SciDAC 2006 Dr. William M Tang doi:10.1088/1742-6596/46/1/E01 Tag this article Abstract Full text PDF (39 KB)

Scientific Discovery through Advanced Computing Michael Strayer doi:10.1088/1742-6596/46/1/E02 Tag this article Abstract Full text PDF (26 KB)

Simulation, computation, and the Global Nuclear Energy Partnership Dr. Victor Reis doi:10.1088/1742-6596/46/1/E03 Tag this article Abstract Supplementary data Full text PDF (32 KB)

1 Simulation of lean premixed turbulent combustion J Bell, M Day, A Almgren, M Lijewski, C Rendleman, R Cheng and I Shepherd doi:10.1088/1742-6596/46/1/001 Tag this article Abstract References Full text PDF (545 KB)

16 Large eddy simulation of turbulence-chemistry interactions in reacting flows J C Oefelein, T G Drozda and V Sankaran doi:10.1088/1742-6596/46/1/002 Tag this article Abstract References Full text PDF (12.42 MB)

28 Turbulent liquid spray mixing and combustion–fundamental simulations Christopher J Rutland and Yunliang Wang doi:10.1088/1742-6596/46/1/003 Tag this article Abstract References Full text PDF (1.19 MB)

38 Direct numerical simulations of turbulent lean premixed combustion Ramanan Sankaran, Evatt R Hawkes, Jacqueline H Chen, Tianfeng Lu and Chung K Law doi:10.1088/1742-6596/46/1/004 Tag this article Abstract References Cited by Full text PDF (513 KB)

43 Simulation of premixed turbulent flames M Day and J Bell doi:10.1088/1742-6596/46/1/005 Tag this article Abstract References Full text PDF (722 KB)

48 A low-numerical dissipation, patch-based adaptive-mesh-refinement method for large-eddy simulation of compressible flows C Pantano, R Deiterding, D J Hill and D I Pullin doi:10.1088/1742-6596/46/1/006 Tag this article Abstract References Full text PDF (189 KB)

53 A computational facility for reacting flow science H N Najm, J Ray, M Valorani, F Creta and D A Goussis doi:10.1088/1742-6596/46/1/007 Tag this article Abstract References Cited by Full text PDF (569 KB)

58 Atomistic simulation of the Rayleigh-Taylor instability J L Barber, K Kadau, T C Germann, P S Lomdahl, B L Holian and B J Alder doi:10.1088/1742-6596/46/1/008 Tag this article Abstract References Cited by Full text PDF (731 KB)

63 Computing nonlinear magnetohydrodynamic edge localized instabilities in fusion plasmas D P Brennan, S E Kruger, D D Schnack, C R Sovinec and A Pankin doi:10.1088/1742-6596/46/1/009 Tag this article Abstract References Cited by Full text PDF (854 KB)

73 Gyrokinetic particle simulation of fusion plasmas: path to petascale computing W W Lee, S Ethier, W X Wang, W M Tang and S Klasky doi:10.1088/1742-6596/46/1/010 Tag this article Abstract References Cited by Full text PDF (1.74 MB)

82 Quasilinear evolution of non-thermal distributions in ion cyclotron resonance heating of tokamak plasmas E F Jaeger, R W Harvey, V E Lynch, N Ershov, L A Berry, P T Bonoli, V Tang and R D Moore doi:10.1088/1742-6596/46/1/011 Tag this article Abstract References Cited by Full text PDF (322 KB)

87 Gyrokinetic particle simulation of neoclassical transport in the pedestal/scrape-off region of a tokamak plasma S Ku, C-S Chang, M Adams, J Cummings, F Hinton, D Keyes, S Klasky, W Lee, Z Lin, S Parker and the CPES team doi:10.1088/1742-6596/46/1/012 Tag this article Abstract References Cited by Full text PDF (697 KB)

92 Arbitrary plasma shape and trapped electron modes in the GEM gyrokinetic electromagnetic turbulence simulation code Yang Chen, Scott Parker and Jianying Lang doi:10.1088/1742-6596/46/1/013 Tag this article Abstract References Full text PDF (144 KB)

97 Massively parallel modeling of the sawtooth instability in tokamaks J A Breslau, W Park and S C Jardin doi:10.1088/1742-6596/46/1/014 Tag this article Abstract References Full text PDF (1.08 MB)

102 Collaborative technologies for distributed science: fusion energy and high-energy physics D P Schissel, E E Gottschalk, M J Greenwald and D McCune doi:10.1088/1742-6596/46/1/015 Tag this article Abstract References Full text PDF (215 KB)

107 Precision lattice QCD calculations and predictions of fundamental physics in heavy quark systems Christine Davies doi:10.1088/1742-6596/46/1/016 Tag this article Abstract References Cited by Full text PDF (645 KB)

122 Lattice simulations of the thermodynamics of strongly interacting elementary particles and the exploration of new phases of matter in relativistic heavy ion collisions Frithjof Karsch doi:10.1088/1742-6596/46/1/017 Tag this article Abstract References Cited by Full text PDF (202 KB)

132 Innovations in lattice QCD algorithms Konstantinos Orginos doi:10.1088/1742-6596/46/1/018 Tag this article Abstract References Full text PDF (178 KB)

142 National software infrastructure for lattice quantum chromodynamics R C Brower, C E DeTar, R G Edwards, D J Holmgren, R D Mawhinney, W Watson III and Y Zhang doi:10.1088/1742-6596/46/1/019 Tag this article Abstract References Full text PDF (109 KB)

147 Predictions with lattice QCD Andreas S Kronfeld for the Fermilab Lattice, MILC, and HPQCD Collaborations doi:10.1088/1742-6596/46/1/020 Tag this article Abstract References Cited by Full text PDF (132 KB)

152 Calculation of the nucleon axial charge in lattice QCD D B Renner, R G Edwards, G Fleming, Ph Hägler, J W Negele, K Orginos, A V Pochinsky, D G Richards and W Schroers doi:10.1088/1742-6596/46/1/021 Tag this article Abstract References Cited by Full text PDF (352 KB)

157 The Blue Gene, GCC and lattice QCD: a case study Andrew Pochinsky doi:10.1088/1742-6596/46/1/022 Tag this article Abstract Full text PDF (59 KB)

161 Kaon physics and CP violation calculations on QCDOC R Mawhinney for the RBC UKQCD collaborations doi:10.1088/1742-6596/46/1/023 Tag this article Abstract References Full text PDF (292 KB)

166 The nuclear structure and low-energy reactions (NSLER) collaboration D J Dean for the NSLER collaboration doi:10.1088/1742-6596/46/1/024 Tag this article Abstract References Full text PDF (236 KB)

171 Extraordinary tools for extraordinary science: the impact of SciDAC on accelerator science and technology Robert D Ryne doi:10.1088/1742-6596/46/1/025 Tag this article Abstract References Cited by Full text PDF (3.31 MB)

190 QuickPIC: a highly efficient fully parallelized PIC code for plasma-based acceleration C Huang, V K Decyk, M Zhou, W Lu, W B Mori, J H Cooley, T M Antonsen Jr, B Feng, T Katsouleas, J Vieira and L O Silva doi:10.1088/1742-6596/46/1/026 Tag this article Abstract References Cited by Full text PDF (675 KB)

200 Petascale self-consistent electromagnetic computations using scalable and accurate algorithms for complex structures John R Cary, D Abell, J Amundson, D L Bruhwiler, R Busby, J A Carlsson, D A Dimitrov, E Kashdan, P Messmer, C Nieter, D N Smithe, P Spentzouris, P Stoltz, R M Trines, H Wang and G R Werner doi:10.1088/1742-6596/46/1/027 Tag this article Abstract References Full text PDF (2.34 MB)

205 Development and validation of self-consistent 3D beam-beam modeling code within SciDAC J Amundson, J Qiang, R Ryne, P Spentzouris, E Stern and A Valishev doi:10.1088/1742-6596/46/1/028 Tag this article Abstract References Full text PDF (262 KB)

210 Beam dynamics D Abell, A Adelmann, J Amundson, A Dragt, C Mottershead, F Neri, I Pogorelov, J Qiang, R Ryne, J Shalf, C Siegerist, P Spentzouris, E Stern, M Venturini and P Walstrom doi:10.1088/1742-6596/46/1/029 Tag this article Abstract References Full text PDF (688 KB)

215 Towards the petascale in electromagnetic modeling of plasma-based accelerators for high-energy physics D L Bruhwiler, T Antonsen, J R Cary, J Cooley, V K Decyk, E Esarey, C G R Geddes, C Huang, A Hakim, T Katsouleas, P Messmer, W B Mori, F S Tsung, J Vieira and M Zhou doi:10.1088/1742-6596/46/1/030 Tag this article Abstract References Cited by Full text PDF (996 KB)

220 Enabling new capabilities and insights from quantum chemistry by using component architectures C L Janssen, J P Kenny, I M B Nielsen, M Krishnan, V Gurumoorthi, E F Valeev and T L Windus doi:10.1088/1742-6596/46/1/031 Tag this article Abstract References Cited by Full text PDF (252 KB)

229 Scalable correlated electronic structure theory Mark S Gordon, Klaus Ruedenberg, Michael W Schmidt, Laimis Bytautas, Timothy J Dudley, Takeshi Nagata, Ryan Olson and Sergey Varganov doi:10.1088/1742-6596/46/1/032 Tag this article Abstract References Cited by Full text PDF (656 KB)

234 Advanced computational methods for simulating chemical reactions D L Thompson, A F Wagner and M Minkoff doi:10.1088/1742-6596/46/1/033 Tag this article Abstract References Full text PDF (91 KB)

239 Advanced software for the calculation of thermochemistry, kinetics, and dynamics R Shepard, A F Wagner and S K Gray doi:10.1088/1742-6596/46/1/034 Tag this article Abstract References Cited by Full text PDF (209 KB)

244 Multiscale dynamical framework for high-level calculations of finite temperature ground and excited state properties Karol Kowalski and Marat Valiev doi:10.1088/1742-6596/46/1/035 Tag this article Abstract References Full text PDF (260 KB)

249 Automated symbolic algebra for quantum chemistry So Hirata doi:10.1088/1742-6596/46/1/036 Tag this article Abstract References Cited by Full text PDF (460 KB)

254 Simulating solidification in metals at high pressure: The drive to petascale computing Frederick H Streitz, James N Glosli, Mehul V Patel, Bor Chan, Robert K Yates, Bronis R de Supinski, James Sexton and John A Gunnels doi:10.1088/1742-6596/46/1/037 Tag this article Abstract References Cited by Full text PDF (1.56 MB)

268 Large-scale first-principles molecular dynamics: moving from terascale to petascale computing François Gygi doi:10.1088/1742-6596/46/1/038 Tag this article Abstract References Cited by Full text PDF (266 KB)

278 Statistical physics of fracture: scientific discovery through high-performance computing Phani Kumar, V V Nukala, Srdan Simunović and Richard T Mills doi:10.1088/1742-6596/46/1/039 Tag this article Abstract References Full text PDF (393 KB)

292 Predicting the electronic properties of 3D, million-atom semiconductor nanostructure architectures A Zunger, A Franceschetti, G Bester, W B Jones, Kwiseon Kim, P A Graf, L-W Wang, A Canning, O Marques, C Voemel, J Dongarra, J Langou and S Tomov doi:10.1088/1742-6596/46/1/040 Tag this article Abstract References Cited by Full text PDF (644 KB)

299 Three-dimensional fracture and fragmentation of artificial kidney stones Alejandro Mota, Jaroslaw Knap and Michael Ortiz doi:10.1088/1742-6596/46/1/041 Tag this article Abstract References Full text PDF (1.05 MB)

304 High performance computing for the application of molecular theories to biological systems Laura J Douglas Frink, Marcus G Martin, Andrew G Salinger and Micheal A Heroux doi:10.1088/1742-6596/46/1/042 Tag this article Abstract References Full text PDF (1.63 MB)

311 Computational challenges for modeling and simulating biomacromolecular assemblies Ed Uberbacher, Philip LoCascio, Sergey Passovets, Pavan Ghattyvenkatakrishna, Pratul Agarwal, Nikita Arnold, Andrew Bordner and Andrey Gorin doi:10.1088/1742-6596/46/1/043 Tag this article Abstract References Full text PDF (1.50 MB)

316 Modeling complex biological flows in multi-scale systems using the APDEC framework David Trebotich doi:10.1088/1742-6596/46/1/044 Tag this article Abstract References Full text PDF (786 KB)

322 Computer models of bacterial cells: from generalized coarsegrained to genome-specific modular models Evgeni V Nikolaev, Jordan C Atlas and Michael L Shuler doi:10.1088/1742-6596/46/1/045 Tag this article Abstract References Cited by Full text PDF (365 KB)

327 Biomolecular simulations on petascale: promises and challenges Pratul K Agarwal and Sadaf R Alam doi:10.1088/1742-6596/46/1/046 Tag this article Abstract References Cited by Full text PDF (1.36 MB)

334 Large-scale simulations of the ribosome: a new landmark in computational biology K Y Sanbonmatsu and C-S Tung doi:10.1088/1742-6596/46/1/047 Tag this article Abstract References Cited by Full text PDF (476 KB)

343 Toward an Earth system model: atmospheric chemistry, coupling, and petascale computing P Cameron-Smith, J-F Lamarque, P Connell, C Chuang and F Vitt doi:10.1088/1742-6596/46/1/048 Tag this article Abstract References Full text PDF (338 KB)

351 A geodesic atmospheric model with a quasi-Lagrangian vertical coordinate Ross Heikes, Celal Konor and David A Randall doi:10.1088/1742-6596/46/1/049 Tag this article Abstract References Full text PDF (1.24 MB)

356 Performance engineering in the community atmosphere model P Worley, A Mirin, J Drake and W Sawyer doi:10.1088/1742-6596/46/1/050 Tag this article Abstract References Cited by Full text PDF (251 KB)

363 Terrestrial biogeochemistry in the community climate system model (CCSM) Forrest Hoffman, Inez Fung, Jim Randerson, Peter Thornton, Jon Foley, Curtis Covey, Jasmin John, Samuel Levis, W Mac Post, Mariana Vertenstein, Reto Stöckli, Steve Running, Faith Ann Heinsch, David Erickson and John Drake doi:10.1088/1742-6596/46/1/051 Tag this article Abstract References Full text PDF (882 KB)

370 Large-scale simulations of turbulent stellar convection flows and the outlook for petascale computation Paul R Woodward, David H Porter, Sarah Anderson, Tyler Fuchs and Falk Herwig doi:10.1088/1742-6596/46/1/052 Tag this article Abstract References Cited by Full text PDF (2.21 MB)

385 New approaches for modeling Type Ia supernovae M Zingale, A S Almgren, J B Bell, M S Day, C A Rendleman and S E Woosley doi:10.1088/1742-6596/46/1/053 Tag this article Abstract References Cited by Full text PDF (942 KB)

393 Modeling core collapse supernovae in 2 and 3 dimensions with spectral neutrino transport S W Bruenn, C J Dirk, A Mezzacappa, J C Hayes, J M Blondin, W R Hix and O E B Messer doi:10.1088/1742-6596/46/1/054 Tag this article Abstract References Cited by Full text PDF (488 KB)

403 Gamma-ray bursts: nature's brightest explosions W Zhang, S E Woosley and A I MacFadyen doi:10.1088/1742-6596/46/1/055 Tag this article Abstract References Cited by Full text PDF (2.35 MB)

408 From microscales to macroscales in 3D: selfconsistent equation of state for supernova and neutron star models W G Newton, J R Stone and A Mezzacappa doi:10.1088/1742-6596/46/1/056 Tag this article Abstract References Cited by Full text PDF (3.50 MB)

413 Surface detonation in type Ia supernova explosions? F K Röpke and S E Woosley doi:10.1088/1742-6596/46/1/057 Tag this article Abstract References Cited by Full text PDF (3.71 MB)

418 Simulations of coherent nonlinear neutrino flavor transformation in the core collapse supernova environment H Duan, G M Fuller and J Carlson doi:10.1088/1742-6596/46/1/058 Tag this article Abstract References Cited by Full text PDF (853 KB)

422 Improving the capabilities of a continuum laser plasma interaction code J A F Hittinger and M R Dorr doi:10.1088/1742-6596/46/1/059 Tag this article Abstract References Cited by Full text PDF (315 KB)

433 Implicit solvers for large-scale nonlinear problems David E Keyes, Daniel R Reynolds and Carol S Woodward doi:10.1088/1742-6596/46/1/060 Tag this article Abstract References Cited by Full text PDF (217 KB)

443 Extending the applicability of multigrid methods J Brannick, M Brezina, R Falgout, T Manteuffel, S McCormick, J Ruge, B Sheehan, J Xu and L Zikatanov doi:10.1088/1742-6596/46/1/061 Tag this article Abstract References Cited by Full text PDF (228 KB)

453 Combinatorial algorithms enabling computational science: tales from the front Sanjukta Bhowmick, Erik G Boman, Karen Devine, Assefaw Gebremedhin, Bruce Hendrickson, Paul Hovland, Todd Munson and Alex Pothen doi:10.1088/1742-6596/46/1/062 Tag this article Abstract References Full text PDF (183 KB)

458 Mesh quality improvement for SciDAC applications P Knupp doi:10.1088/1742-6596/46/1/063 Tag this article Abstract References Cited by Full text PDF (315 KB)

463 A multiscale stabilization of the streamfunction form of the steady state Navier-Stokes equations J A Evans, K E Jansen, M S Shephard and A C Bauer doi:10.1088/1742-6596/46/1/064 Tag this article Abstract References Full text PDF (162 KB)

468 Accelerating the scientific exploration process with scientific workflows Ilkay Altintas, Oscar Barney, Zhengang Cheng, Terence Critchlow, Bertram Ludaescher, Steve Parker, Arie Shoshani and Mladen Vouk doi:10.1088/1742-6596/46/1/065 Tag this article Abstract References Cited by Full text PDF (388 KB)

479 How the common component architecture advances computational science G Kumfert, D E Bernholdt, T G W Epperly, J A Kohl, L C McInnes, S Parker and J Ray doi:10.1088/1742-6596/46/1/066 Tag this article Abstract References Cited by Full text PDF (1.52 MB)

494 Berkeley lab checkpoint/restart (BLCR) for Linux clusters Paul H Hargrove and Jason C Duell doi:10.1088/1742-6596/46/1/067 Tag this article Abstract References Cited by Full text PDF (183 KB)

500 Mining science data Chandrika Kamath doi:10.1088/1742-6596/46/1/068 Tag this article Abstract References Full text PDF (936 KB)

505 High performance statistical computing with parallel R: applications to biology and climate modelling Nagiza F Samatova, Marcia Branstetter, Auroop R Ganguly, Robert Hettich, Shiraj Khan, Guruprasad Kora, Jiangtian Li, Xiaosong Ma, Chongle Pan, Arie Shoshani and Srikanth Yoginath doi:10.1088/1742-6596/46/1/069 Tag this article Abstract References Full text PDF (383 KB)

510 Enabling worldwide access to climate simulation data: the earth system grid (ESG) D E Middleton, D E Bernholdt, D Brown, M Chen, A L Chervenak, L Cinquini, R Drach, P Fox, P Jones, C Kesselman, I T Foster, V Nefedova, A Shoshani, A Sim, W G Strand and D Williams doi:10.1088/1742-6596/46/1/070 Tag this article Abstract References Full text PDF (651 KB)

515 ESnet4: next generation network strategy, architecture, and implementation for DOE Science Michael Collins, Joseph Burrescia, Eli Dart, Jim Gagliardi, Chin Guok, William Johnston, Joe Metzger, Kevin Oberman and Mike O'Connor doi:10.1088/1742-6596/46/1/071 Tag this article Abstract References Full text PDF (3.20 MB)

521 Monitoring the grid with the Globus Toolkit MDS4 Jennifer M Schopf, Laura Pearlman, Neill Miller, Carl Kesselman, Ian Foster, Mike D'Arcy and Ann Chervenak doi:10.1088/1742-6596/46/1/072 Tag this article Abstract References Cited by Full text PDF (620 KB)

526 Quantitative and comparative visualization applied to cosmological simulations James Ahrens, Katrin Heitmann, Salman Habib, Lee Ankeny, Patrick McCormick, Jeff Inman, Ryan Armstrong and Kwan-Liu Ma doi:10.1088/1742-6596/46/1/073 Tag this article Abstract References Cited by Full text PDF (581 KB)

535 Visualization of large scale time-varying scientific data Han-Wei Shen doi:10.1088/1742-6596/46/1/074 Tag this article Abstract References Full text PDF (3.83 MB)

545 Web-based secure high performance remote visualization R J Vickery, A Cedilnik, J P Martin, Y Dandass, T Atkison, R J Moorhead, J Clarke and P Adams doi:10.1088/1742-6596/46/1/075 Tag this article Abstract References Full text PDF (3.45 MB)

550 Multi-scale data visualization for computational astrophysics and climate dynamics at Oak Ridge National Laboratory Sean Ahern, Jamison R Daniel, Jinzhu Gao, George Ostrouchov, Ross J Toedte and Chaoli Wang doi:10.1088/1742-6596/46/1/076 Tag this article Abstract References Full text PDF (444 KB)

556 Understanding the structure of the turbulent mixing layer in hydrodynamic instabilities P-T Bremer, W Cabot, A Cook, D Laney, A Mascarenhas, P Miller and V Pascucci doi:10.1088/1742-6596/46/1/077 Tag this article Abstract References Full text PDF (325 KB)

561 VACET: Proposed SciDAC2 Visualization and Analytics Center for Enabling Technologies W Bethel, C Johnson, C Hansen, S Parker, A Sanderson, C Silva, X Tricoche, V Pascucci, H Childs, J Cohen, M Duchaineau, D Laney, P Lindstrom, S Ahern, J Meredith, G Ostrouchov, K Joy and B Hamann doi:10.1088/1742-6596/46/1/078 Tag this article Abstract References Full text PDF (465 KB)

570 A distributed execution environment for large data visualization Jian Huang, Huadong Liu, Micah Beck, Jinzhu Gao and Terry Moore doi:10.1088/1742-6596/46/1/079 Tag this article Abstract References Cited by Full text PDF (1.32 MB)