Applications > pgi

Publications

Users of this package associated the following 132 publications with the XSEDE allocation/account under which they were running this software. Thus the publications may have come before or after the runs of this software, but the authors considered them to be related to the same line of research.

  • Evgeni Penev, Joel Ireta, Joan-Emma Shea, (2008) "Energetics of Infinite Homopolypeptide Chains: A New Look at Commonly Used Force Fields", The Journal of Physical Chemistry B 112 / 22, 6872-6877. http://dx.doi.org/10.1021/jp800058f
  • David G Ackerman (Cornell University), Frederick A Heberle (Oak Ridge National Laboratory), Gerald W Feigenson (Cornell University), (April2013) "Limited Perturbation of a DPPC Bilayer by Fluorescent Lipid Probes: A Molecular Dynamics Study", The Journal of Physical Chemistry B 117 / 17, 4844-4852. http://dx.doi.org/10.1021/jp400289d
  • Bala Murali Venkatesan, James Polans, Jeffrey Comer (University of Illinois at Urbana-Champaign), Supriya Sridhar, David Wendell, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Rashid Bashir, (2011) "Lipid bilayer coated Al2O3 nanopore sensors: towards a hybrid biological solid-state nanopore", Biomedical Microdevices 13 / 4, 671-682. http://dx.doi.org/10.1007/s10544-011-9537-3
  • Colin P. McNally, Wladimir Lyra (California Institute of Technology), Jean-Claude Passy, (2012) "A WELL-POSED KELVIN-HELMHOLTZ INSTABILITY TEST AND COMPARISON", The Astrophysical Journal Supplement Series 201 / 2, 18. http://dx.doi.org/10.1088/0067-0049/201/2/18
  • Yuan Li (Columbia University in the City of New York), Greg L. Bryan (Columbia University in the City of New York), (2012) "SIMULATING THE COOLING FLOW OF COOL-CORE CLUSTERS", The Astrophysical Journal 747 / 1, 26. http://dx.doi.org/10.1088/0004-637X/747/1/26
  • Mordecai-Mark Mac Low, Simon Glover (University of Heidelberg), (February2012) "THE ABUNDANCE OF MOLECULAR HYDROGEN AND ITS CORRELATION WITH MIDPLANE PRESSURE IN GALAXIES: NON-EQUILIBRIUM, TURBULENT, CHEMICAL MODELS", The Astrophysical Journal 746 / 2, 135. http://dx.doi.org/10.1088/0004-637X/746/2/135
  • Jason Maron (North Carolina Museum of Natural Sciences), Colin McNally (American Museum of Natural History), Mordecai-Mark Mac Low, (May2012) "PHURBAS: AN ADAPTIVE, LAGRANGIAN, MESHLESS, MAGNETOHYDRODYNAMICS CODE. I. ALGORITHM", The Astrophysical Journal Supplement Series 200 / 1, 6. http://dx.doi.org/10.1088/0067-0049/200/1/6
  • Nicholas Malaya, Karl Schulz (University of Texas at Austin), (April2012) "Early Experiences Porting Scientific Applications to the Many Integrated Core (MIC) Platform", TACC-Intel Highly-Parallel Computing Symposium TACC, Austin, TX , .
  • Todd A. Oliver, Nicholas Malaya, Rhys Ulerich, Robert D. Moser, (2014) "Estimating uncertainties in statistics computed from direct numerical simulation", Physics of Fluids 26 / 3, 035101. http://dx.doi.org/10.1063/1.4866813
  • Yuexing Li (American Museum of Natural History), Mordecai-Mark Mac Low, Ralf Klessen (University of Heidelberg), (February2005) "Control of Star Formation in Galaxies by Gravitational Instability", The Astrophysical Journal 620 / 1, L19-L22. http://dx.doi.org/10.1086/428497
  • Alex Hill (Australia Telescope National Facility), Mookwang Joung (Columbia University in the City of New York), Mordecai-Mark Mac Low, Robert A. Benjamin, L. Matthew Haffner, Christian Klingenberg, Knut Waagan, (May2012) "VERTICAL STRUCTURE OF A SUPERNOVA-DRIVEN TURBULENT, MAGNETIZED INTERSTELLAR MEDIUM", The Astrophysical Journal 750 / 2, 104. http://dx.doi.org/10.1088/0004-637X/750/2/104
  • Jeffrey Oishi (American Museum of Natural History), Mordecai-Mark Mac Low, Kristen Menou, (November2007) "Turbulent Torques on Protoplanets in a Dead Zone", The Astrophysical Journal 670 / 1, 805-819. http://dx.doi.org/10.1086/521781
  • Thomas Peters (University of Zurich), Robi Banerjee, Ralf Klessen (University of Heidelberg), Mordecai-Mark Mac Low, Roberto Galván-Madrid, Eric R. Keto, (October2010) "H II REGIONS: WITNESSES TO MASSIVE STAR FORMATION", The Astrophysical Journal 711 / 2, 1017-1028. http://dx.doi.org/10.1088/0004-637X/711/2/1017
  • Colin McNally (American Museum of Natural History), Jason Maron (North Carolina Museum of Natural Sciences), Mordecai-Mark Mac Low, (May2012) "PHURBAS: AN ADAPTIVE, LAGRANGIAN, MESHLESS, MAGNETOHYDRODYNAMICS CODE. II. IMPLEMENTATION AND TESTS", The Astrophysical Journal Supplement Series 200 / 1, 7. http://dx.doi.org/10.1088/0067-0049/200/1/7
  • Mikalai Budzevich, Vasily Zhakhovsky (University of South Florida), Carter White, Ivan Oleynik, (September2012) "Evolution of Shock-Induced Orientation-Dependent Metastable States in Crystalline Aluminum", Physical Review Letters 109 / 12, 125505. http://dx.doi.org/10.1103/PhysRevLett.109.125505
  • Vadim Mozhayskiy, Ilias Tagkopoulos (University of California-Davis), (2012) "Horizontal gene transfer dynamics and distribution of fitness effects during microbial in silico evolution", BMC Bioinformatics 13 / Suppl 10, S13. http://dx.doi.org/10.1186/1471-2105-13-S10-S13
  • Vadim Mozhayskiy, Ilias Tagkopoulos (University of California-Davis), (2012) "Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation", BMC Bioinformatics 13 / Suppl 10, S10. http://dx.doi.org/10.1186/1471-2105-13-S10-S10
  • Scott Callaghan (University of Southern California), Philip Maechling (University of Southern California), Patrick Small (University of Southern California), Kevin Milner (University of Southern California), Gideon Juve (University of Southern California), Thomas Jordan (University of Southern California), Ewa Deelman (University of Southern California), Gaurang Mehta (University of Southern California), Karan Vahi (University of Southern California), D. Gunter, K. Beattie, C. Brooks, (August2011) "Metrics for heterogeneous scientific workflows: A case study of an earthquake science application", International Journal of High Performance Computing Applications 25 / 3, 274-285. http://dx.doi.org/10.1177/1094342011414743
  • Scott Callaghan (University of Southern California), Ewa Deelman (University of Southern California), Dan Gunter, Gideon Juve (University of Southern California), Philip Maechling (University of Southern California), Christopher Brooks, Karan Vahi (University of Southern California), Kevin Milner (University of Southern California), Robert Gall (National Oceanic and Atmospheric Administration), Edward Field, David Okaya (University of Southern California), Thomas Jordan (University of Southern California), (September2010) "Scaling up workflow-based applications", Journal of Computer and System Sciences 76 / 6, 428-446. http://dx.doi.org/10.1016/j.jcss.2009.11.005
  • Robert Graves (US Geological Survey), Thomas Jordan (University of Southern California), Scott Callaghan (University of Southern California), Ewa Deelman (University of Southern California), Edward Field, Gideon Juve (University of Southern California), Carl Kesselman, Philip Maechling (University of Southern California), Gaurang Mehta (University of Southern California), Kevin Milner (University of Southern California), David Okaya (University of Southern California), Patrick Small (University of Southern California), Karan Vahi (University of Southern California), (March2011) "CyberShake: A Physics-Based Seismic Hazard Model for Southern California", Pure and Applied Geophysics 168 / 3-4, 367-381. http://dx.doi.org/10.1007/s00024-010-0161-6
  • Mats Rynge (University of Southern California), Scott Callaghan (University of Southern California), Ewa Deelman (University of Southern California), Gideon Juve (University of Southern California), Gaurang Mehta (University of Southern California), Karan Vahi (University of Southern California), Philip Maechling (University of Southern California), (July2012) "Enabling large-scale scientific workflows on petascale resources using MPI master/worker", Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment on Bridging from the eXtreme to the campus and beyond - XSEDE '12 Chicago, Illinois , 1. http://dx.doi.org/10.1145/2335755.2335846
  • Yifeng Cui (University of California-San Diego), Kim Olsen (San Diego State University), Thomas Jordan (University of Southern California), Kwangyoon Lee (San Diego Supercomputer Center), Jun Zhou (University of California-San Diego), Patrick Small (University of Southern California), Daniel Roten (ETH Zurich), Geoffrey Ely (Argonne National Laboratory), Dhabaleswar Panda (Ohio State University), Amit Chourasia (University of California-San Diego), John Levesque, Steven Day (San Diego State University), Philip Maechling (University of Southern California), (November2010) "Scalable Earthquake Simulation on Petascale Supercomputers", 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis New Orleans, Louisiana , 1-20. http://dx.doi.org/10.1109/SC.2010.45
  • Kim Olsen (San Diego State University), Steven Day (San Diego State University), Jean-Bernard Minster (Scripps Institution of Oceanography), Yifeng Cui (University of California-San Diego), Amit Chourasia (University of California-San Diego), David Okaya (University of Southern California), Philip Maechling (University of Southern California), Thomas Jordan (University of Southern California), (June2008) "TeraShake2: Spontaneous Rupture Simulations of Mw 7.7 Earthquakes on the Southern San Andreas Fault", Bulletin of the Seismological Society of America 98 / 3, 1162-1185. http://dx.doi.org/10.1785/0120070148
  • J. Douglas Zechar, Danijel Schorlemmer, Maria Liukis, John Yu, Fabian Euchner, Philip Maechling (University of Southern California), Thomas Jordan (University of Southern California), (August2010) "The Collaboratory for the Study of Earthquake Predictability perspective on computational earthquake science", Concurrency and Computation: Practice and Experience 22 / 12, 1836-1847. http://dx.doi.org/10.1002/cpe.1519
  • Yosuke Mizuno (National Tsing Hua University), Philip E. Hardee, Ken-Ichi Nishikawa, (March2014) "SPATIAL GROWTH OF THE CURRENT-DRIVEN INSTABILITY IN RELATIVISTIC JETS", The Astrophysical Journal 784 / 2, 167. http://dx.doi.org/10.1088/0004-637X/784/2/167
  • Ken-Ichi Nishikawa, Jacek Niemiec (Polish Academy of Sciences), P. E. Hardee, M. Medvedev, H. Sol, Yosuke Mizuno (National Tsing Hua University), B. Zhang, M. Pohl, M. Oka, D. H. Hartmann, (May2009) "WEIBEL INSTABILITY AND ASSOCIATED STRONG FIELDS IN A FULLY THREE-DIMENSIONAL SIMULATION OF A RELATIVISTIC SHOCK", The Astrophysical Journal 698 / 1, L10-L13. http://dx.doi.org/10.1088/0004-637X/698/1/L10
  • Xiaoming Hu, Petra M. Klein, Ming Xue, Alan Shapiro, Anita Nallapareddy, (2013) "Enhanced vertical mixing associated with a nocturnal cold front passage and its impact on near-surface temperature and ozone concentration", Journal of Geophysical Research: Atmospheres 118 / 7, 2714-2728. http://dx.doi.org/10.1002/jgrd.50309
  • Xiao-Ming Hu, Petra M. Klein, Ming Xue, Julie K. Lundquist, Fuqing Zhang, Youcun Qi, (2013) "Impact of Low-Level Jets on the Nocturnal Urban Heat Island Intensity in Oklahoma City", Journal of Applied Meteorology and Climatology 52 / 8, 1779-1802. http://dx.doi.org/10.1175/JAMC-D-12-0256.1
  • Xiaoming Hu, Petra M. Klein, Ming Xue, (2013) "Evaluation of the updated YSU planetary boundary layer scheme within WRF for wind resource and air quality assessments", Journal of Geophysical Research: Atmospheres 118 / 18, 10,490-10,505. http://dx.doi.org/10.1002/jgrd.50823
  • Petra M. Klein, Xiaoming Hu, Ming Xue, (2014) "Impacts of Mixing Processes in Nocturnal Atmospheric Boundary Layer on Urban Ozone Concentrations", Boundary-Layer Meteorology 150 / 1, 107-130. http://dx.doi.org/10.1007/s10546-013-9864-4
  • Xiao-Ming Hu, Petra M. Klein, Ming Xue, Fuqing Zhang, David C. Doughty, Renate Forkel, Everette Joseph, Jose D. Fuentes, (2013) "Impact of the vertical mixing induced by low-level jets on boundary layer ozone concentration", Atmospheric Environment 70 / undefined, 123-130. http://dx.doi.org/10.1016/j.atmosenv.2012.12.046
  • Rogan Carr (University of Illinois at Urbana-Champaign), Jeffrey Comer (University of Illinois at Urbana-Champaign), Mark D. Ginsberg, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2011) "Modeling Pressure-Driven Transport of Proteins Through a Nanochannel", IEEE Transactions on Nanotechnology 10 / 1, 75-82. http://dx.doi.org/10.1109/TNANO.2010.2062530
  • Jeffrey Comer, Aleksei Aksimentiev, (January2012) "Predicting the DNA Sequence Dependence of Nanopore Ion Current Using Atomic-Resolution Brownian Dynamics", The Journal of Physical Chemistry C 116 / 5, 3376-3393. http://dx.doi.org/10.1021/jp210641j
  • Dooho Choi, Chang Kim, Doron Naveh (Carnegie Mellon University), Suk Chung, Andrew Warren, Noel Nuhfer, Michael Toney, Kevin Coffey, Katayun Barmak, (2012) "Electron mean free path of tungsten and the electrical resistivity of epitaxial (110) tungsten films", Physical Review B 86 / 4, . http://dx.doi.org/10.1103/PhysRevB.86.045432
  • Fangzhou Wei (University of Texas at Austin), Ali Yilmaz (University of Texas at Austin), (July2012) "Parallel truncated multigrid preconditioning of AIM for biolectromagnetics", USNC/URSI Radio Science Meeting Chicago, IL , .
  • Jejoong Yoo, Aleksei Aksimentiev, (2012) "Improved Parametrization of Li+, Na+, K+, and Mg2+Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems", The Journal of Physical Chemistry Letters 3 / 1, 45-50. http://dx.doi.org/10.1021/jz201501a
  • Noa Marom (University of Texas at Austin), Minjung Kim (University of Texas at Austin), James Chelikowsky (University of Texas at Austin), (2012) "Structure Selection Based on High Vertical Electron Affinity for TiO_{2} Clusters", Physical Review Letters 108 / 10, 106801. http://dx.doi.org/10.1103/PhysRevLett.108.106801
  • Thomas Furlani (SUNY at Buffalo), Matthew D. Jones, Steve Gallo (SUNY at Buffalo), Andrew E. Bruno, Charng-Da Lu, Amin Ghadersohi, Ryan J. Gentner, Abani Patra, Robert L. DeLeon, Gregor von Laszewski, Fugang Wang, Ann Zimmerman, (2012) "Performance metrics and auditing framework using application kernels for high-performance computer systems", Concurrency and Computation: Practice and Experience 25 / 7, 918-931. http://dx.doi.org/10.1002/cpe.2871
  • James C. Browne, Thomas Furlani (SUNY at Buffalo), Robert T. McLay, Robert L. DeLeon, Charng-Da Lu, Matthew D. Jones, Steve Gallo (SUNY at Buffalo), Amin Ghadersohi, Abani K. Patra, William Barth (University of Texas at Austin), John Hammond, (November2013) "Enabling comprehensive data-driven system management for large computational facilities", Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis on - SC '13 Denver, CO, USA , 1-11. http://dx.doi.org/10.1145/2503210.2503230
  • B. Dorvel, G. Sigalov, Q. Zhao, Jeffrey Comer (University of Illinois at Urbana-Champaign), V. Dimitrov, U. Mirsaidov, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), G. Timp, (2009) "Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore", Nucleic Acids Research 37 / 12, 4170-4179. http://dx.doi.org/10.1093/nar/gkp317
  • Jeffrey Comer (University of Illinois at Urbana-Champaign), Valentin Dimitrov, Qian Zhao, Gregory Timp, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2009) "Microscopic Mechanics of Hairpin DNA Translocation through Synthetic Nanopores", Biophysical Journal 96 / 2, 593-608. http://dx.doi.org/10.1016/j.bpj.2008.09.023
  • Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Robert Brunner, Eduardo Cruz-Chu, Jeffrey Comer (University of Illinois at Urbana-Champaign), Klaus Schulten, (2009) "Modeling transport through synthetic nanopores", IEEE Nanotechnology Magazine 3 / 1, 20-28. http://dx.doi.org/10.1109/MNANO.2008.931112
  • Kyong Min Yeo (Lawrence Berkeley National Laboratory), David M. Romps, (2012) "Measurement of Convective Entrainment using Lagrangian Particles", Journal of the Atmospheric Sciences undefined / undefined, 120907120245001. http://dx.doi.org/10.1175/JAS-D-12-0144.1
  • Pui-kuen Yeung (Georgia Institute of Technology), Diego Donzis (Texas A&M University), K. R. Sreenivasan, (June2012) "Dissipation, enstrophy and pressure statistics in turbulence simulations at high Reynolds numbers", Journal of Fluid Mechanics 700 / undefined, 5-15. http://dx.doi.org/10.1017/jfm.2012.5
  • Christopher Maffeo (University of Illinois at Urbana-Champaign), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2009) "Structure, Dynamics, and Ion Conductance of the Phospholamban Pentamer", Biophysical Journal 96 / 12, 4853-4865. http://dx.doi.org/10.1016/j.bpj.2009.03.053
  • Ruichang Xiong (University of Delaware), Stanley I. Sandler, Dionisios G. Vlachos, (2011) "Alcohol Adsorption onto Silicalite from Aqueous Solution", The Journal of Physical Chemistry C 115 / 38, 18659-18669. http://dx.doi.org/10.1021/jp205312k
  • Ruichang Xiong (University of Delaware), Stanley I. Sandler, Dionisios G. Vlachos, (2012) "Molecular Screening of Alcohol and Polyol Adsorption onto MFI-Type Zeolites", Langmuir 28 / 9, 4491-4499. http://dx.doi.org/10.1021/la204710j
  • Wendell Horton (University of Texas at Austin), K. D. Kaladze (Physcis Department, GC University, Lahore 54000, Pakistan 3I. Vekua Institute of Applied Mathematics, Tbilisi State University, 2 University str., 0186 Tbilisi, Georgia), L. Z. Kahlon (Physcis Department, GC University, Lahore 54000, Pakistan ), O. Pokhotelov (Institute of Physics of the Earth, 10 B. Gruzinskaya Str., 123995 Moscow, Russia), Oleg O. Onishchenko (Institute of Physics of the Earth, 10 B. Gruzinskaya Str., 123995 Moscow, Russia), (December2013) "Zonal flows and magnetic fields driven by large amplitude Rossby–Alfvén–Khantadze waves in the E–layer ionosphere", Journal of Geophysical Research SPACE PHYSICS, VOL. 118, 1–12, 2013, . http://dx.doi.org/10.1063/1.4831981
  • Luca Larini (University of California-Santa Barbara), Megan Murray Gessel, Nichole E. LaPointe, Thanh Do (University of California-Santa Barbara), Michael Bowers (University of California-Santa Barbara), Stuart C. Feinstein, Joan-Emma Shea (University of California-Santa Barbara), (2013) "Initiation of assembly of tau(273-284) and its ΔK280 mutant: an experimental and computational study", Physical Chemistry Chemical Physics 15 / 23, 8916. http://dx.doi.org/10.1039/C3CP00063J
  • Cameron Hummels (University of Arizona), Greg L. Bryan (Columbia University in the City of New York), Britton Smith (Michigan State University), Matthew Turk (Columbia University in the City of New York), (April2013) "Constraints on hydrodynamical subgrid models from quasar absorption line studies of the simulated circumgalactic medium", Monthly Notices of the Royal Astronomical Society 430 / 3, 1548-1565. http://dx.doi.org/10.1093/mnras/sts702
  • Binquan Luan, Rogan Carr, Martin Caffrey, Aleksei Aksimentiev, (2010) "The effect of calcium on the conformation of cobalamin transporter BtuB", Proteins: Structure, Function, and Bioinformatics 78 / 5, 1153-1162. http://dx.doi.org/10.1002/prot.22635
  • Md Ali (Mount Sinai School of Medicine), Rauf Latif (Mount Sinai School of Medicine), Ramkumarie Baliram (Mount Sinai School of Medicine), Terry Davies (Mount Sinai School of Medicine), Mihaly Mezei (Mount Sinai School of Medicine), (February2013) "MODELLING TSH AND ITS RECEPTOR COMPLEX FOR BINDING AFFINITY", Biophysical Society 57th Annual Meeting Philadelphia , . http://bps2013.conferencespot.org/3416-Pos
  • Jesmin Jahan Tithi (SUNY at Stony Brook), (May2013) "Polarization Energy on a Cluster of Multicores", IPDPSW, HICOMB2013 BOSTON, MA , .
  • M. Ryan Joung, Mary E. Putman, Greg L. Bryan (Columbia University in the City of New York), Ximena Fernández, J. E. G. Peek, (2012) "GAS ACCRETION IS DOMINATED BY WARM IONIZED GAS IN MILKY WAY MASS GALAXIES ATz∼ 0", The Astrophysical Journal 759 / 2, 137. http://dx.doi.org/10.1088/0004-637X/759/2/137
  • C. M. Simpson, Greg L. Bryan (Columbia University in the City of New York), K. V. Johnston, B. D. Smith, M.-M. Mac Low, S. Sharma, J. Tumlinson, (2013) "The effect of feedback and reionization on star formation in low-mass dwarf galaxy haloes", Monthly Notices of the Royal Astronomical Society 432 / 3, 1989-2011. http://dx.doi.org/10.1093/mnras/stt474
  • Fangzhou Wei (University of Texas at Austin), Ali Yilmaz (University of Texas at Austin), (September2012) "Surface-preconditioned AIM-accelerated surface-volume integral equation solution for bioelectromagnetics", 2012 International Conference on Electromagnetics in Advanced Applications Cape Town, South Africa , 869-872. http://dx.doi.org/10.1109/ICEAA.2012.6328757
  • Ricardo Taborda (University of Memphis), Jacobo Bielak (Carnegie Mellon University), (2013) "Ground-Motion Simulation and Validation of the 2008 Chino Hills, California, Earthquake", Bulletin of the Seismological Society of America 103 / 1, 131-156. http://dx.doi.org/10.1785/0120110325
  • Brian Crosby (Michigan State University), Brian O'Shea (Michigan State University), Britton Smith (Michigan State University), Matthew Turk (Columbia University in the City of New York), Oliver Hahn, (2013) "POPULATION III STAR FORMATION IN LARGE COSMOLOGICAL VOLUMES. I. HALO TEMPORAL AND PHYSICAL ENVIRONMENT", The Astrophysical Journal 773 / 2, 108. http://dx.doi.org/10.1088/0004-637X/773/2/108
  • Sara Nichols (University of California-San Diego), Carlos Hernandez (Stanford University), Yi Wang (University of California-San Diego), James McCammon (University of California-San Diego), (June2013) "Structure-based network analysis of an evolved G protein-coupled receptor homodimer interface", Protein Science 22 / 6, 745-754. http://dx.doi.org/10.1002/pro.2258
  • Ricardo Taborda (University of Memphis), Jacobo Bielak (Carnegie Mellon University), (2011) "Large-Scale Earthquake Simulation: Computational Seismology and Complex Engineering Systems", Computing in Science & Engineering 13 / 4, 14-27. http://dx.doi.org/10.1109/MCSE.2011.19
  • Ricardo Taborda (University of Memphis), Jacobo Bielak (Carnegie Mellon University), Dorian Restrepo (Carnegie Mellon University), (2012) "Earthquake Ground-Motion Simulation including Nonlinear Soil Effects under Idealized Conditions with Application to Two Case Studies", Seismological Research Letters 83 / 6, 1047-1060. http://dx.doi.org/10.1785/0220120079
  • Natalie Raettig (Max-Planck-Institut fuer Astronomie), Wladimir Lyra (California Institute of Technology), Hubert Klahr, (2013) "A PARAMETER STUDY FOR BAROCLINIC VORTEX AMPLIFICATION", The Astrophysical Journal 765 / 2, 115. http://dx.doi.org/10.1088/0004-637X/765/2/115
  • Wladimir Lyra (California Institute of Technology), M. Kuchner, (July2013) "Formation of sharp eccentric rings in debris disks with gas but without planets", Nature 499 / 7457, 184-187. http://dx.doi.org/10.1038/nature12281
  • M. Ryan Joung, Greg L. Bryan (Columbia University in the City of New York), Mary E. Putman, (2012) "GAS CONDENSATION IN THE GALACTIC HALO", The Astrophysical Journal 745 / 2, 148. http://dx.doi.org/10.1088/0004-637X/745/2/148
  • Parvez Sukheswalla (Cornell University), (August2013) "Simulation of homogeneous turbulent shear flow at higher Reynolds numbers: numerical challenges and a remedy", Journal of Turbulence 14 / 5, 60-97. http://dx.doi.org/10.1080/14685248.2013.817677
  • Matthew J. Turk, Jeffrey S. Oishi, Tom Abel, Greg L. Bryan (Columbia University in the City of New York), (2012) "MAGNETIC FIELDS IN POPULATION III STAR FORMATION", The Astrophysical Journal 745 / 2, 154. http://dx.doi.org/10.1088/0004-637X/745/2/154
  • Stephanie Tonnesen, Greg L. Bryan (Columbia University in the City of New York), (2012) "Star formation in ram pressure stripped galactic tails", Monthly Notices of the Royal Astronomical Society 422 / 2, 1609-1624. http://dx.doi.org/10.1111/j.1365-2966.2012.20737.x
  • Luca Larini (University of California-Santa Barbara), Lanyuan Lu (University of Utah), Gregory Voth (University of Chicago), (April2010) "The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials", The Journal of Chemical Physics 132 / 16, 164107. http://dx.doi.org/10.1063/1.3394863
  • Yifeng Cui (University of California-San Diego), Reagan Moore (San Diego Supercomputer Center), Kim Olsen (San Diego State University), Amit Chourasia (University of California-San Diego), Philip Maechling (University of Southern California), Jean-Bernard Minster (Scripps Institution of Oceanography), Steven Day (San Diego State University), Yuanfang Hu (San Diego Supercomputer Center), Jing Zhu (San Diego Supercomputer Center), Thomas Jordan (University of Southern California), (July2009) "Toward petascale earthquake simulations", Acta Geotechnica 4 / 2, 79-93. http://dx.doi.org/10.1007/s11440-008-0055-2
  • Rukmani Vijayaraghavan (University of Illinois at Urbana-Champaign), Paul M. Ricker (University of Illinois at Urbana-Champaign), (September2013) "Pre-processing and post-processing in group-cluster mergers", Monthly Notices of the Royal Astronomical Society undefined / undefined, . http://dx.doi.org/10.1093/mnras/stt1485
  • Wladimir Lyra (California Institute of Technology), Mordecai-Mark Mac Low (American Museum of Natural History), (2012) "ROSSBY WAVE INSTABILITY AT DEAD ZONE BOUNDARIES IN THREE-DIMENSIONAL RESISTIVE MAGNETOHYDRODYNAMICAL GLOBAL MODELS OF PROTOPLANETARY DISKS", The Astrophysical Journal 756 / 1, 62. http://dx.doi.org/10.1088/0004-637X/756/1/62
  • Jacobo Bielak (Carnegie Mellon University), Robert Graves (US Geological Survey), Kim Olsen (San Diego State University), Ricardo Taborda (Carnegie Mellon University), Leonardo Ramirez-Guzman (US Geological Survey), Steven Day (San Diego State University), Geoffrey Ely (Argonne National Laboratory), Daniel Roten (ETH Zurich), Thomas Jordan (University of Southern California), Philip Maechling (University of Southern California), John Urbanic (Pittsburgh Supercomputing Center), Yifeng Cui (University of California-San Diego), Gideon Juve (University of Southern California), (November2009) "The ShakeOut earthquake scenario: Verification of three simulation sets", Geophysical Journal International 180 / 1, 375-404. http://dx.doi.org/10.1111/j.1365-246X.2009.04417.x
  • Christopher Maffeo (University of Illinois at Urbana-Champaign), Robert Schöpflin, Hergen Brutzer, René Stehr, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Gero Wedemann, Ralf Seidel, (2010) "DNA–DNA Interactions in Tight Supercoils Are Described by a Small Effective Charge Density", Physical Review Letters 105 / 15, 158101. http://dx.doi.org/10.1103/PhysRevLett.105.158101
  • Yuan Zhang (Columbia University in the City of New York), (2012) "Identifying Highly Conserved and Unique Structural Elements in Myosin VI", CELLULAR AND MOLECULAR BIOENGINEERING , .
  • Thomas Peters (University of Zurich), Pamela D. Klaassen, Mordecai-Mark Mac Low, Ralf Klessen (University of Heidelberg), Robi Banerjee, (November2012) "ARE MOLECULAR OUTFLOWS AROUND HIGH-MASS STARS DRIVEN BY IONIZATION FEEDBACK?", The Astrophysical Journal 760 / 1, 91. http://dx.doi.org/10.1088/0004-637X/760/1/91
  • Shawn P Coleman (University of Arkansas), Mehrdad M. M Sichani, Douglas E Spearot (University of Arkansas), (2014) "A Computational Algorithm to Produce Virtual X-ray and Electron Diffraction Patterns from Atomistic Simulations", JOM 66 / 3, 408-416. http://dx.doi.org/10.1007/s11837-013-0829-3
  • Yongen Yu (Illinois Institute of Technology), Zhiling Lan (Illinois Institute of Technology), Jingjin Wu (Illinois Institute of Technology), Nicholas Gnedin (University of Chicago), Andrey Kravtsov (University of Chicago), (May2013) "A Transparent Collective I/O Implementation", IPDPS Boston, MA , .
  • Rogan Carr (University of Illinois at Urbana-Champaign), Jeffrey Comer (University of Illinois at Urbana-Champaign), Mark D. Ginsberg, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2011) "Modeling Pressure-Driven Transport of Proteins Through a Nanochannel", IEEE Transactions on Nanotechnology 10 / 1, 75-82. http://dx.doi.org/10.1109/TNANO.2010.2062530
  • Utkur Mirsaidov, Jeffrey Comer (University of Illinois at Urbana-Champaign), Valentin Dimitrov, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Gregory Timp, (2010) "Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix", Nanotechnology 21 / 39, 395501. http://dx.doi.org/10.1088/0957-4484/21/39/395501
  • Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Robert Brunner, Eduardo Cruz-Chu, Jeffrey Comer (University of Illinois at Urbana-Champaign), Klaus Schulten, (2009) "Modeling transport through synthetic nanopores", IEEE Nanotechnology Magazine 3 / 1, 20-28. http://dx.doi.org/10.1109/MNANO.2008.931112
  • Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Robert Brunner, Eduardo Cruz-Chu, Jeffrey Comer (University of Illinois at Urbana-Champaign), Klaus Schulten, (2009) "Modeling transport through synthetic nanopores", IEEE Nanotechnology Magazine 3 / 1, 20-28. http://dx.doi.org/10.1109/MNANO.2008.931112
  • Bala Murali Venkatesan, James Polans, Jeffrey Comer (University of Illinois at Urbana-Champaign), Supriya Sridhar, David Wendell, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Rashid Bashir, (2011) "Lipid bilayer coated Al2O3 nanopore sensors: towards a hybrid biological solid-state nanopore", Biomedical Microdevices 13 / 4, 671-682. http://dx.doi.org/10.1007/s10544-011-9537-3
  • Swati Bhattacharya (University of Illinois at Urbana-Champaign), Julien Muzard (Ecole Supérieure de Physique et Chimie Industrielles, ParisTech, Centre National de la Recherche Scientifique, France), Linda Payet (Ecole Supérieure de Physique et Chimie Industrielles, ParisTech, Centre National de la Recherche Scientifique, France), Jerome Mathe (Ecole Supérieure de Physique et Chimie Industrielles, ParisTech, Centre National de la Recherche Scientifique, France), Ulrich Bockelmann (Ecole Supérieure de Physique et Chimie Industrielles, ParisTech, Centre National de la Recherche Scientifique, France), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Virgile Viasnoff (Ecole Supérieure de Physique et Chimie Industrielles, ParisTech, Centre National de la Recherche Scientifique, France), (February2011) "Rectification of the Current in α-Hemolysin Pore Depends on the Cation Type: The Alkali Series Probed by Molecular Dynamics Simulations and Experiments", Journal of Physical Chemistry C 115, 4255. http://pubs.acs.org/doi/abs/10.1021/jp111441p
  • Meni Wanunu (Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States), Swati Bhattacharya (University of Illinois at Urbana-Champaign), Yun Xie (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States), Yitzhak Tor (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Marija Drndik (Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania), (November2011) "Nanopore Analysis of Individual RNA/Antibiotic Complexes", ACS Nano 5, 9345. http://pubs.acs.org/doi/abs/10.1021/nn203764j#cor1
  • Noa Marom (University of Texas at Austin), Jonathan Moussa (University of Texas at Austin), Xinguo Ren, Alexandre Tkatchenko, James Chelikowsky (University of Texas at Austin), (December2011) "Electronic structure of dye-sensitized TiO_{2} clusters from many-body perturbation theory", Physical Review B 84 / 24, 245115. http://dx.doi.org/10.1103/PhysRevB.84.245115
  • Noa Marom (University of Texas at Austin), Xinguo Ren, Jonathan Moussa (University of Texas at Austin), James Chelikowsky (University of Texas at Austin), Leeor Kronik, (2011) "Electronic structure of copper phthalocyanine from G_{0}W_{0} calculations", Physical Review B 84 / 19, 195143. http://dx.doi.org/10.1103/PhysRevB.84.195143
  • Jonathan Moussa (University of Texas at Austin), Noa Marom (University of Texas at Austin), Na Sai (University of Texas at Austin), James Chelikowsky (University of Texas at Austin), (2012) "Theoretical Design of a Shallow Donor in Diamond by Lithium-Nitrogen Codoping", Physical Review Letters 108 / 22, . http://dx.doi.org/10.1103/PhysRevLett.108.226404
  • Swati Bhattacharya (University of Illinois at Urbana-Champaign), Ian M. Derrington (Department of Physics, University of Washington Seattle, 3910 15th Avenue, Seattle, Washington, 98195, United States ), Mikhail Pavlenok (Department of Microbiology, University of Alabama at Birmingham, 609 Bevill Biomedical Research Building, 845 19th Street South, Birmingham, Alabama 35294, United States), Michael Niederweis (Department of Microbiology, University of Alabama at Birmingham, 609 Bevill Biomedical Research Building, 845 19th Street South, Birmingham, Alabama 35294, United States), Jens H. Gundlach (Department of Physics, University of Washington Seattle, 3910 15th Avenue, Seattle, Washington, 98195, United States ), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2012) "Molecular Dynamics Study of MspA Arginine Mutants Predicts Slow DNA Translocations and Ion Current Blockades Indicative of DNA Sequence", ACS Nano 6 / 8, 6960-6968. http://dx.doi.org/10.1021/nn3019943
  • Christopher Maffeo (University of Illinois at Urbana-Champaign), Binquan Luan (University of Illinois at Urbana-Champaign), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2012) "End-to-end attraction of duplex DNA", Nucleic Acids Research 40 / 9, 3812-3821. http://dx.doi.org/10.1093/nar/gkr1220
  • David Wells (University of Illinois at Urbana-Champaign), Volha Abramkina, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2007) "Exploring transmembrane transport through α-hemolysin with grid-steered molecular dynamics", The Journal of Chemical Physics 127 / 12, 125101. http://dx.doi.org/10.1063/1.2770738
  • S. Samudrala (Iowa State University), Olga Wodo (Iowa State University), S.K. Suram (Iowa State University), S. Broderick (Iowa State University), K. Rajan (Iowa State University), B. Ganapathysubramanian (Iowa State University), (2013) "A graph-theoretic approach for characterization of precipitates from atom probe tomography data", Computational Materials Science 77 / undefined, 335-342. http://dx.doi.org/10.1016/j.commatsci.2013.04.038
  • David Wells (University of Illinois at Urbana-Champaign), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2010) "Mechanical Properties of a Complete Microtubule Revealed through Molecular Dynamics Simulation", Biophysical Journal 99 / 2, 629-637. http://dx.doi.org/10.1016/j.bpj.2010.04.038
  • Olga Wodo (Iowa State University), Baskar Ganapathysubramanian (Iowa State University), (2012) "Modeling morphology evolution during solvent-based fabrication of organic solar cells", Computational Materials Science 55 / undefined, 113-126. http://dx.doi.org/10.1016/j.commatsci.2011.12.012
  • Olga Wodo (Iowa State University), Baskar Ganapathysubramanian (Iowa State University), (2011) "Computationally efficient solution to the Cahn–Hilliard equation: Adaptive implicit time schemes, mesh sensitivity analysis and the 3D isoperimetric problem", Journal of Computational Physics 230 / 15, 6037-6060. http://dx.doi.org/10.1016/j.jcp.2011.04.012
  • Jesmin Jahan Tithi (SUNY at Stony Brook), (May2013) "Avoiding Locks and Atomic Instructions in Shared-Memory Parallel BFS Using Optimistic Parallelization", IPDPSW, MTAAP'2013 BOSTON, MA , .
  • Luca Larini (Rutgers, the State University of New Jersey), Joan-Emma Shea (University of California-Santa Barbara), (2013) "Double Resolution Model for Studying TMAO/Water Effective Interactions", The Journal of Physical Chemistry B 117 / 42, 13268-13277. http://dx.doi.org/10.1021/jp403635g
  • Cemil S. Geyik, Fangzhou Wei (University of Texas at Austin), Jackson Massey (University of Texas at Austin), Ali Yilmaz (University of Texas at Austin), (July2012) "FDTD vs. AIM for bioelectromagnetic analysis", Proceedings of the 2012 IEEE International Symposium on Antennas and Propagation Chicago, IL , 1-2. http://dx.doi.org/10.1109/APS.2012.6348964
  • Zheqiang Shi (San Diego State University), Steven M. Day, (March2013) "Rupture dynamics and ground motion from 3-D rough-fault simulations", Journal of Geophysical Research: Solid Earth 118 / 3, 1122-1141. http://dx.doi.org/10.1002/jgrb.50094
  • Fangzhou Wei (University of Texas at Austin), Jackson W. Massey, Cemil S. Geyik, Ali Yilmaz (University of Texas at Austin), (July2012) "Error measures for comparing bioelectromagnetic simulators", Proceedings of the 2012 IEEE International Symposium on Antennas and Propagation Chicago, IL , 1-2. http://dx.doi.org/10.1109/APS.2012.6348016
  • Paul C. Clark, Simon Glover (University of Heidelberg), Ralf Klessen (University of Heidelberg), Ian A. Bonnell, (June2012) "How long does it take to form a molecular cloud?", Monthly Notices of the Royal Astronomical Society 424 / 4, 2599-2613. http://dx.doi.org/10.1111/j.1365-2966.2012.21259.x
  • David Wells (University of Illinois at Urbana-Champaign), Maxim Belkin (University of Illinois at Urbana-Champaign), Jeffrey Comer (University of Illinois at Urbana-Champaign), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (July2012) "Assessing Graphene Nanopores for Sequencing DNA", Nano Letters 12 / 8, 4117-4123. http://dx.doi.org/10.1021/nl301655d
  • Luca Larini (University of California-Santa Barbara), Joan-Emma Shea (University of California-Santa Barbara), (July2012) "Coarse-Grained Modeling of Simple Molecules at Different Resolutions in the Absence of Good Sampling", The Journal of Physical Chemistry B 116 / 29, 8337-8349. http://dx.doi.org/10.1021/jp2097263
  • Luca Larini (University of California-Santa Barbara), Joan-Emma Shea (University of California-Santa Barbara), (August2012) "Role of β-Hairpin Formation in Aggregation: The Self-Assembly of the Amyloid-β(25–35) Peptide", Biophysical Journal 103 / 3, 576-586. http://dx.doi.org/10.1016/j.bpj.2012.06.027
  • Yosuke Mizuno (National Tsing Hua University), Yuri Lyubarsky, Ken-Ichi Nishikawa (University of Alabama, Huntsville), Philip E. Hardee, (August2012) "THREE-DIMENSIONAL RELATIVISTIC MAGNETOHYDRODYNAMIC SIMULATIONS OF CURRENT-DRIVEN INSTABILITY. III. ROTATING RELATIVISTIC JETS", The Astrophysical Journal 757 / 1, 16. http://dx.doi.org/10.1088/0004-637X/757/1/16
  • Brett Olsen (Washington University in St. Louis), Paul H. Schlesinger (Washington University in St. Louis), Daniel S. Ory (Washington University in St. Louis), Nathan A. Baker (Pacific Northwest National Labs), (2011) "25-Hydroxycholesterol Increases the Availability of Cholesterol in Phospholipid Membranes", Biophysical Journal , .
  • Jacobo Bielak (Carnegie Mellon University), Haydar Karaoglu (Carnegie Mellon University), Ricardo Taborda (University of Memphis), (2011) "Memory-efficient displacement-based internal friction for wave propagation simulation", GEOPHYSICS 76 / 6, T131-T145. http://dx.doi.org/10.1190/geo2011-0019.1
  • Yigit Isbiliroglu (Carnegie Mellon University), Ricardo Taborda (University of Memphis), Jacobo Bielak (Carnegie Mellon University), (2013) "Coupled Soil-Structure Interaction Effects of Building Clusters During Earthquakes", Earthquake Spectra undefined / undefined, 131030142624007. http://dx.doi.org/10.1193/102412EQS315M
  • C. Stavis, T. L. Clare, J. E. Butler, A. D. Radadia, Rogan Carr (University of Illinois at Urbana-Champaign), H. Zeng, W. P. King, J. A. Carlisle, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), R. Bashir, R. J. Hamers, (2010) "Surface Chemistry Special Feature: Surface functionalization of thin-film diamond for highly stable and selective biological interfaces", Proceedings of the National Academy of Sciences 108 / 3, 983-988. http://dx.doi.org/10.1073/pnas.1006660107
  • Yongen Yu (Illinois Institute of Technology), Zhiling Lan (Illinois Institute of Technology), Douglas Rudd (University of Chicago), Nicholas Gnedin (University of Chicago), Andrey Kravtsov (University of Chicago), Jingjin Wu (Illinois Institute of Technology), (May2012) "Improving Parallel IO Performance of Cell-based AMR Applications", IPDPS Shanghai, China , .
  • Kim Olsen (San Diego State University), Steven Day (San Diego State University), Luis Dalguer (ETH Zurich), John Mayhew (San Diego State University), Yifeng Cui (University of California-San Diego), Jun Zhou (University of California-San Diego), Victor Cruz-Atienza (Universidad Nacional Autonoma de Mexico), Daniel Roten (ETH Zurich), Philip Maechling (University of Southern California), Thomas Jordan (University of Southern California), David Okaya (University of Southern California), Amit Chourasia (University of California-San Diego), (February2009) "ShakeOut-D: Ground motion estimates using an ensemble of large earthquakes on the southern San Andreas fault with spontaneous rupture propagation", Geophysical Research Letters 36 / 4, . http://dx.doi.org/10.1029/2008GL036832
  • Jackson Massey (University of Texas at Austin), Fangzhou Wei (University of Texas at Austin), Ali Yilmaz (University of Texas at Austin), (July2013) "Mixed basis functions for fast analysis of antennas near voxel-based human models", 2013 USNC-URSI Radio Science Meeting (Joint with AP-S Symposium) Orlando, FL , . http://dx.doi.org/10.1109/USNC-URSI.2013.6715406
  • Fangzhou Wei (University of Texas at Austin), Ali Yilmaz (University of Texas at Austin), (July2013) "A scalable nested preconditioner for improving the AIM-accelerated analysis of antennas near the human body", 2013 USNC-URSI Radio Science Meeting (Joint with AP-S Symposium) Orlando, FL , 214-214. http://dx.doi.org/10.1109/USNC-URSI.2013.6715520
  • Greg Meece (Michigan State University), Britton Smith, Brian O'Shea (Michigan State University), (March2014) "FRAGMENTATION IN DUSTY LOW-METALLICITY STAR-FORMING HALOS", The Astrophysical Journal 783 / 2, 75. http://dx.doi.org/10.1088/0004-637X/783/2/75
  • Greg L. Bryan, Michael L. Norman, Brian O'Shea (Michigan State University), Tom Abel, John H. Wise, Matthew J. Turk, Daniel R. Reynolds, David C. Collins, Peng Wang, Sam Skillman (Stanford University), Britton Smith, Robert P. Harkness, James Bordner, Ji-hoon Kim, Michael Kuhlen, Hao Xu, Nathan Goldbaum, Cameron Hummels, Alexei G. Kritsuk, Elizabeth Tasker, Stephen Skory, Christine M. Simpson, Oliver Hahn, Jeffrey S. Oishi, Geoffrey C. So, Fen Zhao, Renyue Cen, Yuan Li, (April2014) "ENZO: AN ADAPTIVE MESH REFINEMENT CODE FOR ASTROPHYSICS", The Astrophysical Journal Supplement Series 211 / 2, 19. http://dx.doi.org/10.1088/0067-0049/211/2/19
  • Britton Smith, Brian O'Shea (Michigan State University), G. Mark Voit, David Ventimiglia, Sam Skillman (Stanford University), (December2013) "COSMOLOGICAL SIMULATIONS OF ISOTROPIC CONDUCTION IN GALAXY CLUSTERS", The Astrophysical Journal 778 / 2, 152. http://dx.doi.org/10.1088/0004-637X/778/2/152
  • Jejoong Yoo (University of Illinois at Urbana-Champaign), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2012) "Improved Parametrization of Li+, Na+, K+, and Mg2+Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems", The Journal of Physical Chemistry Letters 3 / 1, 45-50. http://dx.doi.org/10.1021/jz201501a
  • Winston Timp, Jeffrey Comer (University of Illinois at Urbana-Champaign), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (May2012) "DNA Base-Calling from a Nanopore Using a Viterbi Algorithm", Biophysical Journal 102 / 10, L37-L39. http://dx.doi.org/10.1016/j.bpj.2012.04.009
  • Q. Zhao, J. Comer, V. Dimitrov, S. Yemenicioglu, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), G. Timp, (2008) "Stretching and unzipping nucleic acid hairpins using a synthetic nanopore", Nucleic Acids Research 36 / 5, 1532-1541. http://dx.doi.org/10.1093/nar/gkm1017
  • Jeffrey Comer (University of Illinois at Urbana-Champaign), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (January2012) "Predicting the DNA Sequence Dependence of Nanopore Ion Current Using Atomic-Resolution Brownian Dynamics", The Journal of Physical Chemistry C 116 / 5, 3376-3393. http://dx.doi.org/10.1021/jp210641j
  • Stefan W. Kowalczyk, David Wells (University of Illinois at Urbana-Champaign), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Cees Dekker, (January2012) "Slowing down DNA Translocation through a Nanopore in Lithium Chloride", Nano Letters 12 / 2, 1038-1044. http://dx.doi.org/10.1021/nl204273h
  • Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Robert Brunner, Jordi Cohen, Jeffrey Comer (University of Illinois at Urbana-Champaign), Eduardo Cruz-Chu, David Hardy, Aruna Rajan, Amy Shih, Grigori Sigalov, Ying Yin, Klaus Schulten (University of Illinois at Urbana-Champaign), (2008) "Nanostructure Design", , 181-234. http://dx.doi.org/10.1007/978-1-59745-480-3_11
  • Grigori Sigalov, Jeffrey Comer (University of Illinois at Urbana-Champaign), Gregory Timp, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2008) "Detection of DNA Sequences Using an Alternating Electric Field in a Nanopore Capacitor", Nano Letters 8 / 1, 56-63. http://dx.doi.org/10.1021/nl071890k
  • Kiran Bhaganagar (University of Texas at San Antonio), Long Chau (University of Texas at San Antonio), (November2012) "Understanding turbulent flow over ripple-shaped random roughness in a channel", Physics of Fluids 24(11), 115102-115102-22.
  • Phillip Dickens (University of Maine), Timothy Morey (University of Maine), (May2013) "Increasing the Scalability of PISM for High Resolution Ice Sheet Models", Workshop on Parallel and Distributed Scientific and Engineering Computing Boston, Mass , . http://cse.stfx.ca/~pdsec13/
  • Wendell Horton (University of Texas at Austin), M. Goniche, Y. Peysson, J. Decker, A. Ekedahl, X. Litaudon, (December2013) "Penetration of lower hybrid current drive waves in tokamaks", Physics of Plasmas 20 / 11, 112508. http://dx.doi.org/10.1063/1.4831981
  • Mirko Palla (Columbia University in the City of New York), Chien-Pin Chen, Yuan Zhang, Jingyuan Li, Jingyue Ju, Jung-Chi Liao, (February2013) "Mechanism of flexibility control for ATP access of hepatitis C virus NS3 helicase", Journal of Biomolecular Structure and Dynamics 31 / 2, 129-141. http://dx.doi.org/10.1080/07391102.2012.698236
  • Rogan Carr (University of Illinois at Urbana-Champaign), Ira A. Weinstock, Asipu Sivaprasadarao, Achim Müller, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2008) "Synthetic Ion Channels via Self-Assembly: A Route for Embedding Porous Polyoxometalate Nanocapsules in Lipid Bilayer Membranes", Nano Letters 8 / 11, 3916-3921. http://dx.doi.org/10.1021/nl802366k
  • Kelly E. McCusker, David S. Battisti, Cecilia M. Bitz, (2012) "The Climate Response to Stratospheric Sulfate Injections and Implications for Addressing Climate Emergencies", Journal of Climate 25 / 9, 3096-3116. http://dx.doi.org/10.1175/JCLI-D-11-00183.1
  • Zhiling Lan (Illinois Institute of Technology), Jingjin Wu (Illinois Institute of Technology), (November2012) "Hierarchical Task Mapping of Cell-based AMR Cosmology Simulations", SC Salt Lake, UT , .
  • N. Goldenson, S. J. Doherty, C. M. Bitz, M. M. Holland, B. Light, A. J. Conley, (2012) "Arctic climate response to forcing from light-absorbing particles in snow and sea ice in CESM", Atmospheric Chemistry and Physics 12 / 17, 7903-7920. http://dx.doi.org/10.5194/acp-12-7903-2012
  • Adarsh D. Radadia, Courtney J. Stavis, Rogan Carr (University of Illinois at Urbana-Champaign), Hongjun Zeng, William P. King, John A. Carlisle, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Robert J. Hamers, Rashid Bashir, (2011) "Control of Nanoscale Environment to Improve Stability of Immobilized Proteins on Diamond Surfaces", Advanced Functional Materials 21 / 6, 1040-1050. http://dx.doi.org/10.1002/adfm.201002251
  • Thomas Körzdörfer, Noa Marom (University of Texas at Austin), (2012) "Strategy for finding a reliable starting point for G_{0}W_{0} demonstrated for molecules", Physical Review B 86 / 4, . http://dx.doi.org/10.1103/PhysRevB.86.041110