Staff Publications

Article Index

Staff Publications (within the last 10 years)

Adams, Andrew

V. Hazlewood, K. Benninger, G. Peterson, J. Charcalla, B. Sparks, J. Hanley, A. Adams, B. Learn, R. Budden, D. Simmel, J. Lappa, J. Yanovich. Developing Applications with Networking Capabilities via End-to-End SDN (DANCES). XSEDE16, Miami, FL, July 17-21, 2016

Andrew K. Adams and Adam J. Lee, Combining Social Authentication and Untrusted Clouds for Private Location Sharing, in Proceedings of the 18th ACM Symposium on Access Control Models and Technologies (SACMAT), June 2013

A. Adams, A. J. Lee, and D. Mosse, Receipt-Mode Trust Negotiation: Efficient Authorization Through Outsourced Interactionsin Proceedings of the Sixth ACM Symposium on Information, Computer, and Communication Security (ASIACCS 2011), March 2010.

V. Paxson, A. Adams, M. Mathis, Experiences with NIMI, Passive and Active Measurement Workshop 2000, Proceedings, April 2000.

Peisert, Sean; Welch, Von; Adams, Andrew; Bevier, RuthAnne; Dopheide, Michael; LeDuc, Rich; Meunier, Pascal; Schwab, Steve; Stocks, Karen. Open Science Cyber Risk Profile (OSCRP).  http://hdl.handle.net/2022/21259, 2017.

 

Begandy, Cheryl

Preparing Teachers to Infuse Computational Science into their Classroom Instruction. Susan Ragan, Charlotte M. Trout, Cheryl Begandy, Nancy R. Bunt, and Scott A. Sinex Journal of Computational Science Education,  Volume 2, Issue 1, pp. 9–14. Dec. 2011. https://doi.org/10.22369/issn.2153-4136/2/1/2

 

Blood, Phil

Seetharam A, Gomez A, Purcell C, Hyde J, Blood P, et al. NCBI-BLAST programs optimization on XSEDE resources for sustainable aquaculture. Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure. ACM. 2015. DOI: 10.1145/2792745.2792749

Ghaffari N, Sanchez-Flores A, Doan R, Garcia-Orozco KD, Chen PL, Ochoa-Leyva A, Lopez-Zavala AA, Carrasco JS, Hong C, Brieba LG, Rudiño-Piñera E, Blood PD, Sawyer JE, Johnson CD, Dindot SV, Sotelo-Mundo RR, Criscitiello MF. Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture. Sci Rep. 2014 Nov 25;4:7081. doi: 10.1038/srep07081. PubMed PMID: 25420880; PubMed Central PMCID: PMC4243063

Blood PD, Marcus S, Schatz MC. Large-scale Sequencing and Assembly of Cereal Genomes Using Blacklight. Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment. ACM. 2014. DOI: 10.1145/2616498.2616502

LeDuc R, Vaughn M, Fonner JM, Sullivan M, Williams JG, Blood PD, Taylor J, Barnett W. Leveraging the national cyberinfrastructure for biomedical research. J Am Med Inform Assoc. 2014 Mar-Apr;21(2):195-9. doi: 10.1136/amiajnl-2013-002059. Epub 2013 Aug 20. PubMed PMID: 23964072; PubMed Central PMCID: PMC3932465

Couger MB, Pipes L, Squina F, Prade R, Siepel A, Palermo R, Katze MG, Mason CE, Blood PD. Enabling large-scale next-generation sequence assembly with Blacklight. Concurr Comput. 2014 Sep 10;26(13):2157-2166. PubMed PMID: 25294974; PubMed Central PMCID: PMC4185199

Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, Macmanes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, Leduc RD, Friedman N, Regev A. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013 Aug;8(8):1494-512. doi: 10.1038/nprot.2013.084. Epub 2013 Jul 11. PubMed PMID: 23845962; PubMed Central PMCID: PMC3875132

Pipes L, Li S, Bozinoski M, Palermo R, Peng X, Blood P, Kelly S, Weiss JM, Thierry-Mieg J, Thierry-Mieg D, Zumbo P, Chen R, Schroth GP, Mason CE, Katze MG. The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics. Nucleic Acids Res. 2013 Jan;41(Database issue):D906-14. doi: 10.1093/nar/gks1268. Epub 2012 Nov 29. PubMed PMID: 23203872; PubMed Central PMCID: PMC3531109

Nystrom N, Welling J, Blood P. Contemporary High Performance Computing: From Petascale Toward Exascale. Vetter JS, editor. Boca Raton, FL: CRC Press; 2013. Blacklight: Coherent Shared Memory for Enabling Science; p.421-439

Peng Y, Knight C, Blood P, Crosby L, Voth GA. Extending parallel scalability of LAMMPS and multiscale reactive molecular simulations. Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment, ACM. 2012. DOI: 10.1145/2335755.2335833

Blood PD, Swenson RD, Voth GA. Factors influencing local membrane curvature induction by N-BAR domains as revealed by molecular dynamics simulations. Biophys J. 2008 Aug;95(4):1866-76. doi: 10.1529/biophysj.107.121160. Epub 2008 May 9. PubMed PMID: 18469070; PubMed Central PMCID: PMC2483763

Ayton GS, Blood PD, Voth GA. Membrane remodeling from N-BAR domain interactions: insights from multi-scale simulation. Biophys J. 2007 May 15;92(10):3595-602. Epub 2007 Feb 26. PubMed PMID: 17325001; PubMed Central PMCID: PMC1853153

 

Chiacchia, Ken

Deriving Effective Sweep Width for Air-scent Dog Teams. Chiacchia KB, Houlahan HE, Hostetter RS.Wilderness Environ Med. 2015 Jun;26(2):142-9. doi: 10.1016/j.wem.2014.10.004. PMID: 25754903

Use of the visual range of detection to estimate effective sweep width for land search and rescue based on 10 detection experiments in North America. Koester RJ, Chiacchia KB, Twardy CR, Cooper DC, Frost JR, Robe RQ. Wilderness Environ Med. 2014 Jun;25(2):132-42. doi: 10.1016/j.wem.2013.09.016

Effectors of visual search efficacy on the Allegheny Plateau. Chiacchia KB, Houlahan HE. Wilderness Environ Med. 2010 Sep;21(3):188-201. doi: 10.1016/j.wem.2010.06.002. Erratum in: Wilderness Environ Med. 2010 Dec;21(4):386

 

Gomez, Roberto

A framework for large-scale relativistic simulations in the characteristic approach. Roberto Gomez, Willians Barreto and Simonetta Frittelli Phys. Rev. D 76, 124029 (2007), DOI: https://doi.org/10.1103/PhysRevD.76.124029, arXiv:0711.0564

Initial-boundary-value problem of the self-gravitating scalar field in the Bondi-Sachs gauge. Simonetta Frittelli and Roberto Gomez  Phys. Rev. D 75, 044021 (2007), DOI: https://doi.org/10.1103/PhysRevD.75.0440216

On Boundary Conditions for the Einstein Equations. Simonetta Frittelli and Roberto Gomez. Lecture Notes in Physics, Vol. 692, pp. 205-222, (2006) Editors: Joerg Frauendiener, Domenico J.W. Giulini, Volker Perlick, Springer Berlin/Heidelberg (2006), ISBN: 3-540-31027-4

 

Hood, Greg

Lee WC, Bonin V, Reed M, Graham BJ, Hood G, Glattfelder K, Reid RC. Anatomy and function of an excitatory network in the visual cortex. Nature. 2016; 532(7599):370-4. NIHMSID: NIHMS757168 PubMed [journal] PMID: 27018655, PMCID: PMC4844839

Glaubius RL, Hood G, Penrose KJ, Parikh UM, Mellors JW, Bendavid E, Abbas UL. Cost-effectiveness of Injectable Preexposure Prophylaxis for HIV Prevention in South Africa. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2016; 63(4):539-47. PubMed [journal] PMID: 27193745, PMCID: PMC4967601

Abbas UL, Glaubius R, Hood G, Mellors JW. Antiretroviral treatment, preexposure prophylaxis, and drug resistance in sub-Saharan Africa: a consensus among mathematical models. The Journal of infectious diseases. 2014; 209(1):164-6. PubMed [journal] PMID: 24133186

Abbas UL, Glaubius R, Mubayi  A, Hood G, Mellors JW. Antiretroviral therapy and pre-exposure prophylaxis: combined impact on HIV transmission and drug resistance in South Africa. The Journal of infectious diseases. 2013; 208(2):224-34. PubMed [journal] PMID: 23570850, PMCID: PMC3895950

Zhang X, Badea C, Hood G, Wetzel A, Qi Y, Stiles J, Johnson GA. High-resolution reconstruction of fluorescent inclusions in mouse thorax using anatomically guided sampling and parallel Monte Carlo computing. Biomedical optics express. 2011; 2(9):2449-60. PubMed [journal] PMID: 21991539, PMCID: PMC3184855

Abbas UL, Hood G, Wetzel AW, Mellors JW. Factors influencing the emergence and spread of HIV drug resistance arising from rollout of antiretroviral pre-exposure prophylaxis (PrEP). PloS one. 2011; 6(4):e18165. PubMed [journal] PMID: 21525976,PMCID: PMC3078109

Bock DD, Lee WC, Kerlin AM, Andermann ML, Hood G, Wetzel AW, Yurgenson S, Soucy ER, Kim HS, Reid RC. Network anatomy and in vivo physiology of visual cortical neurons. Nature. 2011; 471(7337):177-82. NIHMSID: NIHMS263529 PubMed [journal] PMID: 21390124, PMCID: PMC3095821

Zhang X, Badea CT, Hood G, Wetzel AW, Stiles JR, Johnson GA. Free-space fluorescence tomography with adaptive sampling based on anatomical information from microCT. Proceedings of SPIE--the International Society for Optical Engineering. 2010; 7757(775706). NIHMSID: NIHMS304986 PubMed [journal] PMID: 21743784, PMCID: PMC3132136

 

Laghaei, Rozita

Water and Ion Permeability of a Claudin Model: A Computational Study, Rozita Laghaei, Alan S. L Yu and Rob D. Coalson, PROTEINS: Structure, Function, and Bioinformatics 2016, 84, 305-315

Early Oligomerization Stages for the Non-Amyloid Component of Alpha-Synuclein Amyloid. Cindie Eugène, Rozita Laghaei and Normand Mousseau, J. Chem. Phys. 2014; 141,135103

Calculation of Iron Transport through Human H-chain Ferritin.  Rozita Laghaei, William Kowallis, Deborah G. Evans and Rob D. Coalson J. Phys. Chem. A. 2014; 118, 7442−7453

Metal Binding Sites of Human H-chain Ferritin and Iron Transport Mechanism to the Ferroxidase Sites: A Molecular Dynamics Simulation Study Rozita Laghaei, Deborah G. Evans and Rob D. Coalson, Proteins: Structure, Function, and Bioinformatics, 2013; 81, 1042–1050

Langevin Dynamics Simulation of 3D Colloidal Crystal Vacancies and Phase Transitions. Rozita Laghaei,  Sanford A. Asher and Rob D. Coalson, J. Phys. Chem. B, 2013, 117, 5271–5279

Distinct Dimerization for Various Alloforms of the Amyloid-Beta Protein: Aβ1-40, Aβ1-42 and Aβ1-40(D23N), Sébastien Côté, Rozita Laghaei, Philippe Derreumaux and Normand Mousseau, J. Phys. Chem. B, 2012; 116, 4043-4055

Structure and Thermodynamics of Amylin Dimer Studied by Hamiltonian- Temperature Replica Exchange Molecular Dynamics Simulations, Rozita Laghaei,  Normand Mousseau and Guanghong Wei, J. Phys. Chem. B, 2011; 115, 3146–3154

Effect of the Disulfide Bond on the Monomeric Structure of Human Amylin Studied by Combined Hamiltonian and Temperature Replica Exchange Molecular  Dynamics Simulations. Rozita Laghaei,  Normand Mousseau and Guanghong Wei, J. Phys. Chem. B, 2010; 114 , 7071-7077

Spontaneous formation of polyglutamine nanotubes with molecular dynamics simulations. Rozita Laghaei and Normand Mousseau, J. Chem. Phys. 2010; 132, 165102

Replica Exchange Molecular Dynamics Simulations of Coarse-grained Proteins in Implicit Solvent. Yassmine Chebaro, Xiao Dong, Rozita Laghaei, Philippe Derreumaux and Normand MousseauJ. Phys. Chem. B, 2009; 113, 267–274

Computational studies on thermodynamic properties, effective diameters, and free volume of argon using an ab initio potential. Afshin Eskandari Nasrabad and Rozita Laghaei, J. Chem. Phys 2006; 125, 084510

 

Lambert, Michael

Wimberly, F, M Lambert, N Nystrom, A Ropelewski and W Young. Porting Third-Party Applications Packages to the Cray T3D: Programming Issues and Scalability Results. Parallel Computing 22(1996) 1073–1089.

Lambert, MH, ed. A Model for Common Operational Statistics. Request for Comments 1857, Internet Engineering Task Force (1995).

Wimberly, F, S Chitre, C Gonzalez, M Lambert, N Nystrom, A Ropelewski and W Young. Porting Third-Party Applications Packages to the Cray MPP: Experiences at the Pittsburgh Supercomputing Center, In: Thirty-Third Semi-Annual Cray User Group Meeting, San Diego, California, March 1994, 39–43.

Gonzalez, C, A Ropelewski, S Chitre, M Lambert, N Nystrom, D Deerfield, H Nicholas, F Wimberly and A Pai. Use of the Cray T3D Emulator in Implementing Scientific Applications, In: Thirty-First Semi-Annual Cray User Group Meeting, Montreux, Switzerland, March/April 1993, 39–42.

Lambert, MH and TR Chay. Cardiac arrhythmias modelled by Cai-inactivated Ca2+ channels. Biological Cybernetics 61(1989) 21–28.


Madrid, Marcela

Akli L, Alameda J, Gordon SI, Madrid M, Rivera L. XSEDE Training: Achieving Access and Inclusion. Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale. 2016; (Art 55) doi: 10.1145/2949550.2949586

Ribone SR, Schenfeld EM, Madrid M, Pierini AB, Quevedo MA. Evaluation and synthesis of AZT prodrugs with optimized chemical stabilities: experimental and theoretical analyses. New J. Chem.. 2016; 40:2383; doi: 10.1039/C5NJ03002A

Ribone SR, Leen V, Madrid M, Dehaen W, Daelemans D, Pannecouque C, Briñón MC. Synthesis, biological evaluation and molecular modeling of 4,6-diarylpyrimidines and diarylbenzenes as novel non-nucleosides HIV-1 reverse transcriptase inhibitors. Eur J Med Chem. 2012 Dec;58:485-92. doi: 10.1016/j.ejmech.2012.10.036

Wierzbinski E, de Leon A, Yin X, Balaeff A, Davis KL, Rapireddy S, Venkatramani R, Keinan S, Ly DH, Madrid M, Beratan DN, Achim C, Waldeck DH. Effect of backbone flexibility on charge transfer rates in peptide nucleic acid duplexes. J Am Chem Soc. 2012 Jun 6;134(22):9335-42. doi: 10.1021/ja301677z

Ribone SR, Quevedo MA, Madrid M, Briñón MC. Rational approaches for the design of effective human immunodeficiency virus type 1 nonnucleoside reverse transcriptase inhibitors. J Chem Inf Model. 2011 Jan 24;51(1):130-8. doi: 10.1021/ci1001636

He W, Crawford MJ, Rapireddy S, Madrid M, Gil RR, Ly DH, Achim C. The structure of a gamma-modified peptide nucleic acid duplex. Mol Biosyst. 2010 Sep;6(9):1619-29. doi: 10.1039/c002254c

Yeh JI, Shivachev B, Rapireddy S, Crawford MJ, Gil RR, Du S, Madrid M, Ly DH. Crystal structure of chiral gammaPNA with complementary DNA strand: insights into the stability and specificity of recognition and conformational preorganization. J Am Chem Soc. 2010 Aug 11;132(31):10717-27. doi: 10.1021/ja907225d

Goicochea J, Madrid M, Amon C. Hierarchical Modeling of Heat Transfer in Silicon-Based Electronic Devices. Journal of heat transfer. 2010; 132(10):102401/1

Goicochea J, Madrid M, Amon C. Thermal Properties of Bulk Silicon Based on the Determination of Relaxation Times using Molecular Dynamics. Journal of heat transfer. 2010; 132(10):102401/1

He W, Hatcher E, Balaeff A, Beratan DN, Gil RR, Madrid M, Achim C. Solution structure of a peptide nucleic acid duplex from NMR data: features and limitations. J Am Chem Soc. 2008 Oct 8;130(40):13264-73. doi: 10.1021/ja800652h

 

Moses, David

Electrostatic Ring Strain in Crown Ethers, D.J. Moses, J.W. Larson, Abs. Pap. ACS., 179, 27 (1980)

Light Charged Particle Emission and Fission in 238U + 238U Collisions at 1740 MeV.  M. Kaplan, D. J. Moses, D. O. Eriksen, M. Kildir, D. R. G. Logan, M. S. Zisman and R. J. McDonald, Z. Physik A313, 31 (1983)

Multiplicities for Evaporative 4He Emission in Heavy Ion Reactions: Relationships to Spin and Lifetime Expectancy of the Composite Nucleus.   N. N. Ajitanand, J. M. Alexander,  H. Delagrange, E. Duek, D. O. Eriksen, D. Guerreau, M. Kaplan, M. Kildir, L. Kowalski, R. Lacey, D. Logan, D. J. Moses, G. F. Peaslee, L. C. Vaz and M. S. Zisman, Z. Physik A316, 169 (1984)

Mechanisms for Emission of 4He in the Reactions of 334-MeV 40Ar with 238U.  E. Duek, N. N. Ajitanand, J. M. Alexander, D. Logan, M. Kildir, L. Kowalski, L. C. Vaz, D. Guerreau,  M. S. Zisman, M. Kaplan and D. J. Moses, Z. Physik A317, 83 (1984)

Fission Reactions of 469-MeV 56Fe + 238U: Detection of 4He/1H Emission from Pre- and  Post-Fission Sources.  M. Kildir, D. R. G. Logan, D. O. Eriksen, D. J. Moses, M. Kaplan, E. Duek,  L. C. Vaz, N. N. Ajitanand, J. M. Alexander and M. S. Zisman, Z. Physik A317, 291 (1984)

Particle Spectra from Reversed Kinematics: Powerful Probes of Hot Rotating Nuclei.  D. J.  Moses, M. Kaplan, J. M. Alexander, D. Logan, M. Kildir, L. C. Vaz, N. N. Ajitanand, E. Duek and M. S. Zisman, Z. Physik A320, 229 (1985)

Clues to the Shapes of Very Hot Nuclei: Calculated Patterns for Evaporative Emission from Deformed Nuclei.  N. N. Ajitanand, G. La Rana, R. Lacey, D. J. Moses, L. C. Vaz, G. F. Peaslee, D. M. de Castro Rizzo, M. Kaplan, and J. M. Alexander, Phys. Rev. C34, 877 (1986)

Large-Angle Correlations in Evaporative Particle Emission: Shape Distortion? Surface Expansion?  R. Lacey, N. N. Ajitanand, J. M. Alexander, D. M. de Castro Rizzo, G. F. Peaslee,  L. C. Vaz,   G. La Rana, M. Kaplan, D.J. Moses, W. Parker, D. Logan and P. DeYoung, J. Phys. (Paris) Colloq. 4, 289 (1986)

A Need for New Physics in Statistical Models of Nuclear De-excitation.  G. La Rana, D. J. Moses, W. E. Parker, M. Kaplan, D. Logan, R. Lacey, J. M. Alexander, and R. J. Welberry,  Phys. Rev. C35, 373 (1987)

Effects of Nuclear Shape on the Properties of 4He Evaporative Emission.   G. La Rana, R. Lacey, D. J. Moses, N. Ajitanand, M. and and J. M. Alexander, Proc. Int. Symp. Nucl. Fission and Heavy-Ion-Induced Reactions (Rochester, 1986), p. 227, W. U. Schroder, ed., Nucl. Sci. Res. Conf. Ser. Vol. 11, Harwood Academic Publishers (1987)

Light Charged Particle Emission in 485-MeV 56Fe + 197Au Reactions:  Correlations with Heavy Fragments and Relationships to Spin and Lifetime.  D. J. Moses, M. Kaplan, M. Kildir,    D. R. G. Logan, G. La Rana, W. E. Parker, R. Lacey, G. F. Peaslee, J. M. Alexander, N. N. Ajitanand, L. C. Vaz and M. S. Zisman, Nucl. Phys. A465, 339 (1987)

Surprising Properties of the Nuclear Stratosphere Indicated by Energy Spectra and Large-Angle Correlations Between 4He and 1,2,3H or 4He.  R. Lacey, N. N. Ajitanand, J. M. Alexander, D. M. de Castro Rizzo, P. DeYoung, M. Kaplan, L. Kowalski, G. La Rana, D. Logan, D. J. Moses, W. E. Parker, G. F. Peaslee, and L. C. Vaz, Phys. Lett. 191B, 253 (1987).

Nuclear Shape Deformations in 485-MeV 56Fe + 197Au Reactions.  D. J. Moses, M. Kaplan, G. La Rana, W. E. Parker, R. Lacey and J. M. Alexander, Phys. Rev. C36, 422 (1987)

Mechanisms for Light Charged Particle Emission in the Reactions 247- and 337-MeV 40Ar + natAg.  R. Lacey, N. N. Ajitanand, J. M. Alexander, D. M. de Castro Rizzo, G. F. Peaslee, L. C. Vaz,   M. Kaplan, M. Kildir, G. La Rana, D. J. Moses, W. E. Parker, D. Logan, M. S. Zisman, P. DeYoung, and L. Kowalski, Phys. Rev. C37, 2540 (1988)

Large-Angle Correlations Between 4He and 1,2,3H or 4He in the Reactions 247 and 337-MeV 40Ar + natAg: Surprising Properties of the Nuclear Stratosphere.  R. Lacey, N. N. Ajitanand, J. M. Alexander, D. M. de Castro Rizzo, G. F. Peaslee, L. C. Vaz, M. Kaplan, M. Kildir, G. La Rana, D. J. Moses, W. E. Parker, D. Logan, M. S. Zisman, P. DeYoung, and L. Kowalski, Phys. Rev. C37, 2561 (1988)

Are Hot Composite Nuclei Significantly Different from Cold Nuclei?  M. Kaplan, W. E. Parker,  D. J. Moses, G. La Rana, R. J. Welberry, D. Logan, R. Lacey, J. M. Alexander, D. M. de Castro Rizzo, and P. DeYoung, Proceedings of the Texas A&M Symposium on Hot Nuclei (College Station, 1987), p. 115, S. Shlomo, R. P. Schmitt, J. B. Natowitz, eds., World Scientific Publishing Co. (1988)

Sources of Light Charged Particle Emission in the Reaction 480-MeV 56Fe + natAg.  G. F.  Peaslee, N. N. Ajitanand, J. M. Alexander, D. Guerreau, R. Lacey, L. C. Vaz, M. Kaplan, M. Kildir, D. J. Moses, D. Logan, and M. S. Zisman, Phys. Rev. C38, 1730 (1988)

Particle-Particle Coincidence Measurements for 1,2,3H and 4He in the Reaction 480-MeV 56Fe + natAg.  G. F. Peaslee, N. N. Ajitanand, J. M. Alexander, R. Lacey, L. C. Vaz, M. Kaplan, M. Kildir, D. J. Moses, D. Logan, and M. S. Zisman, Phys. Rev. C39, 488 (1989)

Three Paths for Intermediate-Mass Fragment Formation at a Near-Onset Excitation Energy of 1.3-MeV/Nucleon.  J. Boger, S. Kox, G. Auger, J. M. Alexander, A. Narayanan, M. A. McMahan, D. J. Moses, M. Kaplan, and G. P. Gilfoyle Phys. Rev. C41, R801 (1990)

Charged Particle Evaporation from Hot Composite Nuclei: Evidence Over a Broad Z Range for Distortions from Cold Nuclear Profiles.  W. E. Parker, M. Kaplan, D. J. Moses, G. La Rana, D. Logan, R. Lacey, J. M. Alexander, D. M. de Castro Rizzo, P. DeYoung, R. J. Welberry, and  J. Boger, Phys. Rev. C44, 774 (1991)

De-Excitation of Hot, High-Spin Nuclei By Particle Emission and Fission.  M. Kaplan, W. E. Parker, D. J. Moses, E. Vardaci, J. M. Alexander, J. Boger, R. Lacey, and N. Carjan, Advances  in Nuclear Dynamics (Key West, Fla., 1991), p. 8, W. Bauer, J. Kapusta, eds., World Scientific Publishing Co. (1991)

The Role of Reversed Kinematics and Double Kinematic Solutions in Nuclear Reactions Studies.  M. Kaplan, W. E. Parker, D. J. Moses, R. Lacey, and J. M. Alexander, Nucl. Inst. Methods in Phys. Res. A327, 551 (1993)

Mechanisms of Light-Charged-Particle Emission in the Matched Reactions 905 and 1030 MeV 121Sb + 27Al and 550 and 750 MeV 86Kr + 63Cu.  W. E. Parker, M. Kaplan, D. J. Moses, J. M. Alexander, J. T. Boger, R. A. Lacey, and D. M. de Castro Rizzo, Nucl. Phys. A568, 633 (1994)

Light Charged Particle and Intermediate Mass Fragment Emission in the Reaction 640 MeV 86Kr + 63Cu.  J. Boger, J. M. Alexander, G. Auger, A. Elmaani, S. Kox, R. A. Lacey, A. Narayanan, M. Kaplan, D. J. Moses, M. A. McMahan, P. A. DeYoung, C. J. Gelderloos, and G. Gilfoyle, Phys. Rev. C49, 1576 (1994)

Coincidence Correlations Between Light Charged Particles in the Matched Reactions 905 and 1030 MeV 121Sb + 27Al and 550 and 750 MeV 86Kr + 63Cu.  W. E. Parker, M. Kaplan, D. J. Moses, J. M. Alexander, R. A. Lacey, D. M. de Castro Rizzo, J. Boger, A. Narayanan, G. F. Peaslee, and D. G. Popescu, Nucl. Phys. A594, 1 (1995)

Studies of light charged particle emission from fission and ER reactions in the system 344 MeV 28Si + 121Sb 149Tb (E* = 240 MeV).  Morton Kaplan, Craig J. Copi, Paul A. DeYoung, Gerard J. Gilfoyle, Paul J. Karol, David J. Moses, Winifred E. Parker, K. Ernst Rehm, John Sarafa, and Emanuele Vardaci, Nucl. Phys. A686, 109 (2001)

 

Rapier, Chris

Rapier, Chris, and Benjamin Bennett. High speed bulk data transfer using the SSH protocol. Proceedings of the 15th ACM Mardi Gras conference. ACM, 2008 

Rapier, Chris. High speed bulk data transfer on the Grid using the SSH protocol. Proceedings of Gridnets (2007): 17-19

 

Roskies, Ralph

An Overview of the XSEDE Extended Collaborative Support Program with N. Wilkins-Diehr, N and S Sanielevici, J Alameda, J Cazes, L Crosby, M Pierce, R Roskies. High Performance Computer Applications 6th International Conference, ISUM 2015, Mexico City, Mexico, March 9-13, 2015, Revised Selected Papers Gitler, Isidoro, Klapp, Jaime (Eds.) Springer International Publishing. ISBN 978-3-319-32243-8, 3-13, 2016. 10.1007/978-3-319-32243-8

John Towns, Timothy Cockerill, Maytal Dahan, Ian Foster, Kelly Gaither, Andrew Grimshaw, Victor Hazlewood, Scott Lathrop, Dave Lifka, Gregory D. Peterson, Ralph Roskies, J. Ray Scott, Nancy Wilkins-Diehr, XSEDE: Accelerating Scientific Discovery, Computing in Science & Engineering, vol.16, no. 5, pp. 62-74, Sept.-Oct. 2014, doi:10.1109/MCSE.2014.80S

Stewart, Craig A.; Roskies, Ralph; Knepper, Richard; Moore, Richard L.; Whitt, Justin; Cockerill, Timothy M. , XSEDE Value Added, Cost Avoidance, and Return on Investment,  IUScholarWorks, http://dx.doi.org/10.1145/2792745.2792775 (won best paper at XSEDE15).

Nystrom, N. A., Levine, M. J., Roskies, R. Z., and Scott, J. R. 2015. Bridges: A Uniquely Flexible HPC Resource for New Communities and Data Analytics. In Proceedings of the 2015 Annual Conference on Extreme Science and Engineering Discovery Environment (St. Louis, MO, July 26-30, 2015). XSEDE15. ACM, New York, NY, USA. DOI=http://dx.doi.org/10.1145/2792745.2792775.

Catlett, C, R. Roskies et al, TeraGrid: Analysis of Organization, System Architecture, and Middleware Enabling New Types of Applications. In: Advances in Parallel Computing Volume 16, 2008: High Performance Computing and Grids in Action. L. Grandinetti, ed.  IOS Press, Amsterdam, The Netherlands, 2008. Available from: http://hdl.handle.net/2022/14524

 

Sanielevici, Sergiu

An Overview of the XSEDE Extended Collaborative Support Program with N. Wilkins-Diehr, N and S Sanielevici, J Alameda, J Cazes, L Crosby, M Pierce, R Roskies. High Performance Computer Applications 6th International Conference, ISUM 2015, Mexico City, Mexico, March 9-13, 2015, Revised Selected Papers Gitler, Isidoro, Klapp, Jaime (Eds.) Springer International Publishing. ISBN 978-3-319-32243-8, 3-13, 2016. 10.1007/978-3-319-32243-8.

 

James Taylor, Anton Nekrutenko, Nate Coraor, Philip D. Blood, Alex Ropelewski, Zhihui Zhang, Josephine Palencia, Sergiu Sanielevici, Jared Yanovich, and Robert Budden. 2013. A sustainable national gateway for biological computation. In Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery (XSEDE '13). ACM, New York, NY, USA, Article 32 , 3 pages. DOI=http://dx.doi.org/10.1145/2484762.2484817

 

Urbanic, John

Y. Hongfeng, T. Tu, J. Bielak, O. Ghattas, J. Lopez, K. Ma, D. O’Hallaron., L. Ramirez-Guzman, N. Stone, R. Taborda, J. Urbanic 2006.  Analytics challenge- Remote runtime steering of integrated terascale simulation and visualization.  Proceedings of the ACM/IEEE SC2006 Conference on High Performance Networking and Computing

R. Taborda, J. Bielak,  D. O’Hallaron., L. Ramirez-Guzman, J. Lopez, J. Urbanic 2007.  The ShakeOut and its Effects in the Los Angeles and Oxnard Areas.  Conference: Annual Meeting, American Geophysical Union

J. Bielak, R. Graves, K. Olsen, R. Taborda, L. Ramirez, S. Day, G Ely, D Toren, T Jordan, P Maechling, J. Urbanic, Y. Cui, G. Juve. 2010.  The ShakeOut earthquake scenario: Verification of three simulation sets.  Geophysical Journal International 180:375-404

Ebcioglu, K., Sarkar, V., El-Ghazawi, T., Urbanic, J. 2006. An experiment in measuring the productivity of three parallel programming languages. Proceedings of the Third Workshop on Productivity and Performance in High-End Computing: 30-36

S. Koric, G. Arnold, M. Gajbe, J. Urbanic. 2014.  XSEDE OpenACC workshop enables Blue Waters Researchers to Accelerate Key Algorithms.  Conference Paper XSEDE '14

 

Wang, Yang

R. E. Stoller, A. Tamm, L. K. Béland, G. D. Samolyuk, G. M. Stocks, A. Caro, L. V. Slipchenko, Yu. N. Osetsky, A. Aabloo, M. Klintenberg, and Y. Wang, The Impact of Short-range Forces on Defect Production from High-energy Collisions, J. Chem. Theory Comput., 12, 2871 (2016). DOI:10.1021/acs.jctc.5b01194

Fuyang Tian, Dongping Wang, Jiang Shen, Yang Wang, An ab initio investigation of ideal tensile and shear strength of TiVNbMo high-entropy alloy, Materials Letters, 166, 271 (2016). DOI:10.1016/j.matlet.2015.12.064

Xianglin Liu, Yang Wang, Markus Eisenbach, G. Malcolm Stocks, A full-potential approach to the relativistic single-site Green's function, J. Phys.: Condens. Matter 28, 355501 (2016). doi:10.1088/0953-8984/28/35/355501

Fuyang Tian, Yang Wang, Douglas L. Irving, Levente Vitos, Applications of Coherent Potential Approximation to HEAs, Chapter 9, High-Entropy Alloys – Fundamentals and Applications, Michael C. Gao, Jien-Wen Yeh, Peter K. Liaw, Yong Zhang, Eds. Springer, 2016.

M. Claudia Troparevsky, James R. Morris, Markus Daene, Yang Wang, Andrew R. Lupini, and G. Malcolm Stocks, Beyond Atomic Sizes and Hume-Rothery Rules: Understanding and Predicting High-Entropy Alloys, JOM, 67, 2350 (2015). DOI:10.1007/s11837-015-1594-2

Yang Wang, G.M. Stocks, J.S. Faulkner, The single-site Green's function and Krein's theorem, J. Phys.: Condens. Matter 26, 274208 (2014). DOI:10.1088/0953-8984/26/27/274208

A. Rusanu, G.M. Stocks, Yang Wang, J.S. Faulkner, Green's functions in full-potential multiple-scattering theory, Phys. Rev. B 84, 035102 (2011). doi:10.1103/PhysRevB.84.035102

K. Odbadrakh, A. Rusanu, G. M. Stocks, G. D. Samolyuk, M. Eisenbach, Yang Wang, and D. M. Nicholson, Calculated electronic and magnetic structure of screw dislocations in alpha iron, J. Appl. Phys. 109, 07E159 (2011). DOI: 10.1063/1.3562217

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, J. Appl. Phys. 109, 07E120 (2011). DOI: 10.1063/1.3553937

Yang Wang, D.M.C. Nicholson, G.M. Stocks, Aurelian Rusanu, Markus Eisenbach, and R. E. Stoller, A Theoretical Study of the Magnetic Structure of Bulk Iron with Radiation Defects, MRS Proceedings 1363, mrss11-1363-rr01-07 (2011). DOI: 10.1557/opl.2011.1283

Yang Wang, Stocks G.M., Rusanu A., Nicholson D.M.C., Eisenbach M., Qiming Zhang, Liu J.P., Electronic and Magnetic Structure of L10-FePt Nanoparticle Embedded in FePt Random Alloy, IEEE Transactions on Magnetics, 43, 3103 (2007). doi:10.1109/TMAG.2007.893856

 

Welling, Joel

Mark R. Lovell, Jamie E. Pardini, Joel Welling, Michael W. Collins, Jennifer Bakal, Nicole Lazar, Rebecca Roush, William F. Eddy, and James T. Becker. Functional brain abnormalities are related to clinical recovery and time to return-to-play in athletes. Neurosurgery, 61(2):352– 360, August 2007.

Dirk Bartz, Bruno Raffin, Han wei Shen (editors, Hongfeng Yu, Kwan liu Ma, and Joel Welling. I/o strategies for parallel rendering of large time-varying volume data. 2008.

Jamie E. Pardini, Dustin A Pardini, James T. Becker, Kathryn L. Dunfee, William F. Eddy, Mark R. Lovell, and Joel S. Welling. Post-concussive symptoms are associated with compensatory cortical recruitment during a working memory task. Neurosurgery, 67(4):1020–1028, October 2010.

BY Lee, TM Assi, K Rookkapan, DL Connor, J Rajgopal, V Sornsrivichai, ST Brown, BA Welling, Jand Norman, S Chen, RR Bailey, AE Wiringa, AR Wateska, A Jana, WA Van Panhuis, and DS Burke. Replacing the measles multi-dose vaccine presentation with the single-dose presentation in Thailand. Vaccine, 29(21):3811–3817, 2011.

TM Assi, ST Brown, A Djibo, BA Norman, J Rajgopal, JS Welling, SI Chen, RR Bailey, S Kone, H Kenea, DL Connor, AR Wateska, A Jana, SR Wisniewski, WG Van Panhuis, DS Burke, and BY Lee. Impact of changing the measles vaccine vial size on niger’s vaccine supply chain: a computational model. BMC Public Health, 11:425, June 2011.

BY Lee, TM Assi, K Rookkapan, AR Wateska, J Rajgopal, V Sornsrivichai, SI Chen, ST Brown, J Welling, BA Norman, DL Connor, RR Bailey, A Jana, WG Van Panhuis, and DS Burke. Maintaining vaccine delivery following the introduction of the rotavirus and pneumococcal vaccines in Thailand. PLoS One, 6(9):e24673, 2011.

BY Lee, T Assi, J Rajgopal, BA Norman, S Chen, ST Brown, RR Bailey, S Kone, H Kenea, J Welling, DL Connor, AR Wateska, A Jana, AE Wiringa, WA Van Panhuis, and DS Burke. Impact of introducing the pneumococcal and rotavirus vaccines into the routine immunization program in Niger. Am J Public Health, 102(2):269–76, 2011.

TM Assi, K Rookkapan, J Rajgopal, V Sornsrivichai, ST Brown, JS Welling, BA Norman, DL Connor, SI Chen, RB Slayton, Y Laosiritaworn, AR Wateska, SR Wisniewski, and Lee BY. How influenza vaccination policy may affect vaccine logistics. Vaccine, 30(30):4517–23, June 2012.

BY Lee, BE Cakaouros, TM Assi, DL Connor, J Welling, S Kone, A Djibo, AR Wateska, L Pierre, and ST Brown. The impact of making vaccines thermostable in niger’s vaccine supply chain. Vaccine, 30(38):5637, 2012.

L. A. Haidari, D. L. Connor, A. R. Wateska, S. T. Brown, L. E. Mueller, B. A. Norman, M. M. Schmitz, P. Paul, J. Rajgopal, J. S. Welling, J. Leonard, E. G. Claypool, Y. T. Weng, S. I. Chen, and B. Y. Lee. Only adding stationary storage to vaccine supply chains may create and worsen transport bottlenecks. J Public Health Manag Pract, 19 Suppl 2:S65–67, 2013.

Leila A. Haidari, Diana L. Connor, Angela R. Wateska, Shawn T. Brown, Leslie E. Mueller, Bryan A. Norman, Michelle M. Schmitz, Proma Paul, Jayant Rajgopal, Joel S. Welling, Jim Leonard, Sheng-I Chen, and Bruce Y. Lee. Augmenting transport versus increasing cold storage to improve vaccine supply chains. PLoS ONE, 8(5):1–7, 05 2013.

Bruce Y. Lee, Diana L. Connor, Angela R. Wateska, Bryan A. Norman, Jayant Rajgopal, Brigid E. Cakouros, Sheng-I. Chen, Erin G. Claypool, Leila A. Haidari, Veena Karir, Jim Leonard, Leslie E. Mueller, Proma Paul, Michelle M. Schmitz, Joel S. Welling, Yu-Ting Weng, and Shawn T. Brown. Landscaping the structures of GAVI country vaccine supply chains and testing the effects of radical redesign. Vaccine, 33(36):4451 – 4458, 2015.

Leslie E. Mueller, Leila A. Haidari, Angela R. Wateska, Roslyn J. Phillips, Michelle M. Schmitz, Diana L. Connor, Bryan Norman, Shawn Brown, Joel Welling, and Bruce Y. Lee. The impact of implementing a demand forecasting system into a low-income country’s supply chain. Vaccine, 34(32):3663–3669, 2016.

 

Wetzel, Art

Wetzel AW, Bakal J, Dittrich M, Hildebrand DGC, Morgan JL, Lichtman JW, Registering large volume serial-section electron microscopy image sets for neural circuit reconstruction using FFT signal whitening, 45th IEEE Applied Imagery Pattern Recognition Workshop, Cosmos Club, Washington, D.C.  October 18-20, 2016

Wetzel AW, Bakal J, Dittrich M. A Virtual File System for On-Demand Processing of Multidimensional Datasets. Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale; 2016 July 17; Miami, FL, USA

Wetzel A, Badea C, Pomerantz S, Nave D, Mistry N, et al. Measurement and modeling of 4D live mouse heart volumes from CT time series. Videometrics lX Proc. of SPIE-US&T Electronic Imaging. 2007 January; SPIE Vol 6491(64910J-1-64910J-7)