**2001**

K. Abazajian, G. M. Fuller, M. Patel, *"Sterile neutrino hot, warm, and
cold dark matter,"* Physical Review D, 64, 023501, 2001.

P. R. Amestoy, I. S. Duff, J.-Y. L\'Excellent and X.S. Li, *"Analysis
and Comparison of Two General Sparse Solvers for Distributed Memory
Computers,"* ACM Transactions on Mathematical Software, **27**:388-421,
2001.

S. F. Ashby, M. J. Holst, T. A. Manteuffel and P. E. Saylor, *"The Role
of the Inner Product in Stopping Criteria for Conjugate Gradient
Iterations,"* B.I.T., Vol **41**, No. 1, 2001.

N. R. Badnell, and D. C. Griffin, *"Electron-impact excitation of
Fe^20+^, including n=4 levels,"* Journal of Physics B, 34 681, 2001.

N. R. Badnell, D. C. Griffin, and D. M. Mitnik, *"Electron-impact
excitation of Fe^21+^, including n=4 levels,*" Journal of Physics B, 34,
5071, 2001.

M. Baertschy and X. S. Li, *"Solution of a Three-Body Problem in Quantum
Mechanics Using Sparse Linear Algebra on Parallel Computers,"* Proc. of
the SC2001 conference, Denver, Colorado, November 2001.

M. Baker, *"Cluster Computing White Paper,"* International Journal of
High Performance Computing Applications -- special issue Cluster
Computing White Paper, Vol. **15**, No. 2, Summer 2001.

S. Benson, L. Curfman McInnes, and J. More, *"A Case Study in the
Performance and Scalability of Optimization Algorithms,"* ACM
Transactions of Mathematical Software **27**:361-376, 2001.

J. M. Blondin, R. A. Chevalier, D. M. Frierson, *"Pulsar Wind Nebulae in
Evolved Supernova Remnants,"* Astrophysical Journal Letters, 563,
806-815, 2001.

J. M. Blondin, K. J. Borkowski, S. P. Reynolds, *"Dynamics of Fe Bubbles
in Young Supernova Remnants,"* Astrophysical Journal Letters, 557,
782-791, 2001.

M. Borland, H. Braun, S. Doebert, L. Groening, and A. Kabel, *"Recent
Experiments on the Effect of Coherent Synchrotron Radiation on the
Electron Beam of CTF II,"* Proc. of the 2001 Particle Accelerator
Conference, Chicago, Ill., June 2001.

M. Brezina, A. Cleary, R. Falgout, V. Henson, J. Jones, T. Manteuffel,
S. McCormick, and J. Ruge, 2001, *"Algebraic multigrid based on element
interpolation (AMGe)*,*"* SIAM Journal of Scientific Computing,
**22**:1570-1592.

S. W. Bruenn, K. R. De Nisco, A. Mezzacappa, *"General Relativistic
Effects in the Core Collapse Supernova Mechanism,"* Astrophysical
Journal Letters, 560, 326-338, 2001.

D. Bruhwiler, R. Giacone, J. Cary, J. Verboncoeur, P. Mardahl, E.
Esarey, W. Leemans, B. Shadwick, *"Particle-in-Cell Simulations of
Plasma Accelerators and Electron-Neutral Collisions,"* PRST-AB, 4,
101302, 2001.

Z. Cai, T. Manteuffel, S. McCormick and J. Ruge, *"First-order System
LL\* (FOSLL\*): Scalar Elliptic Partial Differential Equations,"* SIAM
Journal on Numerical Analysis, **39**:1418-1445, 2001.

K. Campbell, *"Functional Sensitivity Analysis for Computer Model
Output,"* Proc. of the Seventh Army Conference on Statistics, Santa Fe,
NM, Oct. 2001.

H. Chen, et al., *"Calibrating Scalable Multi-Projector Displays Using
Camera Homography Trees,"* Proc. of Computer Vision and Pattern
Recognition, 2001.

H. Chen, et al., *"Data Distribution Strategies for High-Resolution
Displays,"* Computers & Graphics, **25**(5):811-818, 2001.

T.-Y. Chen, *"Preconditioning sparse matrices for computing eigenvalues
and computing linear systems of equations,"* PhD Dissertation, UC
Berkeley. 2001.

Y. Chen, et al., *"Software Environments for Cluster-based Display
Systems,"* Proc. of the First IEEE/ACM International Symposium on
Cluster Computing and the Grid, 2001.

B. Cheng, J. Glimm, X. L. Li D. H. Sharp, *"Subgrid Models and DNS
Studies of Fluid Mixing,"* Proceedings of the 7th International
Conference on the Physics of Compressible Turbulent Mixing, E. Meshkov,
Y. Yanilkin, V. Zhmailo, eds., p. 385-390, 2001.

E. Chow, *"Parallel Implementation and Practical Use of Sparse
Approximate Inverses With A Priori Sparsity Patterns,"* International
Journal of High Performance Computing Appl., **15**, pp. 56-74, 2001.

S. Chu, and S. Elliott, *"Latitude versus depth simulation of
ecodynamics and dissolved gas chemistry relationships in the central
Pacific,"* Journal of Atmospheric Chemistry, 40**(3)**, 305, 2001.

D. D. Clayton, E. A.-N. Deneault, B. S. Meyer, *"Condensation of Carbon
in Radioactive Supernova Gas,"* Astrophysical Journal Letters, 562,
480-493, 2001.

J. P. Colgan, M. S. Pindzola, D. M. Mitnik, D. C. Griffin, and I. Bray,
*"Benchmark non-perturbative calculations for the electron-impact
ionization of Li(2s) and Li(2p),"* Physical Review Letters, 87, 213201,
2001.

J. P. Colgan, M. S. Pindzola, and F. J. Robicheaux, *"Fully quantal (γ,
2e) calculations for absolute differential cross sections of helium,"*
Journal of Physics B, 34, L457, 2001.

V. K. Decyk and D. E. Dauger, *"Supercomputing for the Masses: A
Parallel Macintosh Cluster,"* Proc. 4th Intl. Conf. on Parallel
Processing and Applied Mathematics, Naleczow, Poland, September, 2001,
Springer-Verlag Lecture Notes in Computer Science 2328, ed. by R.
Wryrzykowski, J. Dongerra, M. Paprzycki, and J. Wasniewski
Springer-Verlag, Berlin, 2002.

C. H. Q. Ding and Y. He, *"Ghost Cell Expansion Method for Reducing
Communications in Solving PDE Problems,"* Proc of SC2001, Denver,
Coloradao, Nov. 2001.

F. Dobrian, *"External Memory Algorithms for Factoring Sparse
Matrices,"* PhD Dissertation, Old Dominion University, 2001.

F. Dobrian and A. Pothen, 2001, *"The Design of I/O-Efficient Sparse
Direct Solvers,"* Proc. of the SC 2001 conference, Denver, Colorado,
2001.

V. Eijkhout, *"Automatic Determination of Matrix Blocks,"* Lapack
Working note 151, Parallel Programming, 2001.

A. Gabric, W. Gregg, R. G. Najjar, D. J. Erickson III and P. Matrai,
*"Modeling the biogeochemical cycle of DMS in the upper ocean: A
review,"* Chemosphere - Global Change Science **3**, 377, 2001.

F. Gerigk, M. Vretenar, and R. D. Ryne*, "Design of the Superconducting
Section of the SPL Linac at CERN,"* Proc. PAC 2001, p. 3909.

J. R. Gilbert, X. S. Li, E. G. Ng and B. W. Peyton, *"Computing Row and
Column Counts for Sparse QR and LU Factorization,"* BIT **41**:693-710,
2001.

J. Glimm, X. L. Li, Y. J. Liu, N. Zhao, *"Conservative Front Tracking
and Level Set Algorithms,"* Proc. National Academy of Sci., p.
14198-14201, 2001.

D. C. Griffin, D. M. Mitnik, J. P. Colgan and M. S. Pindzola*,
"Electron-impact excitation of lithium,"* Physical Review A, 64, 032718,
2001.

D. C. Griffin, D. M. Mitnik and N. R. Badnell, *"Electron-impact
excitation of Ne^+^,"* Journal of Physics B, 34, 4401 2001.

E. D. Held, J. D. Callen, C. C. Hegna, and C. R. Sovinec, *"Conductive
electron heat flow along magnetic field lines,"* Physics of Plasmas
**8**, 1171, 2001.

P. Heggernes, S. Eisenstat, G. Kumfert and A. Pothen, *"The
Computational Complexity of the Minimum Degree Algorithm,"* Proc. of the
Nordic Computer Science Conference (NIK), 2001.

W. D. Henshaw, *"An Algorithm for Projecting Points onto a Patched CAD
Model,"* Proc. of the 10th International Meshing Roundtable, October
2001.

I. Hofmann, O. Boine-Frankenheim, G. Franchetti, J. Qiang, R. Ryne, D.
Jeon, J. Wei, *"Emittance Coupling in High Intensity Beams Applied to
the SNS Linac,"* Proc. of the 2001 Particle Accelerator Conference, p.
2902, Chicago, Ill., June 2001.

I. Hofmann, J. Qiang, R. D. Ryne and R. W. Garnett, *"Collective
Resonance Model of Energy Exchange in 3D Nonequipartitioned Beams,"*
Physical Review Letters **86**, 2313--2316, 2001.

D. J. Holmgren, P. Mackenzie, D. Petravick, R. Rechenmacher and J.
Simone, *"Lattice QCD production on a commodity cluster at Fermilab,"*
Computing in High-Energy Physics and Nuclear, 2, Beijing, China, Sept.
2001.

C. Huang, V. Decyk, S. Wang, E. S. Dodd, C. Ren, W. B. Mori, T.
Katsouleas, and T. Antonsen Jr*., "QuickPIC: A Parallelized Quasi-Static
PIC Code for Modeling Plasma Wakefield Acceleration,"* Proc. of the 2001
Particle Accelerator Conference, Chicago, Ill., June 2001.

E.-J. Im and K. A. Yelick, Paper: *"Optimizing Sparse Matrix-Vector
Multiplication for Register Reuse**,**"* International Conference on
Computational Science, San Francisco, Calif., May 2001

V. Ivanov, A. Krasnykh, *"Confined Flow Multiple Beam Guns for High
Power RF Applications,"* Proc. of the 2nd IEEE International Vacuum
Electronics Conference, Noordwijk, Netherlands, April 2001.

V. Ivanov, A. Krasnykh, *"3D Method for the Design of Multi or Sheet
Beam RF Sources,"* Proc. of the 2001 Particle Accelerator Conference,
Chicago, Ill., June 2001.

A. Kabel*, "Coherent Synchrotron Radiation Calculations Using TRAFIC4:
Multi-processor Simulations and Optics Scans,"* Proc. of the 2001
Particle Accelerator Conference, Chicago, Ill., June 2001.

A. Kabel, *"Quantum Corrections to Intrabeam Scattering,"* Proc. of the
2001 Particle Accelerator Conference, Chicago, Ill., June 2001.

K. Keahey, T. Fredian, Q. Peng, D. P. Schissel, M. Thompson, I. Foster,
M. Greenwald, and D. McCune, *"Computational Grids in Action,"* The
National Fusion Collaboratory Future Generation Computer System, 2001.

S.-D. Kim, T. Manteuffel and S. McCormick, "First-order system least
squares (FOSLS) for spatial linear elasticity: pure traction," SIAM
Journal on Numerical Analysis, 38:1454-1482, 2001.

A. Kuprat, A. Khamayseh, "Volume Conserving Smoothing for Piecewise
Linear Curves, Surfaces, and Triple Lines," Journal of Computational
Physics, 172, p. 99-118, 2001.

C.-L. Lappen and D. A. Randall, *"Toward a Unified Parameterization of
the Boundary Layer and Moist Convection. Part III:Simulations of Clear
and Cloudy Convection,"* Journal of Atmospheric Sciences., **58**, 2052,
2001.

C.-L. Lappen and D. A. Randall *"Toward a Unified Parameterization of
the Boundary Layer and Moist Convection. Part II: Lateral Mass Exchanges
and Subplume-Scale Fluxes,"* Journal of Atmospheric Sciences., **58**,
2037, 2001.

C.-L. Lappen and D. A. Randall, *"Toward a Unified Parameterization of
the Boundary Layer and Moist Convection. Part I: A New Type of Mass-Flux
Model,"* Journal of Atmospheric Science, **58**, 2021, 2001.

J. Larson, R. Jacob, I. Foster, J. Guo, *"The Model Coupling Toolkit,"*
Proc. of the. 2001 International Conference on Computational Science,
eds. V. N. Alexandrov, J. J. Dongarra, C. J. K. Tan, Springer-Verlag,
2001.

S. Lee, T. Katsouleas, R. G. Hemker, E. S. Dodd, and W. B. Mori,
*"Plasma-Wakefield Acceleration of a Positron Beam,"* Physical Review E,
**64**, No. 4, 04550, 2001.

Z. Li, N. Folwell, G. Golub, A. Guetz, B. McCandless, C.-K. Ng, Y. Sun,
M. Wolf, R. Yu and K. Ko*, "Parallel Computations of Wakefields in
Linear Colliders and Storage Rings,"* Proc. of the 2001 Particle
Accelerator Conference, Chicago, Ill., June 2001.

Z. Li, K. L. Bane, R. H. Miller, T. O. Raubenheimer, J. Wang, R. D.
Ruth, *"Traveling Wave Structure Optimization for the NLC,"* Proc. of
the 2001 Particle Accelerator Conference, Chicago, Ill., June 2001.

Z. Li, P. Emma and T. Raubenheimer, *"The NLC L-band Bunch Compressor,"*
Proc. of the 2001 Particle Accelerator Conference, Chicago, Ill., June
2001.

Z. Li, N. Folwell, G. Golub, A. Guetz, B. McCandless, C.-K. Ng, Y. Sun,
M. Wolf, R. Yu and K. Ko, *"Parallel Computations Of Wakefields In
Linear Colliders And Storage Rings,"* Proc. of the 2001 Particle
Accelerator Conference, Chicago, Ill., June 2001.

Z. Liu, et al., *"Progressive View-Dependent Isosurface Propagation,"*
Proc. of the IEEE TCVG Symposium on Visualization, 2001.

W. P. Lysenko et al., *"Characterizing Proton Beam of 6.7 MeV LEDA RFQ
by Fitting Wire-Scanner Profiles to 3-D Nonlinear Simulations,"* Proc.
of the 2001 Particle Accelerator Conference, p. 3051, Chicago, Ill.,
June 2001.

B. S. Meyer, S. S. Gupta, L.-S. The, S. Long, *"Long-Lived Nuclear
Isomers and Short-Lived Radioactivities,"* Meteoritics & Planetary
Science (Supp.) 36, 134, 2001.

D. M. Mitnik, D. C. Griffin and N. R. Badnell*, "Electron-impact
excitation of Ne^5+^,"* Journal of Physics B, 34, 4455, 2001.

P. Muggli, et al., *"Collective refraction of a beam of electrons at a
plasma-gas interface,"* Physical Review Letters Special
Topics-Accelerators & Beams, Vol. **4**, No. 9, pp. 091301-091303, Sept.
2001.

S. Nath et al*., "Comparison of Linac Simulation Codes,"* Proc. of the
2001 Particle Accelerator Conference, p. 264, Chicago, Ill., June 2001.

J. Neiplocha, H. E. Trease, B. J. Palmer, D. R. Rector, *"Building an
Application Domain Specific Programming Framework for Computational
Fluid Dynamics Calculations on Parallel Computers*," Tenth SIAM
Conference on Parallel Processing for Scientific Computing, March 2001.

E. Parker, B. R. de Supinski and D. Quinlan, *"Measuring the Regularity
of Array References,"* Los Alamos Computer Science Institute Symposium
(LACSI 2001), Los Alamos, NM, Oct. 2001.

N. A. Peterson, K. K. Chand, *"Detecting translation errors in CAD
surfaces and preparing geometries for mesh generation,"* Proc. of 10th
Annual Meshing Round Table, Newport Beach, Calif., October 2001.

J. Pruet, K. Abazajian, G. M. Fuller, *"New connection between central
engine weak physics and the dynamics of gamma-ray burst fireballs,"*
Physical Review D, 64, 063002, 2001.

J. Pruet, G. M. Fuller, C. Y. Cardall, *"On Steady State Neutrino-heated
Ultrarelativistic Winds from Compact Objects,"* Astrophysical Journal
Letters, 561, 957-963, 2001.

S. C. Pryor, R. J. Barthelmie, J. T. Schoof, L. L. Sorensen, D. J.
Erickson III, *"Implications of heterogeneous chemistry for nitrogen
deposition to marine ecosystems: Observations and modeling,"*
International Journal of Environmental Pollution, Water, Air and Soil
Pollution, Focus **1**, 99, 2001.

J. Qiang and R. Ryne, *"Parallel 3D Poisson Solver for a Charged Beam in
a Conducting Pipe,"* Computer Physics Communications **138**, 18, 2001.

J. Qiang, R. Ryne, B. Blind, J. Billen, T. Bhatia, R. Garnett, G.
Neuschaefer, H. Takeda, *"High Resolution Parallel Particle-In-Cell
Simulation of Beam Dynamics in the SNS Linac,"* Nuclear Instrument and
Methods Physics, Res. A, 457, 1, 2001.

J. Qiang, I. Hofmann, and R. D. Ryne, *"Cross-Plane Resonance: A
Mechanism for Very Large Amplitude Halo Formation,"* Proc. of the 2001
Particle Accelerator Conference, p. 1735, Chicago, Ill., June 2001.

J. Qiang and R. D. Ryne, *"A Layer-Based Object-Oriented Parallel
Framwork for Beam Dynamics Studies,"* Proc. of the 2001 Particle
Accelerator Conference, p. 3060, Chicago, Ill., June 2001.

J. F. Remacle, M. S. Shephard, J. E. Flaherty, O. Klass, *"Parallel
Algorithm oriented mesh database,"* Proc. 10th International Meshing
Roundtable, p. 341-349, Newport Beach, Calif., October 2001.

R. Samanta, et al., *"Parallel Rendering with K-Way Replication,"* Proc.
of the IEEE Symposium on Parallel and Large-Data Visualization and
Graphics, 2001.

S. L. Scott, M. Brim, R. Flanery, A. Geist and B. Luethke, *"Cluster
Command & Control (C3) Tools Suite,"* Parallel and Distributed Computing
Practices -- special issue, Nova Science Publishers, Inc., ISSN
1097-2803,Volume **4**, Number 4, Dec. 2001.

S. L. Scott, M. Brim and T. Mattson, *"OSCAR: Open Source Cluster
Application Resources,"* 2001 Linux Symposium, Ottawa, Canada, July
2001.

S. L. Scott, M. Brim, G.A. Geist, B. Luethke and J. Schwidder, *"M3C:
Managing and Monitoring Multiple Clusters,"* CCGrid 2001 -- IEEE
International Symposium on Cluster Computing and the Grid, Brisbane,
Australia, May 2001.

M. Seth, K. G. Dyall, R. Shepard, and A. Wagner, *"The Calculation of
f-f Spectra of Lanthanide and Actinide Ions by the MCDF-CI Method,"*
Journal of Physics B: At. Molecular and Optical Physics **34**,
2383-2406 2001.

R. Shepard, A. F. Wagner, J. L. Tilson and M. Minkoff, *"The Subspace
Projected Approximate Matrix (SPAM) Modification of the Davidson
Method*,*"* Journal of Computational Physics **172**, 472-514. 2001.

A. Snavely, *"Modeling Application Performance by Convolving Machine
Signatures with Application Profiles,"* IEEE 4th Annual Workshop on
Workload Characterization, Austin, Texas, Dec. 2001.

C. R. Sovinec, J. M. Finn, and D. del-Castillo-Negrete, *"Formation and
sustainment of spheromaks in the resistive MHD model,"* Physics of
Plasmas **8,** 475, 2001.

L. Sugiyama, W. Park, H. R. Strauss, et al., *"Studies of spherical
tori, stellarators, and anisotropic pressure with the M3D code,"*
Nuclear Fusion **41,** 739, 2001.

K. Teranishi, P. Raghavan and E. G. Ng, *"Scalable Preconditioning Using
Incomplete Factors,"* Proc. of the Tenth SIAM Conference on Parallel
Processing for Scientific Computing, 2001.

T. A. Thompson, A. Burrows and B. S. Meyer, *"The Physics of
Proto-Neutron Star Winds: Implications for r-Process Nucleosynthesis,"*
Astrophysical Journal, **562**:887-908, Dec. 2001.

P. Vanek, M. Brezina and J. Mandel, *"Convergence analysis of algebraic
multigrid based on smoothed aggregation,"* Numerical Mathematics **88,**
559---579, 2001.

R. Vuduc, J. Demmel and J. Bilmes, *"Statistical Models for Automatic
Performance Tuning,"* International Journal of High Performance
Computing Applications, 2001.

T. P. Wangler et al., *"Experimental Study of Proton-Beam Halo Induced
by Beam Mismatch in LEDA,"* Proc. of the 2001 Particle Accelerator
Conference, p. 2923, Chicago, Ill., June 2001.

A. D. Whiteford, N. R. Badnell, C. P. Ballance, M. G. O'Mullane, H. P.
Summers and A. L. Thomas, *"A radiation-damped R-matrix approach to the
electron-impact excitation of helium-like ions for diagnostic
application to fusion and astrophysical plasmas*,*"* Journal of Physics
B, 34, 3179, 2001.

K. Wu, E. J. Otoo, and A. Shoshani, *"A performance comparison of bitmap
indexes,"* Proc. of the 2001 ACM CIKM International Conference on
Information and Knowledge Management, Atlanta, Georgia, USA, Nov. 2001.

**2002**

J. Abate, S. Benson, L. Grignon, P. Hovland, L. McInnes, and B. Norris,
*"Integrating Automatic Differentiation with Object-Oriented Toolkits
for High Performance Scientific Computing,"* From Simulation to
Optimization, G. Corliss, C. Faure, A. Griewank, L. Hascoet and U.
Naumann, eds, p 173-178, Springer-Verlag, New-York, 2002.

A. Adelmann, *"Space Charge Studies at PSI,"* Proc. 20^th^ ICFA Advanced
Beam Dynamics Workshop on High Brightness Hadron Beams (ICFA-HB 2002),
p. 316, Batavia, Ill. April 2002.

A. Adelmann and D. Feichtinger, *"Generic Large Scale 3D Visualization
of Accelerators and Beam Lines,"* Proc. ICCS 2002, p. 362, 2002.

S. Adjerid, K. D. Devine, J. E. Flaherty, L. Krivodonova, *"A posteriori
error estimation for discontinuous Galerkin solutions of hyperbolic
problems,"* Computer Methods in Applied Mechanics and Engineering, 191,
p. 1997-1112, 2002.

V. Akcelik, G. Biros and O. Ghattas, 2002, *"Parallel Multiscale
Gauss-Newton-Krylov Methods for Inverse Wave Propagation,"* Proc. of the
IEEE/ACM SC2002 Conference, Baltimore, Md., Nov. 2002.

W. Allcock, J. Bester, J. Bresnahan, I. Foster, J. Gawor, J. Insley, J.
Link, M. Papka, *"GridMapper: A Tool for Visualizing the Behavior of
Large-Scale Distributed Systems,"* Proc. of the 11th IEEE International
Symposium on High Performance Distributed Computing HPDC-11, 179-188,
2002.

C. K. Allen, K. C. D. Chan, P. L. Colestock, K. R. Crandall, R. W.
Garnett, J. D. Gilpatrick, W. Lysenko, J. Qiang, J. D. Schneider, M. E.
Shulze, R. L. Sheffield, H. V. Smith, and T. P. Wangler, *"Beam-Halo
Measurements in High-Current Proton Beams,"* Physical Review Letters,
**89,** 214802, Nov. 2002.

J. Amundson and P. Spentzouris, *"A Hybrid, Parallel 3D Space Charge
Code with Circular Machine Modeling Capabilities,"* Proc. of the
International Computational Accelerator Physics Conference 2002
(ICAP2002), East Lansing, Michigan, Oct. 2002.

C. P. Ballance, N. R. Badnell, and K. A. Berrington, *"Electron-impact
excitation of H-like Fe at high temperatures,"* Journal of Physics B,
35, 1095, 2002.

G. P. Balls, P. Colella, *"A finite difference domain decomposition
method using local corrections for the colution of Poissons\'s
equation,"* Journal of Computational Physics, **180,** 25, 2002.

D. B. Batchelor, L. A. Berry, M. D. Carter, E. F. Jaeger, C. K.
Phillips, R. Dumont, P. T. Bonoli, D. N. Smithe, R. W. Harvey, D. A.
D\'Ippolito, J. R. Myra, E. D\'Azevedo, L. Gray and T. Kaplan,
*"Tera-scale Computation of Wave-Plasma Interactions in Multidimensional
Fusion Plasmas,"* Plasma Physics and Controlled Nuclear Fusion Research,
2002, Proc. of the 19th International Conference, Lyon, France,
International Atomic Energy Agency, Vienna, 2002.

J. B. Bell, M. S. Day and J. F. Grcar, *"Numerical Simulation of
Premixed Turbulent Methane Combustion,"* Proc. of the Combustion
Institute, **29**:1987, 2002.

J. B. Bell, M. S. Day, J. F. Grcar, W. G. Bessler, C. Shultz, P.
Glarborg and A. D. Jensen, *"Detailed Modeling and Laser-Induced
Fluorescence Imaging of Nitric Oxide in an NH3-seeded non-premixed
methane/air flame,"* Proc. of the Combustion Institute, **29**:2195,
2002.

G. J. O. Beran, S. R. Gwaltney, and M. Head-Gordon, *"Can coupled
cluster singles and doubles be approximated by a valence active space
model?,"* Journal of Chemistry Physics. 117, 3040-3048, 2002.

C. Bernard, et al. (The MILC Collaboration), "*Lattice Calculation of
Heavy-Light Decay Constants with Two Flavors of Dynamical Quarks,"*
Physical Review D **66**, 094501, 2002.

L. A. Berry, E. F. D'Azevedo, E. F. Jaeger, D. B. Batchelor and M. D.
Carter, *"All-Orders, Full-Wave RF Computations Using Localized Basis
Functions,"* 29th EPS Conference on Plasma Phys. and Contr. Fusion, ECA
Vol. **26B**, P-4.109, June 2002.

G. Biros and O. Ghattas, *"Inexactness Issues in
Lagrange-Newton-Krylov-Schur Methods for PDE-Constrained Optimization,"*
Lecture Notes in Computational Science and Engineering, **30**,
Springer-Verlag, 2002.

D. L. Brown, L. Freitag, J. Gilman, *"Creating interoperable meshing and
discretization software: the Terascale Simulation Tools and Technology
Center,"* Proc.of the Eighth International Conference on Numerical Grid
Generation in Computational Field Simulations, Honolulu, Hawaii , June
2002.

X.-C. Cai and D. E. Keyes, *"Nonlinearly Preconditioned Inexact Newton
Algorithms,"* SIAM Journal of Scientific Computing, 24:183-200, 2002.

X.-C. Cai, D. E. Keyes and L. Marcinkowski, *"Nonlinear Additive Schwarz
Preconditioners and Applications in Computational Fluid Dynamics,"*
International Journal of Numerical Methods in Fluids, 40:1463-1470,
2002.

X.-C. Cai, D. E. Keyes and D. P. Young, *"A Nonlinearly Additive Schwarz
Preconditioned Inexact Newton Method for Shocked Duct Flow,"* Proc. of
the 13th International Conference on Domain Decomposition Methods," (N.
Debit et al., eds.) CIMNE pp. 345-352, 2002.

M. D. Carter, F. W. Baity, Jr., G. C. Barber, R. H. Goulding, Y. Mori,
D. O. Sparks, K. F. White, E. F. Jaeger, F. R. Chang-Diaz, and J. P.
Squire, *"Comparing Experiments with Modeling for Light Ion Helicon
Plasma Sources,"* Physics of Plasmas **9**, 5097, 2002.

L. Chatterjee, M. R. Strayer, J. S. Wu, *"Pair production by neutrino
bremsstrahlung,"* Physical Review D, 65, 057302, 2002.

H. Chen, et al., *"Scalable Alignment of Large-Format Multi-Projector
Displays Using Camera Homography Trees,"* Proc. of IEEE Visualization
(VIZ), October 2002.

H. Chen, et al., *"Memory Performance Optimizations for Real-Time
Software HDTV Decoding,"* Proc. of the IEEE International Conference on
Multimedia and Expo, August 2002.

H. Chen, et al., *"A Parallel Ultra-High Resolution MPEG-2 Video Decoder
for PC Cluster Based Tiled Display System,"* Proc. of International
Parallel and Distributed Processing Symposium, 2002.

H. Chen, et al., *"Experiences with Scalability of Display Walls,"*
Proc. of the 7th Annual Immersive Projection Technology Symposium, 2002.

E. Chow, T. A. Manteuffel, C. Tong, B. K. Wallin, *"Algebraic
elimination of slide surface constraints in implicit structural
analysis,"* International Journal for Numerical Methods in Eng., 01,
1-21, 2002.

S. Chu, S. Elliott and M. Maltrud, *"Whole ocean fine resolution carbon
management simulations systems,"* EOS, Transactions, American
Geophysical Union 2002 Spring Meeting, **83**(19), S125, 2002.

C. E. Clayton, B. E. Blue, E. S. Dodd, C. Joshi, K. A. Marsh, W. B.
Mori, S. Wang, P. Catravas, S. Chattopadhyay, E. Esarey, W. P. Leemans,
R. Assmann, F. J. Decker, M. J. Hogan, R. Iverson, P. Raimondi, R. H.
Siemann, D. Walz, T. Katsouleas, S. Lee and P. Muggli, *"Transverse
Envelope Dynamics of a 28.5-GeV Electron Beam in a Long Plasma,"* Phys.
Rev. Lett., **88,** 15 p. 154801/1-4, April 2002.

D. D. Clayton, B. S. Meyer, L.-S. The, M. F. El Eid, *"Iron Implantation
in Presolar Supernova Grains,"* Astrophysical Journal Letters, 578,
L83-L86, 2002.

E. Colby, V. Ivanov, Z. Li, C. Limborg, *"Simulation Issues for RF
Photoinjector,"* Proc. of the International Computational Accelerator
Physics Conference 2002 (ICAP2002), East Lansing, Michigan, Oct. 2002.

J. P. Colgan and M. S. Pindzola, *"(γ, 2e) total and differential cross
section calculations for helium at various excess energies,"* Physical
Review A, 65, 032729, 2002.

J. P. Colgan and M. S. Pindzola, *"Core-excited resonance enhancement in
the two-photon complete fragmentation of helium,"* Physical Review
Letters, 88, 173002, 2002.

J. P. Colgan and M. S. Pindzola, *"Double photoionization of
beryllium,"* Physical Review A, 65, 022709, 2002.

J. P. Colgan and M. S. Pindzola, *"Time-dependent close-coupling studies
of the electron-impact ionization of excited-state Helium,"* Physical
Review A, 66, 062707, 2002.

J. P. Colgan, M. S. Pindzola and F. J. Robicheaux, *"A Fourier transform
method of calculating total cross sections using the time-dependent
close-coupling theory,"* Physical Review A, 66, 012718, 2002.

J. H. Cooley, T. M. Antonsen Jr., C. Huang, V. Decyk, S. Wang, E. S.
Dodd, C. Ren, W. B. Mori, and T. Katsouleas, *"Further Developments for
a Particle-in-Cell Code for Efficiently Modeling Wakefield Acceleration
Schemes,"* Advanced Accelerator Concepts, Tenth Workshop, eds. C. E.
Clayton and P. Muggli, AIP Conf. Proc. No. 647, p. 232-239, 2002.

J. J. Cowan, C. Sneden, S. Burles, I. I. Ivans, T. C. Beers, J. W.
Truran, J. E. Lawler, F. Primas, G. M. Fuller, B. Pfeiffer, K.-L. Kratz,
*"The Chemical Composition and Age of the Metal-poor Halo Star BD
+173248,"* Astrophysical Journal Letters, 572, 861-879, 2002.

T. Cristian, I.-H. Chung and J. K. Hollingsworth, *"Active Harmony:
Towards Automated Performance Tuning,"* Proc. of the SC 2002 conference,
Baltimore, Md., Nov. 2002.

S. Deng, F. Tsung, S. Lee, W. Lu, W. B. Mori, T. Katsouleas, P. Muggli,
B. E. Blue., C. E. Clayton, C. O'Connell, E. Dodd, F. J. Decker, C.
Huang, M. J. Hogan, R. Hemker, R. H. Iverson, C. Joshi, C. Ren, P.
Raimondi, S. Wang and D. Walz, *"Modeling of Ionization Physics with the
PIC Code OSIRIS,"* Advanced Accelerator Concepts, Tenth Workshop, eds.
C. E. Clayton and P. Muggli, AIP Conf. Proc. No. 647, p. 219-223, 2002.

S. Deng, T. Katsouleas, S. Lee, P. Muggli, W. B. Mori, R. Hemker, C.
Ren, C. Huang, E. Dodd, B. E. Blue., C. E. Clayton, C. Joshi, S. Wang,
F-J. Decker, M. J. Hogan, R. H. Iverson, C. O'Connell, P. Raimondi, and
D. Walz, *"3-D Simulation of Plasma Wakefield Acceleration with
Non-Idealized Plasmas and Beams,"* Advanced Accelerator Concepts, Tenth
Workshop, eds. C. E. Clayton and P. Muggli, AIP Conf. Proc. No. 647, p.
592-599. 2002.

L. Derose, K. Ekanadham, J. K. Hollingsworth and S. Sbaraglia, *"SIGMA:
A Simulator to Guide Memory Analysis,"* Proc. of the SC 2002 conference,
Baltimore, Md., Nov. 2002.

D. A. Dimitrov, D. L. Bruhwiler, W. Leemans, E. Esarey, P. Catravas, C.
Toth, B. Shadwick, J. R. Cary, and R. Giacone, *"Simulations of Laser
Propagation and Ionization in l\'OASIS Experiments,"* Proc. Advanced,
Accel. Concepts Workshop, p. 192, Mandalay Beach, CA, 2002.

D. A. Dimitrov, D. L. Bruhwiler, W. P. Leemans, E. Esarey, P. Catravas,
C. Toth, B. A. Shadwick, J. R. Cary and R. E. Giacone, *"Simulations of
Laser Propagation and Ionization in l\'OASIS Experiments,"* Proc.
Advanced Accel. Concepts Workshop, AIP Conf. Proc. 647, eds. C. E.
Clayton and P. Muggli, AIP, New York, 2002.

E. S. Dodd, R. G. Hemker, C.-K.Huang, S. Wang, C. Ren, W. B. Mori, S.
Lee and T. Katsouleas, *"Hosing and Sloshing of Short-Pulse Ge-V-Class
Wakefield Drivers,"* Physical Review Letters, **88**, 125001, March
2002.

E. D. Dolan and J. J. More, *"Benchmarking Optimization Software with
Performance Profiles,"* Mathematical Programming, 91:201-213, 2002.

D. Dolgov, et al. (The LHPC Collaboration):, *"Moments of nucleon light
cone quark distributions calculated in full lattice QCD,"* Physical
Review D **66**, 034506, 2002.

S. C. Doney and M. W. Hecht, *"Antarctic Bottom Water Formation and Deep
Water Chlorofluorocarbon Distributions in a Global Ocean Climate
Model,"* Journal of Physics, Oceanography **32**, 1642, 2002.

R. J. Dumont, C. K. Phillips and D. N. Smithe, *"ICRF wave propagation
and absorption in plasmas with non-thermal populations,"* 29th EPS
Conference on Plasma Phys. and Contr. Fusion, ECA Vol. **26B**, P-5.051,
Montreux, Switzerland, June 2002.

D. J. Erickson, III and J. L. Hernandez, *"A global, high resolution,
satellite-based model of air-sea isoprene flux,"* Gas Transfer at Water
Surfaces, ed. by M. A. Donelan, W. M. Drennan, E. S. Saltzman, and R.
Wanninkhof, American Geophysical Union Monograph **127**, 312, p. 312,
2002.

R. Evard, D. Narayan, J. P. Navarro, and D. Nurmi, *"Clusters as
large-scale development facilities,"* Proc of the 4th IEEE International
Conference on Cluster Computing (CLUSTER02), p. 54, IEEE Computer
Society, 2002.

R. D. Falgout and U. M. Yang, *"hypre*: *a Library of High Performance
Preconditioners,"* in Computational Science - ICCS 2002 Part III, P. M.
A. Sloot, C .J. K. Tan. J. J. Dongarra, and A. G. Hoekstra, eds.,
Lecture Notes in Computer Science, **2331,** p. 632-641,
Springer-Verlag, 2002.

J. E. Flaherty, L. Krivodonova, J. F. Remacle, M. S. Shephard, *"Aspects
of discontinuous Galerkin methods for hyperbolic conservation laws,"*
Finite Elements in Analysis and Design, 38:889-908, 2002.

J. E. Flaherty, L. Krivodonova, J. F. Remacle, M. S. Shephard,
*"High-order adaptive and parallel discontinuous Galerkin methods for
hyperbolic systems,"* WCCM V: Fifth World Congress on Computational
Mechanics, Vienna Univ. of Tech., Vienna, Austria, p. 1:144, 2002.

R. A. Fonseca, et al*., "OSIRIS: A 3D, fully relativistic PIC code for
modeling plasma based accelerators,"* Lect. Notes Comput. Sci, **2331**,
3 p. 342-351. 2002.

T. W. Fredian and J. A. Stillerman, *"MDSplus, Current Developments and
Future Directions,"* The 3rd IAEA Technical Meeting on Control, Data
Acquisition, and Remote Participation for Fusion Research, Fusion
Engineering and Design, 60, 229-233, 2002.

L. Freitag, T. Leurent, P. Knupp, D. Melander, *"MESQUITE Design: Issues
in the Development of a Mesh Quality Improvement Toolkit"*, Proceedings
of the 8th Intl. Conference on Numerical Grid Generation in
Computational Field Simulations, Honolulu, p159-168, 2002.

C. L. Fryer and M. S. Warren, *"Modeling Core-Collapse Supernovae in
Three Dimensions,"* Astrophysical Journal Letters, 574:L65-L68, July
2002.

G. Fubiani, G. Dugan, W. Leemans, E. Esarey, P. Catravas, C. Toth, B.
Shadwick, J. R. Cary, and R. Giacone, *"Semi-analytical 6D Space Charge
Model for Dense Electron Bunches with Large Energy Spreads,"* Proc. of
the Advanced Accelerator Concepts Workshop Mandalay Beach, Calif., 2002.

G. M. Fuller, *"The nuclear physics and astrophysics of the new neutrino
physics,"* AIP Conf. Proc. 610: Nuclear Physics in the 21st Century, p.
231-246, 2002.

A. Gebremedhin, F. Manne, and A. Pothen, *"Parallel Distance- k Coloring
Algorithms for Numerical Optimization,"* Lecture Notes in Computer
Science, 2400, p. 912-921, Springer-Verlag, 2002.

E. George, J. Glimm, X. L. Li, A. Marchese, Z. L. Xu, *"A Comparison of
Experimental, Theoretical and Numerical Simulation Rayleigh-Taylor
Mixing Rates,"* Proc. National Academy of Science, 59, p. 2587-2592,
2002.

S. J. Ghan, X. Bian, A. G. Hunt and A. Coleman, *"The thermodynamic
influence of subgrid orography in a global climate model,"* Climate
Dynamics, **20**, 31-44, 2002.

A. Z. Ghalam, T. Katsouleas, S. Lee, W. B. Mori, C. Huang, V. Decyk and
C. Ren, *"Simulation of Electron-Cloud Instability in Circular
Accelerators using Plasma Models,"* Advanced Accelerator Concepts, Tenth
Workshop, eds. C. E. Clayton and P. Muggli, AIP Conf. Proc. No. 647, p.
224j-231, 2002.

O. Ghattas and L. T. Biegler, *"Parallel Algorithms for Large-Scale
Simulation-based Optimization,"* iModeling and Simulation-Based Life
Cycle Engineering, Spon Press, London, 2002.

T. A. Gianakon, S. E. Kruger, and C. C. Hegna*, "Heuristic closures for
numerical simulation of neoclassical tearing modes,"* Physics of Plasmas
**9,** 536, 2002.

J. Glimm, X. L. Li, A. Lin, "Nonuniform approach to terminal velocity
for single mode Rayleigh-Taylor instability," Acta Mathematicae
Applicatae Sinica, 18, p. 1-8, 2002.

J. Glimm, X. L. Li, Y. J. Liu, "Conservative Front Tracking in One
Dimension," Fluid Flow and Transport in Porous Media: Mathematical and
Numerical Treatment, Contemporary Mathematics, Z. X. Chen, R. Ewing,
eds., American Mathematical Society, 295, p. 253-264, 2002.

L. Griogori and X. S. Li, *"A New Scheduling Algorithm for Parallel
Sparse LU Factorization with Static Pivoting,"* Proc. of the IEEE/ACM
SC2002 Conference, Baltimore, Md., Nov. 2002.

W. Gropp, L. McInnes and B. Smith, *"Chapter 19 of CRPC Handbook of
Parallel Computing,"* Morgan Kaufmann, 2002.

P. T. Haertel and D. A. Randall, *"Could a pile of slippery sacks behave
like an ocean?"* Monthly Weather Review, **130**, 2975, 2002.

A. Heger, S. E.Woosley, T. Rauscher, R. D. Horman, and M. M. Boyes*,
"Massive star evolution: nucleosynthesis and nuclear reaction rate
uncertainties,"* New Astronomy Review, 46:463-468, July 2002.

R. P. Heikes, *"A comparison of vertical coordinate systems for
numerical modeling of the general circulation of the atmosphere,"* Ph.D.
thesis, Colorado State University, 2002.

W. D. Henshaw, *"Generating Composite Overlapping Grids on CAD
Geometries*,*"* Numerical Grid Generation in Computational Field
Simulations, June 2002.

W. D. Henshaw, *"An Algorithm for Projecting Points onto a Patched CAD
Model,"* Engineering with Computers, 18, p. 265-273, 2002.

V. E. Henson and U. M. Yang, *"BoomerAMG: a Parallel Algebraic Multigrid
Solver and Preconditioner,"* Applied Numerical Mathematics, **41,** p.
155-177, 2002.

J. J. Heys, C. G. DeGroff, T. Manteuffel, S. McCormick and W. W.
Orlando, *"First-order system least squares for elastohydrodynamics with
application to flow in compliant blood vessels,"* Biomed. Sci. Instrum.
38, p. 277-282, 2002.

M. J. Hogan, C. D. Barnes, C. E. Clayton, C. O'Connell, F. J. Decker, S.
Deng, P. Emma, C. Huang, R. Iverson, D. K. Johnson, C. Joshi, T.
Katsouleas, P. Krejcik, W. Lu, K. A. Marsh, W. B. Mori, P. Muggli, R. H.
Siemann and D. Walz, *"Acceleration and Focusing of Electrons and
Positrons using a 30 GeV Drive Beam,"* Advanced Accelerator Concepts,
Tenth Workshop, eds. C. E. Clayton and P. Muggli, AIP Conf. Proc. No.
647, pp. 3-10, 2002.

P. Hovland, B. Norris and B. Smith, *"Making Automatic Differentiation
truly Automatic: Coupling PETSc with ADIC,"* Proc. of ICCS 2002,
Amsterdam, Netherlands, 2002.

E. C. Hunke and J. K. Dukowicz, *"The Elastic-Viscous-Plastic Sea Ice
Dynamics Model in General Orthogonal Curvilinear Coordinates on a
Sphere\--Incorporation of Metric Terms,"* Monthly Weather Review,
**130**, 1848, 2002.

C. Joshi, B. Blue, C. E. Clayton, E. Dodd, C. Huang, K. A. Marsh, W. B.
Mori, S. Wang, J. J. Hogan, C. O'Connell, R. Siemann, D. Watz, P.
Muggli, T. Katsouleas and S. Lee, *"High Energy Density Plasma Science
with an Ultrarelativistic Electron Beam,"* Physics of Plasmas, Vol.
**9**, No. 5, p. 1845-1855, May 2002.

J. Ivanic and K. Ruedenberg, *"Deadwood in Configuration Spaces. II. SD
and SDTQ Spaces,"* Theoretical Chemistry Accounts, **107,** 220-228,
2002.

V. Ivanov, N. Folwell, G. Golub, A. Guetz, Z. Li, W. Mi, C.-K. Ng, G.
Schussman, Y. Sun, J. Tran, M. Weiner, M. Wolf and K. Ko,
*"Computational Challenge In Large Scale Accelerator Modeling,"*
ICCM-2002, Novosibirsk, Russia, June 2002.

V. Ivanov, R. Ives, A. Krasnykh, G. Miram, M. Read, *"An Electron Gun
for a Sheet Beam Klystron,"* IVEC-2002, Monterey, Calif., April 2002.

V. Ivanov, G. Schussman, M. Weiner, *"Particle Tracking Algorithms for
3D Parallel Codes in Frequency and Time Domains,"* Proc. of 18th Annual
Review of Progress in Applied Computational Electromagnetics, ACES-2002,
Monterey, Calif., March 2002.

E. F. Jaeger, L. A. Berry, E. D\'Azevedo, D. B. Batchelor, M. D. Carter,
K. F. White and H. Weitzner, *"Advances in Full-Wave Modeling of Radio
Frequency Heated, Multidimensional Plasmas,"* Physics of Plasmas **9**,
1873, 2002.

G. C. Jordan, B. S. Meyer, *"Sensitivity of Isotope Yields to Reaction
Rates in the Alpha Rich Freezeout,"* Proc. of the Workshop on
Astrophysics, Symmetries, and Applied Physics at Spallation Neutron
Sources (ASAP 2002), p. 42. Oak Ridge, Tenn. March 2002.

A. Kabel, *"A Parallel Code for Lifetime Calculations in P/P-Storage
Rings in the Presence of Parasitic Beam-Beam Crossings,"* Proc. of the
International Computational Accelerator Physics Conference 2002
(ICAP2002), East Lansing, Michigan, Oct. 2002.

A. Kabel, *"Parallel Simulation Algorithms for the Strong-Strong
Beam-Beam Interaction,"* Proc. of the International Computational
Accelerator Physics Conference 2002 (ICAP2002), East Lansing, Michigan,
Oct. 2002.

T. Katsouleas, A. Z. Ghalam, S. Lee, W. B. Mori, C. Huang, V. Decyk and
C. Ren, *"Plasma Modeling of Wakefields in Electron Clouds,"* ECLOUD'02
Mini-Workshop on Electron-Cloud Simulations for Proton and Positron
Beams, CERN, Geneva, Switzerland, 2002.

K. Keahey and V. Welch, *"Fine-Grain Authorization for Resource
Management in the Grid Environment,"* Proc. of the 3rd International
Workshop on Grid Computing, 2002.

D. E. Keyes, *"Terascale Implicit Methods for Partial Differential
Equations,"* The Barrett Lectures, University of Tennessee Mathematics
Department, 2001, Contemporary Mathematics 306:29-84, AMS, Providence,
RI, 2002.

D. E. Keyes, P. D. Hovland, L. C. McInnes and W. Samyono, *"Using
Automatic Differentiation for Second-Order Matrix-free Methods in
PDE-constrained Optimization,"* Automatic Differentiation of Algorithms:
From Simulation to Optimization (G. Corliss et al., eds.),
Springer-Verlag, p 35-50, 2002.

A. Khamayseh, A. Kuprat, *"Hybrid Curve Point Distribution Algorithms,"*
SIAM Journal on Scientific Computing, 23, p. 1464-1484, 2002.

A. Klawonn, O. B. Widlund and M. Dryja, *"Dual-Primal FETI Methods for
Three-dimensional Elliptic Problems with Heterogeneous Coefficients,"*
SIAM Journal on Numerical Analysis, **40**:159-179, 2002.

K. Ko*, "High Performance Computing in Accelerator Physics,"* Proc. of
18th Annual Review of Progress in Applied Computational
Electromagnetics, ACES-2002, Monterey, Calif., March 2002.

S. Lee, T. Katsouleas, P. Muggli, W. B. Mori, C. Joshi, R. Hemker, E. S.
Dodd, C. E. Clayton, K. A. Marsh, B. Blue, S. Wang, R. Assmann, F. J.
Decker, M. Hogan, R. Iverson, and D. Walz, *"Energy Doubler for a Linear
Collider,"* Physical Review Special Topics-Accelerators And Beams,
**5**, 1, January 2002.

X. Li, J. Demmel, D. Bailey, G. Henry, Y. Hida, J. Iskandar, W. Kahan,
S. Kang, A. Kapur, M. Martin, B. Thompson, T. Tung and D. Yoo, *"Design,
Implementation and Testing of Extended and Mixed Precision BLAS,"* ACM
Transactions of Mathematical Software **22**:152-205, 2002.

M. Liebendorfer, O. E. B. Messer, A. Mezzacappa, W. R. Hix, F.-K.
Thielemann, K. Langanke, *"The importance of neutrino opacities for the
accretion luminosity in spherically symmetric supernova models,"* Proc.
of the 11^th^ Workshop on Nuclear Astrophysics, p. 126-131,
Max-Planck-Institut fuer Astrophysik, Germany, 2002.

Z. Liu, et al., *"Improving Progressive View-Dependent Isosurface
Propagation,"* Computers and Graphics, **26** (2): 209-218, 2002.

S. D. Loch, M. S. Pindzola and J. P. Colgan, *"Electron-impact
ionization of all ionization stages of krypton,"* Physical Review A, 66,
052708, 2002.

C.-D. Lu and D. A. Reed, *"Compact Application Signatures for Parallel
and Distributed Scientific Codes,"* Proc. of the SC 2002 conference,
Baltimore, Md., Nov. 2002.

X. Luo, M. S. Shephard, J. F. Remacle, R. M. Bara, M. W. Beall, B. A.
Szab, *"p-Version Mesh Generation Issues,"* 11th International Meshing
Roundtable, 2002.

X. Luo, M. S. Shephard, J. F. Remacle, *"The Influence of Geometric
Approximation on the Accuracy of High Order Methods,"* Proc. 8th
International Conference on Numerical Grid Generation in Computational
Field Simulations, Miss. State University, 2002.

W. P. Lysenko, R. W. Garnett, J. D. Gilpatrick, J. Qiang, L. J.
Rybarcyk, R. D. Ryne, J. D. Schneider, H. V. Smith, L. M. Young, and M.
E. Schulze, *"High Order Beam Features and Fitting Quadrupole Scan Data
to Particle Code Model,"* Proc. of the International Computational
Accelerator Physics Conference 2002 (ICAP2002), East Lansing, Michigan,
Oct. 2002.

K.-L. Ma, G. Schussman, B. Wilson, K. Ko, J. Qiang and R. Ryne*,
"Advanced Visualization Technology for Terascale Particle Accelerator
Simulations,"* Proc. of the IEEE/ACM SC2002 Conference, Baltimore, Md.,
Nov. 2002.

J. L. McClean, P.-M. Poulain, J. W. Pelton, and M. E. Maltrud,
*"Eulerian and Lagrangian statistics from surface drifters and a
high-resolution POP simulation in the North Atlantic,"* Journal of
Physical Oceanography, **32**, 2472, 2002.

C. W. McCurdy, P. Cummings, E. Stechel, B. Hendrickson and D. E. Keyes,
*"Theory and Modeling in Nanoscience,"* whitepaper commissioned by the
U.S. DOE Offices of Basic Energy Sciences and Advanced Scientific
Computing, 2002.

C. L. Mendes and D. A. Reed, *"Monitoring Large Systems via Statistical
Sampling,"* LACSI Symposium, Santa Fe, Oct. 2002.

B. S. Meyer, *"r-Process Nucleosynthesis without Excess Neutrons,"*
Physical Review Letters, 89, 231101, 2002.

D. M. Mitnik, D. C. Griffin, and M. S. Pindzola, *"Time-dependent
close-coupling calculations of dielectronic capture in He,"* Physical
Review Letters, 88, 173004, 2002.

J. J. More, *"Automatic Differentiation Tools in Optimization
Software,"* in Automatic Differentiation 2000: From Simulation to
Optimization, G. Corliss, C. Faure, A. Griewank, L. Hascoet, and U.
Naumann, eds, p 25-34, Springer-Verlag, New-York, 2002.

W. B. Mori, *"Recent Advances and Some Results in Plasma-Based
Accelerator Modeling,"* Advanced Accelerator Concepts, Tenth Workshop,
eds. C. E. Clayton and P. Muggli, AIP Conf. Proc. No. 647, p. 11-28,
2002.

P. Muggli, *"Transverse Envelope Dynamics of a 28.5-GeV Electron Beam in
a Long Plasma,"* Physical Review Letters, Vol. **88**, No. 15 pp.
154801/1-4, April 2002.

C. Naleway, M. Seth, R. Shepard, A. F. Wagner, J. L. Tilson, W. C.
Ermler and S. R. Brozell, *"An Ab Initio Study of the Ionization
Potentials and the f-f Spectroscopy of Europium Atoms and Ions,"*
Journal of Chemistry Physics. **116**, 5481-5493. 2002.

J. P. Navarro, R. Evard, D. Nurmi, and N. Desai, *"Scalable cluster
administration - {Chiba City I} approach and lessons learned,"* Proc of
the 4th IEEE International Conference on Cluster Computing (CLUSTER02),
p. 54, IEEE Computer Society, 2002.

J.W. Negele, *"Understanding parton distributions from lattice QCD:
Present limitations and future promise,"* Nuclear Physics **A 711**,
281, 2002.

C.-K. Ng, L. Ge, A. Guetz, V. Ivanov, Z. Li, G. Schussmann, Y. Sun, M.
Weiner, M. Wolf, *"Numerical Studies of Field Gradient and Dark Currents
in SLAC Structures,"* Proc. of the International Computational
Accelerator Physics Conference 2002 (ICAP2002), East Lansing, Michigan,
Oct. 2002.

C.-K. Ng et. al.,*"Modeling HOM Heating in the PEP-II IR with Omega3P,"*
Proc. of the International Computational Accelerator Physics Conference
2002 (ICAP2002), East Lansing, Michigan, Oct. 2002.

B. Norris, S. Balay, S. Benson, L. Freitag, P. Hovland, L. McInnes, and
B. Smith, *"Parallel Components for PDEs and Optimization: Some Issues
and Experiences,"* Parallel Computing 28:1811-1831, 2002.

C. O'Connell et al., *"Dynamic Focusing of an Electron Beam through a
Long Plasma,"* Phys. Rev. STAB, 5, 121301, 2002.

R. J. Oglesby, S. Marshall, D. J. Erickson III, J. O. Roads and F. R.
Robertson, *"Thresholds in atmosphere-soil moisture interactions:
Results from climate model studies,"* Journal of Geophysical Research,.
**107**, 2002.

L. F. Pavarino and O. B. Widlund, *"Balancing Neumann-Neumann methods
for incompressible Stokes equations,"* Comm. Pure Appl. Math.
55:302-335, 2002.

M. S. Pindzola, *"Proton-impact excitation of laser-excited lithium
atoms,"* Physical Review A, 66, 032716, 2002.

P. Ploumans, G. S. Winckelmans, J. K. Salmon, A. Leonard, and M. S.
Warren, *"Vortex Methods for High-Resolution Simulation of
Three-Dimensional Blu® Body Flows; Application to the Sphere at Re=300,
500 and 1000,"* Journal of Computational Physics, 178:427-463, 2002.

J. Pruet and N. Dalal, *"Implications of Neutron Decoupling in Short
Gamma-Ray Bursts,"* ApJ, 573:770-777, July 2002.

J. Pruet, S. Guiles, G. M. Fuller, *"Light-Element Synthesis in
High-Entropy Relativistic Flows Associated with Gamma-Ray Bursts,"*
Astrophysical Journal Letters, 580, 368-373, 2002.

J. Qiang, P. L. Colestock, D. Gilpatrick, H. V. Smith, T. P. Wangler and
M. E. Schulze, *"Macroparticle Simulation Studies of a Proton Beam Halo
Experiment,"* Phys. Rev. ST Accel. Beams, vol **5**, 124201, 2002.

J. Qiang, M. Furman and R. Ryne, *"Strong-Strong Beam-Beam Simulation
Using a Green Function Approach,"* Phys. Rev. ST Accel. Beams, **5**,
104402, Oct. 2002.

J. Qiang and R. Ryne, *"Parallel Beam Dynamics Simulation of Linear
Accelerators,"* Proceedings of the 2002 Applied Computational
Electromagnetics Society (ACES\'2002) Conference, March 2002.

D. A. Randall, T. D. Ringler, R. P. Heikes, P. Jones and J. Baumgardner,
*"Climate modeling with spherical geodesic grids,"* Computing in Science
and Engr., **4**, 32-41. 2002.

T. Rauscher, A. Heger, R. D. Hoffman and S. E. Woosley,
*"Nucleosynthesis in Massive Stars with Improved Nuclear and Stellar
Physics,"* American Physics Journal, 576:323-348, Sept. 2002.

J. F. Remacle, O. Klass, J. E. Flaherty, M. S. Shephard, *"A parallel
algorithm oriented mesh database*," Engineering with Computers, 18,
274,2002.

J. F. Remacle, M. S. Shepard, J. E. Flaherty, *"Some issues on
distributed mesh representations,"* Proc. 8th International Conference
on Numerical Grid Generation in Computational Field Simulations, Miss.
State University, 2002.

J. F. Remacle, O. Klass, M. S. Shephard, *"Trellis: A framework for
adaptive numerical analysis based on multiparadigm programming in C++,"*
WCCM V: Fifth World Congress on Computational Mechanics, Vienna Univ. of
Tech, Vienna, Austria, p. 1-164, 2002.

J. F. Remacle, X. Li, N. Chevaugeon, M. S. Shepard, *"Transient mesh
adaptation using conforming and non-conforming mesh modifications,"*
11th International Meshing Roundtable, 2002.

T. D. Ringler and D. A. Randall, *"The ZM Grid: An Alternative to the Z
Grid,"* Monthly Weather Review, **130**, 1411--1422, 2002.

T. D. Ringler, and D. A. Randall, *"A Potential Enstrophy and Energy
Conserving Numerical Scheme for Solution of the Shallow-Water Equations
on a Geodesic Grid,"* Monthly Weather Review, **130**, 1397--1410, 2002.

F. J. Robicheaux and J. D. Hanson, *"Simulation of the expansion of an
ultracold neutral plasma,"* Physical Review Letters, 88, 055002. 2002.

J. M. Sampaio, K. Langanke, G. Martinez-Pinedo, D. J. Dean,
*"Neutral-current neutrino reactions in the supernova environment,"*
Physics Letters B, 529, 19-25. 2002.

D. P. Schissel, M. J. Greenwald, and W .E. Johnston, *"Fusion Energy
Sciences Networking: A Discussion of Future Requirements,"* DOE High
Performance Network Planning Workshop, 2002.

D. P. Schissel, *"An Advanced Collaborative Environment to Enhance
Magnetic Fusion Research, for the National Fusion Collaboratory
Project,"* Proceedings of the Workshop on Advanced Collaborative
Environments, 2002.

D. P. Schissel, et al., *"Data Management, Code Deployment, and
Scientific Visualization to Enhance Scientific Discovery in Fusion
Research through Advanced Computing,"* The 3rd IAEA Technical Meeting on
Control, Data Acquisition, and Remote Participation for Fusion Research.
Fusion Engineering and Design **60**, 481-486, 2002.

K. L. Schuchardt, J. D. Myers, E. G. Stephan, 2002, *"A web-based data
architecture for problem-solving environments: application of
distributed authoring and versioning the extensible computational
chemistry environment,"* Cluster Computing **5**(3):287-296, 2002.

D. R. Schultz, C. O. Reinhold, P. S. Krstic and M. R. Strayer,
*"Ejected-electron spectrum in low-energy proton-hydrogen collisions,"*
Physical Review A, **65,** 052722, 2002.

G. Schussman and K.-L. Ma*, "Scalable Self-Orienting Surfaces: A
Compact, Texture-Enhanced Representation for Interactive Visualization
Of 3D Vector Fields,"* Proc. of the Pacific Graphics 2002 Conference,
Beijing, China, Oct. 2002.

G. Schussman and K.-L. Ma*, "Scalable Self-Orienting Surfaces: A Compact
Texture-Enhanced Representation for Interactive Visualization Of 3d
Vector Fields,"* Proc. of the 10th Pacific Conference on Computer
Graphics and Applications, IEEE Computer Society, Washington, D.C., Oct.
2002.

S. L. Scott, B. Luethke and T. Naughton, *"C3 Power Tools -- The Next
Generation,"* 4^th^ DAPSYS Conference, Linz, Austria, Sept.--Oct. 2002.

S. L. Scott, B. Luethke, *"HPC Federated Cluster Administration with C3
v3.0,"* Ottawa Linux Symposium (OLS 2002), Ottawa, Canada, July 2002.

S. L. Scott, J. L. Mugler and T. Naughton, *"User Interfaces for
Clustering Tools,"* Ottawa Linux Symposium (OLS 2002), Ottawa, Canada,
July 2002.

S. L. Scott, B. Luethke, *"C3 Power Tools Commodity, High-Performance
Cluster Computing Technologies and Applications,"* Sixth World
Multiconference on Systemics, Cybernetics, and Informatics (ISAS
SCI2002), Orlando, Fla., July 2002.

S. L. Scott, T. Naughton, B. Barrett, J. Squyres, A. Lumsdain and Y. C.
Fang, *"The Penguin in the Pail -- OSCAR Cluster Installation Tool
Commodity, High-Performance Cluster Computing Technologies and
Applications,"* Sixth World Multiconference on Systemics, Cybernetics,
and Informatics (ISAS SCI2002), Orlando, Fla., July 2002.

B. A. Shadwick, G. M. Tarkenton, E. H. Esarey and W. P. Leemans, *"Fluid
simulations of intense laser-plasma interactions,"* IEEE Trans. Plasma
Sci. 30, 38, 2002.

M. S. Shephard, X. Luo, J. F. Remacle, *"Meshing for p-version finite
element methods,"* WCCM V: Fifth World Congress on Computational
Mechanics, Vienna Univ. of Tech, Vienna, Austria, p. 1-464, 2002.

A. Snavely, et al., *"A Framework for Application Performance Modeling
and Prediction,"* Proc. of the SC 2002 conference, Baltimore, Md., Nov.
2002.

P. Spentzouris, J. Amundson, J. Lackey, L. Spentzouris, R. Tomlin,
*"Space Charge Studies and Comparison with Simulations Using the FNAL
Booster,"* Proc. of the International Computational Accelerator Physics
Conference 2002 (ICAP2002), East Lansing, Michigan, Oct. 2002.

N. Sullivan, A. D. Jensen, P. Glarborg, M. S. Day, J. F. Grcar, J. B.
Bell, C. J. Pope, and R. J. Kee, *"Ammonia Conversion and NOx Formation
in Laminar Coflowing Nonpremixed Methane-Air Flames,"* Combustion and
Flame, **131**(3):285, 2002.

Y. Sun, N. Folwell, Z. Li and G. H. Golub, *"High Precision Accelerator
Cavity Design Using the Parallel Eigensolver Omega3p,"* Proc. of 18th
Annual Review of Progress in Applied Computational Electromagnetics,
ACES-2002, Monterey, Calif., March 2002.

Y. Sun, G. Golub and K. Ko, *"Solving the Complex Symmetric Eigenproblem
in Accelerator Structure Design,"* Proc. of the International
Computational Accelerator Physics Conference 2002 (ICAP2002), East
Lansing, Michigan, Oct. 2002.

K. Teranishi, P. Raghavan, and E. G. Ng, *"A New Data-Mapping Scheme for
Latency-Tolerant Distributed Sparse Triangular Solution,"* Proc. of the
IEEE/ACM SC2002 Conference, Baltimore, Md., Nov. 2002.

K. Teranishi, P. Raghavan, and E. G. Ng, *"Reducing Communication Costs
for Parallel Sparse Triangular Solution,"* Proc. of the IEEE/ACM SC2002
Conference, Baltimore, Md., Nov. 2002.

F.-K. Thielemann, D. Argast, F. Brachwitz, G. Martinez-Pinedo, T.
Rauscher, M. Liebendoerfer, A. Mezzacappa, P. Hoflich, K. Nomoto,
*"Nucleosynthesis and Stellar Evolution,"* Astrophysics and Space
Science, 281, 25-37, 2002.

F.-K Thielemann,. D. Argast, F. Brachwitz, G. Martinez-Pinedo, T.
Rauscher, M. Liebendoerfer, A. Mezzacappa, P. Hoflich, K. Iwamoto, K.
Nomoto, *"Nucleosynthesis in Supernovae. (I),"* ASP Conf. Ser. 253:
Chemical Enrichment of Intracluster and Intergalactic Medium, p. 205,
2002.

F.-K. Thielemann, P. Hauser, E. Kolbe, G. Martinez-Pinedo, I. Panov, T.
Rauscher, K.-L. Kratz, B. Pfeiffer, S. Rosswog, M. Liebendoerfer, A.
Mezzacappa, *"Heavy Elements and Age Determinations,"* Space Science
Reviews, 100, 277-296, 2002.

J. L. Tilson, C. Naleway, M. Seth, R. Shepard, A. F. Wagner, and W. C.
Ermler, "*An Ab Initio Study of the f-f Spectroscopy of Americium^+3^,"*
Journal of Chemistry Physics. **116**, 5494-5502, 2002.

S. J. Thomas, J. M. Dennis, H. M. Tufo, P. F. Fischer, *"A Schwarz
preconditioner for the cubed-sphere,"* Proc. of the Copper Mountain
Conference on Iterative Methods, 2002.

H. Trease, L. Trease, J. Fowler, R. Corley, C. Timchalk, K. Minard, D.
Rommeriem, *"A Case Study: Extraction, Image Reconstruction, And Mesh
Generation From NMR Volume Image Data From F344 Rats For Computational
Biology Applications,"* 8th International Conference on Grid Generation
and Computational Physics, 2002.

F. S. Tsung., R. G. Hemker, C. Ren, W. B. Mori, L. O. Silva and T.
Katsouleas, *"Generation of Ultra-Intense, Single-Cycle Laser Pulse
using Photon Deceleration,"* Proceedings of the National Academy of
Sciences., Vol. **99**, pp. 29-32, 2002.

T. Van Voorhis and M. Head-Gordon, *"Implementation of generalized
valence-bond inspired coupled cluster theories,"* Journal of Chemical
Physics, **117**, 9190-9201, 2002.

J. L. Vay, P. Colella, P.McCorquodale, B. Van Straalen, A. Friedman,
D.P. Grote, *"Mesh refinement for particle-in-cell plasma simulations:
Applications to and benefits for heavy ion fusion,"* Laser and Particle
Beams, 20, 4, p. 569-575, 2002.

J. S. Vetter and P. Worley, "*Asserting Performance Expectations,"*
Proc. of the SC 2002 conference, Baltimore, Md., Nov. 2002.

J. S. Vetter and A. Yoo, *"An Empirical Performance Evaluation
of Scalable Scientific Applications,"* Proc. of the SC 2002 conference,
Baltimore, Md., Nov. 2002.

J. S. Vetter, *"Dynamic Statistical Profiling of Communication Activity
in Distributed Applications,"* Proc. of SIGMETRICS 2002: Joint
International Conference on Measurement and Modeling of Computer
Systems, ACM, 2002.

J. S. Vetter and F. Mueller, *"Communication Characteristics of
Large-Scale Scientific Applications for Contemporary Cluster
Architectures,"* Proc. of the International Parallel and Distributed
Processing Symposium, 2002.

R. Vuduc, J. W. Demmel, K. A. Yelick, S. Kamil, R. Nishtala and B. Lee,
*"Performance Optimizations and Bounds for Sparse Matrix-Vector
Multiply,"* Proc. of the IEEE/ACM SC2002 Conference, Baltimore, Md.,
Nov. 2002.

R. Vuduc, S. Kamil, J. Hsu, R. Nishtala, J. W. Demmel and K. A. Yelick,
*"Automatic Performance Tuning and Analysis of Sparse Triangular
Solve,"* ICS 2002: Workshop on Performance Optimization via High-Level
Languages and Libraries, 2002.

G. Wallace, *"Display Wall Cluster Management,"* Proc. of the IEEE
Visualization 2002 Workshop on Commodity-Based Visualization Clusters,
Oct. 2002.

S. Wang, C. E. Clayton, B. E. Blue, E. S. Dodd, K. A. Marsh, W. B. Mori,
C. Joshi, P. Muggli, T. Katsouleas, F. J. Decker, M. J. Hogan, R. H.
Iverson, P. Raimondi, D. Watz, R. Siemann, and R. Assmann, *"X-ray
Emission from Betatron Motion in a Plasma Wiggler,"* Physical Review
Letters, Vol. **88**, No. 13, p. 135004/1-4, April 2002.

A. Wetzels, A. Gurtler, L. D. Noordam, F. Robicheaux, C. Dinu, H. G.
Muller, M. J. J. Vrakking and W. J. van der Zande, *"Rydberg state
ionization by half-cycle-pulse excitation: strong kicks create slow
electrons,"* Physical Review Letters, **89,** 273003. 2002.

A. D. Whiteford, N. R. Badnell, C. P. Ballance, S. D. Loch, M. G.
O'Mullane and H. P. Summers, *"Excitation of Ar^15+^ and Fe^23+^ for
diagnostic application to fusion and astrophysical plasmas,"* Journal of
Physics B, **35,** 3729, 2002.

B. Wilson, K.-L. Ma and P. McCormick, *"A Hardware-Assisted Hybrid
Rendering Technique for Interactive Volume Visualization,"* 2002
Symposium on Volume Visualization and Graphics, Boston, Mass., Oct.
2002.

B. Wilson, K.-L. Ma, J. Qiang, and R. Ryne, *" Interactive Visualization
of Particle Beams for Accelerator Design,"* In Proceedings of the
Workshop on Particle Accelerator Science and Technology, ICCS 2002,
Amsterdam, Netherlands, April 2002.

M. Wingate, et al. (The HPQCD Collaboration), *"Heavy Light Physics
Using NRQCD/Staggered Actions,"* Nuclear Physics B (Proc. Suppl.)
**106**, 379, 2002.

M. Wolf, A. Guetz and C.-K. Ng, *"Modeling Large Accelerator Structures
with the Parallel Field Solver Tau3P,"* Proc. of 18th Annual Review of
Progress in Applied Computational Electromagnetics, ACES-2002, Monterey,
Calif., March 2002.

C. S. Woodward, K. E. Grant and R. Maxwell, *"Applications of
Sensitivity Analysis to Uncertainty Quantification for Variably
Saturated Flow,"* Computational Methods in Water Resources, S.M.
Hassanizadeh, R. J. Schotting, W. G. Gray, and G. F. Pinder, eds.,
vol.**1**, pp. 73-80, Elsevier, Amsterdam, 2002.

S. E. Woosley, A. Heger, and T. A. Weaver, *"The evolution and explosion
of massive stars,"* Reviews of Modern Physics, 74:1015-1071, Nov. 2002.

P. H. Worley, *"Scaling the Unscalable: A Case Study on the AlphaServer
SC,"* Proc. of the IEEE/ACM SC2002 Conference, Baltimore, Md., Nov.
2002.

P. H. Worley, T. H. Dunigan, Jr., M. R. Fahey, J. B. White III, A. S.
Bland, *"Early Evaluation of the IBM p690,"* Proc. of the IEEE/ACM
SC2002 Conference, Baltimore, Md., Nov. 2002.

K. Wu, J. Ekow, E. J. Otoo, and A. Shoshani, *"Compressing bitmap
indexes for faster search operations,"* Proc. of SSDBM'02, p. 99,
Edinburgh, Scotland, 2002.

M. Zingale, L. J. Dursi, J. ZuHone, A. C. Calder, B. Fryxell, T. Plewa,
J. W. Truran, A. Caceres, K. Olson, P. M. Ricker, K. Riley, R. Rosner,
A. Siegel, F. X. Timmes and N. Vladimirova, *"Mapping Initial
Hydrostatic Models in Godunov Codes,"* Astrophysical Journal Supplement,
**143**:539-565, Dec. 2002.

**2003**

S. I. Abarzhi, J. Glimm, A. D. Lin, *"Rayleigh-Taylor instability for
fluids with a finite density contrast,"* Phys. Fluids, 15, p. 2190-2197,
2003.

S. I. Abarzhi, J. Glimm, K. Nishihara, *"Rayleigh-Taylor instability and
Richtmyer-Meshkov instabilities for fluids with a finite density
contrast,"* Phys. Lett. A, 11, p. 1-7, 2003.

M. Adams, M. Brezina, J. Hu, and R. Tuminaro, *"Parallel multigrid
smoothing: polynomial versus Gauss-Seide*l*,"* Journal of Computational
Physics, 188, p. 593-610, 2003.

V. Akcelik, J. Bielak, G. Biros, I. Epanomeritakis, A. Fernandez, O.
Ghattas, E. J. Kim, D. O\'Hallaron and T. Tu, 2003, *"High-resolution
Forward and Inverse Earthquake Modeling on Terascale Computers,"* Proc.
of the ACM/IEEE SC03 conference, Nov. 2003.

C. Alexandrou et al., *"Calculation of the N to Delta electromagnetic
transition matrix element,"* Nuclear Physics B (Proc. Suppl.) **119**,
413, 2003.

P. R. Amestoy, I. S. Duff, J.-Y. L\'Excellent and X. S. Li, *"Impact of
the Implementation of MPI Point-to-Point Communications on the
Performance of Two General Sparse Solvers,"* Parallel Computing,
29:833-849, 2003.

J. Amundson, J. Lackey, P. Spentzouris, G. Jungman, L. Spentzouris*,
"Calibration of the Fermilab Booster ionization profile monitor,"*
Physics Review ST Accel. Beams. **6**, 102801, 2003.

J. Amundson, P. Spentzouris, *"FNAL Booster: Experiment and Modeling,"*
Proc. of IEEE Particle Accelerator Conference 2003, Portland, Ore., May
2003.

J. Amundson, P. Spentzouris*, "SYNERGIA: A Hybrid, Parallel Beam
Dynamics Code with 3D Space Charge,"* Proc. of IEEE Particle Accelerator
Conference 2003, Portland, Ore., May 2003.

C. Aubin, et al. (The MILC Collaboration), *"Chiral logs with staggered
fermions,"* Nuclear Physics B (Proc. Suppl.), **119**, 233, 2003.

N. R. Badnell, D. C. Griffin, and D. M. Mitnik, *"Electron-impact
excitation of B^+^ using the R-matrix with pseudo-states method,"*
Journal of Physics B, 1337 2003.

N. R. Badnell, M. G. O\'Mullane, H. P. Summers, Z. Altun, M. A.
Bautista, J. P. Colgan, T. W. Gorczyca, D. M. Mitnik, M. S. Pindzola,
and O. Zatsarinny, *"Dielectronic recombination data for dynamic
finite-density plasmas: I. Goals and methodology,"* Astronomy and
Astrophysics, **406,** 1151, 2003.

A. B. Balantekin, G. M. Fuller, *"Supernova neutrino nucleus
astrophysics,"* Journal of Physics G, 29, 2513-2522, 2003.

C. P. Ballance, N. R. Badnell and E. S. Symth, *"A pseudo-state
sensitivity study on hydrogenic ions,"* Journal of Physics B, **36**.
3707. 2003.

C. P. Ballance, N. R. Badnell, D. C. Griffin, S. D. Loch and D. M.
Mitnik, *"The effects of coupling to the target continuum on the
electronimpact excitation of Li^+^,"* Journal of Physics B, **36,** 235,
2003.

G. T. Balls, S. B. Baden, P. Colella, *"SCALLOP: A highly scalable
parallel Poisson solver in three dimensions,"* Proc. of ACM/IEEE SC03
conference, Phoenix, Arizona, November, 2003.

M. W. Beall, J. Walsh, M. S. Shephard, *"A comparison of techniques for
geometry access related to mesh generation,"* Proc. 7th US Nat. Congress
on Comp. Mech., p. 62, 2003.

M. W. Beall, J. Walsh, M. S. Shephard., *"Accessing CAD geometry for
mesh generation,"* 12th International Meshing Roundtable, Sandia
National Laboratories, p. 33-42, 2003.

J. B. Bell, M. S. Day, J. F. Grcar, M. J. Lijewski, M. Johnson, R. K.
Cheng and I. G. Shepherd, *"Numerical Simulation of a Premixed Turbulent
V-Flame,"* 19th International Colloquium on the Dynamics of Explosions
and Reactive Systems, July-Aug. 2003.

J. B. Bell, M. S. Day, A. S. Almgren, R. K. Cheng, and I. G. Shepherd,
*"Numerical Simulation of Premixed Turbulent Methane Combustion,"* Proc.
of the Second MIT Conference on Computational Fluid and Solid Mechanics,
June 2003.

J. B. Bell, M. S. Day, J. F. Grcar, and M. J. Lijewski, *"Analysis of
carbon chemistry in numerical simulations of vortex flame
interactions,"* 19th International Colloquium on the Dynamics of
Explosions and Reactive Systems, July-Aug. 2003.

C. Bernard, et al. (The MILC Collaboration), *"Topological
Susceptibility with the Improved Asqtad Action,"* Phys. Rev. D **68**,
114501, 2003.

C. Bernard, et al. (The MILC Collaboration), *"Light hadron properties
with improved staggered quarks,"* Nuclear Physics B (Proc. Suppl.),
**119**, 257, 2003.

C. Bernard, et al. (The MILC Collaboration), *"Topological
susceptibility with the improved Asqtad action,"* Nuclear Physics B
(Proc. Suppl.), **119**, 991, 2003.

C. Bernard, et al. (The MILC Collaboration), *"Static hybrid quarkonium
potential with improved staggered quarks,"* Nuclear Physics B (Proc.
Suppl.), **119**, 598, 2003.

C. Bernard, et al. (The MILC Collaboration), *"High temperature QCD with
three flavors of improved staggered quarks,"* Nuclear Physics B (Proc.
Suppl.), **119**, 523, 2003.

C. Bernard, et al. (The MILC Collaboration), *"Exotic hybrid mesons from
improved Kogut-Susskind fermions,"* Nuclear Physics B (Proc. Suppl.),
**119**, 260, 2003.

C. Bernard, et al. (The MILC Collaboration), *"Heavy--light meson decay
constants with Nf* =*3,"* Nuclear Physics B (Proc. Suppl.), **119**,
613, 2003.

C. Bernard, et al. (The MILC Collaboration), *"Lattice calculation of*
1^−+^ *hybrid mesons with improved Kogut-Susskind fermions,"* Physical
Review D **68**, 074505, 2003.

S. Bhowmick, L. McInnes, B. Norris, and P. Raghavan, 2003, *"The Role of
Multi-Method Linear Solvers in PDE-based Simulations,"* Proc. of the
2003 International Conference on Computational Science and its
Applications, Montreal, Canada, Lecture Notes in Computer Science, 2677,
p. 828-839, V. Kumar, M. L. Gavrilova, C. J. K. Tan, and P. L\'Ecuyer.
eds, May 2003.

L. Biegler, O. Ghattas, M. Heinkenschloss and B. van Bloemen Waanders,
editors, *"PDE-Constrained Optimization: State-of-the-Art,"* Lecture
Notes in Computational Science and Engineering, 30, Springer-Verlag,
2003.

J, M. Blondin, *"The Inherent Asymmetry of Core-Collapse Supernovae,"*
ASP Conf. Ser. 293: 3D Stellar Evolution, p. 290, 2003.

J. M. Blondin, A. Mezzacappa, C. DeMarino, *"Stability of Standing
Accretion Shocks, with an Eye toward Core-Collapse Supernovae,"*
Astrophysical Journal Letters, 584, 971-980, 2003.

B. E. Blue et al., *"Plasma-Wakefield Acceleration of an Intense
Positron Beam,"* Phys. Rev. Lett. **90**, 214801, 2003.

P. A. Boyle, C. Jung and T. Wettig, *"The QCDOC supercomputer: Hardware,
software, and performance,"* Econf **C0303241**, THIT003, 2003.

M. Branstetter, and D. J. Erickson III, *"Continental runoff dynamics in
the CCSM2.0,"* Journal of Geophysical Research 108**(D17)**, 4550, 2003.

D. P. Brennan, R. J. La Haye, A. D. Turnbull, et al., *"A mechanism for
tearing onset near ideal stability boundaries,"* Physics of Plasmas
**10** 1643, 2003.

J. A. Breslau, S. C. Jardin and W. Park, *"Simulation studies of the
role of reconnection in the 'current hole' experiments in the joint
European torus,"* Physics of Plasmas **10** 1665, 2003.

M. Brewer, L. Diachin, T. Leurent, D. Melander, *"The Mesquite Mesh
Quality Improvement Toolkit,"* Proc. of the 12^th^ International Meshing
Roundtable, Santa Fe NM, p. 239-250, 2003.

P. N. Brown, B. Lee, T. A. Manteuffel, *"A moment-parity multigrid
preconditioner for the first-order least-squares formulation of the
Blotzmann transport equations,"* SIAM Journal of Scientific Computing,
**25**, 2, p. 513-533, 2003.

P. N. Brown, P. Vassilevski, and C. S. Woodward, *"On Mesh-Independent
Convergence of an Inexact Newton-Multigrid Algorithm,"* SIAM Journal of
Scientific Computing, **25,** 2, p. 570-590, 2003.

D. L. Bruhwiler, D. A. Dimitrov, J. R. Cary, E. Esarey, W. P. Leemans
and R. E. Giacone, *"Particle-in-cell simulations of tunneling
ionization effects in plasma-based accelerators,"* Physics of Plasmas
**10**, p. 2022, 2003.

D. L. Bruhwiler, D. A. Dimitrov, J. R. Cary, E. Esarey and W. P.
Leemans, *"Simulation of ionization effects for high-density positron
drivers in future plasma wakefield experiments,"* Proc. of IEEE Particle
Accelerator Conference 2003, Portland, Ore., May 2003.

N. Bucciantini, J. M. Blondin, L. Del Zanna, E. Amato, *"Spherically
symmetric relativistic MHD simulations of pulsar wind nebulae in
supernova remnants,"* Astronomy & Astrophysics, 405, 617-626, 2003.

T. Burch and D. Toussaint (The MILC Collaboration), *"Hybrid
configuration content of heavy S-wave mesons*,*"* Physical Review D,
**68**, 094504, 2003.

R. Butler, D. Narayan, A. Lusk and E. Lusk, *"The process management
component of a scalable system software environment,"* Proc. of the 5th
IEEE International Conference on Cluster Computing (CLUSTER03), Kowloon,
Hong Kong, Dec. 2003.

L. Bytautas, J. Ivanic, K. Ruedenberg, *"Split-Localized Orbitals Can
Yield Stronger Configuration Interaction Convergence than Natural
Orbitals,"* Journal of Chemical Physics, **119**, 8217, 2003.

C. Cardall, A. Mezzacappa, *"Conservative formulations of general
relativistic kinetic theory,"* Physical Review D, 68, 023006, 2003.

L. Carrington, A. Snavely, N. Wolter, and X. Gao, *"A Performance
Prediction Framework for Scientific Applications,"* ICCS Workshop on
Performance Modeling and Analysis (PMA03), Melbourne, Australia, June
2003.

M. D. Carter, F. W. Baity Jr., G. C. Barber, R. H. Goulding, Y. Mori, D.
O. Sparks, K. F. White, E. F. Jaeger, F. R. Chang-Diaz and J. P. Squire,
*"Comparing Experiments with Modeling to Optimize Light Ion Helicon
Plasma Sources for VASIMR,"* Proc. of Open Systems, Korea, Transactions
of Fusion Science and Technology **43**(1), 2003.

J. R. Cary, R. E. Giacone, C. Nieter, D. L. Bruhwiler, E. Esarey, G.
Fubiani and W. P. Leemans, *"All-Optical Beamlet Train Generation,"*
Proc. of IEEE Particle Accelerator Conference 2003, Portland, Ore., May
2003.

G. K. L. Chan and M. Head-Gordon, *"Exact solution (in a triple zeta,
double polarization basis) of the Schrödinger electronic equation for
water,"* Journal of Chemical Physics, 118, 8851-8854, 2003.

B. Cheng, J. Glimm, H. Jin, D. H. Sharp, *"Theoretical methods for the
determination of mixing,"* Laser and Particle Beams, 21, p. 429-436,
2003.

N. Chevaugeon, J. E. Flaherty, L. Krivodonova, J. F. Remacle, M. S.
Shephard, *"Adaptive and parallel discontinuous Galerkin method for
hyperbolic conservation law,"* Proc. 7th US Nat. Congress on Comp.
Mech., p. 448, 2003.

N. Chevaugeon, J. F. Remacle, J. E. Flaherty, D. Cler, M. S. Shephard,
*"Application of discontinuous Galerkin method. Large scale problem:
Cannon blast modeling,"* Proc. 7th US Nat. Congress on Comp. Mech., p.
470, 2003.

Y. Choi, S. Elliott, D. R. Blake, F. S. Rowland, et al., *"PCA survey of
whole air hydrocarbon data from the second airborne BIBLE expedition,"*
Journal of Geophysical Research, **108**, 10, 2003.

T. Chartier, R. D. Falgout, V. E. Henson, J. Jones, T. Manteuffel, S.
McCormick, J. Ruge and P. S. Vassilevski, *"Spectral AMGe (ρAMGe),"*
SIAM Journal of Scientific Computing, **25**, p. 1-26, 2003.

E. Chow, *"An Unstructured Multigrid Method Based on Geometric
Smoothness,"* Numer. Linear Algebra Appl., **10**, p. 401-421, 2003.

E. Chow, T. A. Manteuffel, C. Tong and B. K. Wallin, *"Algebraic
Elimination of Slide Surface Constraints in Implicit Structural
Analysis," Intern. Journal on Numerical Analysis,. Meth. Engrg.,
**57***, p. 1129-1144, 2003.

E. Chow and P. Vassilevski, *"Multilevel Block Factorizations in
Generalized Hierarachical Bases,"* Numer. Linear Algebra Appl., **10**,
p. 105-127, 2003.

S. Chu, S. M. Elliott, and M. E. Maltrud, *"Global eddy permitting
simulations of surface ocean nitrogen, iron, sulfur cycling,"*
Chemosphere, **50**, 223, 2003.

S. Chu, S. Elliott, M. Maltrud, F. Chai and F. Chavez, *"Studies of the
consequences of ocean carbon sequestration using Los Alamos ocean
models,"* Proceedings of the DOE 2nd Annual Conference on Carbon
Sequestration, Alexandria, Va., May 2003.

D. L. Cler, N. Chevaugeon, M. S. Shephard, J. E. Flaherty, J. F.
Remacle, *"CFD application to gun muzzle blast - A validation case
study,"* 41st AIAA Aerospace Sciences Meeting and Exhibit, Jan. 2003.

A. Codd, T. Manteuffel and S. McCormick, *"Multilevel first-order system
least squares for nonlinear elliptic partial differential equations,"*
SIAM Journal on Numerical Analysis, **41**, p. 2197-2209, 2003.

A. Codd, T. Manteuffel, S, McCormick and J. Ruge, *"Multilevel
first-order system least squares for elliptic grid generation,"* SIAM
Journal on Numerical Analysis, **41**, pp. 2210-2232, 2003.

J. P. Colgan, M. S. Pindzola, A. D. Whiteford, and N. R. Badnell,
*"Dielectronic recombination data for dynamic finite-density plasmas:
III. The Beryllium isoelectronic sequence,"* Astronomy and Astrophysics,
**412,** 597, 2003.

J. P. Colgan and M. S. Pindzola, *"Total and differential cross section
calculations for the double photoionization of the helium 1x2s^1,3^ S
states,"* Physical Review A, **67,** 012711, 2003.

J. P. Colgan, M. S. Pindzola, and F. J. Robicheaux, *"Time-dependent
studies of single and multiple photoionization of H~2~^+^,"* Physical
Review A, **68,** 063413, 2003.

J. P. Colgan, M. S. Pindzola, and M. C. Witthoeft*, "Time-dependent
electron-impact scattering from He^+^ using variable lattice spacings,"*
Physical Review A, 032713, 2003.

J. P. Colgan, S. D. Loch, M. S. Pindzola, C. P. Ballance, and D. C.
Griffin, *"Electron-impact ionization of all ionization stages of
Beryllium,"* Physical Review A, 032712, 2003.

D. Datta, C. Picu, M. S. Shephard, *"Multiscale simulation of defects
using multigrid atomistic continuum method,"* Proc. 7th US Nat. Congress
on Comp. Mech., p. 814, 2003.

C. Davies, et al. (The HPQCD Collaboration), *"The Determination of
Alpha(s) from Lattice QCD with 2+1 Flavors of Dynamical Quarks,"*
Nuclear Physics B (Proc. Suppl.), **119**, 595, 2003.

J. Demmel and Y. Hida, *"Accurate Floating Point Summation,"* SIAM
Journal of Scientific Computing, **25**, 4, p. 1214--1248, 2003.

S. Dey, L. Couchman, D. Datta, *"Error and convergence of p-refinement
schemes for elastodynamics and coupled elasto-acoustics,"* Proc. 7th US
Nat. Congress on Comp. Mech., , p. 517, 2003.

M. di Pierro et al., *"Charmonium with three flavors of dynamical
quarks,"* Nuclear Physics B (Proc. Suppl.) **119**, 586, 2003.

J. Dongarra, K. London, S. Moore, P. Mucci, D. Terpstra, H. You, and M.
Zhou, *"Experiences and Lessons Learned with a Portable Interface to
Hardware Performance Counters,"* PADTAD Workshop, IPDPS 2003, Nice,
France, April 2003.

J. Dongarra and V. Eijkhout, *"Self-adapting Numerical Software and
Automatic Tuning of Heuristics,"* ICCS 2003, Workshop on Adaptive
Algorithms, Melbourne, Australia, June 2003.

J. Dongarra, A. Malony, S. Moore, P. Mucci, and S. Shende, *"Performance
Instrumentation and Measurement for Terascale Systems,"* ICCS 2003,
Terascale Systems Workshop, Melbourne, Australia, June 2003.

P. Dreher, et al. (The SESAM Collaboration), *"Continuum extrapolation
of moments of nucleon quark distributions in full QCD,"* Nuclear Physics
B (Proc. Suppl.), **119**, 392, 2003.

M. Dryja and O. Widlund, *"A Generalized FETI-DP Method for a Mortar
Discretization of Elliptic Problems,"* Proc of the 14^th^ International
Symposium on Domain Decomposition Methods, Cocoyoc, Mexico, Jan. 2002,
I. Herrera, D. E. Keyes, O. B. Widlund and R. Yates eds., 2003.

R. J. Dumont, C. K. Phillips, A. Pletzer and D.N. Smithe, *"Effects of
Non-Maxwellian Plasma Species on ICRF Wave Propagation and Absorption in
Toroidal Magnetic Confinement Devices,"* invited paper in the 10th
European Fusion Theory Conference, Helsinki, Finland, Sept. 2003.

R. J. Dumont, C. K. Phillips, and D. N. Smithe, *"Effects of
Non-Maxwellian Plasma Species on ICRF Propagation and Absorption,"*
Radio Frequency Power in Plasmas, Proc. 15^th^ Topical Conf., Moran,
Wyoming, 2003, AIP, N. Y., 2003.

T. H. Dunigan, Jr., M. R. Fahey, J. B. White III, P. H. Worley, *"Early
Evaluation of the Cray X1,"* Proc. of the ACM/IEEE SC03 conference,
Phoenix, Ariz., Nov. 2003.

L. J. Dursi, M. Zingale, A. C. Calder, B. Fryxell, F. X. Timmes, N.
Vladimirova, R. Rosner, A. Caceres, D. Q. Lamb, K. Olson, P. M. Ricker,
K. Riley, A. Siegel, and J. W. Truran, *"The Response of Model and
Astrophysical Thermonuclear Flames to Curvature and Stretch,"* ApJ,
595:955-979, Oct. 2003.

S. Dutta, E. George, J. Glimm, X. L. Li, A. Marchese, Z. L. Xu, Y. M.
Zhang, J. W. Grove, D. H. Sharp, *"Numerical methods for the
determination of mixin*g," Laser and Particle Beams, 21, p. 437-442,
2003.

S. Dutta, J. Glimm, J. W. Grove, D. H. Sharp, Y. Zhang, *"A fast
algorithm for moving interface problems,"* International Conference on
Computational Science and Its Applications (ICCSA 2003), Lecture Notes
in Computer Science 2668, V. Kumar et al.., ed., Springer-Verlag,
Berlin/Heidelberg, p. 782-790, 2003.

S. Elliott and S. Chu, *"Comment on 'ocean fertilization experiments
initiate large scale phytoplankton blooms,'"* Geophysical Research
Letters, **30**, 1274, 2003.

S. Elliott, and H. Hanson, *"Syndication of the Earth system,"*
Environmental Science and Policy, **6**, 457, 2003.

S. Elliott, D. R. Blake, F. S. Rowland, et al., *"Whole air sampling as
a window on Pacific biogeochemistry,"* Journal of Geophysical Research,
108**(D3),** 8407, 2003.

D. J. Erickson III, J. Hernandez, P. Ginoux, W. Gregg, C. McClain, and
J. Christian, *"Atmospheric Iron Delivery and surface ocean biological
activity in the Southern Ocean and Patagonian region,"* Geophysical
Research Letter, 30**(12)**, 1609, 2003.

J. Fetter, G. C. McLaughlin, A. B. Balantekin, G. M. Fuller,
*"Active-sterile neutrino conversion: consequences for the r-process and
supernova neutrino detection,"* Astroparticle Physics, 18, 433-448,
2003.

P. Fischer, F. Hecht, Y. Maday, *"A Parareal in Time Semi-implicit
Approximation of the Navier-Stokes Equations,"* Proc. Of the 15th Int.
Conf. on Domain Decomposition Methods, Berlin, 2003.

P. F. Fischer, J. W. Lottes, *"Hybrid* *Schwarz-Multigrid Methods for
the Spectral Element Method: Extensions to Navier-Stokes,"* Proc. Of the
15th Int. Conf. on Domain Decomposition Methods, Berlin, 2003.

N. Folwell, P. Knupp *"Increasing Tau3P Abort-Time via Mesh Quality
Improvement,"* Proceedings of the 12th International Meshing Roundtable,
Santa Fe NM, p. 379-392, 2003.

N. Folwell, P. Knupp and M. Brewer, *"Increasing the TAU3P Abort-time
via Mesh Quality Improvement,"* Proc. of the 12th International Meshing
Roundtable, Sandia National Laboratories, Santa Fe, NM, Sept. 2003.

N. Folwell, P. Knupp, K. Ko, *"Mesh Quality Improvement for Accelerator
Design,"* SIAM Conference on Computational Science and Engineering, San
Diego, Calif., Feb. 2003.

C. L. Fryer and P. Meszaros, *"Neutrino-driven Explosions in Gamma-Ray
Bursts and Hypernovae,"* ApJ Letters, 588:L25-L28, May 2003.

G. Fubiani, E. Esarey, W. Leemans, J. Qiang, R. D. Ryne and G. Dugan,
*"Numerical Studies of Laser-Plasma Produced Electron Beam Transport,"*
Proc. of IEEE Particle Accelerator Conference 2003, Portland, Ore., May
2003.

G. M. Fuller, A. Kusenko, I. Mocioiu, S. Pascoli, *"Pulsar kicks from a
dark-matter sterile neutrino,"* Physical Review D, 68, 103002, 2003.

E. Gabriel, G. Fagg and J. Dongarra, *"Evaluating the Performance of
MPI-2 Dynamic Communicators and One-sided Communication,"* EuroPVM/MPI
2003, Venice, Italy, Sept. 2003.

Z. Gan, Y. Alexeev, R. A. Kendall, and M. S. Gordon, "*The Parallel
Implementation of a Full CI Program,"* Journal of Chemical Physics,
**119**, 47, 2003.

X. Gao and A. Snavely, *"Exploiting Stability to Reduce Time-Space Cost
for Memory Tracing,"* ICCS Workshop on Performance Modeling and Analysis
(PMA03), Melbourne, Australia, June 2003.

E. George, J. Glimm, J. W. Grove, X. L. Li, Y. J. Liu, Z. L. Xu, N.
Zhao, *"Simplification, conservation and adaptivity in the front
tracking method,"* in Hyperbolic Problems: Theory, Numerics,
Applications, T. Hou, E. Tadmor, eds., Springer Verlag, Berlin and New
York, p. 175-184200, 2003.

F. X. Giraldo, J. B. Perot and P. F. Fischer, *"A spectral element
semi-Lagrangian (SESL) method for the spherical shallow water
equations,"* J. of Comp. Phys., 190 2, p. 623-650, 2003.

J. Glimm, S. Hou, Y. Lee, D. Sharp, K. Ye, *"Solution error models for
uncertainty quantification,"* Contemporary Mathematics, 327, p. 115-140,
2003.

J. Glimm, H. Jin, M. Laforest, F. Tangerman, Y. Zhang, *"A two pressure
numerical model of two fluid mixing*,*"* SIAM J. Multiscale Model.
Simul., 1, p. 458-484, 2003.

J. Glimm, Y. Lee, D. H. Sharp, K. Q. Ye, *"Prediction using numerical
simulations, A Bayesian framework for uncertainty quantification and its
statistical challenge,"* in Proceedings of the Fourth International
Symposium on Uncertainty Modeling and Analysis (ISUMA 2003), B. M.
Ayyub, N. O. Attoh-Okine, eds., IEEE Computer Society, 2003.

J. Glimm, X. L. Li, Y. J. Liu, Z. L. Xu, N. Zhao, *"Conservative front
tracking with improved accuracy,"* SIAM J. Numerical Analysis, 41, p.
1926-1947, 2003.

J. Glimm, X. L. Li, W. Oh, A. Marchese, M.-N. Kim, R. Samulyak, C.
Tzanos, *"Jet breakup and spray formation in a diesel engine,"* Proc. of
the Second MIT Conference on Computational Fluid and Solid Mechanics,
Cambridge, Mass., 2003.

P. Goldfeld, 2003, *"Balancing Neumann-Neumann for (In)Compressible
Linear Elasticity and (Generalized) Stokes - Parallel Implementation,"*
Proc of the 14^th^ International Symposium on Domain Decomposition
Methods, Cocoyoc, Mexico, Jan. 2002, I. Herrera, D. E. Keyes, O. B.
Widlund and R. Yates, eds., 2003.

P. Goldfeld, L. F. Pavarino and O. B. Widlund, *"Balancing
Neumann-Neumann Preconditioners for Mixed Approximations of Heterogenous
Problems in Linear Elasticity,"* Numer. Math., **95**, 283-324, 2003.

D. A. Goussis, M. Valorani, F. Creta, and H. N. Najm, *"Inertial
Manifolds with CSP,"* Computational Fluid and Solid Mechanics,
**1**:1951-1955, K. J. Bathe, ed., Elsevier, 2003.

A. Gray, et al. (The HPQCD Collaboration), *"The Upsilon Spectrum from
Lattice QCD with 2+1 Flavors of Dynamical Quarks,"* Nuclear Physics B
(Proc. Suppl.), **119**, 592, 2003.

J. F. Grcar, M. S. Day and J. B. Bell, *"Conditional and opposed
reaction path diagrams for the analysis of fluid-chemistry
interactions,"* 19th International Colloquium on the Dynamics of
Explosions and Reactive Systems, July-Aug. 2003.

D. C. Griffin, J. P. Colgan, S. D. Loch, M. S. Pindzola, and C. P.
Ballance *"Electron-impact excitation of beryllium and its ions,"*
Physical Review A, **68,** 062705, 2003.

A. T. Hagler, et al. (The LHPC Collaboration), *"Moments of nucleon
generalized parton distributions in lattice QCD,"* Physical Review D
**68**, 034505, 2003.

J. C. Hayes, M. L. Norman, *"Beyond Flux-limited Diffusion: Parallel
Algorithms for Multidimensional Radiation Hydrodynamics,"* Astrophysical
Journal Supplement Series, 147, 197-220, 2003.

M. Head-Gordon, T. Van Voorhis, G. Beran and B. Dunietz, *"Local
Correlation Models,"* Computational Science: ICCS 2003, Part IV, Lecture
Notes in Computer Science, Vol. **2660**, p. 96-102, 2003.

A. Heger, C. L. Fryer, S. E. Woosley, N. Langer, and D. H. Hartmann,
*"How Massive Single Stars End Their Life,"* ApJ, 591:288-300, July
2003.

E. D. Held*, "Unified form for parallel ion viscocus stress in
magnetized plasmas,"* Physics of Plasmas, **10,** 4708, 2003.

E. D. Held, J. D. Callen, C. C. Hegna, and C. R. Sovinec, *"Conductive
electron heat flow along an inhomogeneous magnetic field,"* Physics of
Plasmas **10,** 3933, 2003.

B. Hientzsch, 2003, *"Fast Solvers and Schwarz Preconditioners for
Spectral Nedelec Elements for a Model Problem in H(curl),"* Proc of the
14^th^ International Symposium on Domain Decomposition Methods, Cocoyoc,
Mexico, Jan. 2002, I. Herrera, D. E. Keyes, O. B. Widlund and R. Yates,
eds., 2003.

W. R. Hix, O. E. B. Messer, A. Mezzacappa, M. Liebendoerfer, J. Sampaio,
K. Langanke, D. J. Dean, G. Martinez-Pinedo, *"Consequences of Nuclear
Electron Capture in Core Collapse Supernovae,"* Physical Review Letters,
91, 201102, 2003.

W. R. Hix, A. Mezzacappa, O. E. B. Messer, S. W. Bruenn, *"Supernova
science at spallation neutron sources,"* Journal of Physics G, 29,
2523-2542, 2003.

I. Hofmann, G. Franchetti, O. Boine-Frankenheim, J. Qiang, and R. D.
Ryne, *"Space-Charge Resonances in Two- and Three-Dimensional
Anisotropic Beams,"* Physics Rev. ST Accel. Beams, **6**, 024202, 2003.

I. Hofmann, G. Franchetti, J. Qiang and R. D. Ryne, *"Self-Consistency
and Coherent Effects in Nonlinear Resonances,"* Proc. of the 29^th^ ICFA
Advanced Beam Dynamics Workshop on Beam Halo Dynamics, Diagnostics, and
Collimation (HALO'03), Montauk, NY, May 2003.

M. J. Hogan et al., *"Ultrarelativistic-Positron-Beam Transport through
Meter-Scale Plasmas,"* Phys. Rev. Lett. 90, 205002, 2003.

P. Hovland, K. Keahey, L. C. McInnes, B. Norris, L. Freitag and P.
Raghavan, *"A Quality-of-Service Architecture for High-Performance
Numerical Components,"* Proceedings of QoSCBSE2003, Toulouse, France,
June 2003.

C. Hsu, *"Effects of Block Size on the Block Lanczos Algorithm,"* Senior
Thesis, U.C. Berkeley Dept. of Mathematics, June 2003.

P. Hu, N. Chevaugeon, J. E. Flaherty, M. S. Shephard, *"Modelizations of
moving object in a fluid flow using level set,"* Proc. 7th US Nat.
Congress on Comp. Mech., p. 288, 2003.

A. L. Hungerford, C. L. Fryer, and M. S. Warren, *"Gamma-Ray Lines from
Asymmetric Supernovae,"* ApJ, 594:390-403, Sept. 2003.

M. Ikegami, et al., *"Beam Commissioning of the J-PARC Linac Medium
Energy Beam Transport at KEK,"* Proc. of IEEE Particle Accelerator
Conference 2003, Portland, Ore., May 2003.

M. Ikegami, T. Kato, Z. Igarashi, A. Ueno, Y. Kondo, J. Qiang, and R.
Ryne, *"Comparison of Particle Simulation with J-PARC Linac MEBT Beam
Test Results,"* Proc. of the 29^th^ ICFA Advanced Beam Dynamics Workshop
on Beam Halo Dynamics, Diagnostics, and Collimation (HALO'03), Montauk,
NY, May 2003.

J. Ivanic and K. Ruedenberg, *"A MCSCF Method for Ground and Excited
States Based on Full Optimizations of Successive Jacobi Rotations*,*"*
Journal of Computational Chemistry, **24**, 1250-1262, 2003.

V. Ivanov, A. Krasnykh, G. Scheitrum, D. Sprehn, L. Ives, G. Miram, *"3D
Modeling Activity for Novel High Power Electron Guns at SLAC,"* Proc. of
IEEE Particle Accelerator Conference 2003, Portland, Ore., May 2003.

V. Ivanov, C. Adolphsen, N. Folwell, L. Ge, A. Guetz, Z. Li, C.-K. Ng,
G. Schussman, J.W. Wang, M. Weiner, M. Wolf, K. Ko, *"Simulating
Accelerator Structure Operation at High Power,"* Proc. of IEEE Particle
Accelerator Conference 2003, Portland, Ore., May 2003.

V. Ivanov, C. Adolphsen, N. Folwell et al., *"Dark Current Simulation
and Rise Time Effects at High Power,"* Workshop on High Gradient RF,
Chicago, Ill., Oct. 2003.

E. F. Jaeger, L. A. Berry, J. R. Myra, D. B. Batchelor, E. D\'Azevedo,
P. T. Bonoli, C. K. Phillips, D. N. Smithe, D. A. D\'Ippolito, M. D.
Carter, R. J. Dumont, J. C. Wright, R. W. Harvey, *"Sheared Poloidal
Flow Driven by Mode Conversion in Tokamak Plasmas,"* Physical Review
Letters, **90**, 195001, 2003.

A. Jensen, V. Ivanov, A. Krasnykh, G. Scheitrum, *"An Improved Version
of TOPAZ3D,"* Proc. of IEEE Particle Accelerator Conference 2003,
Portland, Ore., May 2003.

N. A. C. Johnston, F. S. Rowland, S. Elliott, K. S. Lackner, et al.,
*"Chemical transport modeling of CO2 sinks,"* Energy Conversion and
Management, **44**, 681, 2003.

J. E. Jones, P. S. Vassilevski, and C. S. Woodward, *"Nonlinear
Schwarz-FAS Methods for Unstructured Finite Element Problems,"* Proc. of
the Second M.I.T. Conference on Computational Fluid and Solid Mechanics,
Cambridge, Mass., June 2003.

R. M. Jones, Z. Li, R. H. Miller, T. O. Raubenheimer, *"Optimized
Wakefield Suppression & Emittance Dilution-Imposed Alignment Tolerances
in X-Band Accelerating Structures for the JLC/NLC,"* Proc. of IEEE
Particle Accelerator Conference 2003, Portland, Ore., May 2003.

G. C. Jordan, S. S. Gupta, B.S. Meyer, *"Nuclear reactions important in
alpha-rich freeze-outs,"* Physical Review C, 68, 065801, 2003.

A. Kabel, *"Maxwell-Lorentz Equations in General Frenet-Serret
Coordinates,"* Proc. of IEEE Particle Accelerator Conference 2003,
Portland, Ore., May 2003.

A. Kabel, *"Parallel Simulation Algorithms for the Three-dimensional
Strong-Strong Beam-Beam Interaction,"* Proc. of IEEE Particle
Accelerator Conference 2003, Portland, Ore., May 2003.

A. Kabel, *"Particle Tracking and Bunch Population in TRAFIC4 2.0,"*
Proc. of IEEE Particle Accelerator Conference 2003, Portland, Ore., May
2003.

A. Kabel, Y. Cai, B. Erdelyi, T. Sen, and M. Xiao*, "A Parallel Code for
Lifetime Simulations in Hadron Storage Rings in the Presence of
Parasitic Weak-strong Beam-beam Interactions,"* Proc. of IEEE Particle
Accelerator Conference 2003, Portland, Ore., May 2003.

K. Keahey, *"Fine Grain Authorization Policies in the Grid: Design and
Implementation,"* Proc. of the Middleware 2003 Conference, 2003.

E. Kim, J. Bielak, and O. Ghattas, *"Large-scale Northridge Earthquake
simulation using octree-based multiresolution mesh method,"* Proc. of
16^th^ ASCE Engineering Mechanics Conference, Seattle, Wash., July 2003.

L. Krivodonova, J. E. Flaherty, *"Error estimation for discontinuous
Galerkin solutions of multidimensional hyperbolic problems,"* Advances
in Computational Mathematics, 19, 57, 2003.

K. Langanke, D. J. Dean, W. Nazarewicz, *"Shell model Monte Carlo
studies of nuclei in the A\~80 mass region,"* Nuclear Physics A, 728,
109-117, 2003.

K. Langanke, G. Martinez-Pinedo, J. M. Sampaio, D. J. Dean, W. R. Hix,
O. E. B. Messer, A. Mezzacappa, M. Liebendorfer, H.-T. Janka, M. Rampp,
*"Electron Capture Rates on Nuclei and Implications for Stellar Core
Collapse,"* Physical Review Letters, 90, 241102, 2003.

B. S. Lee McCormick, B. Philip, and D. Quinlan, *"Asynchronous fast
adaptive composite-grid methods: numerical results,"* SIAM Journal of
Scientific Computing, **25,** p. 682-700, 2003.

S. Lefantzi and J. Ray, *"A Component-based Scientific Toolkit for
Reacting Flows,"* Computational Fluid and Solid Mechanics,
**2**:1401-1405, K. J. Bathe, Ed., Elsevier, 2003.

S. Lefantzi, J. Ray and H. Najm, *"Using the Common Component
Architecture to Design High Performance Scientific Simulation Codes,"*
Proc. of the Parallel and Distributed Processing Symposium, June 2003.

J. Li, *"A Dual-Primal FETI Method for Solving Stokes/Navier-Stokes
Equations,"* Proc of the 14^th^ International Symposium on Domain
Decomposition Methods, Cocoyoc, Mexico, Jan. 2002, I. Herrera, D. E.
Keyes, O. B. Widlund and R. Yates, eds., 2003.

L. Li, J. Glimm, X. L. Li, *"All isomorphic distinct cases for
multi-component interfaces in a block,"* J. Comp. Appl. Mathematics,
152, p. 263-276, 2003.

X. S. Li and J. W. Demmel, *"SuperLU_DIST: A Scalable Distributed-memory
Sparse Direct Solver for Unsymmetric Linear Systems,"* ACM Transactions
on Math. Software, 29:110-140, 2003.

X. Li, M. S. Shephard, M. W. Beall, *"General mesh adaptation using mesh
modifications,"* Proc. 7th US Nat. Congress on Comp. Mech., p. 17, 2003.

X. Li, M. S. Shephard, M. W. Beall, *"Accounting for curved domains in
mesh adaptation,"* International Journal for Numerical Methods in
Engineering, 58, p. 246-276, 2003.

Z. Li, C. Adolphsen, D. L. Burke, V. Dolgashev, R. M. Jones, R. H.
Miller, C. Nantista, C.-K. Ng, T. O. Raubenheimer, R. D. Ruth, P. T.
Tenenbaum, J. W. Wang, N. Toge, T. Higo, *"Optimization of the X-band
Structure for the JLC/NLC,"* Proc. of IEEE Particle Accelerator
Conference 2003, Portland, Ore., May 2003.

Z. Li, R. Johnson, S. R. Smith, T. Naito, J. Rifkin, *"Cavity BPM with
Dipole-mode-selective coupler,"* Proc. of IEEE Particle Accelerator
Conference 2003, Portland, Ore., May 2003.

M. Liebendoerfer, A. Mezzacappa, O. E. B. Messer, G. Martinez-Pinedo, W.
R. Hix, F.-K Thielemann, *"The neutrino signal in stellar core collapse
and postbounce evolution,"* Nuclear Physics A, 719, 144-152, 2003.

Y. Lin et al., *"Ion Cyclotron Range of Frequencies Mode Conversion
Electron Heating in Deuterium-Hydrogen Plasmas in the Alcator C-Mod
Tokamak,"* Plasma Phys. Control. Fusion **45**, (6) 1013, 2003.

Y. Lin, S. J. Wukitch, P. T. Bonoli, A. Mazurenko, E. Nelson-Melby, M.
Porkolab, J. C. Wright, I. H. Hutchinson, E. S. Marmar, D. Mossessian,
S. Wolfe, C. K. Phillips, G. Schilling, and P. Phillips, *"Study of Ion
Cyclotron Range of Frequencies in the Alcator C-Mod Tokamak,"* Radio
Frequency Power in Plasmas, Proc. 15^th^ Topical Conf., Moran, Wyoming,
2003.

S. D. Loch, J. P. Colgan, and M. S. Pindzola, M. Westermann, F.
Scheuermann, K. Aichele, D. Hathiramani, and E. Salzborn,
*"Electron-impact ionization of O^q+^ ions for q=1-4,"* Physical Review
A, **67,** 042714, 2003.

Y. Luo, I. Malik, Z. Li, M S. Shephard, *"Adaptive mesh refinement in
accelerator modeling with OMEGA3P*," Proc. 7th US Nat. Congress on Comp.
Mech., p. 50, 2003.

W. P. Lysenko, J. Qiang, R. W. Garnett, T. P. Wangler, *"Challenge of
Benchmarking Simulation Codes for the LANL Beam-Halo Experiment,"* Proc.
of IEEE Particle Accelerator Conference 2003, Portland, Ore., May 2003.

K.-L. Ma, *"Visualizing Time-Varying Volume Data,"* IEEE Computing in
Science and Engineering," 5**(2),** p. 34, March/April 2003.

M. Macri, S. De, M. S. Shephard, *"Hierarchical tree-based
discretization for the method of spheres,"* Computers and Structures,
81(8-11), p. 789-803, 2003.

G. G. Maisuradze, and D. L. Thompson, *"Interpolating Moving
Least-Squares Method for Fitting Potential Energy Surfaces: Illustrative
Approaches and Applications,"* Journal of Physical Chemistry A **107**,
7118-7124, 2003.

G. G. Maisuradze, D. L. Thompson, A. F. Wagner, and M. Minkoff,
*"Interpolating Moving Least-Squares Method for Fitting Potential Energy
Surfaces:* *Detailed Analysis of One Dimensional Applications,"* Journal
of Chemical Physics **119,** 10002-10014, 2003.

T. Manteuffel, S. McCormick, and C. Pflaum, *"Improved discretization
error estimates for first-order system least squares (FOSLS),"* Journal
on Numerical Analysis, Math., **11,** p. 163-177, 2003.

J. Marathe, F. Mueller, T. Mohan, B. R. de Supinski, S.A. McKee and A.
Yoo, *"METRIC: Tracking Down Inefficiencies in the Memory Hierarchy Via
Binary Rewriting,"* International Symposium on Code Generation and
Optimization 2003,\
San Francisco, Calif., March 2003.

E. S. Marmar, B. Bai, R. L. Boivin, P. T. Bonoli, C. Boswell, R.
Bravenec, B. Carreras, D. Ernst, C. Fiore, S. Gangadhara, K. Gentle, J.
Goetz, R. Granetz, M. Greenwald, K. Hallatschek, J. Hastie, J. Hosea, A.
Hubbard, J. W. Hughes, I. Hutchinson, Y. In, J. Irby, T. Jennings, D.
Kopon, G. Kramer, B. LaBombard, W. D. Lee, Y. Lin, B. Lipschultz, J.
Liptac, A. Lynn, K. Marr, R. Maqueda, E. Melby, D. Mikkelsen,
D. Mossessian, R. Nazikian, W. M. Nevins, R. Parker, T. S. Pedersen, C.
K. Phillips, P. Phillips, C. S. Pitcher, M. Porkolab, J. Ramos, M. Redi,
J. Rice, B. N. Rogers, W. L. Rowan, M. Sampsell, G. Schilling, S. Scott,
J. Snipes, P. Snyder, D. Stotler, G. Taylor, J. L. Terry, H. Wilson, J.
R. Wilson, S. M. Wolfe, S. Wukitch, X. Q. Xu, B. Youngblood, H. Yuh, K.
Zhurovich and S. Zweben, *"Overview of recent Alcator C-Mod research,"*
Nucl. Fusion **43**, 1610, 2003.

G. Martinez-Pinedo, D. J. Dean, K. Langanke, J. Sampaio,
*"Neutrino-nucleus interactions in core-collapse supernova,"* Nuclear
Physics A, 718, 452-454, 2003.

W. Maslowski, and W. H. Lipscomb, *"High-resolution simulations of
Arctic sea ice during 1979-93,"* Polar Research, **22**, 67, 2003.

L. McInnes, B. Norris, S. Bhowmick, and P. Raghavan, 2002, *"Adaptive
Sparse Linear Solvers for Implicit CFD Using Newton-Krylov Algorithms,"*
Proc. of the Second MIT Conference on Computational Fluid and Solid
Mechanics, Boston, Mass., June 2003.

D. J. McGillicuddy, L. A. Anderson, S. C Doney and M. E. Maltrud,
*"Eddy-driven sources and sinks of nutrients in the upper ocean: results
from a 0.1 degree resolution model of the North Atlantic,"* Global
Biogeochemical Cycles, **17**, 1035, 2003.

O. E. B. Messer, W. R. Hix, M. Liebendorfer, A. Mezzacappa, *"Electron
capture and shock formation in core-collapse supernovae,"* Nuclear
Physics, A. 718, 449-451, 2003.

O. E. B. Messer, M. Liebendorfer, W. R. Hix, A. Mezzacappa, S. W.
Bruenn, *"The Impact of Improved Weak Interaction Physics in
Core-Collapse Supernova Simulations,"* From Twilight to Highlight: The
Physics of Supernovae, W. Hillebrandt, D. Leibundgut, eds., p. 70,
Springer-Verlag, 2003.

B. S. Meyer, *"Neutrinos, supernovae, molybdenum, and extinct 92Nb,"*
Nuclear Physics A, 719, 13-20, 2003.

A. Mezzacappa, *"The Road to Prediction: Toward Gravitational Wave
Signatures from Core Collapse Supernovae,"* AIP Conf. Proc. 686: The
Astrophysics of Gravitational Wave Sources, p. 29-39, 2003.

A. Mezzacappa, J. M. Blondin, *"A New Twist on the Core Collapse
Supernova Mechanism?"* in From Twilight to Highlight: The Physics of
Supernovae, W. Hillebrandt, D. Leibundgut, eds., p. 63, Springer-Verlag,
2003.

D. Mika, P. Myers, A. Majorell, L. Jiang, S. Kocak, J. Wan, M. S.
Shephard, *"Alloy 718 extrusion modeling - unstable flow and mesh
enrichment,"* Proc. 7th US Nat. Congress on Comp. Mech., p. 342, 2003.

A. J. Miller, M. A. Alexander, G. J. Boer, F. Chai, K. Denman, D. J.
Erickson III, R. Frouin, A. Gabric, E. Laws, M. Lewis, Z. Liu, R.
Murtugudde, S. Nakamoto, D. J. Neilson, J. R. Norris, C. Ohlmann, I.
Perry, N. Schneider, K. Shell and A. Timmermann, *"Potential feedbacks
between Pacific Ocean ecosystems and interdecadel climate variations,"*
Bulletin of the American Meteorology, Soc. **84**, 617, 2003.

G. H. Miller, *["An iterative Riemann solver for systems of hyperbolic
conservation laws, with application to hyperelastic solid
mechanics](http://seesar.lbl.gov/anag/publications/colella/Miller-2003.pdf),"*
Journal of Computational Physics **193,** p. 198-225, 2003.

D. M. Mitnik, D. C. Griffin, C. P. Ballance, and N. R. Badnell, *"An
R-matrix with pseudo-states calculation of electron-impact excitation in
C^2+^,"* Journal of Physics B, **36,** 717, 2003.

T. Mohan, B. R. de Supinski, S. A. McKee, F. Mueller, A. Yoo, M. Schulz,
*"Identifying and Exploiting Spatial Regularity in Data Memory
References,"* Proc. of ACM/IEEE SC03 conference, Phoenix, Ariz., Nov.
2003.

J. Mueller, S. Nagrath, X. Li, J. E. Jansen, M. S. Shephard, *"Efficient
computational methods for the investigation of vascular disease,"* Proc.
7th US Nat. Congress on Comp. Mech., p. 195, 2003.

J. D. Myers, C. Pancerella, C. Lansing, K. L. Schuchardt and B. Didier,
*"Multi-scale science: Supporting emerging practice with
semantically-derived provenance,"* Proc. of the Workshop on Semantic Web
Technologies for Searching and Retrieving Scientific Data, Sanibel
Island, Fla., Oct. 2003.

J. D. Myers, A. Chappell, M. Elder, A. Geist, J. Schwidder,
*"Re-integrating the research record,"* IEEE Computing in Science and
Engineering, **5**(3):44-50, 2003.

D. Narayan, R. Bradshaw, R. Evard and A. Lusk, *"Bcfg: a configuration
management tool for heterogeneous environments,"* Proc. of the 5th IEEE
International Conference on Cluster Computing (CLUSTER03), Kowloon, Hong
Kong, Dec. 2003.

E. Nelson-Melby, M. Porkolab, P. T. Bonoli, Y. Lin, A. Mazurenko, and S.
J. Wukitch, *"Experimental Observations of Mode-Converted Ion Cyclotron
Waves in a Tokamak Plasma by Phase Contrast Imaging,"* Physical Review
Letters, **90**, 155004, 2003.

R. M. Olson, M. W. Schmidt, M. S. Gordon and A. P. Rendell, *"Enabling
the Efficient Use of SMP Clusters: The GAMESS/DDI Model,"* Proc. of the
ACM/IEE SC03 conference, Phoenix, Ariz., Nov. 2003.

E. Ong, J. Larson and R. Jacob, *"A Real Application of the Model
Coupling Toolkit,"* Proc. of the 2002 International Conference on
Computational Science, eds. P. Sloot, C. J. K. Tan, J. J. Dongarra, A.
Hoekstra, Springer-Verlag, 2003.

C. M. Pancerella, J. Hewson, W. Koegler D. Leahy, M. Lee, L. Rahn, C.
Yang, J. D. Myers, D. Didier, R. McCoy, *"Metadata in the collaboratory
for multi-scale chemical science,"* Proc, of the 2003 Dublin Core
Conference: Supporting Communities of Discourse and Practice-Metadata
Research and Applications, Seattle, Wash., Sept.-Oct. 2003.

W. Park, J. Breslau, J. Chen, et al,, *"Nonlinear simulation studies of
tokamaks and STs,"* Nuclear Fusion **43,** 483, 2003.

M. S. Pindzola, T. Minami, and D. R. Schultz, *"Laser-modified
charge-transfer processes in proton collisions with lithium atoms,"*
Physical Review A, **68,** 013404, 2003.

M. S. Pindzola and F. Texier, *"Collective modes of ground and
dark-soliton states of Bose-Einstein condensates in anisotropic traps,"*
Journal of Physics B, **36,** 1783, 2003.

A. Pochinsky, et al., *"Large scale commodity clusters for lattice
QCD,"* Nuclear Physics B (Proc. Suppl.) **119**, 1044, 2003.

J. Pruet, *"Neutrinos from the Propagation of a Relativistic Jet through
a Star,"* ApJ, 591:1104-1109, July 2003.

J. Pruet and G. M. Fuller, *"Estimates of Stellar Weak Interaction Rates
for Nuclei in the Mass Range A=65-80,"* Astrophysical Journal
Supplement, 149:189-203, Nov. 2003.

J. Pruet, S. E. Woosley, and R. D. Hoffman, *"Nucleosynthesis in
Gamma-Ray Burst Accretion Disks,"* ApJ, 586:1254-1261, April 2003.

J. Qiang and R. W. Garnett, *"Smooth Approximation with Acceleration in
an Alternating Phase Focusing Superconducting Linac,"* Nuclear
Instruments and Methods in Physics Res. A 496, 33, 2003.

J. Qiang, M. Furman and R. Ryne*, "Parallel Particle-In-Cell Simulation
of Colliding Beams in High Energy Accelerators,"* Proc. of the ACM/IEEE
SC03 conference, Phoenix, Ariz., Nov. 2003.

J. Qiang, M. Furman, R. D. Ryne, W. Fischer, T. Sen, M. Xiao, *"Parallel
Strong-Strong/Strong-Weak Simulations of Beam-Beam Interactions in
Hadron Accelerators,"* Proc. of the 29^th^ ICFA Advanced Beam Dynamics
Workshop on Beam Halo Dynamics, Diagnostics, and Collimation (HALO'03),
Montauk, NY, May 2003.

J. Qiang, R. D. Ryne, and I. Hofmann, *"Space-Charge Driven Emittance
Growth in a 3D Mismatched Anisotropic Beam,"* Proc. of IEEE Particle
Accelerator Conference 2003, Portland, Ore., May 2003.

J. Qiang, R. D. Ryne, T. Sen, M. Xiao, *"Macroparticle Simulations of
Antiproton Lifetime at 150 GeV in the Tevatron,"* Proc. of IEEE Particle
Accelerator Conference 2003, Portland, Ore., May 2003.

D. Quinlan and M. Schordan, *"A Source-to-Source Architecture for
User-Defined Optimizations,"* Joint Modular Languages Conference,
Austria, Lecture Notes in Computer Science, **2789**, p. 214-223,
Springer-Verlag, Aug. 2003.

D. Quinlan, M. Schordan, B. Miller and M. Kowarschik, *"Parallel
Object-Oriented Framework Optimization,"* Special Issue of Concurrency:
Practice and Experience, **16**, 2-3, p. 293-302, 2003.

D. Quinlan, M. Schordan, Q. Yi, and B. R. de Supinski*, "Semantic-driven
Parallelization of Loops Operating on User-Defined Containers,"* 16th
Annual Workshop on Languages and Compilers for Parallel Computing,
College Station, Texas, Oct. 2003.

D. Quinlan, M. Schordan, Qing Li, and B. R. de Supinski, *"A C++
Infrastructure for Automatic Introduction and Translation of OpenMP
Directives,"* Proc. of the Workshop on Open MP Applications and Tools
(WOMPAT'03), Lecture Notes in Computer Science, **2716**, p. 13-25,
Springer-Verlag, June 2003.

P. Raghavan, K. Teranishi, and E. G. Ng, *"A Latency Tolerant Hybrid
Sparse Solver Using Incomplete Cholesky Factorization,"* Numerical
Linear Algebra with Applications **10,** p. 541-560, 2003.

S. Ratkovic, S. Iyer Dutta, M. Prakash, *"Differential neutrino rates
and emissivities from the plasma process in astrophysical systems,"*
Physical Review D, 67, 123002, 2003.

D. A. Reed, C. L. Mendes and C. Lu, *"Intelligent Application Tuning and
Adaptation,"* Chapter in The Grid: Blueprint for a New Computing
Infrastructure, 2nd edition, I. Foster & C. Kesselman eds., Morgan
Kaufmann, Nov. 2003.

D. A. Reed, C. Lu, C. L. Mendes, *"Big Systems and Big Reliability
Challenges,"* Proc. of Parallel Computing 2003, Dresden, Germany, Sept.
2003.

J. F. Remacle, J. E. Flaherty, M. S. Shephard, *"An adaptive
discontinuous Galerkin technique with an orthogonal basis applied
compressible flow problems,"* SIAM Review, 45(1), p. 53-72, 2003.

J. F. Remacle, M. S. Shephard, *"An algorithm oriented mesh database,"*
International Journal for Numerical Methods in Engineering, 58, p.
349-374, 2003.

J. Rikovska Stone, J. C. Miller, R. Koncewicz, P. D. Stevenson, M. R.
Strayer, *"Nuclear matter and neutron-star properties calculated with
the Skyrme interaction,"* Physical Review C, 68, 034324, 2003.

F. J. Robicheaux and J. D. Hanson, *"Simulated expansion of an ultracold
neutral plasma,"* Physics of Plasmas, **10,** 2217, 2003.

T. M. Rogers, G. A. Glatzmaier, and S. E. Woosley, *"Simulations of
two-dimensional turbulent convection in a density-stratified fluid,"*
Physical Review E, **67**(2):026315, Feb. 2003.

G. Rosa, E. Lum, K.-L. Ma, and K. Ono*, "An Interactive Volume
Visualization System for Transient Flow Analysis,"* Proc. of the Volume
Graphics 2003 Workshop, Tokyo, Japan, July 2003.

A. L. Rosenberg, J. E. Menard, J. R. Wilson, S. Medley, R. Andre, D.
Darrow, R. Dumont, B. P. LeBlanc, C. K. Phillips, M. Redi, T. K. Mau, E.
F. Jaeger, P. M. Ryan, D. W. Swain, R. W. Harvey, J. Egedal, and the
NSTX Team, *"Characterization of Fast Ion Absorption of the High
Harmonic Fast Wave in the National Spherical Torus Experiment,"* Radio
Frequency Power in Plasmas, Proc. 15^th^ Topical Conf., Moran, Wyoming,
AIP, N. Y., 185, 2003.

G. Rumolo, A. Z. Ghalam, et al., *"Electron Cloud Effects on Beam
Evolution in a Circular Accelerator,"* Phys. Rev. STAB, 6, 081002, 2003.

J. M. Sampaio, K. Langanke, G. Martinez-Pinedo, E. Kolbe, D. J. Dean,
*"Electron capture rates for core collapse supernovae,"* Nuclear Physics
A, 718, 440-442, 2003.

R. Samtaney, *"Suppression of the Richtmyer-Meshkov instability in the
presence of a magnetic field,"* Physics of Fluids **15,** L53-56, 2003.

S. Sankaran, J. M. Squyres, B. Barrett, A. Lumsdaine, J. Duell, P.
Hargrove and E. Roman, *"The LAM/MPI Checkpoint/Restart Framework:
System-Initiated Checkpointing,"* LACSI Symposium, Santa Fe, NM, Oct.
2003.

D. P. Schissel, *"National Fusion Collaboratory - Advancing the Science
of Fusion Research,"* Proc. of the 2003 DOE SciDAC PI Meeting, 2003.

M. Schnell, G. Gwinner, N. R. Badnell, M. E. Bannister, S. Bohm, J. P.
Colgan, S. Kieslich, S. D. Loch, D. Mitnik, A. Muller, M. S. Pindzola,
S. Schippers, D. Schwalm, W. Shi, A. Wolf and S. G. Zhou, *"Observation
of trielectronic recombination in Be-like Cl ions,"* Physical Review
Letters, **91,** 043001, 2003.

M. Schordan and D. Quinlan, *"A Source-to-Source Architecture for
User-Defined Optimizations,"* Proc, of the Joint Modular Languages
Conference (JMLC'03), Lecture Notes in Computer Science, **2789,** p.
214-223, Springer-Verlag, June 2003.

D. R. Schultz and P. S. Krstic, *"Ionization of Helium by antiprotons:
Fully correlated, four-dimensional lattice approach,"* Physical Review
A, 022712, 2003.

G. L. Schussman, *"Interactive And Perceptually Enhanced Visualization
Of Large, Complex Line-Based Datasets,"* Ph.D. thesis, University of
California Davis. Dec. 2003.

S. L. Scott, B. Luethke and J. Mugler, *"Cluster & Grid Tools: C3 Power
Tools with C2G,"* Newsletter of the IEEE Task Force on Cluster
Computing, **4**, 2, March/April 2003.

S. L. Scott, C. Leangsuksun, L Chen and T. Lui, *"Building High
Availability and Performance Clusters with HA-OSCAR Toolkits,"* 2003
High Availability and Performance Workshop, Santa Fe, NM, Oct. 2003.

S. L. Scott, C. Leangsuksun, L. Shen, T. Liu and H. Song, *"Availability
Prediction and Modeling of High Availability OSCAR Cluster,"* Proc. of
the 5th IEEE International Conference on Cluster Computing (CLUSTER03),
Kowloon, Hong Kong, Dec. 2003.

S. L. Scott, B. Luethke and T. Naughton, *"OSCAR Cluster Administration
With C3,"* Proc. of the 17^th^ Annual International Symposium on High
Performance Computing Systems and Applications and the 1^st^ Annual
OSCAR Symposium, Quebec, Canada, May 2003.

S. L. Scott, C. Leangsuksun, L. Shen, H. Song and I. Haddad, *"The
Modeling and Dependability Analysis of High Availability OSCAR Cluster
System,"* Proc. of the 17^th^ Annual International Symposium on High
Performance Computing Systems and Applications and the 1^st^ Annual
OSCAR Symposium, Quebec, Canada, May 2003.

S. L. Scott, T. Naughton, B. Ligneris and N. Gorsuch*, "Open Source
Cluster Application Resources (OSCAR): Design, Implementation and
Interest for the \[Computer\] Scientific Community,"* Proc. of the
17^th^ Annual International Symposium on High Performance Computing
Systems and Applications and the 1^st^ Annual OSCAR Symposium, Quebec,
Canada, May 2003.

S. L. Scott, B. Luethke, *"Scalable C3 Power Tools,"* Cluster World
Conference and Expo (CWCE 2003) and 4^th^ Linux Cluster Institute
Conference (LCI), San Jose, Calif., June 2003.

S. L. Scott, J. Mugler, T. Naughton, B. Barrett, A. Lumsdaine, J.
Squyres, B. Ligneris, F. Giraldeau and C. Leangsuksun, *"OSCAR
Clusters,"* Proc. of the Ottawa Linux Symposium (OLS\'03), Ottawa,
Canada, July 2003.

S. L. Scott, C. Leangsuksun, L. Shen, T. Liu and H. Song,
*"Dependability Prediction of High Availability OSCAR Cluster Server,"*
2003 International Conference on Parallel and Distributed Processing
Techniques and Applications (PDPTA'03), Las Vegas, Nevada, June 2003.

S. L. Scott, I. Haddad and C. Leangsuksun*, "HA-OSCAR: The birth of a
Highly Available OSCAR,"* Linux Journal, **2003**, 115, Seattle, Wash.,
Nov. 2003.

S. L. Scott, T. Naughton, Y. C. Fang, P. Pfeiffer, B. Ligneris, and C.
Leangsuksun, *"The OSCAR Toolkit: Current and Future Developments,"*
Dell Power Solution magazine, Nov. 2003.

S. L. Scott, T. Naughton, B. Barrett, J. Squyres, A. Lumsdaine, Y. C.
Fang, and V. Mashayekhi *"Looking Inside the OSCAR Cluster Toolkit,"*
Dell Power Solution magazine, Nov. 2003.

A. Snavely, L. Carrington, N. Wolter, C. Lee, J. Labarta, J. Gimenez,
and P. Jones, *"Performance Modeling of HPC Applications, Mini-symposium
on Performance Modeling,"* Proc. of Parallel Computing 2003, Dresden,
Germany, Sept. 2003.

C. Sneden, J. J. Cowan, J. E. Lawler, I. I. Ivans, S. Burles, T. C.
Beers, F. Primas, V. Hill, J. W. Truran, G. M. Fuller, B. Pfeiffer,
K.-L. Kratz, *"The Extremely Metal-poor, Neutron Capture-rich Star CS
22892-052: A Comprehensive Abundance Analysis,"* Astrophysical Journal
Letters, 591, 936-953, 2003.

C. R. Sovinec, T. A. Gianakon, E. D. Held, S. E. Kruger, D. D. Schnack
and the NIMROD Team, *"NIMROD: a computational laboratory for studying
nonlinear fusion magnetohydrodynamics,"* Physics of Plasmas **10,**
1727, 2003.

C. R. Sovinec, B. I. Cohen, G. A. Cone, E. B. Hooper, and H. S. McLean,
*"Numerical investigation of transients in the SSPX spheromak,"*
Physical Review Letters **94,** 035003, 2003.

P. Spentzouris, J. Amundson, *"FNAL Booster: experiment and modeling,"*
Proc. of IEEE Particle Accelerator Conference 2003, Portland, Ore., May
2003.

N. Stojic, J. W. Davenport, M. Komelj, J. Glimm, *"Surface magnetic
moment in\\alpha-uranium by density-functional theory,"* Phys. Rev. B,
68, 094407, 2003.

P. H. Stoltz, M. A. Furman, J. -L. Vay, A. W. Molvik, R. H. Cohen,
*"Numerical Simulation of the Generation of Gecondary Electrons in the
High Current Experiment,"* Physics Rev. ST Accel. Beams. Vol **6**,
054701. 2003.

A. Stompel, K.-L. Ma, J. Bielak, O. Ghattas and E. Kim, *"Visualizing
Large-Scale Earthquake Simulations,"* Proc. of the ACM/IEEE SC03
conference, Phoenix, Ariz., Nov. 2003.

A. Stompel, K.-L. Ma, E. Lum, J. Ahrens, and J. Patchett, *"SLIC:
Scheduled Linear Image Compositing for Parallel Vollume Rendering,"*
Proc. of the 2003 Symposium on Parallel Visualization and Graphics,
Seattle, WA, Oct. 2003.

D. W. Swain, M. D. Carter, J. R. Wilson, P. M. Ryan, J. B. Wilgen, J.
Hosea and A. Rosenberg, *"Loading and Asymmetry Measurements and
Modeling for the National Spherical Torus Experiment Ion Cyclotron Range
of Frequencies System,"* Fusion Science and Technology, **43**, 503,
2003.

K. Takahashi, K. Sato, A. Burrows, and T. Thompson, *"Supernova
neutrinos, neutrino oscillations, and the mass of the progenitor star,"*
Phys. Rev. D, 68:113009, 2003.

T. J. Tautges, *"MOAB-SD: Integrated Structured and Unstructured Mesh
Representation,"* 6th U.S. Congress on Computational Mechanics, Trends
in Unstructured Mesh Generation, Albuquerque, NM, July 2003.

F.-K. Thielemann, D. Argast, F. Brachwitz, W. R. Hix, P. Hoflich, M.
Liebendorfer, G. Martinez-Pinedo, A. Mezzacappa, I. Panov, T. Rauscher,
"Nuclear cross sections, nuclear structure and stellar nucleosynthesis,"
Nuclear Physics A, 718, 139-146, 2003.

F.-K. Thielemann, D. Argast, F. Brachwitz, W. R. Hix, P. Hoflich, M.
Liebendorfer, G. Martinez-Pinedo, A. Mezzacappa, K. Nomoto, I. Panov, I.
*"Supernova Nucleosynthesis and Galactic Evolution,"* From Twilight to
Highlight: The Physics of Supernovae, W. Hillebrandt, D. Leibundgut,
eds., p. 331, Springer-Verlag, 2003.

S. J. Thomas, J. M. Dennis, H. M. Tufo, P. F. Fischer, *"A Schwarz
Preconditioner for the Cubed-Sphere,"* SIAM J. Sci. Comp., 25, p.
442-453, 2003.

M. Thompson, *"Fine-grained Authorization for Job and Resource
Management using Akenti and Globus,"* Proceedings of the 2003 Conference
for Computing in High Energy and Nuclear Physics, 2003.

T. A. Thompson, A. Burrows, and P. A. Pinto, *"Shock Breakout in
Core-Collapse Supernovae and Its Neutrino Signature,"* Astrophysical
Journal, 592:434-456, July 2003.

C. Tse, S. T. Teoh, and K.-L. Ma, *"An Interactive Isosurface
Visualization Cluster,"* Proc. of High Performance Computing 2003
Symposium, Orlando, Fla., March 2003.

M. Valorani, F. Creta and D. A. Goussis, *"Local and Global Manifolds in
Stiff Reaction-Diffusion Systems,"* Computational Fluid and Solid
Mechanics 2003, 1548-1551, K. J. Bathe, ed., Elsevier, 2003.

M. Valorani, H. N. Najm and D. A. Goussis, *"CSP Analysis of a Transient
Flame-Vortex Interaction: Time Scales and Manifolds,"* Combustion and
Flame, **134**(1-2):35-53, July 2003.

J. S. Vetter and F. Mueller, *"Communication Characteristics of
Large-Scale Scientific Applications for Contemporary Cluster
Architectures,"* Journal of Parallel and Distributed Computing, **63**,
p. 853-865, 2003.

R. Vuduc, *"Automatic Performance Tuning of Sparse Matrix Kernels,"*
Ph.D. thesis, U.C. Berkeley Dept. of Computer Science, Dec. 2003.

R. Vuduc, A. Gyulassy, J. W. Demmel and K. A. Yelick, *"Memory Hierarchy
Optimizations and Performance Bounds for Sparse A^T^A\*x,"* Proc. of
ICCS 2003: Workshop on Parallel Linear Algebra, Melbourne, Australia,
June 2003.

G. Wallace, et al., *"DeskAlign: Automatically Aligning a Tiled Windows
Desktop,"* Proc. of the IEEE International Workshop on Projector-Camera
Systems (PROCAMS), Oct. 2003.

G. Wallace, et al., *"Color Gamut Matching for Tiled Display Walls,"*
Proc. of the Immersive Projection Technology Workshop (IPT), May 2003.

J. Wan, S. Kocak, M. S. Shephard, *"Automated adaptive forming
simulations,"* 12th International Meshing Roundtable, Sandia National
Laboratories, p. 323-334, 2003.

J. Wan, S. Kocak, M. S. Shephard, *"Controlled mesh enrichments for
evolving geometries,"* Proc. 7th US Nat. Congress on Comp. Mech., p. 42,
2003.

T. P. Wangler, K. R. Crandall, R. W. Garnett, D. Gorelov, P. Ostroumov,
J. Qiang, R. Ryne, R. York, *"Advanced Beam-Dynamics Simulation Tools
for the RIA Driver Linac, Part I: Low Energy Beam Transport and
Radiofrequency Quadrupole,"* Proc. RIA R&D Workshop, Washington, D.C.,
Aug. 2003.

A. Wetzels, A. Gurtler, F. Rosca-Pruna, S. Zamith, M. J. J. Vrakking, F.
Robicheaux and W. J. van der Zande, *"Two-dimensional momentum imaging
of Rydberg states using half-cycle pulse ionization and velocity map
imaging,"* Physical Review A, **68,** 041401, 2003.

M. Wingate, et al. (The HPQCD Collaboration), *"Bs Mesons Using
Staggered Light Quarks,"* Nuclear Physics B (Proc. Suppl.) **119**, 604,
2003.

M. C. Witthoeft, J. P. Colgan, and M. S. Pindzola, *"Electron-impact
excitation of Li to high principal quantum number,"* Physical Review A,
**68,** 022711, 2003.

F. Wolf, B. Mohr, *"Automatic performance analysis of hybrid MPI/OpenMP
applications,"* Journal of Systems Architecture, Special Issue:
Evolutions in Parallel Distributed and Network-Based Processing, A.
Clematis, D. D'Agostino, eds., Elsevier, **49**(10-11), p. 421-439, Nov.
2003.

P. H. Worley, T. H. Dunigan, *"Early Evaluation of the Cray X1* *at Oak
Ridge National Laboratory,"* Proc. of the 45th Cray User Group
Conference, Columbus, Ohio, May 2003.

J. C. Wright, P. T. Bonoli, M. Brambilla, F. Meo, E. D\'Azevedo, D. B.
Batchelor, E. F. Jaeger, L. A. Berry, C. K. Phillips and A. Pletzer,
*"Full Wave Simulations of Fast Wave Mode Conversion and Lower Hybrid
Wave Propagation in Tokamaks,"* Bull. Am. Phys. Soc. **48**, 127, 2003.

K. Wu, W. Koegler, J. Chen and A. Shoshani, *"Using bitmap index for
interactive exploration of large datasets,"* Proc. of SSDBM 2003, p. 65,
Cambridge, Mass, USA, 2003.

K. Wu, W.-M. Zhang, A. Sim, J. Gu and A. Shoshani, *"Grid collector: An
event catalog with automated file management,"* Proc. of IEEE Nuclear
Science Symposium 2003, 2003.

R. G. Zepp, T. V. Callaghan and D. J. Erickson III, *"Interactive
effects of ozone depletion and climate change on biogeochemical
cycles,"* Journal of Photochemistry, Photobiol. **2**, 51, 2003.

O. Zatsarinny, T. W. Gorczyca, K. T. Korista, N. R. Badnell and D. W.
Savin, *"Dielectronic recombination data for dynamic finite-density
plasmas: II. The Oxygen isoelectronic sequence,"* Astronomy and
Astrophysics, **412,** 587, 2003.

M. Zeghal, U. El Shamy, M. S. Shephard, R. Dobry, J. Fish, T. Abdounm,
*"Micro-mechanical analysis of saturated granular soils,"* Journal of
Multiscale Computational Engineering, 1(4), p. 441-460, 2003.

W. Zhang, S. E. Woosley, and A. I. MacFadyen, *"Relativistic Jets in
Collapsars,"* Astrophysical Journal, 586:356-371, March 2003.

**2004**

A. Adelmann, J. Amundson, P. Spentzouris, J. Qiang, R. D. Ryne, *"A Test
Suite of Space-charge Problems for Code Benchmarking,"* Proc. of EPAC
2004, Lucerne, Switzerland, p. 1942, 2004.

P. K. Agarwal, R. A. Alexander, E. Apra, S. Balay, A. S. Bland, J.
Colgan, E. F. D\'Azevedo, J. J. Dongarra, T. H. Dunigan, Jr., M. R.
Fahey, R. A. Fahey, A. Geist, M. Gordon, R. J. Harrison, D. Kaushik, M.
Krishnakumar, P. Lusczek, A. Mezzacappa, J. A. Nichols, J. Nieplocha, L.
Oliker, T. Packwood, M. S. Pindzola, T. C. Shulthess, J. S. Vetter, J.
B. White III, T. L. Windus, P. H. Worley, T. Zacharia, *"ORNL Cray X1,"*
Proc. of the 46th Cray User Group Conference, Knoxville, TN, May 2004.

V. Akcelik, J. Bielak, G. Biros, I. Epanomeritakis, O. Ghattas, L.
Kallivokas and E. Kim, *"An Online Framework for Inversion-Based 3D Site
Characterization,"* Lecture Notes in Computer Science, **3038**, p. 717,
Springer-Verlag, 2004.

# M. A. Albao, D.-J. Liu, C. H. Choi, M. S. Gordon and J. W. Evans, "*Atomistic modeling of morphological evolution during simultaneous etching and oxidation of Si(100),"* Surface Science 555, 51, 2004.

A. Alexakis, A. C. Calder, A. Heger, E. F. Brown, L. J. Dursi, J. W.
Truran, R. Rosner, D. Q. Lamb, F. X. Timmes, B. Fryxell, M. Zingale, P.
M. Ricker and K. Olson, *"On Heavy Element Enrichment in Classical
Novae,"* ApJ, 602:931-937, Feb. 2004.

C. Alexandru, et al., *"N to Delta electromagnetic transition form
factors from lattice QCD,"* Physical Review D, **69**, 114506, 2004.

C. Alexandrou, et al., *"gamma N -- Delta transition form factors in
quenched and N(F) = 2 QCD,"* Nuclear Physics (Proc. Suppl.) **129-130**,
302, 2004.

J. Amundson, P. Spentzouris, *"[Emittance dilution and halo creation
during the first milliseconds after injection at the Fermilab
Booster,](http://cd-amr.fnal.gov/aas/hb04/hb04_proc_spentzouris.pdf)"*
Proc. 33rd ICFA Advanced Beam Dynamics Workshop on High Intensity & High
Brightness Hadron Beams, Bensheim, Germany, Oct. 2004.

J. Amundson, P. Spentzouris, J. Qiang, R. D. Ryne, A. Adelmann, *"A test
suite of space-charge problems for code benchmarking,"* 9th European
Particle Accelerator Conference (EPAC 2004), Lucerne, Switzerland, July
2004.

A. Andrady, P. J. Aucamo, A. F. Bais, C. L. Ballare, L. O. Bjorn, J. F.
Bornman, M. Caldwell, A. P. Cullen, D. J. Erickson III, F. R. de Gruijl,
D.-P. Hader, M. ilyas, G. Kulandaivelu, H. D. Kumar, J. Longstreth, R.
L. McKenzie, M. Norval, H. H. Redhwi, R. C. Smith, K. R. Solomon, Y.
Takizawa, X. Tang, A. H. Teramura, A. Torikai, J. C. van der Leun, S.
Wilson, R. C. Worrest, and R. G. Zepp, "*Environmental effects of ozone
depletion and its interactions with climate change: Progress Report
2003,"* Photochemical and Photobiological Sciences. **3**, 1-5, 2004.

C. Aubin, et al. (The HPQCD, MILC and UKQCD Collaborations), *"First
determination of the strange and light quark masses from full lattice
QCD*,*"* Physical Review D, **70,** 031504(R), 2004.

C. Aubin, et al. (The MILC Collaboration), *"Light hadrons with improved
staggered quarks: approaching the continuum limit,"* Physical Review D
**70**, 094505, 2004.

C. Aubin, et al. (The MILC Collaboration), *"Light pseudoscalar decay
constants, quark masses, and low energy constants from three-flavor
lattice QCD*,*"* Physical Review D, **70**, 114501, 2004.

C. Aubin, et al. (The MILC Collaboration), *"Pion and kaon physics with
improved staggered quarks*,*"* Nuclear Physics B (Proc. Suppl.),
**129-130**, 227, 2004.

T. Austin, T. Manteuffel, and S. McCormick, *"A robust approach to
minimizing H(div) dominated functionals in an H^1^-conforming finite
element space,"* Journal on Numerical Analysis, Lin. Alg. App. **11**,
p. 115, 2004.

I. Baraffe, A. Heger, and S. E. Woosley, *"Stability of Supernova Ia
Progenitors against Radial Oscillations,"* ApJ, 615:378-382, Nov. 2004.

S. Basak, et al. (The LHPC Collaboration), *"Baryon operators and
spectroscopy in lattice QCD,"* Nuclear Physics (Proc. Suppl.)
**129-130**, 186, 2004.

S. Basak, et al. (The LHPC Collaboration), *"Mass spectrum of N\* and
source optimization*,*"* Nuclear Physics (Proc. Suppl.) **129-130**,
209, 2004.

D. B. Batchelor, E. F. Jaeger, L. A. Berry, E. D'Azevedo, M. D. Carter,
R. W. Harvey, R. J. Dumont, J. R. Myra, A. A. D'Ippolito, D. N. Smithe,
C. K. Phillips, P. T. Bonoli and J. C. Wright, *"Integrated modeling of
wave-plasma interactions in fusion systems,"* Theory of Fusion Plasmas,
Proc. of the Joint Varenna-Lausanne International Workshop Varenna,
Italy, Aug.-Sept. 2004.

M. W. Beall, J. Walsh, M. S. Shephard, *"A comparison of techniques for
geometry access related to mesh generation,"* Engineering with
Computers, 20(3), p. 210-221, 2004.

J. B. Bell, M. S. Day, C. A. Rendleman, S. E. Woosley, and M. A.
Zingale, *"Direct Numerical Simulations of Type Ia Supernovae Flames II:
The Rayleigh-Taylor Instability,"* Astrophysical Journal, **608,** 883,
2004.

J. B. Bell, M. S. Day, C. A. Rendleman, S. E. Woosley, and M. A.
Zingale, *"Direct Numerical Simulations of Type Ia Supernovae Flames I:
The Landau-Darrieus Instability,"* Astrophysical Journal, **606**, 1029,
2004.

J. B. Bell, M. S. Day, C. A. Rendleman, S. E. Woosley, and M. A.
Zingale, *"Adaptive low Mach number simulations of nuclear flame
microphysics,"* Journal of Computational Physics, 195:677-694, April
2004.

J. B. Bell, M. S. Day, J. F. Grcar, and M. J. Lijewski, *"Stochastic
Algorithms for the Analysis of Numerical Flame Simulations,"* Journal of
Computational Physics, **202**, 262, 2004.

S. Belviso, L. Bopp, C. Moulin, J. C. Orr, T. R. Anderson, O. Aumont, S.
Chu, S. Elliott, M. E. Maltrud and R. Simó, *"Comparison of global
climatological maps of sea surface dimethylsulfide,"* Global
Biogeochemical Cycles, **18(**3**)**, GB3013, 2004.

S. J. Benson, L. Curfman McInnes, J. J. Moré and J. Sarich, *"Scalable
Algorithms in Optimization: Computational Experiments,"* AIAA
Multidisciplinary Analysis and Optimization Conference, 2004.

G. J. O. Beran and M. Head-Gordon, *"Extracting dominant pair
correlations from many-body wavefunctions,"* Journal of Chemical
Physics, 121, 78-88, 2004.

C. Bernard, et al. (The MILC Collaboration), *"Quark Loop Effects in
Semileptonic Form Factors for Heavy-Light Mesons*,*"* Nuclear Physics B
(Proc. Suppl.), **129-130**, 364, 2004.

C. Bernard, et al. (The MILC Collaboration), *"The Phase Diagram of High
Temperature QCD with Three Flavors of Improved Staggered Quarks*,*"*
Nuclear Physics B (Proc. Suppl.), **129-130**, 626, 2004.

C. Bernard, et al. (The MILC Collaboration), *"Excited States in
Staggered Meson Propagators*,*"* Nuclear Physics B (Proc. Suppl.),
**129-130**, 230, 2004.

S. Bhowmick, P. Raghavan, L. McInnes, and B. Norris, *"Faster PDE-based
Simulations Using Robust Composite Linear Solvers,"* Future Generation
Computer Systems, The International Journal of Grid Computing: Theory,
Methods and Applications, 20, p. 373-387, 2004.

B. Billeter, C. DeTar, and J. Osborn, *"Topological susceptibility in
staggered fermion chiral perturbation theory,"* Physical Review D,
**70**, 077502, 2004.

L. Bonaventura, and T. D. Ringler, *"Analysis of discrete shallow-water
models on geodesic Delaunay grids with C-type staggering,"* Monthly
Weather Review, **133**, 2351, 2004.

P. T. Bonoli et al., *"Full-wave Electromagnetic Field Simulations in
the Lower-Hybrid Range of Frequencies,"* Bull. American Phys. Soc.
**49**, 325, RI13, 2004.

M. Brezina, R. Falgout, S. MacLachlan, T. Manteuffel, S. McCormick and
J. Ruge, *"[Adaptive Smoothed Aggregation
(αSA)](http://www.llnl.gov/CASC/linear_solvers/pubs/aSA.pdf),"* SIAM
Journal of Scientific Computing, **25,** 1896-1920, 2004.

S. W. Bruenn, "Issues with Core-Collapse Supernova Progenitor Models,"
in Open Issues in Core Collapse Supernova Theory, Proc. of the Institute
for Nuclear Theory, Vol. 14, p. 99, University of Washington, Seattle,
Wash., June 2004.

N. Bucciantini, R. Bandiera, J. M. Blondin, E. Amato, L. Del Zanna,
*"The effects of spin-down on the structure and evolution of pulsar wind
nebulae,"* Astronomy & Astrophysics, 422, 609-619, 2004.

A. Burrows, S. Reddy, and T. A. Thompson, *"Neutrino Opacities in
Nuclear Matter,"* Nuclear Physics A, in press, 2004.

J. R. Burruss, et al., *"Remote Computing on the National Fusion Grid,"*
The 4th IAEA Technical Meeting on Control, Data Acquisition, and Remote
Participation for Fusion Research. Fusion Engineering and Design 71,
251-255, 2004.

L. Bytautas and K. Ruedenberg, *"Correlation Energy Extrapolation
Through Intrinsic Scaling. I,"* Journal of Chemical Physics, **121**,
10905, 2004.

L. Bytautas and K. Ruedenberg, *"Correlation Energy Extrapolation
Through Intrinsic Scaling. II,"* Journal of Chemical Physics, **121**,
10919, 2004.

L. Bytautas and K. Ruedenberg, *"Correlation Energy Extrapolation
Through Intrinsic Scaling. III. Compact Wavefunctions,"* Journal of
Chemical Physics, **121**, 10852, 2004.

A. C. Calder, L. J. Dursi, B. Fryxell, T. Plewa, V. G. Weirs, T. Dupont,
H. F. Robey, R. P. Drake, B. A. Remington, G. Dimonte, J. Hayes, J. M.
Stone, P. M. Ricker, F. X. Timmes, M. Zingale and K. Olson*, "Issues
with Validating an Astrophysical Simulation Code,"* Computing in Science
and Engineering, **6**(5):10, 2004.

C. Y. Cardall, A. O. Razoumov, E. Endeve, A. Mezzacappa, *"The Long
Term: Six-dimensional Core-collapse Supernova Models,"* in Open Issues
in Core Collapse Supernova Theory, Proc. of the Institute for Nuclear
Theory, Vol. 14, p. 196, University of Washington, Seattle, Wash., June
2004.

G. R. Carr, I. L. Carpenter, M. J. Cordery, J. B. Drake, M. W. Ham, F.
M. Hoffman and P. H. Worley, *"Porting and Performance of the Community
Climate System Model (CCSM3) on the Cray X1,"* Proc. of the 11th
Workshop on High Performance Computing in Meteorology, Reading, UK, Oct.
2004.

L. Carrington, N. Wolter, A. Snavely and C. B. Lee, *"Applying an
Automated Framework to Produce Accurate Blind Performance Predictions of
Full-Scale HPC Applications,"* DOD User Group Conference 2004,
Williamsburg, Va., June 2004.

Y. Chen, et al., *"Chiral Logs in Quenched QCD,"* Physical Review D**,
70,** 034502, 2004.

Z. Chen, J. Dongarra, P. Luszczek, and K. Roche, *"LAPACK for Clusters
Project: An Example of Self Adapting Numerical Software,"* Hawaii
International Conference on System Sciences (HICSS-37), Jan. 2004.

S. Chu, M. Maltrud, S. Elliott, J. L. Hernandez and D. J. Erickson III,
*"Ecodynamic and eddy resolving dimethyl sulfide simulations in a global
ocean biogeochemistry/circulation model,"* Earth Interactions, **8**
(11), 1, 2004.

S. Chu, S. Elliott, M. E. Maltrud, F. Chavez and F. Chai, *"Ecodynamics
of multiple Southern Ocean iron enrichments simulated in a global*,
*eddy permitting GCM,"* in Environmental Sciences and Environmental
Computing Vol. **II,** The EnviroComp Institute, 2004.

S. Chu, S. Elliott, M. E. Maltrud, F. Chavez, and F. Chai, *"Southern
Ocean Iron Enrichments Simulated in a global, eddy permitting GCM,"* in
Environmental Sciences and Environmental Computing Vol. **II**, ed. P.
Zannetti, The EnviroComp Institute, 2004.

I.-H. Chung, and J. K. Hollingsworth, *"Using Information from Prior
Runs to Improve Automated Tuning Systems,"* Proc. of ACM/IEEE SC2004
conference, Pittsburgh, Penn., Nov. 2004.

I.-H. Chung, and J. K. Hollingsworth, *"Automated Cluster-Based Web
Service Performance Tuning,"* Proceedings of IEEE Conference on High
Performance Distributed Computing (HPDC), June 2004.

J. P. Colgan, M. S. Pindzola, and N. R. Badnell, *"Dielectronic
recombination data for dynamic finite-density plasmas: V. The Lithium
isoelectronic sequence,"* Astronomy and Astrophysics, **417,** 1183,
2004.

J. P. Colgan and M. S. Pindzola, *"Double photoionization of helium at
high photon energies,"* Journal of Physics B, **37,** 1153, 2004.

D. Crawford, K.-L. Ma, M.-Y. Huang, S. Klasky and S. Ethier,
*"Visualizing Gyrokinetic Simulations,"* Proc. of the IEEE Visualization
2004 conference, Austin, Texas, Oct. 2004.

T. L. Dahlgren, P. T. Devanbu, *"Adaptable Assertion Checking for
Scientific Software Components,"* Proc. of the First International
Workshop on Software Engineering for High Performance Computing System
Applications, Edinburgh, Scotland, UK, p 64-69, May 2004.

D. Datta, R. C. Picu, M. S. Shephard, *"Composite Grid Atomistic
Continuum Method: An adaptive approach to bridge continuum with
atomistic analysis,"* Journal of Multiscale Computational Engineering,
2(3), p. 401-420, 2004.

C. T. H. Davies, et al., *"High-Precision Lattice QCD Confronts
Experiment,"* Physical Review Letters, **92**, 022001, 2004.

T. A. Davis, J. R. Gilbert, S. I. Larimore, and E. G. Ng, *"A column
approximate minimum degree ordering algorithm,"* ACM Transactions of
Mathematical Software **30**, p. 353-376, 2004.

T. A. Davis, J. R. Gilbert, S. I. Larimore, and E. G. Ng, *"Algorithm
836: COLAMD, a column approximate minimum degree ordering algorithm,"*
ACM Transactions of Mathematical Software **30**, p. 377-380, 2004.

D. J. Dean, *"Intersections of Nuclear Physics and Astrophysics,"* in
The Future Astronuclear Physics, A. Jorissen, S. Goriely, M. Rayet, L.
Siers, J. Boffin, eds., EAS Publications Series, p. 175-189, 2004.

H. de Sterck, T. Manteuffel, S. McCormick, and L. Olson, *"Least-squares
finite element methods and algebraic multigrid solvers for linear
hyperbolic PDEs,"* SIAM Journal of Scientific Computing, **26**, 31-54,
2004.

S. Deng et al., *"Plasma wakefield acceleration in self-ionized gas or
plasmas,"* Physical Review E 68, 047401, 2004.

Y. Deng, J. Glimm, J. Davenport, X. Cai, E. Santos, *"Performance models
on QCDOC for molecular dynamics with coulomb potentials,"* International
Journal of High Performance Computing Applications, 18, p. 183-198,
2004.

M. di Pierro et al., *"Properties of charmonium in lattice QCD with 2+1
flavors of improved staggered sea quarks*,*"* Nuclear Physics (Proc.
Suppl.) **129-130**, 340. 2004.

M. di Pierro, et al., *"Ds spectrum and leptonic decays with Fermilab
heavy quarks and improved staggered light quarks,"* Nuclear Physics
(Proc. Suppl.) **129-130**, 328, 2004.

J. B. Drake, P. H. Worley, I. Carpenter, M. Cordery, *"Experience with
the Full CCSM,"* Proc. of the 46th Cray User Group Conference,
Knoxville, TN, May 2004.

M. Dryja, A. Gantner, O. Widlund, and B. I. Wohlmuth, *"Multilevel
Additive Schwarz Preconditioner for Nonconforming Mortar Finite Element
Methods,"* Journal on Numerical Analysis, Math., **12**, 1, 23-38, 2004.

S. Dutta, J. Glimm, J. W. Grove, D. H. Sharp, Y. Zhang, "*Error
comparison in tracked and untracked spherical simulations,"* Computers
and Mathematics with Applications, 48, p. 1733-1747, 2004.

S. Dutta, J. Glimm, J. W. Grove, D. H. Sharp, Y. Zhang, *"Spherical
Richtmyer-Meshkov instability for axisymmetric flow,"* Mathematics and
Computers in Simulations, 65, p. 417-430, 2004.

S. I. Dutta, S. Ratkovic, M. Prakash, *"Photoneutrino process in
astrophysical systems,"* Physical Review D, 69, 023005, 2004.

R. G. Edwards, G. Fleming, D. G. Richards, H. R. Fiebig and The LHPC
Collaboration, *"Lattice QCD and nucleon resonances*,*"* Nuclear Physics
A**, 737**, 167, 2004.

T. H. Dunigan, Jr., J. S. Vetter, and P. H. Worley, *"Performance
Evaluation of the Cray X1 Distributed Shared Memory Architecture,"*
Proc. of IEEE Hot Interconnects, 2004.

S. Elliott, S. Chu, M. Maltrud and A. McPherson, *"Animation of global
marine chlorophyll distributions from fine grid
biogeochemistry/transport modeling,"* in Environmental Sciences and
Environmental Computing Vol. **II** (Edited by P. Zannetti), The
EnviroComp Institute, 2004.

S. Ethier and Z. Lin, *"Porting the 3D gyrokinetic particle-in-cell code
GTC to the NEC SX-6 vector architecture: perspectives and challenges,"*
Computer Physics Communications, **164**, 456, 2004.

R. D. Falgout and P. S. Vassilevski, *"[On Generalizing the AMG
Framework](http://www.llnl.gov/CASC/linear_solvers/pubs/gamg.pdf),"*
SIAM Journal on Numerical Analysis, **42**, p. 1669-1693, 2004.

D. G. Fedorov, R. M. Olson, K. Kitaura, M. S. Gordon, and S. Koseki, *"A
new hierarchical parallelization scheme: Generalized distributed data
interface (GDDI), and an application to the fragment molecular orbital
method (FMO),"* Journal of Computational Chemistry, **25**, 872, 2004.

S. Flanagan, et al., *"A General Purpose Data Analysis Monitoring System
with Case Studies from the National Fusion Grid and the DIII-D MDSplus
between Pulse Analysis System,"* 4th IAEA Technical Meeting on Control,
Data Acquisition, and Remote Participation for Fusion Research, Fusion
Engineering and Design 71, 263-267, 2004.

E. Follana, et al. (The HPQCD Collaboration), *"Improvement and taste
symmetry breaking for staggered quarks*,*"* Nuclear Physics (Proc.
Suppl.) **129-130**, 384, 2004.

N. Folwell, L. Ge, A. Guetz, V. Ivanov, et al., *"Electromagnetic System
Simulation -- Prototyping Through Computation,"* SciDAC PI meeting,
2004.

C. L. Fryer, *"Neutron Star Kicks from Asymmetric Collapse,"* ApJ
Letters, 601:L175-L178, Feb. 2004.

C. L. Fryer, D. E. Holz, and S. A. Hughes, *"Gravitational Waves from
Stellar Collapse: Correlations to Explosion Asymmetries,"* ApJ,
609:288-300, July 2004.

C. L. Fryer and M. S. Warren, *"The Collapse of Rotating Massive Stars
in Three Dimensions,"* American Physics Journal, 601:391-404, Jan. 2004.

L. Ge, L.-Q. Lee, Z. Li, C.-K. Ng, K. Ko, Y. Luo and M. Shephard,
*"Adaptive Mesh Refinement For High Accuracy Wall Loss Determination In
Accelerating Cavity Design,"* Proc. of the Eleventh Biennial IEEE
Conference on Electromagnetic Field Computation, Seoul, Korea, June
2004.

L. Ge, L. Lee, L. Zenghai, L. Ng, C. Ko, K., Y. Luo, M. S. Shephard,
"*Adaptive Mesh Refinement for High Accuracy Wall Loss Determination in
Accelerating Cavity Design,"* IEEE Conf. on Electromagnetic Field
Computations, June 2004.

C. G. R. Geddes, C. Toth, J. van Tilborg, E. Esarey, C. B. Schroeder, D.
Bruhwiler, C. Nieter, J. Cary and W. P. Leemans, *"High-quality electron
beams from a laser wakefield accelerator using plasma-channel guiding,"*
Nature 431, p.538-541, 2004.

J. Glimm, J. W. Grove, Y. Kang, T. Lee, X. Li, D. H. Sharp, Y. Yu, K.
Ye, M. Zhao, *"Statistical riemann problems and a composition law for
errors in numerical solutions of shock physics problems,"* SIAM Journal
on Scientific Computing, 26, p. 666-697, 2004.

J. Glimm, S. Hou, Y. Lee, D. Sharp, K. Ye, *"Sources of uncertainty and
error in the simulation of flow in porous media,"* Comp. and Applied
Mathematics, 23, p. 109-120, 2004.

J. Glimm, H. Jin, Y. Zhang, *"Front tracking for multiphase fluid
mixing,"* Computational Methods in Multiphase Flow II, A. A. Mammoli, C.
A. Brebbia, eds., p. 13-22, WIT Press, Southampton, UK, 2004.

J. N. Goswami, K. K. Marhas, M. Chaussidon, M. Gounelle, B. Meyer,
*"Origin of Short-lived Radionuclides in the Early Solar System*,"
Workshop on Chondrites and the Protoplanetary Disk, p. 9120, 2004.

J. F. Grcar, P. Glarborg, J. B. Bell, M. S. Day, A. Loren, and A. D.
Jenson, *"Effects of Mixing on Ammonia Oxidation in Combustion
Environments at Intermediate Temperatures,"* Proceedings of the
Combustion Institute, **30**:1193, 2004.

L. Grigori and X. S. Li, *"Performance Analysis of Parallel
Right-looking Sparse LU Factorization on Two-dimensional Grids of
Processors,"* Proceedings of the PARA\'04 Workshop on State-of-the art
in Scientific Computing, Springer Lecture Notes in Computer Science,
2004.

Y. Guo, A. Kawano, D. L. Thompson, A. F. Wagner and M. Minkoff,
*"Interpolating Moving Least-Squares Methods for Fitting Potential
Energy Surfaces: Applications to Classical Dynamics Calculations,"*
Journal of Chemical Physics, **121**, 5091-5097, 2004.

A. Gurtler, F. Robicheaux, W. J. van der Zande and L. D. Noordam,
*"Asymmetry in the strong field ionization of Rydberg atoms by few-cycle
pulses,"* Physical Review Letters, 033002, 2004.

A. Gurtler, F. Robicheaux, M. J. J. Vrakking, W. J. van der Zande and L.
D. Noordam, *"Carrier phase dependence in the ionization of Rydberg
atoms by short radio-frequency pulses: a model system for high order
harmonic generation,"* Physical Review Letters, 92, 063901, 2004.

S. W. Hadley, D. J. Erickson III, J. L. Hernandez and S. Thompson,
*"Future U.S. energy use for 2000-2025 as computed with temperatures
from a global climate prediction model and energy demand model,"* Proc.
of the 24th Annual North American Conference of the USAEE/IAEE, United
States Association for Energy Economics, Cleveland, OH, 2004.

P. T. Haertel, D. A. Randall and T. G. Jensen, *"Toward a Lagrangian
ocean model: Simulating upwelling in a large lake using slippery
sacks,"* Monthly Weather Review, **132**, 66, 2004.

A. T. Hagler, et al. (The LHPC Collaboration), *"Transverse structure of
nucleon parton distributions from lattice QCD*,*"* Physical Review
Letters, **93**, 112001, 2004.

W. C. Haxton, *"Supernova Neutrino-Nucleus Physics and the r-Process,"*
The r-Process: The Astrophysical Origin of the Heavy Elements and
Related Rare Isotope Accelerator Physics, Proc. of the First
Argonne/MSU/JINA/INT R/A Workshop, p. 73, World Scientific, 2004.

Y. He and C. Ding, *"MPI and OpenMP Paradigms on Cluster of SMP
Architectures*: *the Vacancy Tracking Algorithm for Multi-Dimensional
Array Transpose,"* Journal of Parallel and Distributed Computing
Practice, **2**, 5, 2004.

E. D. Held, J. D. Callen, C. C. Hegna, C. R. Sovinec, T. A. Gianakon, S.
E. Kruger, *"Nonlocal closures for plasma fluid simulations,"* Physics
of Plasmas **11,** 2419, 2004.

J. J. Heys, C. G. DeGroff, T. Manteuffel, S. McCormick, and H. Tufo,
*"Modeling 3-d compliant blood flow with FOSLS,"* Biomed Sci Instrum.
**40**, p. 193-9, 2004.

J. Heys, T. Manteuffel, S. McCormick, and L. Olson, *"Algebraic
multigrid (AMG) for higher-order finite elements,"* Journal of
Computational Physics **195**, p. 560-575, 2004.

J. Heys, T. Manteuffel, S. McCormick, and J. Ruge, *"First-order system
least squares (FOSLS) for coupled fluid-elasticity problems,"* Journal
of Computational Physics **195**, p. 560-575, 2004.

D. Higdon, M. Kennedy, J. C. Cavendish, J. A. Cafeo, R. D. Ryne,
*"Combining Field Data and Computer Simulations for Calibration and
Prediction,"* SIAM Journal on Scientific Computing, **26**, 2, p.
448-466, March 2004.

W. R. Hix, O. E. B. Messer, A. Mezzacappa, *"The interplay between
nuclear electron capture and fluid dynamics in core collapse
supernovae,"* in Cosmic explosions in Three Dimensions, P. Hoflich, P.
Kumar, J. C. Wheeler, eds., p. 307, Cambridge University Press, 2004.

F. M. Hoffman, M. Vertenstein, H. Kitabata, J. B. White III, P. H.
Worley, J. B. Drake, M. Cordery, *"Adventures in Vectorizing the
Community Land Model,"* Proc. of the 46th Cray User Group Conference,
Knoxville, TN, May 2004.

I. Hofmann, G. Franchetti, J. Qiang, R. D. Ryne*, "Dynamical Effects of
the Montague Resonance,"* Proc. EPAC 2004, Lucerne, Switzerland, p.
1960, 2004.

I. Hofmann, G. Franchetti, M. Giovannozzi, M. Martini, E. Metral, J.
Qiang, R. D. Ryne, *"Simulation aspects of the code benchmarking based
on the CERN-PS Montague-resonance experiment,"* Proc. 33rd ICFA Advanced
Beam Dynamics Workshop on High Intensity & High Brightness Hadron Beams,
Bensheim, Germany, Oct. 2004.

D. J. Holmgren, P. Mackenzie, A. Singh and J. Somine, *"Lattice QCD
clusters at Fermilab,"* Computing in High-Energy Physics (CHEP '04),
Interlaken, Switzerland, Sept. 2004.

U. Hwang, J. M. Laming, C. Badenes, F. Berendse, J. Blondin, D. Cio, T.
DeLaney, D. Dewey, R. Fesen, K. A. Flanagan, C. L. Fryer, P. Ghavamian,
J. P. Hughes, J. A. Morse, P. P. Plucinsky, R. Petre, M. Pohl, L.
Rudnick, R. Sankrit, P. O. Slane, R. K. Smith, J. Vink, and J. S.
Warren, *"A Million Second Chandra View of Cassiopeia A.,"* ApJ Letters,
615, L117-L120, Nov. 2004.

A. V. Ilin, F. R. Chang-Diaz, J. P. Squire, A. G. Tarditi, M. D. Carter,
*"Improved simulation of the ICRF waves in the VASIMR plasma,"*
Proceedings of the 18^th^ International conference on the numerical
Simulation of Plasmas, Computer Physics Communications **164**, 251,
2004.

E.-J. Im, I. Bustany, C. Ashcraft, J. Demmel and K. Yelick, *"Toward
automatic performance tuning of matrix triple products based on matrix
structure,"* PARA\'04 Workshop on State-of-the-art in Scientific
Computing, Copenhagen, Denmark, June 2004.

E.-J. Im, K. A. Yelick and R. Vuduc, *"SPARSITY: An Optimization
Framework for Sparse Matrix Kernels,"* International Journal of High
Performance Computing Applications, **18** (1)**,** p. 135-158, Feb.
2004.

J. P. Iorio, P. B. Duffy, B. Govindasamy, S. L. Thompson, M.
Khairoutdinov and D. A. Randall, *"Effects of model resolution and
subgrid-scale physics on the simulation of daily precipitation in the
continental United States,"* Climate Dynamics, **23**, 243, 2004.

L. Ives, T. Bui, W. Vogler, A. Bauer, M. Shephard, "*Operation and
performance of a 3D finite element charged particle code with adaptive
meshing Source,"* 5th IEEE Int. Vacuum Electronics Conf. (IVEC 2004), p.
316-317, 2004.

C. Jablonowski, *"Adaptive grids in weather and climate modeling*,"
University of Michigan thesis, 2004.

C. Jablonowski, M. Herzog, J. E. Penner, R. Oehmke, Q. F. Stout, B. van
Leer, *"Adaptive grids for weather and climate models,"* ECMWF Seminar
Proceedings on Recent Developments in Numerical Methods for Atmospheric
and Ocean Modelling, Reading, UK, Sept. 2004.

S. C. Jardin, *"A triangular finite element with first-derivative
continuity applied to fusion MHD applications,"* Journal of
Computational Physics **200,** 133, 2004.

G. C. Jordan, B. S. Meyer, *"Nucleosynthesis in Fast Expansions of
High-Entropy, Proton-rich Matter,"* Astrophysical Journal Letters, 617,
L131-L134, 2004.

G. C. Jordan, B. S. Meyer, *"Nuclear Reaction Rates and the Production
of Light p-Process Isotopes in Fast Expansions of Proton-Rich Matter,"*
The r-Process: The Astrophysical Origin of the Heavy Elements and
Related Rare Isotope Accelerator Physics, Proc. of the First
Argonne/MSU/JINA/INT R/A Workshop, p. 157, World Scientific, 2004.

R. Katz, M. Knepley and B. Smith, *"Developing a Geodynamics Simulation
with PETSc,"* in Numerical Solution of Partial Differential Equations on
Parallel Computers, A. M. Bruaset, P. Bjorstad, and A. Tveito, eds., p.
413, Springer-Verlag, 2004.

S. R. Kawa, D. J. Erickson III, S. Pawson, and Z. Zhu, *"Global CO~2~
transport simulations using meteorological data from the NASA data
assimilation system,"* Journal of Geophysical Research, **109.** D18,
2004.

K. Keahey et al., *"Agreement Based Interactions for Experimental
Science,"* Proc. of Europar 2004 conference, 2004.

K. Keahey, et al., *"Grids for Experimental Science: The Virtual Control
Room,"* Proc. of the CLADE 2004 Workshop, 2004.

K. Keahey, et al., *"Fine-Grained Authorization for Job Execution in the
Grid: Design and Implementation,"* Concurrency and Computation: Practice
and Experience 16 (5), 477-488, 2004.

J. P. Kenny, S. J. Benson, Y. Alexeev, J. Sarich, C. L. Janssen, L.
Curfman McInnes, M. Krishnan, J. Nieplocha, E. Jurrus, C. Fahlstrom and
T. L. Windus, *"Component-Based Integration of Chemistry and
Optimization Software,"* Journal of Computational Chemistry, 25,
1717-1725, 2004.

M. E. Kowalski, C.-K. Ng, L.-Q. Lee, Z. Li and K. Ko, *"Time-Domain
Calculation of Guided Electromagnetic Wave Propagation on Unstructured
Grids,"* U. S. National Committee of the International Union of Radio
Science (URSI) National Radio Science Meeting, Boulder, Colo., Jan.
2004.

B. C. Lee, R. Vuduc, J. Demmel and K. Yelick, *"Performance Models for
Evaluation and Automatic Tuning of Symmetric Sparse Matrix-Vector
Multiply,"* International Conference on Parallel Processing, Montreal,
Quebec, Canada, Aug. 2004.

L.-Q. Lee, L. Ge, M. Kowalski, Z. Li, C.-K. Ng, G. Schussman, M. Wolf
and K. Ko, *"Solving Large Sparse Linear Systems In End-To-End
Accelerator Structure Simulations,"* Proc. of the 18th International
Parallel and Distributed Processing Symposium, Santa Fe, NM, April 2004.

T. Lee, Y. Yu, M. Zhao, J. Glimm, X. Li, K. Ye, *"Error analysis of
composite shock interaction problems,"* Proc. of PMC04 Conference, 2004.

W. W. Lee, *"Theoretical and numerical properties of a gyrokinetic
plasma: implications on transport scale simulation,"* Computer Physics
Communications, **164**, 244, 2004.

W. W. Lee, *"Steady State Global Simulations of Microturbulence,"*
American Physical Society Division of Plasma Physics, Savannah, Ga.,
Nov. 2004.

J. Li and O. Widlund, *"FETI\--DP, BDDC, and Block Cholesky Methods,"*
International Journal on Numerical Analysis, Methods Engineering, 2004.

N. Li, Y. Saad and E. Chow*, "[Crout Versions of ILU for General Sparse
Matrices](http://www.llnl.gov/CASC/people/chow/pubs/crout.ps),"* SIAM
Journal of Scientific Computing, **25**, p. 716-728, 2004.

X. Li, J. F. Remacle, N. Chevaugeon, M. S. Shephard, *"Anisotropic Mesh
Gradation Control,"* 13th International Meshing Roundtable, Sandia
National Laboratories, p. 401-412, 2004.

Z. Li, N. T. Folwell, L. Ge, A. Guetz, V. Ivanov, M. Kowalski, L.-Q.
Lee, C.-K. Ng, G. Schussman, R. Uplenchwar, M. Wolf and K. Ko, *"X-Band
Linear Collider R&D In Accelerating Structures Through Advanced
Computing,"* Proc. of the 9th European Particle Accelerator Conference,
Lucerne, Switzerland, July 2004.

Z. Li, N. Folwell, L. Ge, A. Guetz, V. Ivanov, M. Kowalski, L.-Q. Lee,
C.-K. Ng, G. Schussman, R. Uplenchwar, M. Wolf, L. Xiao and K. Ko,
*"High Performance Computing In Accelerator Structure Design And
Analysis,"* Proc. of the 8th International Computational Accelerator
Physics Conference, St. Petersburg, Russia, June 2004.

M. Liebendoerfer, O. E. B. Messer, A. Mezzacappa, S. W. Bruenn, C. Y.
Cardall, F.-K. Thielemann, *"A Finite Difference Representation of
Neutrino Radiation Hydrodynamics in Spherically Symmetric General
Relativistic Spacetime,"* Astrophysical Journal Supplement Series, 150,
263-316, 2004.

Y. Lin, S. Wukitch. P. Bonoli, E. Nelson-Melby, M. Porkolab, J. C.
Wright, N. Basse, A. E. Hubbard, J. Irby, L. Lin, E. S. Marmar, A.
Mazurenko, D. Mossessian, A. Parisot, J. Rice, S. Wolfe, C. K. Phillips,
G. Schilling, J. R. Wilson, P. Phillips and A. Lynn, *"Investigation of
Ion Cyclotron Range of Frequencies Mode Conversion at the Ion-Ion Hybrid
Layer in Alcator C-Mod,"* Physics of Plasmas **11** (5) 2466-2472, 2004.

Z. Lin and T. S. Hahm, *"Turbulence spreading and transport scaling in
global gyrokinetic particle simulations,"* Physics of Plasmas, **11**,
1099, 2004.

Z. Lin et al., *"Electron Thermal Transport in Tokamaks: ETG or TEM
Turbulence?"* International Atomic Energy Agency Conference,
IAEA-CN/TH/8-4, Vilamoura, Portugal, 2004.

W. Lipscomb and T. D. Ringler, *"An incremental remapping transport
scheme on a spherical geodesic grid,"* Monthly Weather Review, **133**,
2335, 2004.

E. Livne, A. Burrows, R. Walder, I. Lichtenstadt and T. A. Thompson,
*"Two-dimensional, Time-dependent, Multigroup, Multiangle Radiation
Hydrodynamics Test Simulation in the Core-Collapse Supernova Context,"*
Astrophysical Journal, 609:277-287, July 2004.

S. D. Loch, C. J. Fontes, J. P. Colgan, M. S. Pindzola, C. P. Ballance,
D. C. Griffin, M. G. O'Mullane and H. P. Summers, *"A
collisional-radiative study of lithium plasmas,"* Physical Review E, 69,
066405, 2004.

C. Lu and D. Reed, *"Assessing Fault Sensitivity in MPI Applications,"*
Proc. of the ACM/IEEE SC2004 conference, Pittsburgh, Penn., Nov. 2004.

X. J. Luo, M. S. Shephard, R. M. O'Bara, R. Nastasia, M. W. Beall,
"*Automatic p-version mesh generation for curved domains,"* Book of
Abstracts: ICOSAHOM 4004, Brown University, June, 2004.

X. J. Luo, M. S. Shephard, R. M. O'Bara, R. Nastasia, M. W. Beall.,
*"Automatic p-version mesh generation for curved domains,"* Engineering
with Computers, 20(3), p. 273-285, 2004.

K.-L. Ma and E. Lum*, "Techniques for Visualizing Time-Varying Volume
Data,"* in Visualization Handbook, C. Hansen and C. Johnston, eds.,
Academic Press, Oct. 2004.

K.-L. Ma, G. Schussman and B. Wilson, *"Visualization for Computational
Accelerator Physics,"* in Visualization Handbook, C. Hansen and C.
Johnston, eds., Academic Press, Oct. 2004.

H. MacMillan, T. Manteuffel and S. McCormick, *"First-order system least
squares and electrical impedance tomography,"* SIAM Journal on Numerical
Analysis, **42**, p. 461-483, 2004.

G. Mahinthakumar, M. Sayeed, J. Blondin, P. Worley, W. Hix and A.
Mezzacappa, *"Performance Evaluation and Modeling of a Parallel
Astrophysics Application,"* Proc. of the High Performance Computing
Symposium 2004, The Society for Modeling and Simulation International,
Arlington, Va., 2004.

G. G. Maisuradze, A. Kawano, D. L. Thompson, A. F. Wagner, and M.
Minkoff, *"Interpolating Moving Least-Squares Methods for Fitting
Potential Energy Surfaces: Analysis of an Application to a
Six-Dimensional System,"* Journal of Chemical Physics, **121**,
10329-10338, 2004.

G. Martinez-Pinedo, K. Langanke, J. M. Sampaio, D. J. Dean, W. R. Hix,
O. E. B. Messer, A. Mezzacappa, M. Liebendorfer, H.-T. Janka, M. Rampp,
*"Weak Interaction Processes in Core-Collapse Supernovae,"* IAU Colloq.
192: Cosmic Explosions, On the 10th Anniversary of SN1993J, p. 321,
2005.

N. Mathur, et al., *"A Study of Pentaquarks on the Lattice with Overlap
Fermions,"* Physical Review D, **70,** 074508, 2004.

B. S. Lee McCormick, B. Philip, and D. Quinlan, *"Asynchronous fast
adaptive composite-grid methods for elliptic problems: theoretical
foundations,"* SIAM Journal on Numerical Analysis, **42**, p. 130-152,
2004.

P. McCorquodale, P. Colella, D. P. Grote, J.-L. Vay, *"A node-centered
local refinement algorithm for Poisson\'s equation in complex
geometries,"* Journal of Computational Physics, **201**, p. 34-60, 2004.

E. Métral, C. Carli, M. Giovannozzi, M. Martini, R. R. Steerenberg, G.
Franchetti, I. Hofmann, J. Qiang, R. D. Ryne, *"Intensity Dependent
Emittance Transfer Studies at the CERN Proton Synchrotron,"* Proc. EPAC
2004, Lucerne, Switzerland, p. 1894, 2004.

E. Métral, M. Giovannozzi, M. Martini, R. R. Steerenberg, G. Franchetti,
I. Hofmann, J. Qiang, R. D. Ryne, *"Space-Charge Experiments at the CERN
Proton Synchrotron,"* Proc. 33rd ICFA Advanced Beam Dynamics Workshop on
High Intensity & High Brightness Hadron Beams, Bensheim, Germany, Oct.,
2004.

B. S. Meyer, *"Synthesis of Short-lived Radioactivities in a Massive
Star,"* ASP Conf. Ser. 341: Chondrites and the Protoplanetary Disk, p.
515, 2005.

B. S. Meyer, "*Online Tools for Astronomy and Cosmochemistry,"* 36th
Annual Lunar and Planetary Science Conference, p. 1457, 2005.

B. S. Meyer, *"Nucleosynthesis of Short-lived Radioactivities in Massive
Stars,"* Workshop on Chondrites and the Protoplanetary Disk, p. 9089,
2004.

P. A. Milne, A. L. Hungerford, C. L. Fryer, T. M. Evans, T. J. Urbatsch,
S. E. Boggs, J. Isern, E. Bravo, A. Hirschmann, S. Kumagai, P. A. Pinto,
and L.-S. The, *"Unified One-Dimensional Simulations of Gamma-Ray Line
Emission from Type Ia Supernovae,"* Astrophysical Journal,
613:1101-1119, Oct. 2004.

P. Mucci, J. Dongarra, R. Kufrin, S. Moore, F. Song, F. Wolf,
*"Automating the Large-Scale Collection and Analysis of Performance,"*
Proc. of the 5th LCI International Conference on Linux Clusters: The HPC
Revolution, Austin, Texas, May 2004.

P. Muggli, B. E. Blue, C. E. Clayton, S. Deng, F.-J. Decker, M. J.
Hogan, C. Huang, R. Iverson, C. Joshi, T. C. Katsouleas, S. Lee, W. Lu,
K. A. Marsh, W. B. Mori, C. L. O\'Connell, P. Raimondi, R. Siemann, and
D. Walz, *"Meter-Scale Plasma-Wakefield Accelerator Driven by a Matched
Electron Beam,"* Physical Review Special Topics-Accelerators and Beams
**93**, 014802, 2004.

J. W. Murphy, A. Burrows and A. Heger, *"Pulsational Analysis of the
Cores of Massive Stars and Its Relevance to Pulsar Kicks,"*
Astrophysical Journal, 615:460-474, Nov. 2004.

J. D. Myers, T. C. Allison, S. Bittner, D. Didier, M. Frenklach, W. H.
Green, Jr., Y.-L. Ho, J. Hewson, W. Koegler, C. Lansing, D. Leahy, M.
Lee, R. McCoy, M. Minkoff, S. Nijsure, G. von Laszewski, D. Montoya, L.
Oluwole, C. Pancerella, R. Pinzon, W. Pitz, L. A. Rahn, B. Ruscic, K.
Schuchardt, E. Stephan, A. Wagner, T. Windus, C. Yang, *"A collaborative
informatics infrastructure for multi-scale science,"* Challenges of
Large Applications in Distributed Environments (CLADE) Workshop,
Honolulu, Hawaii, June 2004.

J. R. Myra, L. A. Berry, D. A. D'Ippolito, E. F. Jaeger, *"Nonlinear
Fluxes and Forces from Radio-Frequency Waves with Application to Driven
Flows in Tokamaks,"* Physics of Plasmas **11**, 1786, 2004.

D. Narayan, R. Bradshaw, A. Lusk and E. Lusk, *"MPI cluster system
software,"* Recent Advances in Parallel Virtual Machine and Message
Passing Interface*,* Lecture Notes in Computer Science, 3241, p.
277-286. Springer-Verlag, 2004.

D. Narayan, R. Bradshaw, A. Lusk, E. Lusk and R. Butler,
*"Component-based cluster systems software architecture: A case study,"*
Proc. of the 6th IEEE International Conference on Cluster Computing
(CLUSTER04), p. 319-326, IEEE Computer Society, 2004.

J. W. Negele, et al. (The LHPC Collaboration), *"Insight into nucleon
structure from generalized parton distributions,"* Nuclear Physics
(Proc. Suppl.) **129-130**, 910, 2004.

J. W. Negele, et al., *"Insight into nucleon structure from lattice
calculations of moments of parton and generalized parton
distributions,"* Nuclear Physics (Proc. Suppl.) **128**, 170, 2004.

J. W. Negele, *"What we are learning about the quark structure of
hadrons from lattice QCD,"* 3rd International Symposium on the
Gerasimov-Drell-Hearn Sum Rule and its Extensions (GDH 2004), Norfolk,
Virginia, June 2004.

C.-K. Ng, N. Folwell, A. Guetz, V. Ivanov, L.-Q. Lee, Z. Li, G.
Schussman and K. Ko*,* *"Simulating Dark Current In Nlc Structures,"*
Proc. of the 8th International Computational Accelerator Physics
Conference, St. Petersburg, Russia, June 2004.

M. A. Nobes and H. D. Trottier, *"Progress in automated perturbation
theory for heavy quark physics,"* Nuclear Physics (Proc. Suppl.)
**129-130**, 355, 2004.

B. Norris, J. Ray, R. C. Armstrong, L. C. McInnes, D. E. Bernholdt, W.
R. Elwasif, A. D. Malony and S. Shende, *"Computational quality of
service for scientific components,"* Proc. of the International
Symposium on Component-Based Software Engineering (CBSE7), Edinburgh,
Scotland, May 2004.

K. Ohmi, M. Tawada, Y. Cai, S. Kamada, K. Oide, J. Qiang, *"Beam-beam
limit in e+e- circular colliders,"* Physical Review Letters **92**,
214801, 2004.

K. Ohmi, M. Tawada, Y. Cai, S. Kamada, K. Oide, and J. Qiang,
*"Luminosity limit due to the beam-beam interactions with or without
crossing angle,"* Physical Review ST Accel. Beams, vol **7**, 104401,
2004.

C. D. Ott, A. Burrows, E. Livne and R. Walder, *"Gravitational Waves
from Axisymmetric, Rotating Stellar Core Collapse,"* Astrophysical
Journal, 600:834-864, Jan. 2004.

S. Ovtchinnikov and X.-C. Cai, *"One-level Newton-Krylov-Schwarz
algorithm for unsteady nonlinear radiation diffusion problem,"*
Numerical Linear Alg. Applic., 11, 867-881, 2004.

P. P. Pebay, H. N. Najm, and J. Pousin, *"A Non-Split Projection
Strategy for Low Mach Number Reacting Flow,"* International Journal of
Multiscale Computational Eng*.*, **2**(3):445-460, Aug. 2004.

P. Petreczky and K. Petrov, *"Free energy of a static quark anti-quark
pair and the renormalized Polyakov loop in three flavor QCD,"* Physical
Review D, **70**, 054503, 2004.

M. Prakash, et al., *"Neutrino Processes in Supernovae and Neutron Stars
in Their Infancy and Old Age,"* in Compact Stars: The Quest for New
States of Dense Matter, Proc. of the KIAS-APTCP International Symposium
on Astro-Hadron Physics, Seoul, Korea, p. 476, 2004.

J. Pruet, R. Surman and G. C. McLaughlin, *"On the Contribution of
Gamma-Ray Bursts to the Galactic Inventory of Some Intermediate-Mass
Nuclei,"* Astrophysical Journal Letters, 602:L101-L104, Feb. 2004.

J. Pruet, T. A. Thompson and R. D. Hoffman, *"Nucleosynthesis in
Outflows from the Inner Regions of Collapsars,"* Astrophysical Journal,
606:1006-1018, May 2004.

J. Qiang, M. Furman and R. Ryne, *"A Parallel Particle-In-Cell Model for
Beam-Beam Interactions in High Energy Ring Colliders,"* Journal of
Computational Physics vol. **198**, 278, 2004.

J. Qiang and R. Gluckstern, *"Three-Dimensional Poisson Solver for a
Charged Beam with Large Aspect Ratio in a Conducting Pipe,"* Computer
Physics Communications, **160**, 120, 2004.

J. Qiang, R. D. Ryne, I. Hofmann, *"Space-charge driven emittance growth
in a 3D mismatched anisotropic beam,"* Physical Review Letters, **92**,
174801, 2004.

J. Qiang, *"Halo formation due to beam-beam interactions of beams
optically mismatched at injection,"* Physical Review ST Accel. Beams,
vol **7**, 031001, 2004.

J. Qiang, *"Strong-strong beam-beam simulation on parallel computer,"*
ICFA Beam Dynamics Newsletter, No. **34**, p.19-26, 2004.

D. Quinlan, M. Schordan, Q. Yi and A. Saebjornsen, *"Classification and
Utilization of Abstractions for Optimization,"* First International
Symposium on Leveraging Applications of Formal Methods, Paphos, Cyprus,
Oct. 2004.

 

D. A. Randall, *"The new CSU dynamical core," Seminar on Recent
Developments in Numerical Methods of Atmosphere and Ocean Modeling,"*
European Centre for Mid-Range Weather Forecasting, UK, Sept. 2004.

D. A. Randall and W. H. Schubert, *"Dreams of a stratocumulus sleeper,"*
Atmospheric Turbulence and Mesoscale Meteorology, E. Fedorovich, R.
Rotuno and G. Stevens, eds., p. 71, Cambridge University Press, 2004.

K. Robinson, L. J. Dursi, P. M. Ricker, R. Rosner, A. C. Calder, M.
Zingale, J. W. Truran, T. Linde, A. Caceres, B. Fryxell, K. Olson, K.
Riley, A. Siegel and N. Vladimirova, *"Morphology of Rising Hydrodynamic
and Magnetohydrodynamic Bubbles from Numerical Simulations,"*
Astrophysical Journal, 601:621-643, Feb. 2004.

A. L. Rosenberg, J. E. Menard, J. R. Wilson, S. Medley, R. Andre, D.
Darrow, R. Dumont, B. P. LeBlanc, C. K. Phillips, M. Redi, T. K. Mau, E.
F. Jaeger, P. M. Ryan, D. W. Swain, R. W. Harvey, J. Egedal and the NSTX
Team, *"Fast Ion Absorption of the High Harmonic Fast Wave in the
National Spherical Torus Experiment,"* Physics of Plasmas **11**, 2441,
2004.

B. Ruscic, *"Active Thermochemical Table,"* in 2005 Yearbook of Science
and Technology, an annual update to the McGraw-Hill Encyclopedia of
Science and Technology, McGraw-Hill, New York, 2004.

B. Ruscic, R. E. Pinzon, M. L. Morton, G. von Laszewski, S. Bittner, S.
G. Nijsure, K. A. Amin, M. Minkoff, A. F. Wagner. 2004, *"Introduction
to active thermochemical tables: Several "key" enthalpies of formation
revisited,"* Journal of Physical Chemistry A, **108**:9979-9997, 2004.

R. S. Samtaney, S. Jardin, P. Colella, D. F. Martin, *"3D adaptive mesh
refinement simulations of pellet injection in tokamaks,"* Computer
Physics Communications **164** 1-3 220, 2004.

A. R. Sanderson, et al., *"Display of Vector Fields Using a
Reaction-Diffusion Model,"* Proc. of the 2004 IEEE Visualization
Conference, 115-122, 2004.

D. P. Schissel, *"The National Fusion Collaboratory Project,"* Proc. of
the 2004 DOE SciDAC PI Meeting, 2004.

D. P. Schissel, *"The National Fusion Collaboratory Project: Applying
Grid Technology for Magnetic Fusion Research,"* Proc. of the Workshop on
Case Studies on Grid Applications at GGF10, 2004.

D. P. Schissel, et al., *"Building the U.S. National Fusion Grid:
Results from the National Fusion Collaboratory Project,"* The 4th IAEA
Technical Meeting on Control, Data Acquisition, and Remote Participation
for Fusion Research. Fusion Engineering and Design **71**, 245-250,
2004.

W. Schroers, et al. (The LHPC Collaboration), *"Moments of nucleon
spin-dependent generalized parton distributions*,*"* Nuclear Physics
(Proc. Suppl.) **129-130**, 907, 2004.

W. H. Schubert, *"Generalization of Ertel\'s potential vorticity to a
moist atmosphere,"* Meteorologische Zeitschrift, **13**, (Hans Ertel
Special Issue), 465, 2004.

G. Schussman and K.-L. Ma, *"Anisotropic Volume Rendering for Extremely
Dense, Thin Line Data,"* Proc. of the IEEE Visualization 2004
Conference, Austin, Texas, Oct. 2004.

S. L. Scott, C. B. Leangsuksun, T. Roa, J. Xu, and R. Libby,
*"Experiments and Analysis towards effective cluster management
system,"* 2004 High Availability and Performance Workshop (HAPCW), Santa
Fe, NM, Oct. 2004.

S. L. Scott, C. Leangsuksun, T. Lui and R. Libby, *"HA-OSCAR Release 1.0
Beta: Unleashing HA-Beowulf,"* Proc.of 2^nd^ Annual OSCAR Symposium,
Winnipeg, Manitoba Canada, May 2004.

S. L. Scott, I. Haddad and C. Leangsuksun, *"HA-OSCAR: Towards Highly
Available Linux Clusters,"* Linux World Magazine, **2**, 3, March 2004.

M. S. Shephard, M. W. Beall, R. M. O'Bara, B. E. Webster, *"Toward
simulation-based design,"* Finite Elements in Analysis and Design, 40,
p. 1575-1598, 2004.

M. S. Shephard, M. W. Beall, B. E. Webster, *"Supporting Simulations to
Guide Engineering Design,"* AIAA-2004-4448, AIAA, Richmond, Va., 2004.

J. Shigemitsu, et al. (The HPQCD collaboration), *"Heavy-light Meson
Semileptonic Decays with Staggered Light Quarks*,*"* Nuclear Physics
(Proc. Suppl.) **129-130**, 331, 2004.

L. O. Silva et al., *"Proton shock acceleration in laser-plasma
interactions,"* Physical Review Letters, 92, 015002, 2004.

F. Song, F. Wolf, N. Bhatia, J. Dongarra, S. Moore, *"An Algebra for
Cross-Experiment Performance Analysis,"* 2004 International Conference
on Parallel Processing (ICCP-04), Montreal, Quebec, Canada, Aug. 2004.

C. R. Sovinec, A. H. Glasser, D. C. Barnes, T. A. Gianakon, R. A. Nebel,
S. E. Kruger, D. D. Schnack, S. J. Plimpton, A. Tarditi, M. S. Chu and
the NIMROD Team, *"Nonlinear magnetohydrodynamics with high-order finite
elements,"* Journal Of Computational Physics **195,** 355, 2004.

H. R. Strauss, A. Pletzer, W. Park, S. Jardin, J. Breslau, and L.
Sugiyama*, "MHD simulations with resistive wall and magnetic
separatrix,"* Computer Physics Communications **164,** 1-3 40-45, 2004.

H. R. Strauss, L. Sugiyama, G. Y. Fu, W. Park, J. Breslau, *"Simulation
of two fluid and energetic particle effects in stellarators,"* Nuclear
Fusion **44,** 9, 1008-1014, 2004.

M. M. Strout and P. D. Hovland, *"Metrics and Models for Reordering
Transformations,"* Proc. of the Second ACM SIGPLAN Workshop on Memory
System Performance (MSP), June 2004.

 

M. M. Strout and P. D. Hovland, *"Metrics and Models for Reordering
Transformations*,*"* Proc. of the Second ACM SIGPLAN Workshop on Memory
System Performance (MSP), June 2004.

F. D. Swesty, E. S. Myra, *"Advances in Multi-Dimensional Simulation of
Core-Collapse Supernovae,"* in Open Issues in Core Collapse Supernova
Theory, Proc. of the Institute for Nuclear Theory, Vol. 14, p. 176,
University of Washington, Seattle, Wash., June 2004.

T. J. Tautges, "MOAB-SD: Integrated Structured and Unstructured Mesh
Representation," Engineering With Computers, 20:286-293, 2004.

S. Thompson, B. Govindasamy, A. Mirin, K. Caldeira, C. Delire, J.
Milovich, M. Wickett and D. J. Erickson III, *"Quantifying the effects
of CO2-fertilized vegetation on future global climate and carbon
dynamics,"* Geophysical Research Letters, **31**, L23211, 2004.

M. M. Tikir, J. K. Hollingsworth, *"Using Hardware Counters to
Automatically Improve Memory Performance,"* Proc. of ACM/IEEE SC2004
conference, Pittsburgh, Penn., Nov. 2004.

 

J. L. Tilson, C. Naleway, M. Seth, R. Shepard, A. F. Wagner, and W. C.
Ermler, *"An Ab Initio Study of AmCl^+^: f-f Spectroscopy and Chemical
Binding,"* Journal of Chemical Physics, **121**, 5661-5675, 2004.

A. Toselli and O. Widlund, *"Domain Decomposition Methods - Algorithms
and Theory,"* Springer Series in Computational Mathematics, **34**, Oct.
2004.

H. D. Trottier, *"Higher-order perturbation theory for highly-improved
actions,"* Nuclear Physics (Proc. Suppl.) **129-130**, 142, 2004.

F. S. Tsung et al., *"Near-GeV-energy laser-wakefield acceleration of
self-injected electrons in a centimeter-scale channel"* Physical Review
Letters 93, 185002, 2004.

S. Vadlamani, S. E. Parker, Y. Chen, *"The Particle-Continuum method: an
algorithmic unification of particle-in-cell and continuum methods,"*
Computer Physics Communications, **164**, 209, 2004.

J.-L. Vay, P. Colella, J. W. Kwan, P. McCorquodale, D. B. Serafini, A.
Friedman, D. P. Grote, G. Westenskow, J. C. Adam, A. Héron and I. Haber,
*"Application of adaptive mesh refinement to particle-in-cell
simulations of plasmas and beams,"* Physics of Plasmas 11, 2928, 2004.

J-L. Vay, P. Colella, A. Friedman, D. P. Grote, P. McCorquodale, D. B.
Serafini, *"Implementations of mesh refinement schemes for
particle-in-cell plasma simulations,"* Computer Physics Communications
**164,** p. 297-305, 2004.

M. Vertenstein, K. Oleson, S. Levis, and F. M. Hoffman, *"Community Land
Model Version 3.0 (CLM3.0) User\'s Guide,"* National Center for
Atmospheric Research, June 2004.

R. Vuduc, J. W. Demmel and J. A. Bilmes*, "Statistical Models for
Empirical Search-Based Performance Tuning,"* International Journal of
High Performance Computing Applications, **18** (1), p. 65-94, February
2004.

G. Wallace, et al., *"Automatic* *Alignment of Tiled Displays for a
Desktop Environment,"* Journal of Software. **15**(12): 1776-1786, Dec.
2004.

W. X. Wang, et al., *"Global delta-f particle simulation of neoclassical
transport and ambipolar electric field in general geometry,"* Computer
Physics Communications, **164**, 178, 2004.

T. P. Wangler, C. K. Allen, K. C. D. Chan, P. L. Colestock, K. R.
Crandall, R. W. Garnett, J. D. Gilpatrick, W. Lysenko, J. Qiang, J. D.
Schneider, M. E. Schulze, R. L. Sheffield, H. V. Smith, *"Beam-Halo in
Mismatched Proton Beams,"* Instrument Methods Physics Res. A 519, 425,
2004.

J. Wei, A. Fedotov, W. Fischer, N. Malitsky, G. Parzen, J. Qiang,
*"Intra-beam Scattering Theory and RHIC Experiments,"* Proc. 33rd ICFA
Advanced Beam Dynamics Workshop on High Intensity & High Brightness
Hadron Beams, Bensheim, Germany, Oct. 2004.

M. Wingate, et al. (The HPQCD collaboration), *"Progress Calculating
Decay Constants with NRQCD and AsqTad actions,"* Nuclear Physics (Proc.
Suppl.) **129-130**, 325, 2004.

M. Wingate, et al. (The HPQCD Collaboration), *"The Bs and Ds decay
constants in 3 flavor lattice QCD*,*"* Physical Review Letters **92**,
162001, 2004.

F. Wolf, B. Mohr, J. Dongarra, S. Moore, *"Efficient Pattern Search in
Large Traces through Successive Refinement,"* Proc. of Euro-Par 2004,
Pisa, Italy, Aug.-Sept. 2004.

S. E. Woosley, A. Heger, A. Cumming, R. D. Hoffman, J. Pruet, T.
Rauscher, J. L. Fisker, H. Schatz, B. A. Brown and M. Wiescher, *"Models
for Type I X-Ray Bursts with Improved Nuclear Physics,"* Astrophysical
Journal Supplement, 151:75-102, March 2004.

S. E. Woosley, S. Wunsch and M. Kuhlen, *"Carbon Ignition in Type Ia
Supernovae: An Analytic Model,"* Astrophysical Journal, 607:921-930,
June 2004.

P. H. Worley, J. Levesque, *"The Performance Evolution of the Parallel
Ocean Program on the Cray X1,"* Proc. of the 46th Cray User Group
Conference, Knoxville, TN, May 2004.

J. C. Wright, P. T. Bonoli, M. Brambilla, F. Meo, E. D'Azevedo, D. B.
Batchelor, E. F. Jaeger, L. A. Berry, C. K. Phillips and A. Pletzer,
*"Full Wave Simulations of Fast Wave Mode Conversion and Lower Hybrid
Wave Propagation in Tokamaks,"* Physics of Plasmas **11**, 2473, 2004.

J. C. Wright, P. T. Bonoli, E. D\'Azevedo and M. Brambilla, *"Ultrahigh
resolution simulations of mode converted ion cyclotron waves and lower
hybrid waves,"* Proc. of the 18^th^ International Conference on the
Numerical Simulation of Plasmas, Computer Physics Communications
**164**, 330, 2004.

K. Wu, J. Ekow, E. J. Otoo, and A. Shoshani, *"On the performance of
bitmap indices for high cardinality attributes,"* Proc. of the Thirtieth
International Conference on Very Large Data Bases, Toronto, Canada,
Morgan Kaufmann, Sept. 2004.

K. Wu, W.-M. Zhang, V. Perevoztchikov, J. Lauret and A. Shoshani, *"The
grid collector: Using an event catalog to speed up user analysis in
distributed environment,"* Proc. of Computing in High Energy and Nuclear
Physics (CHEP), Interlaken, Switzerland, Sept. 2004.

S. Wunsch and S. E. Woosley*, "Convection and Core-Center Ignition in
Type Ia Supernovae,"* Astrophysical Journal, 616:1102-1108, Dec. 2004.

D. Xu and B. Bode, *"Performance Study and Dynamic Optimization Design
for Thread Pool Systems,"* Proc. of the International Conference on
Computing, Communications and Control Technologies (CCCT'2004), Austin,
Texas, Aug. 2004.

C. Yang, W. Gao, Z. Bai, X. Li, L. Lee, P. Husbands and E. Ng.,
*"Algebraic Sub-structuring for Large-scale Electromagnetic
Applications,"* PARA\'04 Workshop on State-of-the-art in Scientific
Computing, Copenhagen, Denmark, June 2004.

U. M. Yang, *"[On the Use of Relaxation Parameters in Hybrid
Smoothers](http://www.llnl.gov/CASC/linear_solvers/pubs/relaxfinal.pdf),"*
Numer. Linear Algebra Appl., **11**, p. 155-172, 2004.

Q. Yi, K. Kennedy, H. You, K. Seymour, and J. Dongarra, *"Automatic
Blocking of QR and LU Factorizations for Locality,"* Second ACM SIGPLAN
Workshop on Memory System Performance, Washington, D.C., June 2004.

Q. Yi and D. Quinlan, *"Applying Loop Optimizations to Object-Oriented
Abstractions Through General Classification of Array Semantics,"* 17th
International Workshop on Languages and Compilers for Parallel
Computing, West Lafayette, Ind., Sept. 2004.

H. Yu, K.-L. Ma and J. Welling, *"A Parallel Visualization Pipeline for
Terascale Earthquake Simulations,"* Proc. of the ACM/IEEE SC04
conference, Pittsburgh, Penn., Nov. 2004.

H. Yu, K.-L. Ma and J. Welling, *"I/O Strategies for Parallel Rendering
of Large Time-Varying Volume Data,"* Proc. of the Eurographics/ACM
SIGGRAPH Symposium on Parallel Graphics and Visualization, June 2004.

O. Zatsarinny, T. W. Gorczyca, K. T. Korista, N. R. Badnell and D. W.
Savin, *"Dielectronic recombination data for dynamic finite-density
plasmas: IV. The Carbon isoelectronic sequence,"* Astronomy and
Astrophysics, 417, 1173, 2004.

H. Zhang, et al., *"Providing Data Transfer with QoS as Agreement-Based
Service,"* Proc. of the IEEE International Conference on Services
Computing, 2004.

W. Zhang, S. E. Woosley and A. Heger, *"The Propagation and Eruption of
Relativistic Jets from the Stellar Progenitors of Gamma-Ray Bursts,"*
Astrophysical Journal, 608:365-377, June 2004.

**2005-2006**

G. Abla, et al., *"Shared Display Wall Based Collaboration Environment
in the Control Room of the DIII-D National Fusion Facility,"* Fifth
Annual Workshop on Advanced Collaborative Environments (WACE2005), 2005.

G. Abla, et al., *"Advanced Tools for Enhancing Control Room
Collaborations,"* The 5th IAEA Technical Meeting on Control, Data
Acquisition, and Remote Participation for Fusion Research, 2005.

Mark Adams, *"Ax=b: The Link Between Gyrokinetic Particle Simulations of
Turbulent Transport in Burning Plasmas and Micro-FE Analysis of Whole
Vertebral Bodies in Orthopaedic Biomechanics,"* invited talk, SciDAC
Conference, San Francisco, Calif., June 2005.

C. M. Aikens, G. D. Fletcher, M. W. Schmidt and M. S. Gordon, *"Scalable
Implementation Of Analytic Gradients For Second-Order Z-Averaged
Perturbation Theory Using The Distributed Data Interface,"* Journal of
Chemical Physics., 124, 014107, 2006.

V. Akcelik, J. Bielak, I. Epanomeritakis, O. Ghattas and E. Kim, *"High
fidelity forward and inverse earthquake modeling in large basins,"*
Proc. of the Sixth European Conference on Structural Dynamics
EURODYN\'05, Paris, France, Sept. 2005.

V. Akcelik, G. Biros, A. Dragenescu, J. Hill, O. Ghattas and B. van
Bloemen Waanders, *"Dynamic data-driven inversion for terascale
simulations: Real-time identification of airborne contaminants,"* Proc.
of, ACM/IEEE SC2005 conference, Seattle, Wash., Nov. 2005.

V. Akcelik, G. Biros, O. Ghattas, D. Keyes, K. Ko, L.-Q. Lee and E. Ng,
*"Adjoint Methods For Electromagnetic Shape Optimization Of The Low-Loss
Cavity For The International Linear Collider,"* Proc. of SciDAC 2005
Conference, San Francisco, Calif., June 2005.

V. Akcelik, G. Biros, O. Ghattas, D. Keyes, K. Ko, L.-Q. Lee and E. G.
Ng, *"Adjoint Methods for Electromagnetic Shape Optimization of the
Low-Loss Cavity for the International Linear Collider,"* Proc. of SciDAC
2005, San Francisco, Calif., June 2005.

V. Akcelik, G. Biros, O. Ghattas, J. Hill, D. Keyes, and B. van Bloeman
Waanders, *"Parallel PDE constrained optimization,"* in Frontiers of
Parallel Computing, M. Heroux, P. Raghaven, and H. Simon, eds, SIAM, to
appear 2006.

H. Akiba, K.-L. Ma, and J. Clyne, *"End-to-end Data Reduction and
Hardware Accelerated Rendering Techniques for Visualizing Time-Varying
Non-uniform Grid Volume Data,"* Proc. of the International Workshop on
Volume Graphics 2005, Stony Brook, NY, June 2005.

M. A. Albao, D.-J. Liu, C. H. Choi, M. S. Gordon and J. W. Evans,

*"Competitive Etching and Oxidation of Vicinal Si(100) Surfaces,"* MRS
Proceedings Vol. **859E,** JJ3.6., 2005.

M. A. Albao, M. M. R. Evans, J. Nogami, D. Zorn, M. S. Gordon and J. W.
Evans, *"Atomistic processes mediating growth of one-dimensional Ga rows
on Si(100),"* Physical Review B **72**, 035426, 2005.

M. A. Albao, D.-J. Liu, M. S. Gordon and J. W. Evans, *"Simultaneous
Etching and Oxidation of Vicinal Si(100) Surfaces: Atomistic Lattice-Gas
Modeling of Morphological Evolution,"* Physical Review B **72,** 195420,
2005.

A. Alexandru, et al., *"Progress on a Canonical Finite Density
Algorithm,"* Nuclear Physics B (Proc. Suppl.) **140,** 517, 2005.

C. Alexandru, et al. (The LHPC Collaboration), *"First principles
calculations of nucleon and pion form factors: Understanding the
building blocks of nuclear matter from lattice QCD,"* Journal of Physics
Conf. Ser. **16**, 174, 2005.

C. Alexandrou, et al., *"Momentum dependence of the N to Delta
transition form factors,"* Nuclear Physics B (Proc. Suppl.) **140**,
293, 2005.

I. F. Allison et al. (The HPQCD Collaboration), *"Mass of the B/c meson
in three-flavor lattice QCD,"* Physical Review Letters **94**, 172001,
2005.

I. F. Allison et al. (The HPQCD Collaboration), *"A precise
determination of the B/c mass from dynamical lattice QCD,"* Nuclear
Physics (Proc. Suppl.) **140**, 440, 2005.

A. S. Almgren, J. B. Bell, C. A. Rendleman, and M. Zingale*, "Low Mach
Number Modeling of Type Ia Supernovae,"* ApJ, 637, 922, 2006.

J. Amundson, P. Spentzouris*,"Space charge experiments and simulation in
the Fermilab Booster,"* Proc. of Particle Accelerator Conference (PAC
05), Knoxville, Tenn., May 2005.

J. Amundson, P. Spentzouris, J.Qiang and R. Ryne, *"Synergia: An
accelerator modeling tool with 3-D space charge,"* Journal of
Computational Physics vol. **211**, 229, 2006.

A. Andrady, P. J. Aucamo, A. F. Bais, C. L. Ballare, L. O. Bjorn, J. F.
Bornman, M. Caldwell, A. P. Cullen, D. J. Erickson III, F. R. de Gruijl,
D.-P. Hader, M. ilyas, G. Kulandaivelu, H. D. Kumar, J. Longstreth, R.
L. McKenzie, M. Norval, H. H. Redhwi, R. C. Smith, K. R. Solomon, Y.
Takizawa, X. Tang, A. H. Teramura, A. Torikai, J. C. van der Leun, S.
Wilson, R. C. Worrest and R. G. Zepp, *"Environmental effects of ozone
depletion and its interactions with climate change: Progress Report
2004,"* Photochem. Photobiol. Sci., 2005.

D. J. Antonio et al. (The RBC and UKQCD Collaborations), *"Baryons in
2+1 flavour domain wall QCD,"* Proc. of XXIII International Symposium on
Lattice Field Theory (Lattice 2005), 098, 2005.

C. Aubin, et al. (The MILC Collaboration), *"Properties of light quarks
from lattice QCD simulations,"* Journal of Physics: Conference
Proceedings, **16,** 160, 2005.

C. Aubin, et al. (The Fermilab Lattice, MILC, and HPQCD Collaborations),
"*Semileptonic decays of D mesons in three-flavor lattice QCD,"*
Physical Review Letters **94**, 011601, 2005.

C. Aubin, et al. (The Fermilab Lattice, MILC, and HPQCD Collaborations),
*"Charmed meson decay constants in three flavor lattice QCD,"* Physical
Review Letters **95,** 122002, 2005.

C. Aubin, et al. (The MILC Collaboration), *"Topological susceptibility
with three flavors of staggered quarks,"* Nuclear Physics. B (Proc.
Suppl.) **140**, 600, 2005.

C. Aubin, et al. (The MILC Collaboration), *"Results for light
pseudoscalars from three-flavor simulations,"* Nuclear Physics. B (Proc.
Suppl.) **140**, 231, 2005.

C. Aubin, et al. (The MILC Collaboration), *"The scaling dimension of
low lying Dirac eigenmodes and of the topological charge density,"*
Nuclear Physics. B (Proc. Suppl.) **140**, 626, 2005.

B. Bader, O. Ghattas, B. van Bloemen Waanders and K. Willcox, *"An
optimization framework for goal-oriented model-based reduction of
large-scale systems,"* 44th IEEE Conference on Decision and Control,
Seville, Spain, Dec. 2005.

D. H. Bailey and A. S. Snavely, *"Performance Modeling: Understanding
the Present and Predicting the Future,"* Proc. of SIAM PP04, 2005.

A. H. Baker, E. R. Jessup, and T. A. Manteuffel, *"A technique for
accelerating the convergence of GMRES,"* SIAM J. Mat. Anal. & App.,
**26**, 4, p. 962, 2005.

S. Basak, et al., *"Combining quark and link smearing to improve
extended baryon operators,"* Proc. of XXIII International Symposium on
Lattice Field Theory (Lattice 2005), 076, 2005.

S. Basak, et al. (The LHPC Collaboration), *"Baryonic sources using
irreducible representations of the double-covered octahedral group,"*
Nuclear Physics. (Proc. Suppl.) **140**, 281, 2005.

S. Basak, et al. (The LHPC Collaboration), *"Analysis of N\* spectra
using matrices of correlation functions based on irreducible baryon
operators,"* Nuclear Physics (Proc. Suppl.) **140**, 278, 2005.

S. Basak, et al. (The LHPC Collaboration), *"Group-theoretical
construction of extended baryon operators,"* Nuclear Physics. (Proc.
Suppl.) **140**, 287, 2005.

S. Basak, et al. (The LHPC Collaboration), *"Group-theoretical
construction of extended baryon operators in lattice QCD,"* Physical
Review D, **72**, 094506, 2005.

S. Basak, et al. (The LHPC Collaboration), *"Clebsch-Gordan construction
of lattice interpolating fields for excited baryons,"* Physical Review
D**, 72**, 074501, 2005.

A. C. Bauer, M. S. Shephard, M., Nuggehally, *"Design overview of the
TSTT integrated field approximation for numerical simulation (FANS)
library,"* Proc. 8th US Nat. Congress on Comp. Mech., 2005.

J. B. Bell, M. S. Day, J. F. Grcar, and M. J. Lijewski, *"Active Control
for Statistically Stationary Turbulent Premixed Flame Simulations,"*
Communications in Applied Mathematics and Computational Science, **1**,
29, 2006.

J. B. Bell, M. S. Day, I. G. Shepherd, M. Johnson, R. K. Cheng, J. F.
Grcar, V. E. Beckner, and M. J. Lijewski, *"Numerical Simulation of a
Laboratory-Scale Turbulent V- flame,"* Proceedings of the National
Academy of Sciences, **102** (29) 10006, 2005.

G. J. O. Beran, B. Austin, A. Sodt, and M. Head-Gordon*, "Unrestricted
perfect pairing: The simplest wave-function-based model chemistry beyond
mean field,"* Journal of Physical Chemistry A, **109,** 9183-9192, 2005.

C. Bernard, et al. (The MILC Collaboration), *"The locality of the
fourth root of staggered fermion determinant in the interacting case,"*
XXIII International Symposium on Lattice Field Theory (Lattice 2005),
299, 2005.

C. Bernard, et al. (The MILC Collaboration), *"More evidence of
localization in the low-lying Dirac spectrum,"* XXIII International
Symposium on Lattice Field Theory (Lattice 2005), 299, 2005.

C. Bernard, et al. (The MILC Collaboration), *"The Equation of State for
QCD with 2+1 Flavors of Quarks,"* Proceedings of Science, Lattice 2005,
156, 2005.

C. Bernard, et al. (The MILC Collaboration), *"Update on pi and K
Physics,"* XXIII International Symposium on Lattice Field Theory
(Lattice 2005), 025, 2005.

C. Bernard, et al. (TheMILC Collaboration), *"QCDThermodynamics with
Three Flavors of Improved Staggered Quarks,"* Physical Review D, **71**,
034504, 2005.

C. Bernard, et al. (The MILC Collaboration), *"Heavy-light decay
constants using clover valence quarks and three flavors of dynamical
improved staggered quarks,"* Nuclear Physics. B (Proc. Suppl.) **140**,
449, 2005.

C. Bernard, et al. (The MILC Collaboration), *"Three Flavor QCD at High
Temperatures,"* Nuclear Physics B (Proc. Suppl.) **140**, 538, 2005.

M. Berndt, T. Manteuffel, and S. McCormick, and G. Starke*, "Analysis of
first-order system least squares (FOSLS) for elliptic problems with
discontinuous coefficients: Part I,"* SIAM Journal on Numerical
Analysis, **43**, p. 386-408, 2005.

M. Berndt, T. Manteuffel and S. McCormick, *"Analysis of first-order
system least squares (FOSLS) for elliptic problems with discontinuous
coefficients: Part II,"* SIAM Journal on Numerical Analysis, **43**, p.
409-436, 2005.

M. Barad, P. Colella, [*"A fourth-order accurate local refinement method
for Poisson\'s
equation,"*](http://seesar.lbl.gov/anag/publications/colella/A_1_58.pdf)
J. Comput. Phys. **209**, p. 1-18, 2005.

N. Bhatia, F. Song, F. Wolf, J. Dongarra, B. Mohr, S. Moore, *"Automatic
Experimental Analysis of Communication Patterns in Virtual Topologies,"*
Proc. of the International Conference on Parallel Processing (ICPP-05),
Oslo, Norway, June 2005.

B. Bhattacharjee, P. Lemonidis, W. H. Green, and P. I. Barton, *"Global
Solution of Semi-Infinite Programs,*" Mathematical Programming, 103,
283, 2005.

G. Biros and O. Ghattas, *"Parallel Lagrange-Newton-Krylov-Schur Methods
for PDE-Constrained Optimization. Part I: The Krylov-Schur Solver,"*
SIAM Journal on Scientific Computing, 27, 687, 2005.

G. Biros and O. Ghattas, *"Parallel Lagrange-Newton-Krylov-Schur Methods
for PDE-Constrained Optimization. Part II: The Lagrange-Newton Solver,
and its Application to Optimal Control of Steady Viscous Flows,"* SIAM
Journal on Scientific Computing, 27, 714, 2005.

B. Bistrovic, et al. (The LHPC Collaboration), *"Understanding hadron
structure from lattice QCD in the SciDAC era,"* Journal of Physics Conf.
Ser. **16**, 150, 2005.

J. M. Blondin, *"Discovering new dynamics of core-collapse supernova
shock waves,"* Journal of Physics Conference Series, 16, 370-379, 2005.

J. M. Blondin, A. Mezzacappa, *"The Spherical Accretion Shock
Instability in the Linear Regime,"* ArXiv Astrophysics e-prints, July
2005.

T. Blum, *"Lattice calculation of the lowest-order hadronic contribution
to the muon anomalous magnetic moment,"* Nuclear Physics B (Proc.
Suppl.) **140**, 311, 2005.

T. Blum and P. Petreczky, *"Cutoff effects in meson spectral
functions,"* Nuclear Physics B (Proc. Suppl.) **140**, 553, 2005.

F.D.R. Bonnet, et al. (The LHPC Collaboration), *"Lattice computations
of the pion form factor,"* Phys. Rev. D **72**, 054506, 2005.

P. A. Boyle, et al., *"Overview of the QCDSP and QCDOC computers,"* IBM
Research Journal **49**, 351, 2005.

P. A. Boyle, et al., *"QCDOC: Project status and first results,"*
Journal of Physics Conf. Ser. **16**, 129, 2005.

P. A. Boyle, et al., *"Localisation and chiral symmetry in 2+1 flavour
domain wall QCD,"* Proc. of XXIII International Symposium on Lattice
Field Theory (Lattice 2005), 141, 2005.

P. A. Boyle, et al., *"The QCDOC project,"* Nuclear Physics (Proc.
Suppl.) **140**, 169, 2005.

J. Brannick, M. Brezina, S. MacLachlan, T. Manteuffel, S. McCormick, and
J. Ruge, *"An energy-based AMG coarsening strategy,"* Journal on
Numerical Analysis,. Lin. Alg. Appl., 13, 133, 2006.

D. P. Brennan, S. E. Kruger, T. A. Gianakon, and D. D. Schnack, *"A
categorization of tearing mode onset in tokamaks via nonlinear
simulation,"* Nuclear Fusion **45.** 1178, 2005.

M. Brezina, R. Falgout, S. MacLachlan, T. Manteuffel, S. McCormick and
J. Ruge, *"Adaptive Smoothed Aggregation (αSA),"* SIAM Review: SIGEST,
**47,** p. 317, 2005.

M. Brezina, R. Falgout, S. MacLachlan, T. Manteuffel, S. McCormick and
J. Ruge, *"Adaptive Algebraic Multigrid,"* SIAM Journal of Scientific
Computing, 27, 1534, 2006.

M. Brezina, C. Tong, R. Becker, *"Parallel Algebraic Multigrids for
Structural Mechanics,"* SIAM Journal of Scientific Computing, to appear.

R. C. Brower, H. Neff, and K. Orginos, *"Moebius fermions: Improved
domain wall chiral fermions,"* Nuclear Physics. (Proc. Suppl.) **140**,
686, 2005.

J. R. Burruss, et al., *"Security on the U. S. Fusion Grid,"* The 5th
IAEA Technical Meeting on Control, Data Acquisition, and Remote
Participation for Fusion Research, 2005.

J. R. Burruss, et al., *"Simplifying FusionGrid Security,"* Proc.
Challenges of Large Applications in Distributed Environments, 95-105,
2005.

J. R. Burruss, *"The Resource Oriented Authorization Manager (ROAM),"*
Proc. 14th IEEE International Symposium on High Performance Distributed
Computing, 308-309, 2005.

J. R. Burruss, et al., "*Developments in Remote Collaboration and
Computation,"* The 14th ANS Topical Meeting on the Technology of Fusion
Energy, Fusion Science and Technology, **47**, 3, 814, 2005.

L. Bytautas and K. Ruedenberg, *"Correlation Energy Extrapolation
through Intrinsic Scaling. IV. Accurate Binding Energies of the
Homonuclear Diatomic Molecules Carbon, Nitrogen, Oxygen and Fluorine,"*
Journal of Chemical Physics, **122**, 154110, 2005.

X.-C. Cai, L. Marcinkowski, and P. Vassilevski, *"An element
agglomeration nonlinear additive Schwarz preconditioned Newton method
for unstructured finite element problems,"* Applications of Mathematics,
50, p. 247-275, 2005.

C. Y. Cardall, E. J. Lentz, A. Mezzacappa, *"Conservative special
relativistic radiative transfer for multidimensional astrophysical
simulations: Motivation and elaboration,"* Physical Review D, 72,
043007, 2005.

C. Y. Cardall, A. O. Razoumov, E. Endeve, E. J. Lentz, A. Mezzacappa,
*"Toward five-dimensional core-collapse supernova simulations,"* Journal
of Physics Conference Series, 16, 390-394, 2005.

G. R. Carr, M. J. Cordery, J. B. Drake, M. W. Ham, F. M. Hoffman and P.
H. Worley, *"Porting and Performance of the Community Climate System
Model (CCSM3) on the Cray X1,"* Proc. of the 47th Cray User Group
Conference, Albuquerque, NM, May 2005.

L. Carrington, M. Laurenzano, A. Snavely, R. Campbell and L. Davis,
*"How well can simple metrics represent the performance of HPC
applications?"* Proc. of the ACM/IEEE SC05 conference, Seattle, Wash.,
Nov. 2005.

T. Chartier, R. Falgout, V. E. Henson, J. Jones, T. Manteuffel, S.
McCormick, J. Ruge and P. Vassilevski, *"Spectral element agglomerate
AMGe,"* Lecture Notes in Computational Science and Engineering, to
appear.

J. Chen, S. C. Jardin, and H. R. Strauss*, "Solving anisotropic
transport equations on misaligned grids,"* Lecture Notes In Computer
Science, **3516,** 1076-1079, 2005.

J. Chen, J. Breslau, G. Fu, S. Jardin, W. Park, *"Symmetric solution in
M3D,"* Computer Physics Communications **164,** 1-3, 468-471, 2005.

H. Chen, et al., *"Memory Performance Optimizations for Real-Time
Software HDTV Decoding,"* The Journal of VLSI Signal Processing, **21**,
2, 193-207, 2005.

L. Chen, F. Zonca, and Z. Lin, *"Nonlinear Toroidal Mode Coupling: A New
Paradigm for Drift Wave Turbulence in Toroidal Plasmas,"* Plasma Phys.
Contr. Fusion **47**, B71, 2005.

M. Cheng, et al. (The RBC-Bielefeld Collaboration), *"Scaling test of
the P4-improved staggered fermion action,"* Proc. of XXIII International
Symposium on Lattice Field Theory (Lattice 2005), 045, 2005.

N. Chevaugeon, P. Hu, X. Li, J. Xin, D. Cler, J. E. Flaherty, M. S.
Shephard, "Discontinuous Galerkin methods applied to shock and blast
problems," Journal of Scientific Computing, 22, p. 227-243, 2005.

E. Chow, *"An Aggregation Multilevel Method Using Smooth Error
Vectors,"* SIAM Journal of Scientific Computing, 27, 1727, 2006.

M. Choi, V. S. Chan, V. Tang, P. Bonoli, R. I. Pinsker*, "Monte-Carlo
Orbit/Full Wave Simulation of Fast Alfvén (FW) Damping on Resonant Ions
in Tokamaks,"* Radio Frequency Power in Plasmas, Proc. 16^th^ Topical
Conf., Park City, Utah, 2005.

M. A. Clark, P. de Forcrand and A. D. Kennedy, *"Algorithm shootout: R
versus RHMC,"* Proc. of XXIII International Symposium on Lattice Field
Theory (Lattice 2005), 115, 2005.

C. S. Co, A. Friedman, D. P. Grote, J.-L.Vay, W. Bethel, K. I. Joy,
*"Interactive Methods for Exploring Particle Simulation Data,"* Proc. of
EuroVis 2005 conference, 2005.

B. Cohen, E. B. Hooper, R. H. Cohen, D. N. Hill, H. S. McLean, R. D.
Wood, S. Woodruff, C. R. Sovinec, and G. A. Cone, *"Simulation of
spheromak evolution and energy confinement,"* Physics of Plasmas,
**12,** 056106, 2005.

S. Cohen, *"Preliminary Study of BK on 2+1 flavor DWF lattices from
QCDOC,"* Proc. of XXIII International Symposium on Lattice Field Theory
(Lattice 2005), 346, 2005.

P. Colella, D. T. Graves, B. J. Keen, D. Modiano, *"[A cartesian grid
embedded boundary method for hyperbolic conservation
laws,"](http://seesar.lbl.gov/anag/publications/colella/LBNL-56420.pdf)*
Journal of Computational Physics, **211,** p. 347-366, 2006.

I. R. Corey, J. R. Johnson and J. S. Vetter, *"Performance Assertions
and Sensitivity Analysis: A Technique for Developing Adaptive Grid
Applications,"* Proceedings of the Eleventh IEEE International Symposium
on High Performance Distributed Computing, (HPDC), Edinburgh, Scotland,
July 2006.

A. P. Craig, R. L. Jacob, B. Kauffman, T. Bettge, J. Larson, E. Ong, C.
Ding, and Y. He, *"CPL6: The New Extensible, High-Performance Parallel
Coupler for the Community Climate System Model,"* International Journal
of High Performance Computing Applications, **19**, 3, p. 309, Aug.
2005.

R. K. Crockett, P. Colella, R. Fisher, R. I. Klein, C. F. McKee, [*"An
unsplit, cell-centered Godunov method for ideal
MHD,"*](http://seesar.lbl.gov/anag/publications/colella/A_1_56.pdf) J.
Comput. Phys. **203,** p. 422-448, 2005.

C.T.H. Davies, G. P. Lepage, F. Niedermayer and D. Toussaint*,* (The
HPQCD, MILC and UKQCD Collaborations), *"The Quenched Continuum Limit,"*
Nuclear Physics B (Proc. Suppl.) **140**, 261, 2005.

M. S. Day, J. B. Bell, J. F. Grcar, and V. E. Beckner, *"Numerical
Control of 3D Turbulent Premixed Flame Simulations,"* 20th International
Colloquium on the Dynamics of Explosions and Reactive Systems, July-Aug,
2005.

H. de Sterck, T. Manteuffel, S. McCormick and L. Olson*, "Numerical
conservation properties of H(div)-conforming least-squares finite
element methods for the Burgers equation,"* SIAM Journal of Scientific
Computing, 26, p. 1573-1597, 2005.

H. de Sterck, R. Markel and R. Knight, *"TaskSpaces: a software
framework for parallel bioinformatics on computational grids,"* in
Parallel Computing in Bioinformatics and Computational Biology, A.
Zomaya, editor, J. Wiley and Sons, 2005.

J. Demmel, J. Dongarra, V. Eijkhout, E. Fuentes, A. Petitet, R. Vuduc,
R. C. Whaley, and K. Yelick***,** "Self-Adapting Linear Algebra
Algorithms and Software,"* Proc. of the IEEE, Special Issue on Program
Generation, Optimization, and Platform Adaptation, **93**(2), Feb. 2005.

N. Desai, R. Bradshaw, S. Matott, S. Bittner, S. Coghlan, R. Evard, C.
Luenighoener, T. Leggett, J. P. Navarro, G. Rackow, C. Stacey, and T.
Stacey, *"A case study in configuration management tool deployment,"*
Proc. of the Nineteenth System Administration Conference (LISA XIX), San
Diego, Calif., Dec. 2005.

N. Desai, A. Lusk, R. Bradsha, and E. Lusk, *"{MPISH}: A parallel shell
for {MPI} programs,"* Proc. of the 1st Workshop on System Management
Tools for Large-Scale Parallel Systems (IPDPS \'05), Denver, Colo.,
2005.

Z. M. Djurisic, D. Amusin, T. Bereknyei, T. C. Allison, M. Frenklach,
*"Reporting of experimental data for development and validation of
chemical kinetic models,"* Fall Meeting of the Western States Section of
the Combustion Institute, Stanford, CA, Oct. 2005.

J. B. Drake, P. W. Jones, G. R. Carr Jr., *"Overview of the Software
Design of the Community Climate System Model,"* International Journal of
High Performance Computational Application, **19**, 177, 2005.

T. Draper, et al., *"Improved Measure of Local Chirality,"* Nuclear
Physics B (Proc. Suppl.) **140,** 623, 2005.

T. Draper, et al., *"Locality and Scaling of Quenched Overlap
Fermions,"* Draper, et al., Proc. of XXIII International Symposium on
Lattice Field Theory (Lattice 2005), 120, 2005.

H. Duan, G. M. Fuller, Y.-Z. Qian, *"Collective Neutrino Flavor
Transformation In Supernovae,"* ArXiv Astrophysics e-prints, Nov. 2005.

J. Dudek, R. G. Edwards and D. G. Richards, *"Radiative transitions in
charmonium,"* Proc. of XXIII International Symposium on Lattice Field
Theory (Lattice 2005), 210, 2005.

T. J. Dudley, R. M. Olson, M. W. Schmidt, and M .S. Gordon, *"Parallel
Coupled Perturbed CASSCF Equations and Analytic CASSCF Second
Derivatives,"* Journal of Computational Chemistry, 27, 352, 2006.

T. H. Dunigan, Jr., J. S. Vetter and P. H. Worley, *"Performance
Evaluation of the SGI Altix 3700,"* Proc. of the 2005 International
Conference on Parallel Processing, Oslo, Norway, June 2005.

T. H. Dunigan, Jr., J. S. Vetter, J. B. White III, and P. H. Worley*,
"Performance Evaluation of the Cray X1 Distributed Shared-Memory
Architecture,"* IEEE Micro, **25**(1), p. 30, Jan./Feb. 2005.

R. J. Dumont, C. K. Phillips and D. N. Smithe, *"Effects of
non-Maxwellian species on ion cyclotron wave propagation and absorption
in magnetically confined plasmas,"* Physics of Plasmas **12**, 042508,
2005.

R. G. Edwards, et al. (The LHPC Collaboration), *"Hadron structure with
light dynamical quarks,"* Proc. of XXIII International Symposium on
Lattice Field Theory (Lattice 2005), 056, 2005.

R. G. Edwards et al. (The LHPC and UKQCD Collaborations), *"The Chroma
Software System for Lattice QCD,"* Nuclear Physics (Proc. Suppl.)
**140**, 832, 2005.

S. Ethier, *"Gyrokinetic Particle-in-Cell Simulations of Plasma
Microturbulence on Advanced Computing Platforms,"* keynote talk, SciDAC
Conference, San Francisco 2005.

J. W. Evans, *"Kinetic* *Monte Carlo Simulation of Non-Equilibrium
Lattice-Gas Models: Basic and Refined Algorithms applied to Surface
Adsorption Processes,"* in Handbook of Materials Modeling, Part A, Ch.
5.12, ed. S. Yip, Springer, Berlin, 2005.

M. R. Fahey, S. Alam, T. H. Dunigan, Jr., J. S. Vetter and P. H. Worley,
*"Early Evaluation of the Cray XD1,"* Proc. of the 47th Cray User Group
Conference, Albuquerque, NM, May 2005.

R. Falgout, J. Brannick, M. Brezina, T. Manteuffel, and S. McCormick,
*"New multigrid solver advances in TOPS,"* Proceedings of SciDAC 2005,
Journal of Physics: Conference Series, Institute of Physics, San
Francisco, Calif., June 2005.

R. D. Falgout, J. E. Jones, and U. M. Yang, *"The Design and
Implementation of hypre, a Library of Parallel High Performance
Preconditioners,"* chapter in Numerical Solution of Partial Differential
Equations on Parallel Computers, A. M. Bruaset, P. Bjørstad, and A.
Tveito, eds., Springer-Verlag, 2006.

R. D. Falgout, J. E. Jones, and U. M. Yang, *"[Conceptual Interfaces in
hypre](http://www.llnl.gov/CASC/linear_solvers/pubs/concif.pdf),"*
Future Generation Computer Systems, Special Issue on PDE software,
**22**, p. 239-251, 2005.

R. D. Falgout, J. E. Jones and U. M. Yang*, "Pursuing Scalability for
hypre\'s Conceptual Interfaces,"* ACM Transactions of Mathematical
Softw., **31**, p. 326-350, 2005.

R. D. Falgout, P. S. Vassilevski, and L. T. Zikatanov, *"[On Two-Grid
Convergence
Estimates](http://www.llnl.gov/CASC/linear_solvers/pubs/sharp_TG_NLA2.pdf),"*
Numer. Linear Algebra Appl., **12**, p. 471-494, 2005.

D.G. Fedorov, K. Kitaura, H. Li, J. H. Jernsen, and M. S. Gordon, *"The
polarizable continuum model (PCM) interfaced with the fragment molecular
orbital method (FMO),"* Journal of Computational Chemistry, in press.

J. Feng, W. Wan, J. Qiang, A. Bartelt, A. Comin, A. Scholl, J. Byrd, R.
Falcone, G. Huang, A. MacPhee, J. Nasiatka, K. Opachich, D. Weinstein,
T. Young and H. A. Padmore, *"An Ultra-Fast X-Ray Streak Camera for the
Study of Magnetication Dynamics,"* Proceedings of SPIE, 2005.

G. Fleming, et al. (The LHPC Collaboration), *"Pion form factor using
domain wall valence and asqtad sea quarks,"* Nuclear Physics (Proc.
Suppl.) **140**, 302 2005.

G. Folatelli, C. Contreras, M. M. Phillips, S. E. Woosley, S. Blinnikov,
N. Morrell, N. B. Suntzeff, B. L. Lee, M. Hamuy, S. Gonzalez, W.
Krzeminski, M. Roth, W. Li, A. V. Filippenko, W. L. Freedman, B. F.
Madore, S. E. Persson, D. Murphy, S. Boissier, G. Galaz, L. Gonzalez, P.
J. McCarthy, A. McWilliam and W. Pych, *"SN 2005bf: A Transition Event
Between Type Ib/c Supernovae and Gamma Ray Bursts,"* ArXiv Astrophysics
e-prints, Sept. 2005.

I. Foster, *"Service-Oriented Science,"* Science Magazine, **308**,
5723, 814-817, May 2005.

N. Fout, H. Akiba, K.-L. Ma, A. Lefohn, and J. Kniss, *"High Quality
Rendering of Compressed Volume Data Formats,"* Proc. of the
Eurographics/IEEE-VGTC Symposium on Visualization (EuroVis 2005), Leeds,
UK, June 2005.

N. Fout, K.-L. Ma, and J. Ahrens, *"Time-Varying Multivariate Volume
Data Reduction,"* Proc. of the ACM Symposium on Applied Computing 2005,
p. 1224-1230, Santa Fe, NM, March 2005.

C. L. Fryer and A. Heger, *"Binary Merger Progenitors for Gamma-Ray
Bursts and Hypernovae,"* ApJ, 623:302-313, April 2005.

C. L. Fryer, G. Rockefeller, A. Hungerford, and F. Melia, *"The Sgr B2
X-ray Echo of the Galactic Center Supernova Explosion that Produced Sgr
A East,"* ArXiv Astrophysics e-prints, June 2005.

G. M. Fuller, Y.-Z. Qian, *"Simultaneous Flavor Transformation of
Neutrinos and Antineutrinos with Dominant Potentials from
Neutrino-Neutrino Forward Scattering,"* ArXiv Astrophysics e-prints, May
2005.

E. Gamiz, et al. (The HPQCD Collaboration), *"Dynamical Determination of
BK from Improved Staggered Quarks,"* Proc. of XXIII International
Symposium on Lattice Field Theory (Lattice 2005), 47 2005.

E. Gamiz, et al. (The HPQCD Collaboration), *"BK from Improved Staggered
Quarks,"* Nuclear Physics (Proc. Suppl.) **140**, 353, 2005.

W. Gao, X. S. Li, C. Yang, Z. Bai, *"Performance Evaluation of a
Multilevel Sub-structuring Method for Sparse Eigenvalue Problems,"*
Proc. of the 16th International Conference on Domain Decomposition
Methods, 2005.

X. Gao, B. Simon, and A. Snavely, *"ALITER: An Asynchronous Lightweight
Instrumentation Tool for Event Recording,"* Workshop on Binary
Instrumentation and Applications, St. Louis, Mo. Sept. 2005.

X. Gao, M. Laurenzano, B. Simon, and A. Snavely, *"Reducing Overheads
for Acquiring Dynamic Traces,"* International Symposium on Workload
Characterization (ISWC05), Austin, Texas, Sept. 2005.

R. Garnett, J. Billen, T. Wangler, P. Ostroumov, J. Qiang, R. Ryne, R.
York, K. Crandall, *"Advanced Beam-Dynamics Simulation Tools for RIA,"*
Proc. PAC2005, Knoxville,

Tenn., May 2005.

C. Gatti-Bono, P. Colella, ["An anelastic allspeed projection method for
gravitationally stratified
flows,"](http://seesar.lbl.gov/anag/publications/colella/LBNL-57158.pdf)
Journal of Computational Physics, in press.

L. Ge, L.-Q. Lee, Z. Li, C.-K. Ng, G. Schussman, L. Xiao and K. Ko*,
"Advanced Eigensolver For Electromagnetic Modeling Of Accelerator
Cavities,"* The 15th Conference on the Computation of Electromagnetic
Fields, Shenyang, China, June 2005.

L. Ge, L.-Q. Lee, Z. Li, C.-K. Ng, K. Ko, E. Seol, A. C. Bauer and M.
Shephard, *"Adaptive Mesh Refinement In Accelerator Cavity Design,"*
SIAM Conference on Computational Science & Engineering, Orlando, Fla.,
Feb. 2005.

C. G. R. Geddes, C. Toth, J. van Tilborg, E. Esarey, C. B. Schroeder, D.
Bruhwiler, C. Nieter, J. Cary, and W. P. Leemans, *"Production of high
quality electron bunches by dephasing and beam loading in channeled and
unchanneled laser plasma accelerators,"* Physics of Plasmas, **12**, 5,
p. 56709, May 2005.

S. J. Ghan, and T. Shippert, *"Load balancing and scalability of a
subgrid orography scheme in a global climate model,"* International
Journal of High Performance Computer Applications., **19**, 237, 2005.

J. Glimm, X. L. Li, Z. L. Xu, *"Front* *tracking algorithm using
adaptively refined meshes,"* Proc. of the 2003 Chicago Workshop on
Adaptive Mesh Refinement Methods, Lecture Notes in Computational Science
and Engineering, 41, 83-90, 2005.

M. S. Gordon and M. W. Schmidt, *"Advances in Electronic Structure
Theory: GAMESS a Decade Later,"* Theory and Applications of
Computational Chemistry, Ch. 41, C. E. Dykstra, G. Frenking, K. S. Kim,
G. E. Scuseria, Eds., Elsevier, 2005.

S. Gottlieb, et al., *"Onium masses with three flavors of dynamical
quarks,"* Proc. of XXIII International Symposium on Lattice Field Theory
(Lattice 2005), 203, 2005.

D. A. Goussis and M. Valorani, *"An efficient iterative algorithm for
the approximation of the fast and slow dynamics of stiff systems,"*
Journal of Computational Physics, 214, 316, 2006.

D. A. Goussis, and M. Valorani, F. Creta and H. N. Najm, *"Reactive and
Reactive/Diffusive Time Scales in Stiff Reaction-Diffusion Systems,"*
Prog. in Computational Fluid Dynamics, **5**(6):316-326, Sept. 2005.

A. Gray, et al. (The HPQCD Collaboration), *"The B meson decay constant
from unquenched lattice QCD,"* Physical Review Letters **95**, 212001,
2005.

A. Gray, et al. (The HPQCD Collaboration), *"The Upsilon spectrum and
m(b) from full lattice QCD,"* Physical Review D, **72**, 094507, 2005.

A. Gray, et al. (The HPQCD Collaboration), *"B Leptonic Decays and B−B
Mixing with 2+1 Flavors of Dynamical Quarks,"* Nuclear Physics (Proc.
Suppl.) **140**, 446, 2005.

J. F. Grcar, M. S. Day, and J. B. Bell, *"A Taxonomy of Integral
Reaction Path Analysis,"* Combust. Theory Modelling, to appear.

C. M. Greenfield, *"Advanced Tokamak Research at the DIII-D National
Fusion Facility in Support of ITER,"* Proceedings of SciDAC 2005,
Journal of Physics: Conference Series, Institute of Physics, San
Francisco, Calif., June 2005.

M. Greenwald, D. P. Schissel, J. R. Burruss, T. Fredian, J. Lister and
J. Stillerman, *"Visions for Data Management and Remote Collaboration on
ITER,"* Proc. of ICALEPCS05, 2005.

E. Gulez, et al. (The HPQCD Collaboration), *"B Semileptonic Decays with
2+1 Dynamical Quark Flavors,"* Proc. of XXIII International Symposium on
Lattice Field Theory (Lattice 2005), 220, 2005.

O. D. Gurcan, P. H. Diamond, T. S. Hahm and Z. Lin, *"Dynamics of
Turbulence Spreading in Magnetically Confined Plasmas,"* Physics of
Plasmas, **12**, 032303, 2005.

A. T. Hagler, et al. (The LHPC Collaboration), *"Helicity dependent and
independent generalized parton distributions of the nucleon in lattice
QCD,"* European Physics Journal, **A24S1**, 29, 2005.

T. S. Hahm, P. H. Diamond, Z. Lin, G. Rewoldt, O. Gurcan, and S. Ethier,
*"On the Dynamics of Edge-Core Coupling,"* Physics of Plasmas, **12**,
090903, 2005.

K. Hashimoto, T. Izubuchi and J. Noaki, *"The static quark potential in
2+1 flavour domain wall QCD from QCDOC,"* Proc. of XXIII International
Symposium on Lattice Field Theory (Lattice 2005), 093, 2005.

J. C. Hayes, S. W. Bruenn, *"Toward 2-D and 3-D simulations of
core-collapse supernovae with magnetic fields,"* Journal of Physics
Conference Series, 16, 395-399, 2005.

Y. He and C. Ding, *"Coupling Multi-Component Models with MPH on
Distributed Memory Computer Architectures,"* International Journal of
High Performance Computing Applications, **19**, 3, p. 329, 2005.

M. Head-Gordon, G. J. O. Beran, A. Sodt and Y. Jung, *"Fast electronic
structure methods for strongly correlated molecular systems,"* Journal
of Physics: Conf. Ser. 16, 233-242, 2005.

A. Heger, E. Kolbe, W. C. Haxton, K. Langanke, G. Martinez-Pinedo and S.
E. Woosley, *"Neutrino nucleosynthesis,"* Physics Letters B, **606**,
258-264, Jan. 2005.

A. Heger, S. E. Woosley and H. C. Spruit*, "Presupernova Evolution of
Differentially Rotating Massive Stars Including Magnetic Fields,"* ApJ,
626:350-363, June 2005.

J. J. Heys, C. G. DeGroff, T. Manteuffel, and S. McCormick,
*"First-order system least squares (FOSLS) for modeling blood flow,"*
Med. Eng. Phys., to appear.

A. C. Hindmarsh, P. N. Brown, K. E. Grant, S. L. Lee, R. Serban, D. E.
Shumaker, and C. S. Woodward, *"SUNDIALS: Suite of Nonlinear and
Differential/Algebraic Equation Solvers,"* ACM Transactions on
Mathematical Software, 31(3), p. 363-396, 2005.

W. R. Hix, O. E. B. Messer, A. Mezzacappa, M. Liebendoerfer, D. J. Dean,
K. Langanke, J. Sampaio, G. Martinez-Pinedo, *"Terascale input physics:
the role of nuclear electron capture in core collapse supernovae,"*
Journal of Physics Conference Series, 16, 400-404, 2005.

W. R. Hix, B. S. Meyer, *"Thermonuclear Kinetics in Astrophysics,"*
Nuclear Physics A, in press, Sept. 2005.

F. M. Hoffman, W. W. Hargrove, D. J. Erickson III and W. Oglesby,
*"Using clustered climate regimes to analyze and compare predictions
from fully coupled general circulation models,"* Earth Interactions,
**9**, 1, 2005.

F. M. Hoffman, M. Vertenstein, H. Kitabata, and J. B. White III.
*"Vectorizing the Community Land Model (CLM),"* International Journal of
High Performance Computing Applications, **19**(3), 247, Aug. 2005.

F. M. Hoffman, W. W. Hargrove, D. J. Erickson, and R. J. Oglesby,
*"Using Clustered Climate Regimes to Analyze and Compare Predictions
from Fully Coupled General Circulation Models,"* Earth Interactions,
**9**(10), 1-27, Aug. 2005.

I. Hofmann, G. Franchetti, A. U. Luccio, M. Giovannozzi, E. Métral, J.
F. Amundson, P. Spentzouris, S. Machida, J. Qiang, R. Ryne, S. M.
Cousineau, J. A. Holmes, F. Jones, *"Benchmarking of Simulation Codes
Based on the Montague Resonance in the CERN-PS,"* Proc. PAC2005,
Knoxville, Tenn., May 2005.

M. J. Hogan, C. D. Barnes, C. E. Clayton, F. J. Decker, S. Deng, P.
Emma, C. Huang, R. H. Iverson, D. K. Johnson, C. Joshi, T. Katsouleas,
P. Krejcik, W. Lu, K. A. Marsh, W. B. Mori, P. Muggli, C. L. O'Connell,
E. Oz, R. H. Siemann and D. Walz, *"Multi-GeV Energy Gain in a
Plasma-Wakefield Accelerator,"* Physical Review Letters 95, 054802,
2005.

J. Hollingsworth, A. Snavely, S. Sbaraglia, and K. Ekanadham, *"EMPS: An
Environment for Memory Performance Studies,"* IPDPS 2005, Next
Generation Software Workshop, to appear.

D. J. Holmgren, *"PC clusters for lattice QCD,"* Nuclear Physics (Proc.
Suppl.) **140**, 183, 2005.

D. J. Holmgren, *"U.S. Lattice Clusters and the USQCD Project,"* Proc.
of XXIII International Symposium on Lattice Field Theory (Lattice 2005),
105, 2005.

C. Homescu, L. Petzold, and R. Serban*, "Error estimation for reduced
order models of dynamical systems,"* SIAM Journal on Numerical Analysis,
43, 1693, 2005.

E. B. Hooper, R. A. Kopriva, B. I. Cohen, D. N. Hill, H. S. McLean, R.
D. Wood, S. Woodruff and C. R. Sovinec, *"A magnetic meconnection event
in a driven spheromak,"* Physics of Plasmas **12,** 092503, 2005.

I. Horvath, et al., *"Inherently Global Nature of Topological Charge
Fluctuations in QCD,"* Physics Letters B, **612,** 21, 2005.

I. Horvath, et al., *"The Negativity of the Overlap-Based Topological
Charge Density Correlator in Pure-Glue QCD and the Non-Integrable Nature
of its Contact Part,"* Physics Letters B, **617**, 49, 2005.

M. Huang, and B. Bode, *"A Performance Comparison of Tree and Ring
Topologies in Distributed Systems,"* Parallel and Distributed Scientific
and Engineering Computing PDSEC-05, Denver, Colo., April 2005.

A. L. Hungerford, C. L. Fryer, and G. M. Rockefeller, *"Gamma-Rays from
Single Lobe Supernova Explosions,"* ArXiv Astrophysics e-prints, July
2005.

F.-N. Hwang, and X.-C. Cai, *"Parallel fully coupled Schwarz
preconditioners for saddle point problems,"* Electronic Transactions on
Numerical Analysis, 2005.

F.-N. Hwang, and X.-C. Cai, *"A parallel nonlinear additive Schwarz
preconditioned inexact Newton algorithm for incompressible Navier-Stokes
equations,"* Journal of Computational Physics, **204**, p. 666-691,
2005.

F.-N. Hwang, and X.-C. Cai, *"A combined linear and nonlinear
preconditioning technique for incompressible Navier-Stokes equations,"*
J. Dongarra, K. Madsen, and J. Wasniewski, eds., Lecture Notes in
Computer Science, 3732, p. 313-322, Springer-Verlag, 2005.

E. Ipek, B. R. de Supinski, M. Schulz and S. A. McKee, *"An Approach to
Performance Prediction for Parallel Applications,"* Euro-Par 2005,
Lisbon, Portugal, Sept. 2005.

R. Jacob, J. Larson, and E. Ong, *"MxN Communication and Parallel
Interpolation in CCSM3 Using the Model Coupling Toolkit,"* International
Journal of High Performance Computational Applications, **19**(3), 293,
2005.

E. F. Jaeger, *"Self-consistent full-wave and Fokker-Planck calculations
for ion cyclotron heating in non-Maxwellian plasmas,"* Bull. American
Physics Society **50**, 257, 2005.

E. F. Jaeger, L. A. Berry, R. W. Harvey, et al., *"Self-Consistent
Full-Wave / Fokker-Planck Calculations for Ion Cyclotron Heating in
non-Maxwellian Plasmas,"* Radio Frequency Power in Plasmas, Proc. 16^th^
Topical Conf., Park City, Utah, 2005.

S. C. Jardin, J. A. Breslau, *"Implicit solution of the four-field
extended-magnetohydrodynamic equations using high-order high-continuity
finite elements,"* Physics of Plasmas **12,** 10, 2005.

J.E. Jones and B. Lee, *"[A Multigrid Method for Variable Coefficient
Maxwell\'s
Equations](http://www.llnl.gov/CASC/linear_solvers/pubs/jones_lee_2004_maxwell_rev.pdf),"*
SIAM Journal on Scientific Computing, 27, 168, 2006.

P. W. Jones, P. H. Worley, Y. Yoshida, J. B. White III and J. Levesque,
*"Practical performance portability in the Parallel Ocean Program
(POP*)*,"* Concurrency Computation-Practice Experiment & Experience,
**17**, 1317, 2005.

C. Jung, *"Thermodynamics using p4-improved staggered fermion action on
QCDOC,"* Proc. of XXIII International Symposium on Lattice Field Theory
(Lattice 2005), 150, 2005.

A. Juodagalvis, D. J. Dean, *"Gamow-Teller GT~+~ distributions in nuclei
with mass A = 90-97,"* Physical Review C, 72, 024306, 2005.

A. Juodagalvis, K. Langanke, G. Martinez-Pinedo, W. R. Hix, D. J. Dean,
J. M. Sampaio, *"Neutral-current neutrino-nucleus cross sections for
A\~50-65 nuclei,"* Nuclear Physics A, 747, 87-108, 2005.

D. J. Kerbyson and P. W. Jones, *"A Performance Model of the Parallel
Ocean Program,"* International Journal of High Performance Computing
Applications, **19**, 261, 2005.

C. C. Kim, C. R. Sovinec, S. E. Parker and the NIMROD Team, *"Hybrid
kinetic-MHD simulations in general geometry,"* Computer Physics
Communications **164,** 1-3, 448, 2005.

S. Klasky, *"Data Management on the Fusion Computational Pipeline,"*
invited talk, SciDAC Conference, San Francisco, Calif., June 2005.

A. Klawonn, O. Rheinbach and O. Widlund, *"Some Computational Results
for Dual-Primal FETI Methods for Elliptic Problems in 3D,"* Proc. of the
15^th^ International Symposium on Domain Decomposition Methods, Berlin,
Germany, July 2003.

A. Klawonn and O. Widlund, *"Selecting Constraints in Dual-Primal FETI
Methods for Elasticity in Three Dimensions,"* Proc. of the 15^th^
International Symposium on Domain Decomposition Methods, Berlin,
Germany, July 2003.

K. Ko, N. Folwell, L. Ge, A. Guetz, L.-Q. Lee, Z. Li, C.-K. Ng, E.
Prudencio, G. Schussman, R. Uplenchwar and L. Xiao, *"Advances in
Electromagnetic Modeling through High Performance Computing,"* Proc. of
12th International Workshop on RF Superconductivity (SRF 2005), Cornell,
New York, July 2005.

K. Ko, N. Folwell, L. Ge, A. Guetz, V. Ivanov, A. Kabel, M. Kowalski, L.
Lee, Z. Li, C. Ng, E. Prudencio, G. Schussman, R. Uplenchwar, L. Xiao,
E. Ng, W. Gao, X. Li, C. Yang, P. Husbands, A. Pinar, D. Bailey, D.
Gunter, L. Diachin, D. Brown, D. Quinlan, R. Vuduc, P. Knupp, K. Devine,
J. Kraftcheck, O. Ghattas, V. Akcelik, D. Keyes, M. Shephard, E. Seol,
A. Brewer, G. Golub, K. Ma, H. Yu, Z. Bai, B. Liao, T. Tautges and H.
Kim, *"Impact of SciDAC on accelerator projects across the Office of
Science through electromagnetic modeling,"* Proc. of SciDAC 2005
meeting, San Francisco, Calif., June 2005.

S. Kronfeld, et al. (The Fermilab Lattice and MILC Collaborations),
*"Predictions from Lattice QCD,"* Proc. of XXIII International Symposium
on Lattice Field Theory (Lattice 2005), 206, 2005.

S. E. Kruger, C. R. Sovinec, D. D. Schnack and E. D. Held,
*"Free-boundary simulations of DIII-D plasmas with the NIMROD code,"*
Computer Physics Communications **164,** 1-3, 34, 2005.

S. E. Kruger, D. D. Schnack and C. R. Sovinec, *"Dynamics of the major
disruption of a DIII-D plasma,"* Physics of Plasmas **12,** 056113,
2005.

M. Kuhlen, S. E. Woosley and G. A. Glatzmaier, *"Carbon Ignition in Type
Ia Supernovae: II. A Three-Dimensional Numerical Model,"* ApJ 640, 407,
2006.

J.-F. Lamarque, J. T. Kiehl, P. G. Hess, W. D. Collins, L. K. Emmons, P.
Ginoux, C. Luo and X. X. Tie, *"Response of a coupled chemistry-climate
model to changes in aerosol emissions*: *Global impact on the
hydrological cycle and the tropospheric burdens of OH, ozone and NOx,"*
Geophysical Research Letter, **32**, 16, L16809, 2005.

C.-L. Lappen and D. A. Randall, *"Using idealized coherent structures to
parameterize momentum fluxes in a PBL mass-flux model,"* Journal of
Atmospheric Sciences, **62**, 2829, 2005.

J. Larson, R. Jacob and E. Ong, *"The Model Coupling Toolkit: A New
Fortran90 Toolkit for Building Multi-Physics Parallel Coupled Models,"*
International Journal of High Performance Computing Applications,
**19**(3), 277-292, 2005.

M. Laurenzano, B. Simon, A. Snavely and M. Gunn, *"Low Cost Trace-driven
Memory Simulation Using SimPoint,"* Workshop on Binary Instrumentation
and Applications, St. Louis, Mo., Sept. 2005.

I. Lee, P. Raghavan, and E. G. Ng, *"Effective Preconditioning Through
Ordering Interleaved with Incomplete Factorization,"* SIAM J. Matrix
Anal. Appls., 27, 106, 2006.

J. C. Lee, H. N. Najm, S. Lefantzi, J. Ray, M. Frenklach, M. Valorani
and D. A. Goussis, *"On chain branching and its role in homogeneous
ignition and premixed flame propagation,"* Computational Fluid and Solid
Mechanics 2005, K. J. Bathe, ed., p. 717, Elsevier, 2005.

L.-Q. Lee, Z. Bai, W. Gao, L. Ge, Z. Li, C.-K. Ng, C. Yang, E. Ng and K.
Ko, *"Nonlinear Eigenvalue Problem in Accelerator Cavity Design,"* SIAM
Annual Meeting, New Orleans, La., July 2005.

L.-Q. Lee, Z. Bai, W. Gao, L. Ge, P. Husbands, M. Kowalski, X. Li, Z.
Li, C.-K. Ng, C. Yang, E. Ng and K. Ko*, "Modeling Rf Cavities With
External Coupling,"* SIAM Conference on Computational Science &
Engineering, Orlando, Fla., Feb. 2005.

L.-Q. Lee, L. Ge, Z. Li, C. Ng, G. Schussman, K. Ko, E. Ng, W. Gao, P.
Husbands, X. Li, C. Yang, V. Akcelik, O. Ghattas, D. Keyes, T. Tautges,
H. Kim, J. Craftcheck, P. Knupp, L. Freitag Diachin, K.-L. Ma, Z. Bai
and G. Golub, *"Achievements in ISICs/SAPP collaborations for
electromagnetic modeling of accelerators,"* Proc. of SciDAC 2005
meeting, San Francisco, Calif., June 2005.

W. P. Leemans, E. Esarey, J. van Tilborg, P. A. Michel, C. B. Schroeder,
C. Toth, C. G. R. Geddes and B. A. Shadwick, *"Radiation from laser
accelerated electron bunches: coherent terahertz and femtosecond
x-rays,"* IEEE Trans. Plasma Sci., **33**, 1, 0093-3813, Feb. 2005.

S. Lefantzi, J. Ray, C. A. Kennedy and H. N. Najm, *"A Component-based
Toolkit for Reacting Flows with Higher Order Spatial Discretizations on
Structured Adaptively Refined Meshes,"* Prog. in Computational Fluid
Dynamics, **5**(6), 298-315, Sept. 2005.

J. L. V. Lewandowski, *"Low-noise collision operators for
particle-in-cell simulations,"* Physics of Plasmas, **12**, 052322,
2005.

J. L. V. Lewandowski, *"Global particle-in-cell simulations of
microturbulence with kinetic electrons,"* invited talk, APS/DPP meeting,
Denver, Colo., 2005.

H. Li, and M. S. Gordon, *"Gradients of the Exchange-Repulsion Energy in
the Effective Fragment Potential Method,"* Theoretical Chemistry
Accounts, in press.

K. Li, et al., *"Dynamic Scalable Visualization for Collaborative
Scientific Applications,"* Proceedings of the Next Generation Software
Workshop, Denver Colo., April 2005.

X. Li, M. S. Shepard, M. W., Beall, *"3-D Anisotropic Mesh Adaptation by
Mesh Modifications,"* Computer Methods in Applied Mechanics and
Engineering, 194(48-49), p. 4915-4950, 2005.

X. S. Li, *"An Overview of SuperLU: Algorithms, Implementation, and User
Interface,"* ACM Trans. on Math. Software, **31**, 3, 2005.

X. S. Li, W. Gao, P. J. R. Husbands, C. Yang and E. G. Ng, *"The Roles
of Sparse Direct Methods in Large-Scale Simulations,"* Proc. of SciDAC
2005 meeting, San Francisco, Calif., June 2005.

Z. Li, A. Kabel, L. Ge, R. Lee, C.-K. Ng, G. Schussman, L. Xiao and K.
Ko, *"Electromagnetic Modeling For The ILC,"* International Linear
Collider Physics and Detector Workshop and 2^nd^ ILC accelerator
Workshop, Snowmass, Colo., Aug. 2005.

M. Liebendoerfer, M. Rampp, H.-T. Janka, A. Mezzacappa, *"Supernova
Simulations with Boltzmann Neutrino Transport: A Comparison of
Methods,"* Astrophysical Journal Letters, 620, 840-860, 2005.

H.-W. Lin and N. H. Christ, *"Non-perturbatively determined relativistic
heavy quark action,"* Proc. of XXIII International Symposium on Lattice
Field Theory (Lattice 2005), 225, 2005.

M.-F. Lin, *"Probing the chiral limit ofM~p~i and f~p~i in 2+1 flavor
QCD with domain wall fermions from QCDOC,"* Proc. of XXIII International
Symposium on Lattice Field Theory (Lattice 2005), 94, 2005.

Y. Lin, S. Wukitch, A. Parisot, J. C. Wright, N. Basse, P. Bonoli, E.
Edlund, L. Lin, M. Porkolab, G. Schilling and P. Phillips, *"Observation
and modeling of ion cyclotron range of frequencies waves in the mode
conversion region of Alcator C-Mod,"* Plasma Phys. and Control. Fusion
**47**, 1207, 2005.

Y. Lin, X. Wang, Z. Lin, and L. Chen, *"A Gyrokinetic Electron and Fully
Kinetic Ion Plasma Simulation Model,"* Plasma Phys. Contr. Fusion
**47**, 657, 2005.

Z. Lin, L. Chen, and F. Zonca, *"Role of Nonlinear Toroidal Coupling in
Electron Temperature Gradient Turbulence,"* Physics of Plasmas, **12**,
056125, 2005.

D.-J. Liu and J. W. Evans, *"From Atomic Scale Ordering to Mesoscale
Spatial Patterns in Surface Reactions: A Heterogeneous Coupled
Lattice-Gas (HCLG) Simulation Approach,"* SIAM Multiscale Modeling and
Simulation, 4, 424, 2005.

K. F. Liu and N. Mathur, *"A Review of Pentaquark Calculations on the
Lattice,"* Proc. of 2005 Int. Conf. on QCD and Hadron Physics, 2005.

X. Luo, L. Yin, M. S. Shephard, R. M. O'Bara, M. W. Beall, *"An
automatic adaptive directional variable p-version method for 3-D curved
domains,"* Proc. 8th US Nat. Congress on Comp. Mech., 2005.

E. Lusk, N. Desai, R. Bradshaw, A. Lusk and R. Butler, *"An
Interoperability Approach to System Software, Tools and Libraries for
Clusters,"* International Journal of High Performance Computing
Applications (to appear 2006).

K. L. Ma, E. B. Lum, H. Yu, H. Akiba, M. Y. Huang, M.-Y. Huang, Y. Wang
and G. Schussman, *"Scientific Discovery through Advanced
Visualization,"* Journal of Physics, **16**, DOE SciDAC 2005 Conference,
San Francisco, Calif., June 2005.

Q. Mason et al. (The HPQCD Collaboration), *"Accurate determinations of
alpha(s) from realistic lattice QCD,"* Physical Review Letters **95**,
052002, 2005.

T. Manteuffel, S. McCormick, J. Ruge and J. G. Schmidt, *"First-order
system LL\* (FOSLL\*) for general scalar elliptic problems in the
plane,"* SIAM Journal on Numerical Analysis, 43, 209, 2005.

T. Manteuffel, S. McCormick, O. Röhrle and J. Ruge, *"Projection
multilevel methods for quasilinear elliptic partial differential
equations: numerical results,"* SIAM Journal on Numerical Analysis, 44,
120, 2006.

T. Manteuffel, S. McCormick and O. Röhrle, *"Projection multilevel
methods for quasilinear elliptic partial differential equations:
theoretical results,"* SIAM Journal on Numerical Analysis, 44, 139,
2006.

J. Marathe, F. Mueller and B. R. de Supinski, *"A Hybrid
Hardware/Software Approach to Efficiently Determine Cache Coherence
Bottlenecks,"* Proc. of the International Conference on Supercomputing,
Heidelberg, Germany, June 2005.

D. F. Martin, P. Colella, M. Anghel, F. Alexander, [*"Adaptive mesh
refinement for multiscale nonequilibrium
physics,"*](http://seesar.lbl.gov/anag/publications/colella/A_1_59.pdf)
Computers in Science and Engineering, **7,** 3, p. 24-31, 2005.

N. Mathur, et al., *"Roper Resonance and S11(1535) from Lattice QCD,"*
Physics Letters B, **605,** 137, 2005.

S. McCormick, *"Projection multilevel methods for quasilinear elliptic
partial differential equations: V-cycle theory,"* SIAM J. Mult. Modeling
Sim., 4, 133, 2006.

P. McCorquodale, P. Colella, G. Balls, S. B. Baden, *"A scalable
parallel Poisson solver with infinite domain boundary conditions,"*
Proc. of the 7th Workshop on High Performance Scientific and Engineering
Computing, Oslo, Norway, June 2005.

D. M. Medvedev, E. M. Goldfield and S. K. Gray, *"An OpenMP/MPI Approach
to the Parallelization of Iterative Four-Atom Quantum Mechanics,"*
Computer Physics Comm. **166,** 94-108, 2005.

D. M. Medvedev, S. K. Gray, A. F. Wagner, M. Minkoff and R. Shepard,
*"Advanced Software for the Calculation of Thermochemistry, Kinetics,
and Dynamics,"* Journal of Physics: Conference Series **16**, 247-251,
2005.

J. E. Menard, R. E. Bell, E. D. Fredrickson, W. Park, et al., *"Internal
kink mode dynamics in high-beta NSTX plasmas,"* Nuclear Fusion **45**
(7), 539-556, 2005.

A. Mezzacappa, *"Ascertaining the Road Ahead,"* Annual Review of Nuclear
and Particle Science, 55, 467-515, 2005.

B. Mohr, A. Khnal, M.-A. Hermanns, F. Wolf, *"Performance Analysis of
One-sided Communication Mechanisms,"* Mini-Symposium *"Tools Support for
Parallel Programming,"* Proc. of Parallel Computing (ParCo), Malaga,
Spain, Sept. 2005.

S. Moore, F. Wolf, J. Dongarra, S. Shende, A. Malony, B. Mohr, *"A
Scalable Approach to MPI Application Performance Analysis,"* Proc. of
the 12th European Parallel Virtual Machine and Message Passing Interface
Conference, Sept. 2005.

S. Moore, F. Wolf, J. Dongarra, B. Mohr, *"Improving Time to Solution
with Automated Performance Analysis,"* Second Workshop on Productivity
and Performance in High-End Computing, 11th International Symposium on
High Performance Computer Architecture (HPCA-2005), San Francisco,
Calif., Feb. 2005.

J. Mueller, O. Sahni, K. E. Jansen, M. S. Shephard, "*An anisotropic
mesh adaption procedure for pulsatile blood flow simulation,"* Proc. 8th
US Nat. Congress on Comp. Mech., 2005.

J. Mueller, O. Sahni, K. E. Jansen, M. S. Shephard, C. A. Taylor, *"A
tool for the efficient FE-simulation of cardio-vascular flow,"* Proc.
2nd NAFEMS CFD Seminar: Simulation of Complex Flows (CFD), April 2005.

B. Mustapha, V. N. Aseev, P. Ostroumov, J. Qiang, R. Ryne, *"RIA Beam
Dynamics: Comparing TRACK to IMPACT,"* Proc. of Particle Accelerator
Conference (PAC 05), Knoxville, Tenn., May 2005.

J. R. Myra, D. A. D'Ippolito, D. A. Russell, L. A. Berry, E. F. Jaeger
and M. D. Carter, *"Nonlinear IRCR-Plasma Interactions,"* Radio
Frequency Power in Plasmas, Proc. 16^th^ Topical Conf., Park City, Utah,
2005.

H. N. Najm, J. C. Lee, M. Valorani, D. A. Goussis and M. Frenklach,
*"Adaptive chemical model reduction,"* Journal of Physics: Conference
Series, **16**, 101-106, June 2005.

D. Narayan, *"Bcfg2: A Pay As You Go Approach to Configuration
Complexity,"* Proc. of the 2005 Australian UNIX Users Group, Sydney,
Australia, Oct. 2005.

D. Narayan, E. Lusk and R. Bradshaw, *"{MPISH2}: Unix integration for
{MPI} programs,"* Proc, of EuroPVM-MPI 2005, Sept. 2005.

H. Nassar, M. Paul, I. Ahmand, J. Ben-Dov, J. Caggiano, S. Ghelberg, S.
Goriely, J. P. Greene, M. Hass, A. Heger, A. Heinz, D. J. Henderson, R.
V. F. Janssens, C. L. Jiang, Y. Kashiv, B. S. Nara Singh, A. Ofan, R. C.
Pardo, T. Pennington, K. E. Rehm, G. Savard, R. Scott and R. Vondrasek,
*"The ^40^Ca(α,γ)^44^Ti reaction in the energy regime of supernova
nucleosynthesis,"* Physical Review Letters, 96, 041102, 2006.

Y. Nishimura, Z. Lin, J. L. V. Lewandowski and S. Ethier, *"A Finite
Element Poisson Solver for Global Gyrokinetic Particle Simulations in a
Global Field Aligned Mesh,"* Journal of Computation & Physics, 214, 657,
2006.

B. Norris, L. McInnes, and I. Veljkovic, *"Computational quality of
service in parallel CFD,"* Proc. of the 17th International Conference on
Parallel Computational Fluid Dynamics, University of Maryland, College
Park, Md., May 2005.

M. Nuggehally, M. Picu, C. Shephard, M. S. Shephard, *"Adaptive model
selection procedure in multiscale problems,"* Proc. 8th US Nat. Congress
on Comp. Mech., 2005.

M. Okamoto, et al. (The Fermilab Lattice, HPQCD and MILC
Collaborations), *"Semileptonic D → Π/K and B → Π /D decays in 2+1
flavor lattice QCD,"* Nuclear Physics B (Proc. Suppl.) **140**, 461,
2005.

L. Oliker, J. Carter, M. Wehner, A. Canning, S. Ethier, A. Mirin, G.
Bala, D. Parks, P. Worley, S. Kitawaki and Y. Tsuda, *"Leading
Computational Methods on Scalar and Vector HEC Platforms,"* Proc. of the
ACM/IEEE SC05 conference, Seattle, Wash., Nov. 2005.

O. O. Oluwole and W. H. Green, *"Rigorous Error Control in Reacting Flow
Simulations Using Reduced Chemistry Models,"* Computational Fluid and
Solid Mechanics: Proceedings of the Third MIT Conference on
Computational Fluid and Solid Mechanics, ed. by K. J. Bathe, Elsevier,
2005.

C. D. Ott, S. Ou, J. E. Tohline and A. Burrows, *"One-armed Spiral
Instability in a Low-T/\|W\| Postbounce Supernova Core,"* ApJ. Letters,
625:L119-L122, June 2005.

C. Ozen, D. J. Dean, *"Shell Model Monte Carlo method in the
pn-formalism and applications to the Zr and Mo isotopes,"* ArXiv Nuclear
Theory e-prints, Aug. 2005.

J. E. Penner, M. Herzog, C. Jablonowski, B. van Leer, R. C. Oehmke, Q.
F. Stout and K. G. Powell, *"Development of an atmospheric climate model
with self-adapting grid and physics,"* Journal of Physics: Conference
Series, **16**, 353, 2005.

P. Petreczky, K. Petrov, D. Teaney and A. Velytsky, *"Heavy quark
diffusion and lattice correlators,"* Proc. of XXIII International
Symposium on Lattice Field Theory (Lattice 2005), 185, 2005.

K. Petrov, A. Jakovac, P. Petreczky and A. Velytsky, *"Bottomonia
correlators and spectral functions at zero and finite temperature,"*
Proc. of XXIII International Symposium on Lattice Field Theory (Lattice
2005), 153, 2005.

J. Petrovic, N. Langer, S.-C. Yoon and A. Heger*, "Which massive stars
are gamma-ray burst progenitors?"* Astronomy & Astrophysics,
435:247-259, May 2005.

L. R. Petzold, Y. Cao, S. Li and R. Serban, *"Sensitivity Analysis of
Differential-Algebraic Equations and Partial Differential Equations,"*
Proc. of the Chemical Process Control Conference, Lake Louise, Alberta,
Canada, Jan. 2006.

J. Pjesivac-Grbovic, T. Angskun, G. Bosilca, G. Fagg, E. Gabriel, J.
Dongarra, *"Performance Analysis of MPI Collective Operations,"* 4th
International Workshop on Performance Modeling, Evaluation, and
Optmization of Parallel and Distributed Systems (PMEO-PDS 2005), Denver,
Colo., April 2005.

A. Pochinsky*, "Domain Wall Fermion Inverter on Pentium 4,"* Nuclear
Physics B (Proc. Suppl.) **140**, 859, 2005.

E. Prudencio, R. Byrd, and X.-C. Cai, *"Parallel full space SQP
Lagrange-Newton-Krylov-Schwarz algorithms for PDE-constrained
optimization problems,"* SIAM Journal of Scientific Computing, 27, 130,
2006.

J. Pruet, S. E. Woosley, R. Buras, H.-T. Janka and R. D. Hoffman,
*"Nucleosynthesis in the Hot Convective Bubble in Core-Collapse
Supernovae,"* ApJ, 623:325-336, April 2005.

J. Qiang, *"Terascale Beam-Beam Simulations for Tevatron, RHIC and
LHC,"* Proc. PAC2005, Knoxville, Tenn., May 2005.

J. Qiang, M. A. Furman, R. D. Ryne, W. Fischer, K. Ohmi, *"Recent
advaces of strong-strong beam-beam simulation,"* Nuclear Instruments &
Methods in Physics Research A, 558, 351, 2006.

J. Qiang, S. M. Lidia, R. Ryne, C. Limborg-Deprey, *"A 3D Parallel Beam
Dynamics Code for Modeling High Brightness Beams in Photoinjectors,"*
Proc. PAC2005, Knoxville, Tenn., May 2005.

J. Qiang, D. Leitner, D. Todd, *"A Parallel 3D Model for the
Multi-Species Low Energy Beam Transport System of the RIA Prototype ECR
Ion Source VENUS,"* Proc. PAC2005, Knoxville, Tenn., May 2005.

P. Raghavan, M. J. Irwin, L. C. McInnes and B. Norris, *"Adaptive
software for scientific computing: Co-managing quality-performance-power
tradeoffs,"* Proc. of the IEEE International Parallel & Distributed
Processing Symposium 2005, IEEE Computer Society Press, 2005.

J. J. Ramos, *"Fluid formalism for collisionless magnetized plasmas,"*
Physics of Plasmas **12,** 052102, 2005.

J. J. Ramos, *"General expression of the gyroviscous force,"* Physics of
Plasmas **12,** 112301, 2005.

N. S. Rao, S. M. Carter, Q. Wu, W. R. Wing, M. Zhu, A. Mezzacappa, M.
Veeraraghavan, J. M. Blondin, *"Networking for large-scale science:
infrastructure, provisioning, transport and application mapping,"*
Journal of Physics Conference Series, 16, 541-545, 2005.

J. Ray, C. Kennedy, J. Steensland and H. Najm, *"Advanced algorithms for
computations on block-structured adaptively refined meshes,"* Journal of
Physics: Conference Series, **16**:113-118, June 2005.

D. A. Reed, C. Lu and C. L. Mendes, *"[Reliability Challenges in Large
Systems](http://dx.doi.org/10.1016/j.future.2004.11.015),"* Future
Generation Computer Systems, 22, 293,2006.

J. F. Remacle, S. S. Frazao, M. S. Shephard, M. S. Flaherty, *"An
Adaptive Discretization of Shallow Water Equations based on
Discontinuous Galerkin Methods,"* International Journal for Numerical
Methods in Fluids, 62(7), pp. 899-923, 2005.

J. F. Remacle, X. Li, M. S. Shephard, J. E. Flaherty, *"Anisotropic
Adaptive Simulation of Transient Flows using Discontinuous Galerkin
Methods,"* International Journal for Numerical Methods in Engineering,
62, pp. 899-923, 2005.

D. B. Renner, et al. (The LHPC Collaboration), *"Hadronic physics with
domain-wall valence and improved staggered sea quarks,"* Nuclear
Physics. (Proc. Suppl.) **140**, 255, 2005.

G. Rewoldt, *"Particle-In-Cell simulations of electron transport,"*
invited talk, SciDAC Conference, San Francisco, Calif., June 2005.

D. G. Richards, *"Lattice studies of baryons,"* Journal of Physics Conf.
Ser. **9**, 238, 2005.

G. Rockefeller, C. L. Fryer, F. K. Baganoff and F. Melia, *"The X-ray
Ridge Surrounding Sgr A\* at the Galactic Center,"* ArXiv Astrophysics
e-prints, June 2005.

G. Rockefeller, C. L. Fryer, and F. Melia, *"Spin-Induced Disk
Precession in Sagittarius A\*,"* ArXiv Astrophysics e-prints, July 2005.

F. K. Roepke, W. Hillebrandt, J. C. Niemeyer, and S. E. Woosley,
*"Multi-spot ignition in type Ia supernova models,"* ArXiv Astrophysics
e-prints, Oct. 2005.

T. M. Rogers and G. A. Glatzmaier, *"Penetrative Convection within the
Anelastic Approximation,"* ApJ, 620:432-441, Feb. 2005.

D. Rotem, K. Stockinger, and K. Wu, *"Optimizing candidate check costs
for bitmap indices,"* Proc. of CIKM 2005, ACM Press, 2005.

D. Rotem, K. Stockinger, and K. Wu, *"Optimizing i/o costs of
multi-dimensional queries using bitmap indices,"* in DEXA, Lecture Notes
in Computer Science **3588,** p. 220. Springer-Verlag, 2005.

B. Ruscic, J. E. Boggs, A. Burcat, A. G. Csaszar, J. Demaison, R.
Janosche, J. M. L. Martin, M. L. Morton, M. J. Rossi, J. F. Stanton**,**
P. G. Szalay, P. R. Westmoreland, F. Zabel, T. Berces, *"IUPAC critical
evaluation of thermochemical properties of selected radicals: Part I,"*
Journal of Physical and Chemical Reference Data, **34**(2), 573-656,
2005.

B. Ruscic, R. E Pinzon, G. Von Laszewski, D. Kodeboyina, A. Burcat, D.
Leahy, D. Montoya, A. F. Wagner**,** *"Active thermochemical tables:
Thermochemistry for the 21st Century,"* Journal of Physics: Conference
Series, **16**:561-570, 2005.

R. Ryne, D. Abell, A. Adelmann, J. Amundson, C. Bohn, J. Cary, P.
Colella, D. Dechow, V. Decyk, A. Dragt, R. Gerber, S. Habib, D. Higdon,
T. Katsouleas, K.-L. Ma, P. McCorquodale, D. Mihalcea, C. Mitchell, W.
Mori, C. T. Mottershead, F. Neri, I. Pogorelov, J. Qiang, R. Samulyak,
D. Serafini, J. Shalf, C. Siegerist, P. Spentzouris, P. Stoltz, B.
Terzic, M. Venturini, P. Walstrom, *"SciDAC Advances and Applications in
Computational Beam Dynamics,"* Proceeding of SciDAC 2005, June 26-30,
San Francisco, Calif., June 2005.

M. J. Savage, *"Nuclear Physics and QCD,"* Proc. of XXIII International
Symposium on Lattice Field Theory (Lattice 2005), 020, 2005.

E. Scannapieco, P. Madau, S. Woosley, A. Heger and A. Ferrara*, "The
Detectability of Pair-Production Supernovae at z \< 6,"* Astrophysical
Journal, 633, 1031, 2005.

D. P. Schissel, *"Advances in Remote Participation for Fusion
Experiments,"* Proc. of the 21st IEEE/NPSS Symposium on Fusion
Engineering, 2005.

D. P. Schissel, et al., *"The Collaborative Tokamak Control Room,"* The
5th IAEA Technical Meeting on Control, Data Acquisition, and Remote
Participation for Fusion Research, 2005.

D. P. Schissel, *"Advances in the Real-Time Interpretation of Fusion
Experiments,"* Proceedings of SciDAC 2005, Journal of Physics:
Conference Series, Institute of Physics, San Francisco, Calif., June
2005.

D. P. Schissel, et al., *"Grid Computing and Collaboration Technology in
Support of Fusion Energy Sciences,"* Physics of Plasmas **12**, 058104,
2005.

D. P. Schissel, et al., *"Advances in Remote Participation for Fusion
Experiments,"* The 23rd Symposium on Fusion Technology, 2005.

W. J. Schroeder, M. S. Shephard, *"Computational Visualization,"*
Encyclopedia of Computational Mechanics, E. Stein, R. DeBorst, T.J.R.
Hughes, eds., Wiley, 2005.

K. Schuchardt, O. Oluwole, W. Pitz, L. A. Rahn, J. William, H. Green, D.
Leahy, C. Pancerella, M. Sjöberg and J. Dec, *"New Approaches for
Collaborative Sharing of Chemical Model Data and Analysis Tools,"* 2005
Joint Meeting of the US Sections of the Combustion Institute, 2005.

K. Schuchardt, O. Oluwole, W. Pitz, L. A. Rahn, J. William, H. Green, D.
Leahy, C. Pancerella, M. Sjöberg, J. Dec, *"Development of the RIOT web
service and information technologies to enable mechanism reduction for
HCCI simulations,"* Journal of Physics: Conference Series,
**16**:107‑112, 2005.

M. Schulz, D. Ahn, A. Bernat, B. R. de Supinski, S. Ko, G. Lee and B.
Rountree, *"Scalable Dynamic Binary Instrumentation for BlueGene/L,"*
Workshop on Binary Instrumentation and Applications, Sept. 2005.

P. Schwartz, D. Adalsteinsson, P. Colella, A. P. Arkin, M. Onsum,
[*"Numerical computation of diffusion on a
surface,"*](http://seesar.lbl.gov/anag/publications/colella/SchwartzETALPNAS.pdf)
Proc. Nat. Acad. Sci*.,* **102**, p. 11151-11156, 2005.

P. Schwartz, M. Barad, P. Colella, T. J. Ligocki, [*"A Cartesian grid
embedded boundary method for the heat equation and Poisson\'s equation
in three
dimensions,"*](http://seesar.lbl.gov/anag/publications/colella/LBNL-56607.pdf)
Journal of Computational Physics **211**, p. 531-550, 2006.

E. S. Seol, M. S. Shephard, *"A Flexible Distributed Mesh Data Structure
to Support Parallel Adaptive Analysis,"* Proc. 8th US Nat. Congress on
Comp. Mech., 2005.

R. Serban and A. C. Hindmarsh, *"CVODES: the Sensitivity-Enabled ODE
Solver in SUNDIALS,"* Proc. of the 5th International Conference on
Multibody Systems, Nonlinear Dynamics and Control, Long Beach, Calif.,
Sept. 2005.

B. A. Shadwick, G. M. Tarkenton, E. Esarey and C. B. Schroeder, *"Fluid
and Vlasov models of low temperature, collisionless laser-plasma
interactions,"* Physics of Plasmas, **12**, 5, p. 56710-18, May 2005.

S. Shende, A. Malony, A. Morris, F. Wolf, *"Performance Profiling
Overhead Compensation for MPI Programs,"* Proc. of the 12th European
Parallel Virtual Machine and Message Passing Interface Conference, Sept.
2005.

M. S. Shephard, A. C. Bauer, E. S. Seol, J. Wa., "*Construction of
Adaptive Simulation Loops,"* Proc. 8th US Nat. Congress on Comp. Mech.,
2005.

M. S. Shephard, J. E. Flaherty, K. E. Jansen, X. Li, X. j. Luo, N.
Chevaugeon, J. F. Remacle, M. W. Beall, R. M. O'Bara, "*Adaptive mesh
generation for curved domains*," Applied Numerical Mathematics, 53(2-3)
p. 251-271, 2005.

R. Shepard, M. Minkoff, and Y. Zhou, *"Software for Computing Eigenvalue
Bounds for Iterative Subspace Methods,"* Computer Physics Comm*.*
**170**, 109-114, 2005.

M. S. Shephard, E. Seol, J. Wan, A. C. Bauer, *"Component-based adaptive
control procedures,"* Proc. from the Conference on Analysis, Modeling
and Computation of PDE and Multiphase Flow, Kluwer Academic Press, 2005.

J. Shigemitsu, et al. (The HPQCD Collaboration)*, "Semileptonic B Decays
with Nf = 2+1 Dynamical Quarks,"* Nuclear Physics (Proc. Suppl.)
**140**, 464, 2005.

J. N. Simone, et al. (The Fermilab Lattice, HPQCD and MILC
Collaborations), *"Leptonic decay constants fDs and fD in three flavor
lattice QCD,"* Nuclear Physics B (Proc. Suppl.) **140**, 443, 2005.

A. Socrates, O. Blaes, A. Hungerford, and C. L. Fryer*, "The Neutrino
Bubble Instability: A Mechanism for Generating Pulsar Kicks,"*
Astrophysical Journal, 632:531-562, Oct. 2005.

C. R. Sovinec, and C. C. Kim, D. D. Schnack, A. Y. Pankin, S. E. Kruger,
E. D. Held, D. P. Brennan, D. C. Barnes, X. S. Li, D. K. Kaushik, S. C.
Jardin and the NIMROD Team, *"Nonlinear Magnetohydrodynamic (MHD)
Simulations using High-Order Finite Elements,"* SciDAC 2005 meeting,
Journal of Physics: Conference Series, **16**, p. 25-34, San Francisco,
Calif., June 2005.

C. Stan, *"The mean meridional circulation: A new potential-vorticity,
potential-temperature perspective,"* Ph.D. thesis, Colorado State
University. 2005.

A. W. Steiner, M. Prakash, J. M. Lattimer, P. J. Ellis, *"Isospin
asymmetry in nuclei and neutron stars,"* Physics Reports, 411, 325-375,
2005.

K. Stockinger, J. Shalf, E. W. Bethel and K. Wu, *"Dex: Increasing the
capability of scientific data analysis pipelines by using efficient
bitmap indices to accelerate scientific visualization,"* Proc. of 2005
Scientific and Statistical Database Management Conference, p. 35, 2005.

K. Stockinger, J. Shalf, E. W. Bethel and K. Wu, *"Query-driven
visualization of large data sets,"* IEEE Visualization 2005,
Minneapolis, MN, Oct. 2005.

K. Stockinger, K. Wu, R. Brun and P. Canal, *"Bitmap indices for fast
end-user physics analysis in Root,"* Nuclear Instruments and Methods in
Physics Research Section A, 539, 99, 2006.

K. Stockinger, K. Wu, S. Campbell, S. Lau, M. Fisk, E. Gavrilov, A.
Kent, C. E. Davis, R. Olinger, R. Young, J. Prewett, P. Weber, T. P.
Caudell, E. W. Bethel and S. Smith, *"Network traffic analysis with
query driven visualization,"* Proc. of the ACM/IEEE SC05 conference,
Seattle, Wash., Nov. 2005.

P. Strack and A. Burrows*, "Generalized Boltzmann formalism for
oscillating neutrinos,"* Physics Rev. D, **71**(9), 093004, May 2005.

L. Sugiyama, W. Park, H. R. Strauss, G. Fu, J. Breslau, J. Chen and S.
Klasky, *"Plasmas beyond MHD: two-fluids and symmetry breaking,"*
Journal of Physics: Conference Series **16,** 54-58, 2005.

F. D. Swesty, E. S. Myra, *"Multigroup models of the convective epoch in
core collapse supernovae,"* Journal of Physics Conference Series, 16,
380-389, 2005.

S. Tamhankar, et al., *"Charmonium Spectrum from Quenched QCD with
Overlap Fermions,"* Nuclear Physics B (Proc. Suppl.), **140,** 434,
2005.

T. A. Thompson, E. Quataert, and A. Burrows, *"Viscosity and Rotation in
Core-Collapse Supernovae,"* Astrophysical Journal, 620:861-877, Feb.
2005.

D. Trebotich, G. H. Miller, P. Colella, D. T. Graves, D. F. Martin, P.
O. Schwartz, *"A tightly coupled particle-fluid model for DNA-laden
flows in complex microscale geometries,"* Proc. of the Third MIT
Conference on Computational Fluid and Solid Mechanics, June 2005.

D. Trebotich, P. Colella, G. H. Miller, *"[A stable and convergent
scheme for viscoelastic flow in contraction
channels,"](http://seesar.lbl.gov/anag/publications/colella/A_1_57.pdf)*
J. Comput. Phys*.* **205**, p. 315-342, 2005.

D. Todd, D. Leitner, C. Lyneis, J. Qiang, D. Grote, *"Particle-in-Cell
Simulations of the VENUS Ion Beam Transport System,"* Proc. PAC2005,
Knoxville, Tenn., May 2005.

D. Toussaint and C. Davies (MILC and UKQCD Collaborations), *"The Ω− and
the strange quark mass,"* Nuclear Physics B (Proc. Suppl.), **140**,
234, 2005.

T. Tu, D. O\'Hallaron, and O. Ghattas, *"Scalable parallel octree
meshing for terascale applications,"* Proceedings of the ACM/IEEE SC05
conference, Seattle, Wash., November 2005.

R. Tweedie, *"Light meson masses and decay constants in a 2+1 flavour
domain wall QCD,"* Proc. of XXIII International Symposium on Lattice
Field Theory (Lattice 2005), 080, 2005.

F. Y. Tzeng and K. L. Ma, *"Intelligent Feature Extraction and Tracking
for Large-Scale 4D Flow Simulations,"* Proc. of the ACM/IEEE SC05
conference, Seattle, Wash., Nov. 2005.

M. Valorani, F. Creta, D. A. Goussis, H. N. Najm, and J. C. Lee,
*"Chemical kinetics mechanism simplification via CSP,"* Computational
Fluid and Solid Mechanics 2005, K. J. Bathe, ed., p. 900, Elsevier,
2005.

M. Valorani, D. A. Goussis, F. F. Creta and H. N. Najm, *"Higher Order
Corrections in the Approximation of Low Dimensional Manifolds and the
Construction of Simplified Problems with the CSP Method,"* Journal of
Computational Physics, **209**(2), 754-786, Nov. 2005.

J-L. Vay, P. Colella, P. McCorquodale, D. Serafini, V. Straalen, A.
Friedman, D. P. Grote, J-C. Adam, A. Héron, *"Application of Adaptive
Mesh Refinement to Particle-In-Cell Simulations of Plasmas and Beams,"*
Workshop on Multiscale Processes in Fusion Plasmas, IPAM, Los Angeles,
Calif., Jan. 2005.

J.-L. Vay, M. Furman, R. Cohen, A. Friedman, D. Grote, *"Initial
self-consistent 3-D electron-cloud simulations of LHC beam with the code
WARP+POSINST,"* Proc. PAC2005, Knoxville, Tenn., May 2005.

J. Vetter, B. R. de Supinski, J. May, L. Kissel and S. Vaidya,
*"Evaluating High Performance Computers,"* in Concurrency: Practice and
Experience, **17,** 1239, 2005.

J. S. Vetter, S. R. Alam, T. H. Dunigan, Jr., M. R. Fahey, P. C. Roth
and P. H. Worley, *"Early Evaluation of the Cray XT3 at ORNL,"* Proc. of
the 47th Cray User Group Conference, Albuquerque, NM, May 2005.

R. Vuduc, J. Demmel and K. Yelick, *"OSKI: A library of automatically
tuned sparse matrix kernels,"* Proc. of SciDAC 2005, Journal of Physics:
Conference Series, San Francisco, Calif., June 2005.

R. Vuduc, and H.-J. Moon, *"Fast sparse matrix-vector multiplication by
exploiting variable block structure,"* Proc. of the International
Conference on High-Performance Computing and Communications, Sorrento,
Italy, Sept. 2005.

G. Wallace, et al*., "Tools and Applications for Large-Scale Display
Walls,"* IEEE Computer Graphics & Applications, Special Issue on Large
Displays, 25, 24, July/Aug. 2005.

R. Walder, A. Burrows, C. D. Ott, E. Livne, I. Lichtenstadt and M.
Jarrah, *"Anisotropies in the Neutrino Fluxes and Heating Profiles in
Two-dimensional, Time-dependent, Multigroup Radiation Hydrodynamics
Simulations of Rotating Core-Collapse Supernovae,"* Astrophysical
Journal, 626:317-332, June 2005.

W. Wan, Y. Chen, S. E. Parker, *"Gyrokinetic delta f simulation of the
collisionless and semicollisional tearing mode instability,"* Physics of
Plasmas **12,** 012311, 2005.

J. Wan, M. S. Shephard, *"Contact Surface Control in Forming
Simulations,"* Proc. 8th US Nat. Congress on Comp. Mech., 2005.

W. X. Wang, *"Neoclassical and turbulent transport in shaped toroidal
plasmas,"* invited talk, APS/DPP meeting, Denver, Colo., 2005.

J. Weinberg, M. O. MCracken, A. Snavely, and E. Strohmaier,
*"Quantifying Locality in the Memory Access Patterns of HPC
Applications,"* Proc. of the ACM/IEEE SC05 conference, Seattle, Wash.,
Nov. 2005.

V. Wheatley, D. I. Pullin and R. Samtaney, *"On the regular refraction
of a MHD shock at a density interface,"* Journal of Fluid Mechanics,
**522,** 179-214, 2005.

V. Wheatley, D. I. Pullin, and R. Samtaney, and R. Samtaney*, "Stability
of an impulsively accelerated density interface in MHD,"* Physical
Review Letters **95,** 12, 2005.

B. S. White, S. A. McKee, B. R. de Supinski, B. Miller, D. Quinlan and
M. Schulz, *"Improving the Computational Intensity of Unstructured Mesh
Applications,"* Proceedings of the International Conference on
Supercomputing, Heidelberg, Germany, June 2005.

B. Willems, M. Henninger, T. Levin, N. Ivanova, V. Kalogera, K. McGhee,
F. X. Timmes, and C. L. Fryer, *"Understanding Compact Object Formation
and Natal Kicks. I. Calculation Methods and the Case of GRO J1655-40,"*
Astrophysical Journal, 625, 324-346, May 2005.

F. Wolf, A. Malony, S. Shende, A. Morris, *"Trace-Based Parallel
Performance Overhead Compensation,"* Proc. of the International
Conference on High Performance Computing and Communications (HPCC),
Sorrento, Italy, Sept.2005.

S. E. Woosley and T. Janka*, "The Physics of Core-Collapse Supernovae,"*
Nature Physics, 1, 147, 2005.

P. H. Worley, S. Alam, T. H. Dunigan, Jr., M. R. Fahey and J. S. Vetter,
*"Comparative Analysis of Interprocess Communication on the X1, XD1, and
XT3,"* Proc. of the 47th Cray User Group Conference, Albuquerque, NM,
May 2005.

P. H. Worley and J. B. Drake, *"Performance Portability in the Physical
Parameterizations of the Community Atmospheric Model,"* International
Journal for High Performance Computer Applications, **19**(3), p. 187,
Aug. 2005.

J. C Wright, L. A. Berry, P. T. Bonoli, D. B. Batchelor, E. F. Jaeger,
M. D. Carter, E. D'Azevedo, C. K. Phillips, H. Okuda, R. W. Harvey, D.
N. Smithe, J. R. Myra, D. A. D'Ippolito, M. Brambilla and R. J. Dumont,
*"Nonthermal particle and full-wave diffraction effects on heating and
current drive in the ICRF and LHRF regimes,"* Nuclear Fusion **45**,
1411, 2005.

J. C. Wright, P. T. Bonoli, M. Brambilla, E. D'Azevedo, L. A. Berry, D.
B. Batchelor, E. F. Jaeger, M. D. Carter, C. K. Phillips, H. Okuda, R.
W. Harvey, J. R. Myra, D. D'Ippolito and D. N. Smithe, *"Full-wave
Electromagnetic Field Simulation of Lower Hybrid Waves in Tokamaks,"*
Radio Frequency Power in Plasmas, Proc. 16^th^ Topical Conf., Park City,
Utah, 2005.

K. Wu, J. Ekow, E. J. Otoo, and A. Shoshani, *"An efficient compression
scheme for bitmap indices,"* ACM Transactions on Database Systems, to
appear.

K. Wu, J. Gu, J. Lauret, A. M. Poskanzer, A. Shoshani, A. Sim, and W. M.
Zhang, *"Grid collector: Facilitating efficient selective access from
data grids,"* Proc. of International Supercomputer Conference,
Heidelberg, Germany, June 2005.

B. Wylie, B. Mohr, F. Wolf, *"Holistic hardware counter performance
analysis of parallel programs short version:,"* Proceedings of Parallel
Computing 2005 (ParCo 2005), Malaga, Spain, Sept. 2005.

A. Yamaguchi, *"Chiral condensate and spectral flows on 2+1 flavours
Domain Wall QCD from QCDOC,"* Proc. of XXIII International Symposium on
Lattice Field Theory (Lattice 2005), 135, 2005.

T. Yamaguchi, *"Entraining cloud-topped boundary layers,"* M.S. Thesis,
Colorado State University, 2005.

C. Yang, *"Solving Large-scale Eigenvalue Problems in SciDAC
Applications,"* SciDAC 2005 meeting, Journal of Physics: Conference
Series, **16**, p. 425-434, San Francisco, Calif., June 2005.

C. Yang, W. Gao, Z. Bai, X. Li, L.-Q. Lee, P. Husbands, and E. Ng, *"An
Algebraic Sub-Structuring for Large-Scale Eigenvalue Calculation,"* SIAM
Journal on Scientific Computing, 27, 873, 2005.

U. M. Yang, *"Parallel Algebraic Multigrid Methods - High Performance
Preconditioners,"* chapter in Numerical Solution of Partial Differential
Equations on Parallel Computers, A. M. Bruaset, P. Bjørstad, and A.
Tveito, eds., Springer-Verlag, 2006.

L. Yin, X. Luo, M. S. Shephard, *"Identifying and meshing thin section
of 3-d curved domains,"* Proc. 14th International Meshing Roundtable, p.
33-54, Springer, 2005.

H. Yu and K.-L. Ma, *"A Study of I/O Techniques for Parallel
Visualization,"* Journal of Parallel Computing, **31**, 2, p. 167-183,
Feb. 2005.

P. A. Young, C. Meakin, D. Arnett, and C. L. Fryer, *"The Impact of
Hydrodynamic Mixing on Supernova Progenitors,"* Astrophysical Journal
Letters, 629:L101-L104, Aug. 2005.

Y. Zhang, X. S. Li, and O. Marques, *"Towards an Automatic and
Application-Based Eigensolver Selection,"* LACSI Symposium 2005, Santa
Fe, NM, 87501, Oct. 2005.

Y. Zhou, R. Shepard and M. Minkoff, *"Computing Eigenvalue Bounds for
Iterative Subspace Methods,"* Computer Physics Comm*.* **167**, 90-102,
2005.

M. Zingale, S. E. Woosley, C. A. Rendleman, M. S. Day, and J. B. Bell,
*"Three-dimensional Numerical Simulations of Rayleigh-Taylor Unstable
Flames in Type Ia Supernovae,"* Astrophysical Journal, 632, 1021-1034,
Oct. 2005.