Staff information

PNNL Publications

2023

• Palmer B.J., A. Almgren, C. Johnson, A.T. Myers, and W.R. Cannon. 2023. "BMX: Biological Modelling and Interface Exchange." Scientific Reports 13. PNNL-SA-189605. doi:10.1038/s41598-023-39150-1

2020

• Chen Y., K.R. Glaesemann, X. Li, B.J. Palmer, R. Huang, and B. Vyakaranam. 2020. "A Generic Advanced Computing Framework for Executing Windows-based Dynamic Contingency Analysis Tool in Parallel on Cluster Machines." In IEEE Power & Energy Society General Meeting (PESGM 2020), August 2-6, 2020, Montreal, Canada, 1-5. Piscataway, New Jersey:IEEE. PNNL-SA-149017. doi:10.1109/PESGM41954.2020.9281477

2019

• Huang Q., R. Huang, B.J. Palmer, Y. Liu, S. Jin, R. Diao, and Y. Chen, et al. 2019. "A Generic Modeling and Development Approach for WECC Composite Load Model." Electric Power Systems Research 172. PNNL-SA-125265. doi:10.1016/j.epsr.2019.02.027

2018

• Chen Y., B.J. Palmer, P. Sharma, Y. Yuan, B. Mathew, and Z. Huang. 2018. "A High Performance Computational Framework for Dynamic Security Assessment under Uncertainty." In IEEE Electronic Power Grid (eGrid 2018), November 12-14, 2018, Charleston, SC. Piscataway, New Jersey:IEEE. PNNL-SA-138783. doi:10.1109/eGRID.2018.8598684
• Palmer B.J. 2018. "Coarse-Grained Hydrodynamics from Correlation Functions." Physical Review E 97, no. 2:Article No. 022106. PNNL-SA-115670. doi:10.1103/PhysRevE.97.022106
• Palmer B.J. 2018. "Coarse-Grained Hydrodynamics from Correlation Functions." Physical Review E 97, no. 2:Article No. 022106. PNNL-SA-127413. doi:10.1103/PhysRevE.97.022106

2017

• Bylaska E.J., E. Apra, K. Kowalski, M. Jacquelin, W.A. De Jong, A. Vishnu, and B.J. Palmer, et al. 2017. "Transitioning NWChem to the Next Generation of Manycore Machines." In Exascale Scientific Applications: Scalability and Performance Portability, edited by TP Straatsma, KB Antypas and TJ Williams. 165-186. New York, New York:Chapman and Hall/CRC. PNNL-SA-130902.
• Huang R., S. Jin, Y. Chen, R. Diao, B.J. Palmer, Q. Huang, and Z. Huang. 2017. "Faster than Real-Time Dynamic Simulation for Large-Size Power System with Detailed Dynamic Models using High-Performance Computing Platform." In IEEE Power & Energy Society General Meeting, July 16-20, 2017, Chicago, Illinois. Piscataway, New Jersey:IEEE. PNNL-SA-122263. doi:10.1109/PESGM.2017.8274505

2016

• Chen Y., E.B. Fitzhenry, S. Jin, B.J. Palmer, P. Sharma, and Z. Huang. 2016. "An Integrated Software Package to Enable Predictive Simulation Capabilities." In 19th Power Systems Computation Conference (PSCC 2016), June, 20-24 2016, Genoa Italy. Piscataway, New Jersey:IEEE. PNNL-SA-113618. doi:10.1109/PSCC.2016.7540951
• Jin S., Y. Chen, R. Diao, Z. Huang, W.A. Perkins, and B.J. Palmer. 2016. "Power Grid Simulation Applications Developed Using the GridPACKTM High Performance Computing Framework." Electric Power Systems Research 141. PNNL-SA-115344. doi:10.1016/j.epsr.2016.06.024
• Makarov Y.V., D. Meng, B. Vyakaranam, R. Diao, B.J. Palmer, and Z. Huang. 2016. "Direct methods to estimate the most limiting voltage level and thermal violations in coordinates of power transfers on critical transmission paths." In 49th Hawaii International Conference on System Sciences (HICSS 2016), January 5-8, 2016, Kauai, Hawaii, 2466-2471. Piscataway, New Jersey:IEEE. PNNL-SA-111006. doi:10.1109/HICSS.2016.308
• Palmer B.J., W.A. Perkins, Y. Chen, S. Jin, D. Callahan, K.A. Glass, and R. Diao, et al. 2016. "GridPACK™ : A Framework for Developing Power Grid Simulations on High-Performance Computing Platforms." International Journal of High Performance Computing Applications 30, no. 2:223-240. PNNL-SA-109336. doi:10.1177/1094342015607609

2015

• Krishnamoorthy S., J.A. Daily, A. Vishnu, and B.J. Palmer. 2015. "Global Arrays." In Programming Models for Parallel Computing. 113-128. Cambridge, Massachusetts:MIT Press. PNNL-SA-111177.
• Scheibe T.D., E.M. Murphy, X. Chen, A.K. Rice, K.C. Carroll, B.J. Palmer, and A.M. Tartakovsky, et al. 2015. "An Analysis Platform for Multiscale Hydrogeologic Modeling with Emphasis on Hybrid Multiscale Methods." Groundwater 53, no. 1:38-56. PNNL-SA-93006. doi:10.1111/gwat.12179
• Scheibe T.D., K.L. Schuchardt, K. Agarwal, J.M. Chase, X. Yang, B.J. Palmer, and A.M. Tartakovsky, et al. 2015. "Hybrid multiscale simulation of a mixing-controlled reaction." Advances in Water Resources 83. PNNL-SA-105960. doi:10.1016/j.advwatres.2015.06.006
• Wood L.S., J.A. Daily, M.J. Henry, B.J. Palmer, K.L. Schuchardt, D.A. Dazlich, and R.P. Heikes, et al. 2015. "A Global Climate Model Agent for High Spatial and Temporal Resolution Data." International Journal of High Performance Computing Applications 29, no. 1:107-116. PNNL-SA-94300. doi:10.1177/1094342013518808

2014

• Daily J.A., A. Vishnu, B.J. Palmer, H.J. van Dam, and D.J. Kerbyson. 2014. "On the Suitability of MPI as a PGAS Runtime." In 21st International Conference on High Performance Computing, (HiPC 2014), December 17-20, 2014, Dona Paula, India, 1-10. Piscataway, New Jersey:IEEE. PNNL-SA-104811. doi:10.1109/HiPC.2014.7116712
• Scheibe T.D., X. Yang, K.L. Schuchardt, K. Agarwal, J.M. Chase, B.J. Palmer, and A.M. Tartakovsky. 2014. "A Many-Task Parallel Approach for Multiscale Simulations of Subsurface Flow and Reactive Transport." In 7th Workshop on Many-Task Computing on Clouds, Grids, and Supercomputers (MTAGS 2014), November 16, 2014, New Orleans, Louisiana. New York, New York:ACM. PNNL-SA-105263.

2013

• Bandara D.C., A.M. Tartakovsky, M. Oostrom, B.J. Palmer, J.W. Grate, and C. Zhang. 2013. "Smoothed Particle Hydrodynamics pore-scale simulations of unstable immiscible flow in porous media." Advances in Water Resources 62, no. Part C:356-369. PNNL-SA-97277. doi:10.1016/j.advwatres.2013.09.014
• Palmer B.J., W.A. Perkins, K.A. Glass, Y. Chen, S. Jin, and C.D. Callahan. 2013. "GridPACK Toolkit for Developing Power Grid Simulations on High Performance Computing Platforms." In Proceedings of the 3rd International Workshop on High Performance Computing, Networking, and Analytics for the Power Grid (HiPCNA-PG '13), November 17-21, 2013, Denver, Colorado, Article No. 3. New York, New York:ACM. PNNL-SA-99768. doi:10.1145/2536780.2536782
• Scheibe T.D., Z. Hou, B.J. Palmer, and A.M. Tartakovsky. 2013. "Pore-Scale Simulation of Intragranular Diffusion: Effects of Incomplete Mixing on Macroscopic Manifestations." Water Resources Research 49, no. 7:4277-4294. PNNL-SA-91962. doi:10.1002/wrcr.20333

2012

• Vishnu A., J.A. Daily, and B.J. Palmer. 2012. "Designing Scalable PGAS Communication Subsystems on Cray Gemini Interconnect." In 19th International Conference on High Performance Computing (HiPC), December 18-22, 2012, Pune, India. Piscataway, New Jersey:Institute of Electrical and Electronics Engineers. PNNL-SA-89704. doi:10.1109/HiPC.2012.6507506

2011

• Agarwal K., J.M. Chase, K.L. Schuchardt, T.D. Scheibe, B.J. Palmer, and T.O. Elsethagen. 2011. "Design and Implementation of “Many Parallel Task” Hybrid Subsurface Model." In MTAGS '11: Proceedings of the 2011 ACM International Workshop on Many Task Computing on Grids and Supercomputers, November 12-18, 2011, Seattle, Washington, 25-32. New York, New York:Association for Computing Machinery. PNNL-SA-83048. doi:10.1145/2132876.2132884
• Bandara U.C., A.M. Tartakovsky, and B.J. Palmer. 2011. "Pore-scale study of capillary trapping mechanism during CO2 injection in geological formations." International Journal of Greenhouse Gas Control 5, no. 6:1566-1577. PNNL-SA-79776. doi:10.1016/j.ijggc.2011.08.014
• Nieplocha J., M. Krishnan, B.J. Palmer, V. Tipparaju, R.J. Harrison, and D. Chavarría-Miranda. 2011. "Global Arrays Parallel Programming Toolkit." In Encyclopedia of Parallel Computing, edited by D Padua. 779-787. New York, New York:Springer. PNNL-SA-76024.
• Palmer B.J., A.S. Koontz, K.L. Schuchardt, R.P. Heikes, and D.A. Randall. 2011. "Efficient data IO for a Parallel Global Cloud Resolving Model." Environmental Modelling & Software 26, no. 12:1725-1735. PNNL-SA-73200. doi:10.1016/j.envsoft.2011.08.007
• Scheibe T.D., A.M. Tartakovsky, U.C. Bandara, B.J. Palmer, M. Oostrom, C. Zhang, and A. Bonneville. 2011. "Physical and Numerical Models of Pore-Scale Trapping of CO2." In Les Rencontres Scientifiques d’IFP Energies Nouvelles: International Conference on Flows and Mechanics in Natural Porous Media from Pore to Field Scale - Pore2Field, November 16-18, 2011, Rueil-Malmaison, France. Paris:IFP Energies Nouvelles. PNNL-SA-83932.

2010

• Daily J.A., K.L. Schuchardt, and B.J. Palmer. 2010. "Efficient Extraction of Regional Subsets from Massive Climate Datasets using Parallel IO." In American Geophysical Union, Fall Meeting 2010, Paper No. IN41A-1360. Washington Dc:American Geophysical Union. PNNL-SA-71307.
• Gurumoorthi V., A.M. Tartakovsky, T.D. Scheibe, and B.J. Palmer. 2010. "A Component-Based Framework for Smoothed Particle Hydrodynamics Simulations of Reactive Fluid Flow in Porous Media." International Journal of High Performance Computing Applications 24, no. 2:228-239. PNNL-SA-65869. doi:10.1177/1094342009358415
• Scheibe T.D., B.J. Palmer, K.L. Schuchardt, Y. Fang, and A.M. Tartakovsky. 2010. "Simulations of Subsurface Flow and Transport at the Pore and Continuum Scales." In SciDAC 2010 Scientific Discovery Through Advanced Computing, July 11-15, 2010, Chattanooga, Tennessee. Washington Dc:US Department of Energy, Office of Science. PNNL-SA-74118.

2009

• Gurumoorthi V., M. Krishnan, Y. Fang, B.J. Palmer, and D. Chavarría-Miranda. 2009. "Multiple Component Multiple Data Programming in Subsurface Simulations: The CCA Approach." In Proceedings of the Workshop on Component-Based High Performance Computing (CBHPC 2009). New York, New York:ACM Press. PNNL-SA-68966.
• Palmer B.J., Y. Fang, V. Gurumoorthi, G.E. Hammond, J.A. Fort, and T.D. Scheibe. 2009. "Developing a Component-Based Framework for Subsurface Simulation using the Common Component Architecture." In SciDAC 2009: Journal of Physics: Conference Series, 180, Paper No. 012064. London:IOP Publishing. PNNL-SA-66756. doi:10.1088/1742-6596/180/1/012064
• Schuchardt K.L., J.M. Chase, J.A. Daily, T.O. Elsethagen, B.J. Palmer, and T.D. Scheibe. 2009. "Application of SALSSA Framework to the Validation of Smoothed Particle Hydrodynamics Simulations of Low Reynolds Number Flows." Journal of Physics: Conference Series 180, no. 1:Article No. 012065. PNNL-SA-66754. doi:10.1088/1742-6596/180/1/012065

2008

• Kathmann S.M., B.J. Palmer, G.K. Schenter, and B.C. Garrett. 2008. "Activation Energies and Potentials of Mean Force for Water Cluster Evaporation." Journal of Chemical Physics 128, no. 6:Art. No. 064306. PNNL-SA-56857. doi:10.1063/1.2837282
• Scheibe T.D., A.M. Tartakovsky, D.M. Tartakovsky, G.D. Redden, P. Meakin, B.J. Palmer, and K.L. Schuchardt. 2008. "Hybrid numerical methods for multiscale simulations of subsurface biogeochemical processes." Journal of Physics: Conference Series 125, no. 1:Article No. 012054. PNNL-SA-60981. doi:10.1088/1742-6596/125/1/012054

2007

• Palmer B.J., S.M. Kathmann, M. Krishnan, V. Tipparaju, and J. Nieplocha. 2007. "The Use of Processor Groups in Molecular Dynamics Simulations to Sample Free-Energy States." Journal of Chemical Theory and Computation 3, no. 2:583-592. PNNL-SA-51253. doi:10.1021/ct600260u
• Palmer B.J., Y. Fang, G.E. Hammond, and V. Gurumoorthi. 2007. "Component-Based Framework for Subsurface Simulations." In SciDAC 2007. Published in Journal of Physics: Conference Series, 78, 012056 (5 pages). Bristol:IOP Publishing. PNNL-SA-56016. doi:10.1088/1742-6596/78/1/012056
• Schuchardt K.L., B.J. Palmer, J. Daily, T.O. Elsethagen, and A.S. Koontz. 2007. "IO strategies and data services for petascale data sets from a global cloud resolving model." Journal of Physics: Conference Series 78. PNNL-SA-55926. doi:10.1088/1742-6596/78/1/012089
• Tipparaju V., M. Krishnan, B.J. Palmer, F. Petrini, and J. Nieplocha. 2007. "Towards Fault Resilient Global Arrays." In Parallel Computing: Architectures, Algorithms and Applications: NIC Series, 38, 339-345. Julich:John von Neumann Institute for Computing. PNNL-SA-54426.

2006

• Nieplocha J., B.J. Palmer, V. Tipparaju, M. Krishnan, H.E. Trease, and E. Apra. 2006. "Advances, Applications and Performance of the Global Arrays Shared Memory Programming Toolkit." International Journal of High Performance Computing Applications 20, no. 2:203-231. PNNL-SA-45378.
• Wang W., L.Q. Wang, B.J. Palmer, G.J. Exarhos, and A.D. Li. 2006. "Cyclization and Catenation Directed by Molecular Self-Assembly." Journal of the American Chemical Society 128, no. 34:11150-11159. PNNL-SA-52118.

2005

• Gdanitz J., G.D. Black, C.S. Lansing, B.J. Palmer, and E.F. Schuchart. 2005. "Registering the Amica Electronic Structure Code in the Extensible Computational Chemistry Environment." Journal of Computational Chemistry 26, no. 3:214-225. PNNL-SA-42203.
• Nieplocha J., M. Krishnan, B.J. Palmer, V. Tipparaju, and Y. Zhang. 2005. "Exploiting Processor Groups to Extend Scalability of the GA Shared Memory Programming Model." In Proceedings of the 2nd Conference on Computing Frontiers, May 4-6, Ischia, Italy, 262 - 272. New York, New York:Association for Computing Machinery. PNNL-SA-44286. doi:10.1145/1062261.1062305

2004

• Krishnan M., V. Tipparaju, B.J. Palmer, and J. Nieplocha. 2004. "Processor-Group Aware Runtime Support for Shared-and Global-Address Space Models." In 33rd International Conference on Parallel Processing (ICPP-2004). Workshop on Compile and Runtime Techniques for Parallel Computing, 15-18 August 2004, Montreal, Quebec, Canada, 506-513. Piscataway, New Jersey:Institute of Electrical and Electronics Engineers. IEEE Computer Society. PNNL-SA-41767.
• Palmer B.J., and D.R. Rector. 2004. "Erratum: Lattice-Boltzmann algorithm for simulating thermal two-phase flow [ Phys. Rev. E 61, 5295 (2000) ]." Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics 69, no. 4:Article no: 049903. PNNL-SA-42306. doi:10.1103/PhysRevE.69.049903

2003

• Black G.D., K.L. Schuchardt, D.K. Gracio, and B.J. Palmer. 2003. "The Extensible Computational Chemistry Environment: A Problem Solving Environment for High Performance Theoretical Chemistry." In 3rd International Conference on Computational Science - ICCS 2003, Saint Petersburg, Russian Federation and Melbourne, Australia; Lecture notes in computer science, edited by Sloot, P., 2660, 122-131. Berlin:Springer. PNNL-SA-38140.

2002

• Nieplocha J., R.J. Harrison, M. Kumar, B.J. Palmer, V. Tipparaju, and H.E. Trease. 2002. "Combining Distributed and Shared Memory Models: Approach and Evolution of the Global Arrays Toolkit." In Workshop on Performance Optimization for High-Level Languages and Libraries in conjunction with the16th Annual ACM International Conference on Supercomputing (ICS'02). No Publisher Listed):(Web publication. PNNL-SA-37535. Combining Distributed and Shared Memory Models: Approach and Evolution of the Global Arrays Toolkit

2001

• Fulton J.L., M.M. Hoffman, J.G. Darab, B.J. Palmer, and E.A. Stern. 2001. "Ion Hydration and Ion-Pair Formation in Water." In Advanced Photon Source Forefront 1, ANL/APS/TB-42. 83-85. Argonne, Illinois:Argonne National Laboratory. PNNL-SA-35115.
• Yonker C.R., and B.J. Palmer. 2001. "Investigation of CO2-Fluorine Interactions through the Intermolecular Effects on theH-1and F-19 Shielding of CH3F and CHF3 at Various Temperatures and Pressures." Journal of Physical Chemistry A 105, no. 2:308-314. PNNL-SA-33558.

2000

• Fulton J.L., M.M. Hoffmann, J.G. Darab, B.J. Palmer, and E.A. Stern. 2000. "Copper(I) and Copper(II) Coordination Structure under Hydrothermal Conditions at 325 degrees C: An X-ray Absorption Fine Structure and Molecular Dynamics Study." Journal of Physical Chemistry A 104, no. 49:11651-11663. PNNL-SA-33219.
• Palmer B.J., and D.R. Rector. 2000. "Lattice Boltzmann Algorithm for Simulating Thermal Flow in Compressible Fluids." Journal of Computational Physics 161, no. 1:1-20. PNNL-SA-29454.
• Palmer B.J., and D.R. Rector. 2000. "Lattice-Boltzmann Algorithm for Simulating Thermal Two-Phase Flow." Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics 61, no. 5:5295-5306. PNNL-SA-31554.

1999

• Hoffmann M.M., J.G. Darab, B.J. Palmer, and J.L. Fulton. 1999. "A Transition in the Ni2+ Complex Structure from Six-to Four- Coordinate upon Formation of Ion Pair Species in Supercritical Water: An X-ray Absorption Fine Structure, Near-infrared, and Molecular Dynamics Study." Journal of Physical Chemistry A 103, no. 42:8471-8482. PNNL-SA-30916.
• Palmer B.J., J. Liu, and J.W. Virden. 1999. "Simulations of the Effect of Diblock Surfactant Spacer Molecules on Micelle Structure and Function." Langmuir 15, no. 22:7426-7431. PNNL-SA-30713.

1998

• Palmer B.J. 1998. "Direct Simulation of Hydrodynamic Relaxation in Microchannels." Journal of Chemical Physics 109, no. 1:196-207. PNNL-SA-29392. doi:10.1063/1.476549