Publications by PSC Staff

Article Index
Publications by PSC Staff
2010 publications
2009 publications
Earlier publications
All Pages

2012

  1. D. Bourilkov, P. Avery, M.Cheng, Y. Fu, B. Kim, J. Palencia, R. Budden, K. Sullivan, J. Scott, J. Rodriquez, D. Dykstra, N. Seenu, "Secure wide area network access to CMS analysis data using the Lustre filesystem". J. Phys.: Conf. Ser. In press.
  2. D. Bourilkov, P. Avery, M.Cheng, Y. Fu, B. Kim, J. Palencia, R. Budden, K. Benninger, J. Kochmar, "Using virtual Lustre clients on the WAN for analysis of data from high energy experiments". J. Phys.: Conf. Ser. In press.
  3. B.Y. Lee, T.M. Assi, A. Djibo, J. Rajgopal, B.A. Norman, S.I. Chen, S.T. Brown, R.R. Bailey, A.E. Wiringa, J.S. Welling, D.L. Connor, A.R. Wateska, A. Jana, W.G. Van Panhuis, D.S. Burke. “Impact of introducing the pneumococcal and rotavirus vaccines into the routine immunization program in Niger” Am J Public Health. 2012 Feb; 102(2):269-76.

2011

  1. B.Y. Lee, B.A. Norman, T.M. Assi, S.I. Chen, R.R. Bailey, J. Rajgopal, S.T. Brown, A.S. Wiringa, D.S. Burke, “Single vs multi-dose vaccine vials: an economic computational model”. Vaccine. 2011; 28 (32):5292-300. PubMed PMID: 21439313.
  2. B. Y. Lee, T. M. Assi, K. Rookkapan, D. L. Connor, J. Rajgopal, V. Sornsrivichai, S. T. Brown, J. S. Welling, B. A. Norman, S. I. Chen, R. R. Bailey, A. E. Wiringa, A. R. Wateska, A. Jana, W. G. Van Panhuis and D. S. Burke. “Replacing the measles ten-dose vaccine presentation with the single-dose presentation in Thailand”. Vaccine 2011 May 12;29(21):3811-7.
  3. S.T. Brown , J.H. Tai, R.R. Bailey, P.C. Cooley, W.D. Wheaton, M.A. Potter, R.E. Voorhees, M. Lejeune, J.J. Grefenstette, D.S. Burke, S.M. McGlone, B.Y. Lee. Would school closure for the 2009 H1N1 influenza epidemic have been worth the cost?: a computational simulation of Pennsylvania. BMC Public Health. 2011 May 2011(1):353. [Epub ahead of print] PubMed PMID: 21599920.
  4. B.Y. Lee, D.L. Connor, S.B. Kitchen, K.M. Bacon, M. Shah, S.T. Brown, R.R. Bailey, Y. Laosiritaworn, D.S. Burke, D.A. Cummings. Economic value of dengue vaccine in Thailand. Am J Trop Med Hyg. 2011 May;84(5):764-72. PubMed PMID: 21540387; PubMed Central PMCID: PMC3083745.
  5. B.Y. Lee, S.M. McGlone, K.F. Wong, S.L. Yilmaz, T.R. Avery, Y. Song, R. Christie, S. Eubank, S.T. Brown, J.M. Epstein, J.I. Parker, D.S. Burke, R. Platt, S.S. Huang. Modeling the Spread of Methicillin-Resistant Staphylococcus aureus (MRSA) Outbreaks throughout the Hospitals in Orange County, California. Infect Control Hosp Epidemiol. 2011 Jun;32(6):562-72. PubMed PMID: 21558768.
  6. J. Rajgopal, D.L. Connor, T.M. Assi, B.A. Norman, S. Chen, R.R. Bailey, A.R. Long, A.R. Wateska, K.M. Bacon, S.T. Brown, D.S. Burke, B.Y. Lee,  The optimal number of routine vaccines to order at health clinics in low or middle income.  Vaccine.  2011; 11(1):425. [Epub ahead of print] PubMed PMID: 21635774\
  7. B.Y. Lee, S.T. Brown, R.R. Bailey, R.K. Zimmerman, M.A. Potter, S.M. McGlone, P.C. Cooley, J.J. Grefenstette, S.M. Zimmer, W.D. Wheaton, S.C. Quinn, R.E. Voorhees, D.S. Burke. The benefits to all of ensuring equal and timely access to influenza vaccines in poor communities. Health Aff (Millwood). 2011 Jun; 30(6):1141-50. PubMed PMID: 21653968.
  8. Davi D. Bock, Wei-Chung Allen Lee, Aaron M. Kerlin, Mark L. Andermann, Greg Hood, Arthur W. Wetzel, Sergey Yurgenson, Edward R. Soucy, Hyon Suk Kim, and R. Clay Reid, “Network anatomy and in vivo physiology of visual cortical neurons”, Nature, Volume: 471, pp. 177-182, March 10, 2011, doi:10.1038/nature09802.
  9. S.R. Ribone, M.A. Quevedo, M. Madrid, and M.C. Brinon, “Rational Approaches for the Design of Effective Human Immunodeficiency Virus Type 1 Nonnucleoside Reverse Transcriptase Inhibitors”, Journal of Chemical Information and Modeling 51(1), 130-138, 2011.
  10. U.L. Abbas, G. Hood, A.W. Wetzel, J.W. Mellors, “Factors Influencing the Emergence and Spread of HIV Drug Resistance Arising from Rollout of Antiretroviral Pre-Exposure Prophylaxis (PrEP).” PLoS One. 2011 Apr 15;6(4):e18165. PMID: 21525976 PMCID: PMC307810; http://www.ncbi.nlm.nih.gov/pubmed/21525976.
  11. S.T. Brown, J.H. Tai, R.R. Bailey, P.C. Cooley, W.D. Wheaton, M.A. Potter, R.E. Voorhees, M. Lejeune, J.J. Grefenstette, D.S. Burke, S.M. McGlone, B.Y. Lee. “Would school closure for the 2009 H1N1 influenza epidemic have been worth the cost?: a computational simulation of Pennsylvania”. BMC Public Health. 2011 May 20;11(1):353. [Epub ahead of print] PubMed PMID: 21599920.
  12. U. Kleinekathofer, B. Isralewitz, M. Dittrich, and K. Schulten, “Domain Motion of Individual F_1-ATPase beta-Subunits during Unbiased Molecular Dynamics Simulations”, J Phys Chem A, 2011 Apr 1 (epub).
  13. Lee, B.Y., Brown, S. T., Korch, G., Cooley, P.C., Zimmerman, R.K., Wheaton, W.D., Zimmer, S.M., Grefenstette, J.J., Bailey, R.R., Assi, T.M., Burke, D.S., “A computer simulation of vaccine prioritization, allocation, and rationing during the 2009 H1N1 influenza pandemic”. Vaccine. 2010; 28 (31):4875-9. PubMed PMID: 20483192.
  14. Lee BY, Brown ST, Cooley P, Grefenstette JJ, Zimmerman RK, Zimmer SM, Potter MA, Rosenfeld R, Wheaton WD, Wiringa AE, Bacon KM, Burke DS. Vaccination deep into a pandemic wave potential mechanisms for a “third wave” and the impact of vaccination. American journal of preventive medicine. 2010 Nov; 39 (5): e21-9. PubMed Central PMCID: PMC2975455. PubMed PMID: 20965375.
  15. Lee, B.Y., Norman, B.A., Assi, T.M., Chen, S.I., Bailey, R.R., Rajgopal, J., Brown, S.T., Wiringa, A.S., Burke, D.S., “Single vs multi-dose vaccine vials: an economic computational model”. Vaccine. 2011; 28 (32):5292-300. PubMed PMID: 21439313.
  16. B. Y. Lee, T. M. Assi, K. Rookkapan, D. L. Connor, J. Rajgopal, V. Sornsrivichai, S. T. Brown, J. S. Welling, B. A. Norman, S. I. Chen, R. R. Bailey, A. E. Wiringa, A. R. Wateska, A. Jana, W. G. Van Panhuis and D. S. Burke. “Replacing the measles ten-dose vaccine presentation with the single-dose presentation in Thailand”. Vaccine 2011 May 12;29(21):3811-7.
  17. Lee BY, Connor DL, Kitchen SB, Bacon KM, Shah M, Brown ST, Bailey RR, Laosiritaworn Y, Burke DS, Cummings DA. “Economic value of dengue vaccine in Thailand”. Am J Trop Med Hyg. 2011 May;84(5):764-72. PubMed PMID: 21540387; PubMed Central PMCID: PMC3083745.
  18. Lee, B. Y., Assi, T. M., Djibo A., Rajgopal, J., Norman, B. A., Chen, S. I., Brown, S. T., Bailey, R. R., Wiringa, A. E., Welling, J. S., Connor, D. L., Wateska, A. R., Jana A., Van Panhuis, W. G., Burke, D. S. “Impact of Introducing the Pneumococcal and Rotavirus Vaccines into the Routine Immunization Program in Niger” American Journal of Public Health. In press.
  19. Lee B.Y., McGlone S.M., Wong K.F., Yilmaz S.L., Avery T.R., Song Y., Christie R., Eubank S., Brown S.T., Epstein J.M., Parker J.I., Burke D.S., Platt R., Huang S.S.  “Modeling the Spread of Methicillin-Resistant Staphylococcus aureus (MRSA) Outbreaks throughout the Hospitals in Orange County, California”. Infect Control Hosp Epidemiol. 2011 Jun;32(6):562-72. PubMed PMID: 21558768.
  20. B.Y. Lee, S.T. Brown, R.R. Bailey, R.K. Zimmerman, M.A. Potter, S.M. McGlone, P.C. Cooley, J.J. Grefenstette, S.M. Zimmer, W.D. Wheaton, S.C. Quinn, R.E. Voorhees, D.S. Burke. “The benefits to all of ensuring equal and timely access to influenza vaccines in poor communities”. Health Aff (Millwood). 2011 Jun; 30(6):1141-50. PubMed PMID: 21653968.
  21. J Rajgopal, DL Connor, TM Assi, BA Norman, S Chen, RR Bailey,  AR Long, AR Wateska,  KM Bacon, ST Brown, DS Burke, BY Lee.  “The optimal number of routine vaccines to order at health clinics in low or middle income”.  Vaccine.  2011; 11(1):425. [Epub ahead of print] PubMed PMID: 21635774
  22. Samarth S. Raut, Anirban Jana, Ender A. Finol, “Effects Of Shape Versus Material Model Variations On AAA Wall Mechanics”, Sixth M.I.T. Conference on Computational Fluid and Solid Mechanics, Boston, MA, June 2001 (Peer-reviewed abstract and presentation)

 

2010

  1. BY  Lee, ST Brown, P Cooley, JJ Grefenstette, RK Zimmerman, SM Zimmer, MA Potter, R Rosenfeld, WD Wheaton, AE Wiringa, KM Bacon, DS. Burke Vaccination deep into a pandemic wave potential mechanisms for a “third wave” and the impact of vaccination. American journal of preventive medicine. 2010 Nov; 39 (5): e21-9. PubMed Central PMCID: PMC2975455. PubMed PMID: 20965375.
  2. Josephine Palencia, Robert Budden and Kevin Sullivan, “Kerberized Lustre 2.0 over the WAN”, TeraGrid 2010, Pittsburgh, PA, August 2-5, 2010, accepted for ACM Publication Copyright 2010 ACM  978-1-60558-818-6/10/0. [PSC]
  3. Joanne I. Yeh, Boris Shivachev, Srinivas Rapireddy, Matthew J. Crawford, Roberto R. Gil, Shoucheng Du, Marcela Madrid, and Danith H. Ly, “Crystal Structure of Chiral γPNA with Complementary DNA Strand—Insights into the Stability and Specificity of Recognition and Conformational Preorganization”, Journal of the American Chemical Society, in press. [PSC]
  4. Palencia, J., Budden, R., and Sullivan, K. 2010. Kerberized Lustre 2.0 over the WAN. In Proceedings of the 2010 TeraGrid Conference (Pittsburgh, Pennsylvania, August 02 - 05, 2010). TG’10. ACM, New York, NY, 1-5. DOI= http://doi.acm.org/10.1145/1838574.1838589
  5. Wei He, Matthew J. Crawford, Srinivas Rapirredy, Marcela Madrid, Roberto R. Gil, Danith H. Ly, Catalina Achim, “The Structure of a γ-Modified Peptide Nucleic Acid Duplex”, Mol. BioSyst. 6, 1619, 1629, 2010.
  6. Javier V. Goicochea, Marcela Madrid, and Cristina Amon, “Hierarchical Modeling of Heat Transfer in Silicon-Based Electronic Devices”, ASME Journal of Heat Transfer 132, 102401 (2010).
  7. Kh. Odbadrakh, A. Rusanu, G. M. Stocks, and G. D. Samolyuk, M. Eisenbach, Yang Wang, D.M. Nicholson, “Calculated Electronic and Magnetic Structure of Screw Dislocations in Alpha Iron”, Journal of Applied Physics (accepted for publication).
  8. Alexander J. Ropelewski, Hugh B. Nicholas, Jr. and Ricardo R. Gonzalez Mendez, “MPI-PHYLIP: Parallelizing Computationally Intensive Phylogenetic Analysis Routines for the Analysis of Large Protein Families”, PLoS One-http://dx.plos.org/10.1371/journal.pone.0013999.
  9. Yang Wang, D.M.C. Nicholson, G.M. Stocks, Aurelian Rusanu, Markus Eisenbach, and R. E. Stoller, “A study of radiation damage effects on the magnetic structure of bulk Iron”, Journal of Applied Physics, (accepted for publication).

 

2009

  1. B.Y. Lee., ST Brown, G Korch, P.C. Cooley, R.K Zimmerman, W.D. Wheaton, S.M.  Zimmer, J.J. Grefenstette, R.R. Bailey, T.M. Assi, D.S. Burke, “A computer simulation of vaccine prioritization, allocation, and rationing during the 2009 H1N1 influenza pandemic”. Vaccine. 2010; 28 (31):4875-9. PubMed PMID: 20483192.

  2. J. Bielak, R.W. Graves, K.B. Olsen, R. Taborda, L. Ramírez-Guzmán , S.M. Day, G.P. Ely, D. Roten, T.H. Jordan, P.J. Maechling , J. Urbanic, Y. Cui & G. Juve, "The ShakeOut earthquake scenerio: Verification of three simulation sets", Geophysical Journal International 180(1), 375-404 (2010).
  3. J. Bent, G. Gibson, G. Grider, B. McClelland, P. Nowoczynski, J. Nunez, M. Polte & M. Wingate, "PLFS: A Checkpoint Filesystem for Parallel Applications". In: Proceedings of Supercomputing '09; 2009 Nov 14-20; Portland OR, USA.
  4. J. Goicochea, M. Madrid & C. Amon, "Effects of quantum corrections and isotope scattering on silicon thermal properties", In: Proceedings of the 15th International Workshop on Thermal Investigations of ICs and Systems 2009 Oct 7-9; Leuven, Belgium.
  5. S. Chandra, A. Jana, & E. Finol, "Individual anisotropic FSI modeling of aortic aneurysms. Phase-contrast and dynamic MRI validation" (Poster session), Presented at the 2009 Biomedical Engineering Society Annual Fall Meeting; 2009 Oct 7-10; Pittsburgh PA, USA.
  6. S. Raut, S. Chandra, A. Jana, S. Muluk, & E. Finol, Effect of Local Infrarenal Flow Conditions on Intra Aneurysmal Flow Dynamics. (PDF) (Poster session) Presented at the 2009 Biomedical Engineering Society Annual Fall Meeting; 2009 Oct 7-10; Pittsburgh PA, USA.
  7. P. Blood, & R. Reddy, "Performance engineering of parallel applications", Presented at Virtual School of Computational Science and Engineering: Scaling to Petascale; 2009 Aug. 3-7; National Center for Supercomputing Applications, Urbana-Champaign IL, USA.
  8. R. Roskies, "Impact of the TeraGrid on science and engineering research", Presented at the 2009 TeraGrid Conference; 2009 June 22-26; Arlington VA, USA.
  9. D.L. Hart, E. Hanna, R. Light, & JP. Navarro, "Simplifying TeraGrid resource integration with the Resource Description Repository", Presented at the 2009 TeraGrid Conference; 2009 June 22-26; Arlington VA, USA.
  10. J. Palencia, E. Mei, A. Dilger, P. Braam, J.R. Scott, K. Sullivan, B. Bennett, D. Thorp, J. Bennett, S. Sakai & P. Rivers, "JWAN: PSC's secure, federated, distributed Lustre filesystem on the TeraGrid WAN", Presented at the 2009 TeraGrid Conference; 2009 June 22-25; Arlington VA, USA.
  11. J. Palencia, "JWAN: PSC's secure, federated, distributed Lustre filesystem on the WAN (TeraGrid)", (Poster session) Presented at the 2009 TeraGrid Conference; 2009 June 22-26; Arlington VA, USA.
  12. P. Blood, R. Flaus, B. Gill, T. Maiden, S. Seshadri, N. Stone & J. Urbanic, "Computation exploration: An introduction to high-performance computing", Presented at the 2009 TeraGrid Conference; 2009 June 22-26; Arlington VA, USA.
  13. M. Mathis, "Thinking about the big problem", Presented to the Internet Congestion Control Research Group (ICCRG); 2009 May 20; Akihabara, Tokyo, Japan.
  14. M. Mathis, "Relentless congestion control", Presented to Protocols for Large-Scale and Diverse Network Transports (PFLDNeT); 2009 May 21; Akihabara, Tokyo, Japan.
  15. Y. Wang, G.M. Stocks, A. Rusanu, DMC. Nicholson & M. Eisenbach, "Toward petaflop computing for electronic structure calculations", Invited Talk at American Chemical Society Spring National Meeting; Mar 22-26 2009; Salt Lake City UT, USA.
  16. Y. Wang, A. Rusanu, G.M. Stocks & J.S. Faulkner, "New approach on calculating Green's functions in full-potential multiple scattering methods", Presented at American Physical Society March Meeting; 2009 Mar 16-20; Pittsburgh PA, USA.
  17. J. Hempel, A. Kraut & T. Wymore, "Gamma glutamyl semialdehyde dehydrogenase: Simulations on native and mutant forms support the importance of outer shell lysines" Chem Biol Interact 178(1), 75-8 (2009)
  18. Hempel J, Kraut A, Wymore T. Gamma glutamyl semialdehyde dehydrogenase: simulations on native and mutant forms support the importance of outer shell lysines. Chem Biol Interact.. 2009; Mar 16;178(1-3):75-8.

 

 

2008

  1. C. Vizino, "Enabling contiguous node scheduling on the Cray XT3"(PDF). Presented at the Cray User Group Meeting 2008; 2008 May 5-8; Helsinki, Finland. 
    Presentation slides (PDF).

 

2006

  1. N. Stone,  (PDF). Presented at the Cray User Group Meeting 2006 (CUG'06); 2006 May 8-11; Lugano, Switzerland.
  2. C. Vizino, N. Stone, and J.R. Scott, "XT3 Operational Enhancements" (PDF). Presented at the Cray User Group Meeting 2006 (CUG'06); 2006 May 8-11; Lugano, Switzerland.
  3. D. Weisser, N. Nystrom, C. Vizino, S.T. Brown, and J. Urbanic, "Optimizing Job Placement on the Cray XT3"(PDF). Presented at the Cray User Group Meeting 2006 (CUG'06); 2006 May 8-11; Lugano, Switzerland.
  4. N. Stone, D. Balog, B. Gill, B. Johanson, J. Marsteller, P. Nowoczynski, D. Porter, R. Reddy, J.R. Scott, D. Simmel, J. Sommerfield, K. Vargo, & C. Vizino.  "PDIO: High-Performance Remote File I/O for Portals-Enabled Compute Nodes". In: Proceedings of the 2006 International Conference on Parallel and Distributed Processing Techniques and Applications. (PDPTA'06/ISBN #:1-932415-89-0/CSREA), Editor: Hamid R. Arabnia, pp. 925-930, Las Vegas, USA, 2006. 

2005

  1. N. Stone, B. Gill, J. Kochmar, R. Light, P. Nowoczynski, J.R. Scott, J. Sommerfield, & C. Vizino,  DMOVER: Portable Data Migration Tools for Mainstream Users" (PDF), In: Proceedings of Workshop on Grid Applications: from Early Adopters to Mainstream Users. Held in conjunction with GGF14, Document GFD-I.068 (pp. 50-59), Chicago, IL June 2005 (available at www.ggf.org/documents/GFD68.pdf (PDF) ). 
  2. C. Vizino, J. Kochmar, N. Stone, & J.R. Scott, "Batch scheduling on the Cray XT3" (PDF). Presented at the Cray User Group Meeting 2005; 2005 May; Albuquerque, NM, USA. 
  3. C. Vizino, J. Kochmar, J.R. Scott, "Custom Features of a Large Cluster Batch Scheduler" (PDF), In: Proceedings of the 2005 International Conference on Parallel and Distributed Processing Techniques and Applications.

2004

  1. J.W. Heffner, "Qsockets", Pittsburgh Supercomputing Center, 2004 December. 
    CMU-PSC-TR-2004-01

2003

  1. C. Vizino, "Visualization resource scheduling with AlphaServer SC" (PowerPoint). Presented at the HP Consortium for Advanced Scientific and Technical Computing Users Group (HP-CAST) meeting; 2003 Sept.
  2. N. Stone, J. Kochmar, P. Nowoczynski, J.R. Scott, D. Simmel, J. Sommerfield, & C. Vizino, "Terascale I/O Solutions" (PDF). Presented at the International Conference on Computational Science (ICCS); 2003 June.

2002

  1. C. Vizino, "Comprehensive system resource management on AlphaServer SC", Presented at the Compaq Alpha Scientific and Technical Users Group (CAST) meeting; 2002 April.
  2. J. Kochmar, "A QsNet API for non-RMS applications", Presented at the Compaq Alpha Scientific and Technical Users Group (CAST) meeting; 2002 April. 

2001

  1. N. Stone, "The PSC checkpoint-recovery system" (PowerPoint), Presented at Supercomputing 2001; 2001 November.
  2. N. Stone, J. Kochmar, R. Reddy, J.R. Scott, J. Sommerfield, & C. Vizino, "A Checkpoint and Recovery System for the Pittsburgh Supercomputing Center Terascale Computing System", Pittsburgh Supercomputing Center, November 2001. Presented at Supercomputing 2001. 
    PDF version
    >Microsoft Word version
    PowerPoint slides used for the presentation 
    CMU-PSC-TR-2001-0002
  3. N. Stone, J.R. Scott, J. Kochmar, J. Sommerfield, R. Subramanya, R. Reddy & K. Vargo," Mass storage on the Terascale Computing System", Presented at the 18th IEEE Symposium on Mass Storage; 2001 April. 
    PDF version
    PowerPoint slides used for the presentation. 
  4. C. Vizino, "Open portable batch system in a Compaq AlphaServer SC environment" (PowerPoint), Presented at Supercomputing 2001; 2001 November.
  5. N. Stone, "A HUBS program review on the PSC Intelligent Archiver" (PowerPoint), Presented 2001 June.

2000

  1. N. Stone, "Collaboratory tools" (PowerPoint), Presented at the PSC Collaboratory Workshop; 2000 October.
  2. N. Stone, "Shared low-latency medical imaging and high bandwidth for the masses: Current and future collaborative projects" (PowerPoint), Presented at the Third HLRS Metacomputing Workshop; 2000 June.
  3. N. Stone, The integrated source management system" (PowerPoint), 2000 May.
  4. J. Semke, "PSC TCP kernel monitor", Pittsburgh Supercomputing Center, 2000 May. CMU-PSC-TR-2000-0001
  5. J. Semke, "Implementation issues of the autotuning fair share algorithm", Pittsburgh Supercomputing Center, 2000 May. CMU-PSC-TR-2000-0002

1999

  1. J. Urbanic and C. Vizino, "Achieving Maximum Disk Performance on Large T3Es: Hardware, Software and Users" (PDF), Presented at the Cray User Group T3E Workshop; October 1999; Princeton, NJ, USA.

1997

  1. P. Cizmas, R. Subramanya, "Parallel computation of rotor-stator interaction" (PDF), Presented at: VIIIth International Symposium on Aerodynamics and Aeroelasticity of Turbomachines; Sept 1997; Stockholm, Sweden.

1996

  1. C. Vizino, "J90 Performance and Tuning" (PDF), Presented at the Cray User Group Meeting Fall 1996; 1996 Oct. 14-18; Charlotte, NC, USA.
Last Updated on Thursday, 16 January 2014 14:58