and an Interactive Visualization Interface." In 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), August 26-30, 2014, Chicago, IL, pp. 3304 - 3307.  IEEE, Piscataway, NJ.  doi:10.1109/EMBC.2014.6944329


  • Einstein DR, AP Kuprat, X Jiao, JP Carson, DM Einstein, RA Corley, and RE Jacob. 2013. "An Efficient Algorithm for Mapping Imaging Data to 3D Unstructured Grids in Computational Biomechanics." International Journal for Numerical Methods in Biomedical Engineering 29(1):1-16.  doi:10.1002/cnm.2489
  • Kleese van Dam K, JP Carson, AL Corrigan, DR Einstein, ZC Guillen, BS Heath, AP Kuprat, IT Lanekoff, CS Lansing, J Laskin, D Li, Y Liu, MJ Marshall, EA Miller, G Orr, P Pinheiro da Silva, S Ryu, CJ Szymanski, and M Thomas. 2013. "Velo and REXAN - Integrated Data Management and High Speed Analysis for Experimental Facilities." In Proceedings of the IEEE 8th International Conference on EScience, October 8-12, 2012, Chicago, Illinois.  IEEE Press, Los Alamitos, CA.  doi: 10.1109/eScience.2012.6404463
  • Kuprat AP, S Kabilan, JP Carson, RA Corley, and DR Einstein. 2013. "A Bidirectional Coupling Procedure Applied to Multiscale Respiratory Modeling." Journal of Computational Physics 244:148-167.  doi:10.1016/
  • Renslow RS, JT Babauta, AP Kuprat, J Schenk, C Ivory, JK Fredrickson, and H Beyenal. 2013. "Modeling biofilms with dual extracellular electron transfer mechanisms." Physical Chemistry Chemical Physics. PCCP 15(44):19262-19283.  doi:10.1039/c3cp53759e


  • Carson JP, AP Kuprat, SM Colby, CA Davis, C Basciano, K Greene, JT Feo, and A Kennedy. 2012. "Detecting Distance between Injected Microspheres and Target Tumor via 3D Reconstruction of Tissue Sections." In 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), August 28 - September 1, San Diego, California, pp. 1149-1152.  IEEE, Piscataway, NJ.  doi:10.1109/EMBC.2012.6346139
  • Corley RA, S Kabilan, AP Kuprat, JP Carson, KR Minard, RE Jacob, C Timchalk, RW Glenny, S Pipavath, TC Cox, C Wallis, R Larson, M Fanucchi, E Postlewait, and DR Einstein. 2012. "COMPARATIVE COMPUTATIONAL MODELING OF AIRFLOWS AND VAPOR DOSIMETY IN THE RESPIRATORY TRACTS OF RAT, MONKEY, AND HUMAN." Toxicological Sciences 128(2):500-516.  doi:10.1093/toxsci/kfs168
  • Minard KR, AP Kuprat, S Kabilan, RE Jacob, DR Einstein, JP Carson, and RA Corley. 2012. "Phase-Contrast MRI and CFD Modeling of Apparent 3He Gas Flow in Rat Pulmonary Airways." Journal of Magnetic Resonance 221:129-138.  doi:10.1016/j.jmr.2012.05.007
  • Thomas M, BS Heath, J Laskin, D Li, EC Liu, KL Hui, AP Kuprat, K Kleese van Dam, and JP Carson. 2012. "Visualization of High Resolution Spatial Mass Spectrometric Data during Acquisition." In 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), August 28 - September 1, San Diego, California, pp. 5545-5548.  IEEE, Piscataway, NJ.  doi:10.1109/EMBC.2012.6347250


  • Kabilan S, AP Kuprat, MP Hlastala, RA Corley, and DR Einstein. 2011. "A Multiscale Bidirectional Coupling Framework ." In Proceedings of the 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, August 30-September 3, 2011, Boston, Massachusetts, pp. 2414-2417.  IEEE, Piscataway, NJ. 


  • Carson JP, AP Kuprat, X Jiao, F del Pin, and DR Einstein. 2010. "An Anisotropic Fluid-Solid Model of the Mouse Heart." In Computers in Cardiology 2009, Park City, Utah September 13-16, 2009, vol. 36, pp. 377-380.  Computers in Cardiology and IEEE, Piscataway, NJ. 
  • Carson JP, AP Kuprat, X Jiao, V Dyedov, F del Pin, JM Guccione, MB Ratcliffe, and DR Einstein. 2010. "Adaptive Generation of Multimaterial Grids from imaging data for Biomedical Lagrangian Fluid-Structure Simulations." Biomechanics and Modeling in Mechanobiology 9(2):187-201.  doi:10.1007/S10237-009-0170-5
  • Hsu EW, LJ Healy, DR Einstein, and AP Kuprat. 2010. "Imaging-Based Assessment and Modeling of the Structures of the Myocardium." Chapter 2 in Computational Cardiovascular Mechanics: Modeling and Applications in Heart Failure, pp. 23-29.  Springer, New York, NY. 
  • Wischgoll T, DR Einstein, AP Kuprat, X Jiao, and GS Kassab. 2010. "Vascular Geometry Reconstruction and Grid Generation." Chapter 7 in Computational Cardiovascular Mechanics: Modeling and Applications in Heart Failure, pp. 103-119.  Springer, New York, NY. 


  • Corley RA, KR Minard, S Kabilan, DR Einstein, AP Kuprat, JR harkema, J Kimbell, ML Gargas, and JH Kinzell. 2009. "Magnetic resonance imaging and computational fluid dynamics (CFD) simulations of rabbit nasal airflows for the development of hybrid CFD/PBPK models ." Inhalation Toxicology 21(5-7):512-518. 
  • Corley RA, KR Minard, S Kabilan, DR Einstein, AP Kuprat, JR Harkema, J Kimbell, ML Gargas, and JH Kinzell. 2009. "Magnetic Resonance Imaging and Computational Fluid Dynamics (CFD) Simulations of Rabbit Nasal Airflows for the Development of Hybrid CFD/PBPK Models." Inhalation Toxicology 21(6):512-518. 
  • Dyedov V, DR Einstein, X Jiao, AP Kuprat, JP Carson, and F del Pin. 2009. "Variational Generation of Prismatic Boundary-Layer Meshes for Biomedical Computing." International Journal for Numerical Methods in Engineering 79(8):907-945.  doi:10.1002/nme.2583
  • Einstein DR, F del Pin, X Jiao, AP Kuprat, JP Carson, K Kunzelman, RP Cochran, JM Guccione, and MB Ratcliffe. 2009. "Fluid-Structure Interactions of the Mitral Valve and Left Heart: Comprehensive Strategies, Past, Present and Future." International Journal for Numerical Methods in Biomedical Engineering 26(3-4):348-380.  doi:10.1002/cnm.1280
  • Kuprat AP, and DR Einstein. 2009. "An Anisotropic Scale-Invariant Unstructured Mesh Generator Auitable for Volumetric Imaging Data." Journal of Computational Physics 228(3):619-640.  doi:10.1016/


  • Einstein DR, B Neradilak, N Pollisar, KR Minard, C Wallis, M Fanucchi, JP Carson, AP Kuprat, S Kabilan, R Jacob, and R Corley. 2008. "An Automated Self-similarity Analysis of the Pulmonary Tree of the Sprague-Dawley Rat." The Anatomical Record 291(12):1628-1648.  doi:10.1002/ar.20771
  • Khamayseh A, and AP Kuprat. 2008. "Deterministic point inclusion methods for computational applications with complex geometry." Computational Science and Discovery 1(Published Online Only):Art. No. 015004.  doi:10.1088/1749-4699/1/1/015004
  • Minard KR, RE Jacob, G Laicher, DR Einstein, AP Kuprat, and RA Corley. 2008. "MR Imaging of Apparent 3He Gas Transport in Narrow Pipes and Rodent Airways ." Journal of Magnetic Resonance 194(2):182-191.  doi:10.1016/j.jmr.2008.07.006


  • Minard KR, DR Einstein, RE Jacob, S Kabilan, AP Kuprat, C Timchalk, LL Trease, and RA Corley. 2006. "Application of Magnetic Resonance (MR) Imaging for the Development and Validation of Computational Fluid Dynamic (CFD) Models of the Rat Respiratory System." Inhalation Toxicology 18(10):787-794.  doi: 10.1080/08958370600748729

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