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Fundamental and Computational Sciences Directorate

Staff information

Andrew

Andrew Kuprat

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

PNNL Publications

2019

  • Rod K.A., W. Um, S.M. Colby, M.L. Rockhold, C.E. Strickland, A.P. Kuprat, and S. Han. 2019. "Relative permeability for water and gas through fractures in cement." PLoS One 14, no. 1:Article Number: e0210741. PNNL-SA-124005. doi:10.1371/journal.pone.0210741

2016

  • Asgharian B., O. Price, S. Kabilan, R.E. Jacob, D.R. Einstein, A.P. Kuprat, and R.A. Corley. 2016. "Development of a Zealand white rabbit deposition model to study inhalation anthrax." Inhalation Toxicology 28, no. 2:80-88. PNNL-SA-121795. doi:10.3109/08958378.2016.1140850
  • Colby S.M., S. Kabilan, R.E. Jacob, A.P. Kuprat, D.R. Einstein, and R.A. Corley. 2016. "Comparison of realistic and idealized breathing patterns in computational models of airflow and vapor dosimetry in the rodent upper respiratory tract." Inhalation Toxicology 28, no. 4:192-202. PNNL-SA-121794. doi:10.3109/08958378.2016.1150367
  • Kabilan S., H.B. Jung, A.P. Kuprat, A. Beck, T. Varga, C.A. Fernandez, and W. Um. 2016. "Numerical Simulation of Permeability Change in Wellbore Cement Fractures after Geomechanical Stress and Geochemical Reactions Using X-ray Computed Tomography Imaging." Environmental Science & Technology 50, no. 12:6180-6188. PNNL-SA-115077. doi:10.1021/acs.est.6b00159
  • Kabilan S., S.R. Suffield, K.P. Recknagle, R.E. Jacob, D.R. Einstein, A.P. Kuprat, and J.P. Carson, et al. 2016. "Computational Fluid Dynamics Modeling of Bacillus anthracis Spore Deposition in Rabbit and Human Respiratory Airways." Journal of Aerosol Science 99. PNNL-SA-108616. doi:10.1016/j.jaerosci.2016.01.011

2015

  • Corley R.A., S. Kabilan, A.P. Kuprat, J.P. Carson, R.E. Jacob, K.R. Minard, and J.G. Teeguarden, et al. 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, no. 1:65-88. PNNL-SA-106531. doi:10.1093/toxsci/kfv071
  • Jung H., K. Carroll, S. Kabilan, D.J. Heldebrant, D.W. Hoyt, L. Zhong, and T. Varga, et al. 2015. "Stimuli-Responsive/Rheoreversible Hydraulic Fracturing Fluids as a Greener Alternative to Support Geothermal and Fossil Energy Production." Green Chemistry 17, no. 5:2799-2812. PNNL-SA-106027. doi:10.1039/c4gc01917b
  • Renslow R.S., J.T. Babauta, A.P. Kuprat, J. Schenk, C. Ivory, J.K. Fredrickson, and H. Beyenal. 2015. "MATHEMATICAL MODELING OF EXTRACELLULAR ELECTRON TRANSFER IN BIOFILMS." In Biofilms in Bioelectrochemical Systems: From Laboratory Practice to Data Interpretation. Hoboken, New Jersey:John Wiley & Sons, Inc. PNNL-SA-101138. doi:10.1002/9781119097426.ch9
  • Shao H., S. Kabilan, S.A. Stephens, N. Suresh, A. Beck, T. Varga, and P.F. Martin, et al. 2015. "Environmentally Friendly, Rheoreversible, Hydraulic-fracturing Fluids for Enhanced Geothermal Systems." Geothermics 58. PNNL-SA-105984. doi:10.1016/j.geothermics.2015.07.010
  • Thomas M., K. Kleese van Dam, M.J. Marshall, A.P. Kuprat, J.P. Carson, C.S. Lansing, and Z.C. Guillen, et al. 2015. "Towards adaptive, streaming analysis of x-ray tomography data." Synchrotron Radiation News 28, no. 2:10-14. PNNL-SA-107653. doi:10.1080/08940886.2015.1013414

2014

  • Jung H., S. Kabilan, J.P. Carson, A.P. Kuprat, W. Um, P.F. Martin, and M.E. Dahl, et al. 2014. "Wellbore cement fracture evolution at the cement-basalt caprock interface during geologic carbon sequestration." Applied Geochemistry 47. PNNL-SA-106261. doi:10.1016/j.apgeochem.2014.04.010
  • Thomas M., M.J. Marshall, E.A. Miller, A.P. Kuprat, K. Kleese van Dam, and J.P. 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, 3304 - 3307. Piscataway, New Jersey:IEEE. PNNL-SA-103381. doi:10.1109/EMBC.2014.6944329

2013

  • Einstein D.R., A.P. Kuprat, X. Jiao, J.P. Carson, D.M. Einstein, R.A. Corley, and R.E. 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, no. 1:1-16. PNNL-SA-85247. doi:10.1002/cnm.2489
  • Kleese van Dam K., J.P. Carson, A.L. Corrigan, D.R. Einstein, Z.C. Guillen, B.S. Heath, and A.P. Kuprat, et al. 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. Los Alamitos, California:IEEE Press. PNNL-SA-89470. doi:10.1109/eScience.2012.6404463
  • Kuprat A.P., S. Kabilan, J.P. Carson, R.A. Corley, and D.R. Einstein. 2013. "A Bidirectional Coupling Procedure Applied to Multiscale Respiratory Modeling." Journal of Computational Physics 244. PNNL-SA-91838. doi:10.1016/j.jcp.2012.10.021
  • Renslow R.S., J.T. Babauta, A.P. Kuprat, J. Schenk, C. Ivory, J.K. Fredrickson, and H. Beyenal. 2013. "Modeling biofilms with dual extracellular electron transfer mechanisms." Physical Chemistry Chemical Physics. PCCP 15, no. 44:19262-19283. PNNL-SA-94504. doi:10.1039/c3cp53759e

2012

  • Carson J.P., A.P. Kuprat, S.M. Colby, C.A. Davis, C. Basciano, K. Greene, and J.T. Feo, et al. 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, 1149-1152. Piscataway, New Jersey:IEEE. PNNL-SA-86493. doi:10.1109/EMBC.2012.6346139
  • Corley R.A., S. Kabilan, A.P. Kuprat, J.P. Carson, K.R. Minard, R.E. Jacob, and C. Timchalk, et al. 2012. "COMPARATIVE COMPUTATIONAL MODELING OF AIRFLOWS AND VAPOR DOSIMETY IN THE RESPIRATORY TRACTS OF RAT, MONKEY, AND HUMAN." Toxicological Sciences 128, no. 2:500-516. PNNL-SA-83274. doi:10.1093/toxsci/kfs168
  • Minard K.R., A.P. Kuprat, S. Kabilan, R.E. Jacob, D.R. Einstein, J.P. Carson, and R.A. Corley. 2012. "Phase-Contrast MRI and CFD Modeling of Apparent 3He Gas Flow in Rat Pulmonary Airways." Journal of Magnetic Resonance 221. PNNL-SA-85956. doi:10.1016/j.jmr.2012.05.007
  • Thomas M., B.S. Heath, J. Laskin, D. Li, E.C. Liu, K.L. Hui, and A.P. Kuprat, et al. 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, 5545-5548. Piscataway, New Jersey:IEEE. PNNL-SA-86504. doi:10.1109/EMBC.2012.6347250

2011

  • Kabilan S., A.P. Kuprat, M.P. Hlastala, R.A. Corley, and D.R. 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, 2414-2417. Piscataway, New Jersey:IEEE. PNNL-SA-79152.

2010

  • Carson J.P., A.P. Kuprat, X. Jiao, F. del Pin, and D.R. Einstein. 2010. "An Anisotropic Fluid-Solid Model of the Mouse Heart." In Computers in Cardiology 2009, Park City, Utah September 13-16, 2009, 36, 377-380. Piscataway, New Jersey:Computers in Cardiology and IEEE. PNNL-SA-68145.
  • Carson J.P., A.P. Kuprat, X. Jiao, V. Dyedov, F. del Pin, J.M. Guccione, and M.B. Ratcliffe, et al. 2010. "Adaptive Generation of Multimaterial Grids from imaging data for Biomedical Lagrangian Fluid-Structure Simulations." Biomechanics and Modeling in Mechanobiology 9, no. 2:187-201. PNNL-SA-66671. doi:10.1007/S10237-009-0170-5
  • Hsu E.W., L.J. Healy, D.R. Einstein, and A.P. Kuprat. 2010. "Imaging-Based Assessment and Modeling of the Structures of the Myocardium." In Computational Cardiovascular Mechanics: Modeling and Applications in Heart Failure. 23-29. New York, New York:Springer. PNWD-SA-8490.
  • Wischgoll T., D.R. Einstein, A.P. Kuprat, X. Jiao, and G.S. Kassab. 2010. "Vascular Geometry Reconstruction and Grid Generation." In Computational Cardiovascular Mechanics: Modeling and Applications in Heart Failure. 103-119. New York, New York:Springer. PNWD-SA-8541.

2009

  • Corley R.A., K.R. Minard, S. Kabilan, D.R. Einstein, A.P. Kuprat, J.R. harkema, and J. Kimbell, et al. 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, no. 5-7:512-518. PNNL-SA-66683.
  • Corley R.A., K.R. Minard, S. Kabilan, D.R. Einstein, A.P. Kuprat, J.R. Harkema, and J. Kimbell, et al. 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, no. 6:512-518. PNWD-SA-7181.
  • Dyedov V., D.R. Einstein, X. Jiao, A.P. Kuprat, J.P. Carson, and F. del Pin. 2009. "Variational Generation of Prismatic Boundary-Layer Meshes for Biomedical Computing." International Journal for Numerical Methods in Engineering 79, no. 8:907-945. PNWD-SA-8252. doi:10.1002/nme.2583
  • Einstein D.R., F. del Pin, X. Jiao, A.P. Kuprat, J.P. Carson, K. Kunzelman, and R.P. Cochran, et al. 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, no. 3-4:348-380. PNWD-SA-8310. doi:10.1002/cnm.1280
  • Kuprat A.P., and D.R. Einstein. 2009. "An Anisotropic Scale-Invariant Unstructured Mesh Generator Auitable for Volumetric Imaging Data." Journal of Computational Physics 228, no. 3:619-640. PNNL-SA-54596. doi:10.1016/j.jcp.2008.09.030

2008

  • Einstein D.R., B. Neradilak, N. Pollisar, K.R. Minard, C. Wallis, M. Fanucchi, and J.P. Carson, et al. 2008. "An Automated Self-similarity Analysis of the Pulmonary Tree of the Sprague-Dawley Rat." The Anatomical Record 291, no. 12:1628-1648. PNNL-SA-58476. doi:10.1002/ar.20771
  • Khamayseh A., and A.P. Kuprat. 2008. "Deterministic point inclusion methods for computational applications with complex geometry." Computational Science and Discovery 1, no. Published Online Only:Art. No. 015004. PNNL-SA-63177. doi:10.1088/1749-4699/1/1/015004
  • Minard K.R., R.E. Jacob, G. Laicher, D.R. Einstein, A.P. Kuprat, and R.A. Corley. 2008. "MR Imaging of Apparent 3He Gas Transport in Narrow Pipes and Rodent Airways." Journal of Magnetic Resonance 194, no. 2:182-191. PNNL-SA-59586. doi:10.1016/j.jmr.2008.07.006

2006

  • Minard K.R., D.R. Einstein, R.E. Jacob, S. Kabilan, A.P. Kuprat, C. Timchalk, and L.L. Trease, et al. 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, no. 10:787-794. PNNL-SA-47732. doi:10.1080/08958370600748729

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