2004 Journal Papers and Book Chapters

• Abdulla, G., T. Critchlow, W. Arrighi, “Simulation Data as Data Streams,” SIGMOD Record, Vol 33, Num 1, March 2004.  UCRL-JC-152697.
• Allesch, M.; E. Schwegler, F.Gygi and G.Galli, “A First-Principles Simulation of Rigid Water”, J. Chem. Phys. 120, p. 5192 (2004). UCRL-JRNL-200807
• Anderson, R.W., Pember, R.B., Elliott, N.S. “A Dynamically Adaptive Lagrangian Eulerian Method for Hydrodynamics,” Computational Fluid and Solid Mechanics 2003.  2003, Elsevier Science, K.J. Bathe (Editor). UCRL-JC-150660, January 2003.
• Armstrong, R., G. Kumfert, L.C. McInnes, S. Parker, B. Allan, M. Sottile, T. Epperly, and T. Dahlgren, “The CCA Component Model for High-Performance Scientific Computing,” The International Journal of Concurrency and Computation: Practice and Experience (2004), to appear.  UCRL-JRNL-208616.
• Baker, A.H., E.R. Jessup, and T. Manteuffel, “A Technique for Accelerating the Convergence of Restarted GMRES,” SIAM Journal on Matrix Analysis and Applications, 2004, to appear.  UCRL-JRNL-202883.
• Bernholdt, D, E., B.A. Allan, R. Armstrong, F. Bertrand, K. Chiu, T.L. Dahlgren, K. Damevski, W.R. Elwasif, T.G.W. Epperly, M. Govindaraju, D.S. Katz, J.A. Kohl, M. Krishnan, G. Kumfert, J.W. Larson, S. Lefantzi, M.J. Lewis, A.D. Malony, L.C. McInnes, J. Nieplocha, B. Norris, S.G. Parker, J. Ray, S. Shende, T.L. Windus, and S. Zhou, “A Component Architecture for High Performance Scientific Computing,” The International Journal of High-Performance Computing Applications (2004), ACTS Collection special issue. UCRL-JRNL-208635
• Bertram, M.,  Mark A. Duchaineau, Bernd Hamann, Kenneth I. Joy, "Generalized B-spline subdivision-surface wavelets for geometry compression", IEEE Transactions on Visualization and Computer Graphics, Volume 10, Issue 3, May 2004, pp 326-338. UCRL-JP-200042.
• Bremer, P.-T. , H. Edelsbrunner, B. H. Edelsbrunner, and V. Pascucci. “A topological hierarchy for functions on triangulated surfaces”. IEEE Transactions on Visualization and Computer Graphics, 10(4):385–396, July/August 2004. UCRL-JRNL-208700
• Brezina, M., R. Falgout, S. MacLachlan, T. Manteuffel, S. McCormick, and J. Ruge, “Adaptive Smoothed Aggregation (aSA),” SIAM Journal on Scientific Computing, 25 (2004), pp. 1896–1920.  Available as LLNL technical report UCRL-JC-151149.
• Brezina, M.; C. Tong, and R. Becker; Parallel Algebraic Multigrids for Structural Mechanics, accepted for publication in SISC, 2004.  UCRL-JRNL-204167.
• Brown, P.N., D.E. Shumaker, and C.S. Woodward, “Fully Implicit Solution of Large-Scale Non-Equilibrium Radiation Diffusion with High Order Time Integration,” Journal on Computational Physics, to appear, 2005, UCRL-JRNL-203809.
• Buehler, M.J.,  A. Hartmaier, H. Gao, M. Duchaineau and F.F. Abraham, "Atomic Plasticity: Description and Analysis of a One-Billion Atom Simulation of Ductile Materials Failure", Computer Methods in Applied Mechanics and Engineering, Vol. 193(48-51), 2004, pp. 5257-5282. UCRL-JRNL-204002
• Buttler, D., T. Critchlow, “Using meta-data to automatically wrap bioinformatics sources”,  Information and Software Technology, Vol. 44, Num 4, Pages 237-239, Mar. 2004.  UCRL-JC-144895.
• Cai, Z., B. Lee, and P. Wang, Least-squares methods for incompressible Newtonian fluid flow: linear stationary problems, SIAM J. Numer. Anal., 42:2 (2004), 843-859.
• Cantú-Paz, E., “Theory of parallel genetic algorithms,” chapter in Parallel Metaheuristics, Springer Verlag. UCRL-MI-206366.  (accepted in 2004) 
• Chand, K., “Component Based Hybrid Mesh Generation,” International Journal for Numerical Methods in Engineering, Published Online Nov. 15, 2004 (print version forthcoming).  UCRL-JC-150594.
• Cheung S.C. and Kamath, C., “Robust background subtraction with foreground validation for urban traffic video”, accepted, Eurasip Journal on applied signal processing. UCRL-JRNL-201916.
• Chiarappa-Zucca, M., R. Finkel, R. Martinelli, J. McAninch, D. Nelson, and K. Turteltaub. Measurement of beryllium in biological samples by accelerator mass spectrometry: Applications for studying chronic beryllium disease. Chem Res Toxicol, 17(12):1614–1620, 12 2004. UCRL-JRNL-203701.
• Chow, E., R.D. Falgout, J.J. Hu, R.S. Tuminaro, and U.M. Yang, "A Survey of parallelization Techniques for Multigrid Solvers", chapter in Frontiers of Parallel Processing For Scientific Computing, M.H. Heroux, P. Raghavan, and H.D. Simon, editors, SIAM, series on Software, Environments, and Tools, 2004, to appear.  UCRL-BOOK-205864.
• Chow, Edmond, “An aggregation multilevel method using smooth error vectors,” SIAM Journal on Scientific Computing, to appear.  UCRL-JRNL-204139.
• Cole-McLaughlin, K. ,  H. Edelsbrunner, J. Harer, V. Natarajan, and V. Pascucci. “Loops in reeb graphs of 2-manifolds”. Discrete and Computational Geometry, 32(2):231–244, July 2004. UCRL-JRNL-208701
• Cook, R.,  Nelson Max, Claudio Silva, and Peter Williams, “Image-Space Visibility Ordering for Cell Projection Volume Rendering of Unstructured Data”, IEEE Transactions on Visualization and Computer Graphics, Vol. 10 No. 6, pp. 695 – 707. UCRL-JC-146582-Rev-1.
• Covello, P., G. Rodrigue, Solving the Eikonal Equation on an Adaptive Mesh, to be published J. App. Comp. Math. Need UCRL number.
• Downing, G.L., P.F. Dubois, T. Cottom, “Data Sharing in Scientific Simulations”, Computing in Science and Engineering, v.6 #3, May 2004. UCRL-JRNL-202641
• Draeger, Erik W.; Jeffrey C. Grossman, Andrew J. Williamson, and Giulia Galli, ”Optical properties of passivated silicon nanoclusters:  the role of synthesis”, J. Chem. Phys. 120, 10807 (2004).  UCRL-JRNL-203580.
• Eder, D. C., Koniges, A. E., Jones, O. S., Marinak M. M., Tobin, M. T., MacGowan, B. J., “Late-time simulations of National Ignition Facility hohlraums, Nucl. Fusion 44, 2004, pp. 709–719. UCRL-JRNL-206693
• Efroymson, R. A., Carlsen, T. M., Jager, H. I., Kostova, T., Carr, E. A., Hargrove, W. W., Kercher, J., and Ashwood, T. L., “Toward a Framework for Assessing Risk to Vertebrate Populations from Brine and Petroleum Spills at Exploration and Production Sites,” chapter in Landscape Ecology and Wildlife Habitat Evaluation:  Critical Information for Ecological Risk Assessment, Land-Use Management Activities, and Biodiversity Enhancement Practices, ASTM STP 1458, L. Kapustka, H. Galbraith, M. Luxon, and G. R. Biddinger, Eds., ASTM International, West Conshohocken, PA, 2004, pp.261-285. UCRL-JC-152537
• Eliassi-Rad, T., C. Baldwin, Abdulla, G., and T. Critchlow, “Statistical Modelig of Large-Scale Scientific Simulation Data,” chapter in New Generation of Data Mining Applications, Wiley/IEEE Press, to appear January 2005. UCRL-BOOK-200992.
• Falgout, R. D., J. E. Jones and U. M. Yang, The Design and Implementation of hypre, a Library of Parallel High Performance Preconditioners, chapter in Numerical Solutions of PDEs on Parallel Computers, Springer-Verlag, to appear. UCRL-JRNL-205459.
• Falgout, R.D. and P.S. Vassilevski, “On Generalizing the AMG Framework,” SIAM Journal on Numerical Analysis, to appear. UCRL-JC-150807, 2003. 
• Falgout, R.D., J.E. Jones, and U.M. Yang, "Conceptual Interfaces in hypre," Future Generation Computer Systems, Special Issue on PDE Software, in press. UCRL-JC-148957, 2002.
• Falgout, R.D., 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.Bjorstad, and A. Tveito, editors, Springer, 2004, to appear.  UCRL-JRNL-205459.
• Fattebert, J.-L., and F. Gygi, “Linear Scaling First-Principles Molecular Dynamics with Controlled Accuracy,” Computer. Physics Communications, 162, 2004, pp. 24–36. UCRL-JRNL-202957.
• Fisher, A., R. Rieben, G. Rodrigue, D. White, A Generalized Mass Lumping Technique for Vector Finite Element Solutions of the Time Dependent Maxwell Equations, to be published IEEE Trans. on Ant. And Prop. UCRL-JRNL-205643
• Gardner, S. N., and Fernandes, M. 2004. Cytostatic anticancer drug development. The Journal of Experimental Therapeutics and Oncology, 4: 9-18. UCRL-JC-149566
• Gardner, S.N., Lam, M.W., Mulakken, N.J., Torres, C.L., Smith, J.R., Slezak, T.R. 2004. Sequencing needs for viral diagnostics. Journal of Clinical Microbiology, 42: 5472-5476. UCRL-JRNL-200926
• Goens, S. D., S. Botero, A. Zemla, C. Ecale Zhou, M. Perdue: "Bovine enterovirus type 2. Complete genomic sequence and molecular modeling of the reference strain and a wild type isolate from endemically infected US cattle", Journal of General Virology, 85, 2004, pp. 3195-3203. UCRL-JRNL-202639
• Govindasamy, B., S. Thompson, A. Mirin, M. Wickett, K. Caldeira, and C. Delire, “Increase of Carbon Cycle Feedback with Climate Sensitivity: Results from a Coupled Climate and Carbon Cycle Model,” Tellus B, 2004, to appear, UCRL-JRNL-203401.
• Gregorski, B., Joshua Senecal, Mark Duchaineau, and Kenneth I. Joy, "Adaptive Extraction of Time-Varying Isosurfaces", IEEE Transactions on Visualization and Computer Graphics, Vol 10, No. 6, Nov-Dec 2004, pp. 683-694. UCRL-JP-200087.
• Grimwood, J., et al, The sequence and biology of human chromosome 19, Nature, 428, 529-535 (2004). UCRL-JRNL-203434
• Grossman , J.C.; E. Schwegler, E.W. Draeger, F. Gygi and G.Galli, “Towards an assessment of the accuracy of density functional theory for first-principles simulations of water”, J. Chem. Phys 120, 300 (2004). UCRL-ABS-202137
• Guerra, C. and V. Pascucci. “Line-based object recognition using Hausdorff distance: from range images to molecular secondary structure”. Image and Vision Computing. To appear. UCRL-JRNL-208551
• Herrnstein, A., G. Rodrigue, M. Wickett, Structured Adaptive Mesh Refinement using Leapfrog Time Integration on a Staggered Grid for Ocean Models, to be published J. of Ocean Modeling. UCRL-JRNL-202368.
• Hillier, L. W., et al, International Chicken Genome Sequencing Consortium, Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution Nature, 432, 695-716 (2004).
• Hillier, L. W., et al, International Human Genome Sequencing Consortium Finishing the euchromatic sequence of the human genome Nature, 431, 931-945 (2004)
• Hillier, L. W., et al, The DNA sequences of human chromosomes 2 and 4, Nature, (accepted, 2005)
• Hillier, L. W., et al, International Chicken Polymorphism Map Consortium, A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms, Nature, 432, 717-722 (2004)
• Hindmarsh, A. C.; P. N. Brown, K. E. Grant, S. L. Lee, R. Serban, D. Shumaker, and C. S. Woodward, “SUNDIALS: Suite of Nonlinear and Differential/Algebraic Equation Solvers,” to appear ACM Transactions on Mathematical Software, 2005, UCRL-JP-200037.
• Hittinger, J.A.F. and P.L. Roe, “Asymptotic Analysis of the Riemann Problem for Constant Coefficient Hyberbolic Systems with Relaxation,” Zeitschrift Für Angewandte Mathematik und Mechanik., 84,  2004, pp. 452-471. UCRL-JC-147811.
• Homescu, C.; L.R. Petzold, and R. Serban, “Error Estimation for Reduced Order Models of Dynamical Systems,” SIAM Journal on Numerical Analysis, to appear, 2004. UCRL-JRNL-201982
• Im, E-J., K. Yelick, and R. Vuduc. “SPARSITY: Optimization framework for sparse matrix kernels.” International Journal of High-Performance Computing Applications, 18(1), pp. 135-158, February 2004.  Need UCRL number.
• Iontcheva, A.H.  and P.S. Vassilevski. “Monotone multigrid methods based on element agglomeration coarsening away from the contact boundary for the Signorini's problem,” Numer. Linear Algebra Appl., 11, (2004), pp. 189-204.  UCRL-JC-153352.
• Isenburg, M., P. Lindstrom, and J. Snoeyink, “Lossless Compression of Predicted Floating-Point Geometry.” Computer-Aided Design, 2004, to appear. UCRL-JRNL-208490-DRAFT.
• Jefferson, David, Aviel Rubin, Barbara Simons, David Wagner,  "Analyzing Internet Voting Security", Communications of the ACM, Vol. 47, No. 10, October, 2004. UCRL-JRNL-209371.
• Kamath, C., Cantú-Paz, E., Cheung, S., Fodor, I.K., Tang, N., “Experiences in mining data from computer simulations,” chapter in New Generation of Data Mining Applications, IEEE Press. August 2003. UCRL-BOOK-200043.
• Kanterdjieff, K. A., Ch. Y. Kim, C. Naranjo, G. S. Waldo, T. P. Lekin, B. W. Segelke, A. Zemla, M. S. Park, T. C. Terwilliger, B. Rupp: "Mycobacterium tuberculosis RmlC epimerase (Rv3465): a promising drug-target structure in the rhamnose pathway", Acta Cryst., 2004, D60, pp. 895-902. UCRL-JRNL-202415
• Kostova, T., Carlsen T., Kercher J., “Individual-Based, Spatially Explicit Model of an Herbivore and its Resource: The Effect of Habitat Reduction and Fragmentation”, Comptes Rendus Biologies, 327, 2004 pp. 261-276. UCRL-JC-148434
• Kostova, T., Ravindran R., and Maria Schonbek, "FitzHugh-Nagumo Revisted," International J.Bifurcation & Chaos, 14(3) 2004, pp. 913-925. UCRL-JC-151668
• Kostova, T., T., Carlsen, “The Effect of Habitat Size and Predation on the Time to Extinction of Prairie Vole Populations: Simulation Studies via SERDYCA”, Ecological Complexity, 2004, to appear. UCRL-JRNL-201153
• Kostova, T., T., Carlsen, “The Effect of Small-Size Habitat Disturbances on Population Density and Time to Extinction of the Prairie Vole”, Nonlinear Analysis: Real World Applications, 2004, to appear. UCRL-JRNL-208647
• Kreiss, Heinz-Otto, and N. Anders Petersson, "A second order accurate embedded boundary method for the wave equation with Dirichlet data," accepted for publication in SIAM Journal on Scientific Computing. UCRL-JRNL-202686, March 2004.
• Kreiss, Heinz-Otto, N. Anders Petersson, and Jacob Ystrom, "Difference Approximations of the Neumann Problem for the Second Order Wave Equation," SIAM J. Numer. Anal, 42, pp. 1292-1323 (2004).  UCRL-JC-153184.
• Lee, B.,  Z. Cai, and P. Wang, “Least-Squares Methods for Incompressible Newtonian Flow: Linear Stationary Problems,”  SIAM J.  Numer. Anal., 42 (2004), pp. 843-859, UCRL-JC-204137.
• Li, Na, Yousef Saad, and Edmond Chow, “Crout versions of ILU for general sparse matrices,” SIAM Journal on Scientific Computing, 25, 2004, pp. 716-728.  UCRL-JC-147917.
• Linsen, L.,  Jevan T. Gray, Valerio Pascucci, Mark A. Duchaineau, Bernd Hamann, Kenneth I. Joy, "Hierarchical Large-scale Volume Representation with Third-Root-of-Two Subdivision and Trivariate B-spline Wavelets", Chapter in Geometric Modeling for Scientific Visualization, Brunnett, G., Hamann, B., Mueller, H. and Linsen, L., eds., Mathematics + Visualization-Series, Springer-Verlag, 2004. UCRL-JC-151004.
• Linsen, L., B. Hamann, K. I. Joy, V. Pascucci, and M. A. Duchaineau. “Wavelet-based multiresolution with n-th-root-of-2”. Computing, 72(1-2):129–142, April 2004. UCRL-JRNL-208695
• Loots, G. G., and I. Ovcharenko, rVISTA 2.0: evolutionary analysis of transcription factor binding sites, Nucleic Acids Research, 32, W217-W221 (2004) UCRL-JRNL-202112
• Manaa, M.R.; E.J.Reed, L.E.Fried, G.Galli and F.Gygi, “Early chemistry in hot and dense nitromethane: Molecular dynamics simulations”, J. Chem. Phys. 120, 10146 (2004). UCRL-JC-153788.
• Max, N.,  “Hierarchical Molecular Modelling with Ellipsoids”, Journal of Molecular Graphics, Vol. 23, No. 3, pp. 233 – 238.  UCRL-CONF-203283.
• McCallen, R., Browand, F., and Ross, J., Eds., The Aerodynamics of Heavy Vehicles: Trucks, Buses, and Trains, Lecture Notes in Applied and Computational Mechanics, Vol. 19, Springer, 2004.
• McInnes, L. C.; B. A. Allan, R. Armstrong, S. J. Benson, D. E. Bernholdt, L Diachin, T. L. Dahlgren, M. Krishnan, J. A. Kohl, J. W. Larson, S. Lefantzi, J. Nieplocha, B. Norris, S. G. Parker, J. Ray, and S. Zhou, Parallel PDE-Based Simulations Using the Common Component Architecture, Argonne National Laboratory preprint ANL/MCS-P1179-0704, to appear in the book Numerical Solution of Partial Differential Equations on Parallel Computers, A. M. Bruaset, P. Bjorstad, and A. Tveito, editors, Springer.
• Mirin, A.A. and W.B. Sawyer, “A Scalable Implementation of a Finite-Volume Dynamical Core in the Community Atmospheric Model,” Int’l. Jour. High Performance Computing Applications, 2004, to appear. UCRL-JRNL-206816.
• Motin,V., A. Georgescu, J. Fitch, P. Gu, D. Nelson, S. Mabery, J. Garnham, B. Sokhansanj, L. Ott, M. Coleman, J. Elliott, L. Kegelmeyer, A. Wyrobek, T. Slezak, R. Brubaker, and E. Garcia. Temporal global changes in gene expression during temperature transition in yersinia pestis. J Bacteriol, 186(18):6298–305, 9 2004.  Need UCRL number.
• Ovcharenko, I., D. Boffelli, G. Loots, eShadow: A Tool for Comparing Closely Related Sequences, Genome Research, 14(6), 1191-1198 (2004) UCRL-JC-154409.
• Ovcharenko, I., G. Loots, B. Giardine, M. Hou, J. Ma, R. Hardison, L. Stubbs, and W. Miller, Mulan: Multiple-Sequence Local Alignment and Visualization for Studying Function and Evolution, Genome Research, 15(1), 184-194 (2005) UCRL-JRNL-205739
• Ovcharenko, I., G. Loots, M. Nobrega, R. Hardison, W. Miller, and L. Stubbs, Evolution and Functional Classification of Vertebrate Gene Deserts, Genome Research, 15(1), 137-145 (2005) UCRL-JRNL-205731
• Ovcharenko, I., G. Loots, R.C. Hardison, W. Miller, Lisa Stubbs, zPicture: Dynamic alignment and visualization tool for analyzing conservation profiles, Genome Research, 14(3), 472-477 (2004) UCRL-JRNL-200708
• Ovcharenko, I., L. Stubbs, and G.G. Loots, Interpreting Mammalian Evolution using Fugu Genome Comparisons, Genomics, 84(5), 890-895 (2004) UCRL-JRNL-203427.
• Pascucci, V., “Topology Diagrams in Scientific Visulization”, Chapter in: Surface Topological Data Structures: An Introduction for Geographical Information Science, pages 121–130. John Wiley & Sons, May 2004. UCRL-BOOK-200013
• Pernice, M., and R. D. Hornung, “Newton-Krylov-FAC Methods for Problems Discretized on Locally-Refined Grids,” Comput. & Visualization in Science, 2004, to appear. UCRL-JC-151614.
• Pierce, T., G. Rodrigue, A Parallel Two-Sided Contact Algorithm in ALE3D, to be published J. of Comp. Meth. In App. Mech. And Eng. UCRL-JC-155219
• Prendergast, D., J.C. Grossman, A.J. Williamson, J.-L. Fattebert, and G. Galli, “Optical properties of silicon clusters in the presence of water: a first-priciples theoretical analysis”, J. Am. Chem. Soc., 126 (42), 2004, pp. 13827–13837. UCRL-JRNL-203548.
• Pudzer, A, A.J. Williamson, F.Gygi and G.Galli, “Self-healing of CdSe nanoparticles: A first-principles study”, Phys. Rev. Lett. 92, 217401 (2004). Need UCRL number.
• Rabenseifner, Rolf, Koniges, Alice E., Prost, Jean-Pierre, and Hedges, Richard, “The Parallel Effective I/O Bandwidth Benchmark: b_eff_io,” chapter 4 in Parallel I/O for Cluster Computing, Kogan Page Ltd., pp. 107–132, 2004. UCRL-JC-143979
• Rieben, R., D. White, G. Rodrigue, "Improved Conditioning of Finite Element Matrices using New High Order Interpolatory Bases," IEEE Transactions on Antennas and Propagation, volume 52, no. 10, pages 2675-2683, October 2004, UCRL-JC-15229
• Rieben, R., G. Rodrigue, D. White, A High Order Mixed Finite Element Method for Solving Time Dependent Maxwell Equations on Unstructured Hexahedral Grids, to be published J. Comp. Phys. UCRL-JRNL-202960
• Rieben, R., G. Rodrigue, D. White, “High Order Symplectic Integration Methods for Finite Element Solutions of Time Dependent Maxwell Equations,” IEEE Transactions on Antennas and Propagation, vol 52, no. 8, pp 2190-2195, August 2004, UCRL-JC-152872
• Rotman, D., C. Atherton, D. Bergmann, P. Cameron-Smith, C. Chuang, P. Connell, J. Dignon, A. Franz, K. Grant, D. Kinnison, C. Molenkamp, D. Proctor, and J. Tannahill, “IMPACT, the LLNL 3-D global atmospheric chemical transport model for the combined troposphere and stratosphere: Model description and analysis of ozone and other trace gases,” Journal of Geophysical Research, 109(D04303), Feb. 2004, pp. 1-42. UCRL-JC-155255.
• Schwegler , E.; J.C. Grossman, F. Gygi and G.Galli, “Towards an assessment of the accuracy of density functional theory for first-principles simulations of water II”, J. Chem. Phys 121, 5400 (2004). UCRL-JRNL-204466
• Sharan, R., A. Ben-Hur, G.G. Loots, and I. Ovcharenko, CREME: Cis-Regulatory Module Explorer for the human genome, Nucleic Acids Research, 32, W253-W256 (2004) UCRL-JRNL-202313
• Shaw, M., W. Williams, R. House, C. Haynam, “Laser Performance Operations Model”, Optical Engineering Vol. 43 No. 12, December 2004. UCRL-JRNL-204642.
• Shestakov, A. I., J. A. Greenough, and L. H. Howell, “Solving the Radiation Diffusion and Energy Balance Equations using Pseudo Transient Continuation,” J.Quantitative Spectroscopy and Radiative Transfer, 90(1) 2005, pp. 1–28. UCRL-JC-138727-REV-1.
• Thompson, S., B. Govindasamy, A. Mirin, K. Caldeira, C. Delire, J. Milovich, M. Wickett, and D. Erickson, “Effect of limited CO2 fertilization on computed future climate: Quantifying Uncertainty in a Coupled Climate-Carbon Model,” Geophysical Research Letters, 2004, to appear, UCRL-TR-203417.
• Thompson, S.L., B. Govindasamy, A. Mirin, K. Caldeira, C. Delire, J. Miolvich, M. Wickett and D. Erickson, “Quantifying the Effects of Limited CO2 Fertilization on Future Global Climate and Carbon Dynamics,” Geophys. Res. Lett., 2004, to appear. UCRL-JRNL-207218.
• Tomascik-Cheeseman, L., M. Coleman, F. Marchetti, D. Nelson, L. Kegelmeyer, J. Nath, and A. Wyrobek. Differential basal expression of genes associated with stress response, damage control, and dna repair among mouse tissues. Mutat Res, 561(1-2):1–14, 7 2004. Need UCRL number.
• Tong, C.; Refinement Strategies for Stratified Sampling Methods, accepted for publication in Reliability Engineering and System Safety, 2004.  UCRL-JRNL-204408.
• Trebotich, D., P. Colella and G. H. Miller, “A Stable and Convergent Scheme for Viscoelastic Flow in Contraction Channels”, accepted in J. Comput. Phys. (2004). UCRL-JC-1001385.
• van Kreveld, M. J. , R. van Oostrum, C. L. Bajaj, V. Pascucci, and D. R. Schikore. “Efficient contour tree and minimum seed set construction”, Chapter in: Surface Topological Data Structures: An Introduction for Geographical Information Science, pages 71–86. John Wiley & Sons, May 2004. UCRL-BOOK-200018
• Vetter, Jeffrey, Bronis R. de Supinski, John May, Lynn Kissel, and Sheila Vaidya, "Evaluating High Performance Computers," Concurrency and Computation: Practice & Experience, (to appear). (UCRL-JC-151967).
• Vuduc, R., J. Demmel, and J. Bilmes, “Statistical Models for Empirical Search-Based Performance Tuning.” International Journal of High-Performance Computing Applications, 18(1), pp. 65-94, February 2004. Need UCRL number.
• Wijesinghe, H. S., R. D. Hornung, A. L. Garcia, and N.G. Hadjiconstantinou, “Three-dimensional Hybrid Continuum-Atomistic Simulations for Multiscale Hydrodynamics,” J. Fluids. Eng., 126, 2004, pp. 768–777. UCRL-JRNL-203681.
• Williams, E. A., B. I. Cohen, L. Divol, M. R. Dorr, J. A. Hittinger, D. E. Hinkel, A. B. Langdon, R. K. Kirkwood, D. H. Froula, and S. H. Glenzer, “Effects of Ion Trapping on Crossed-Laser-Beam Stimulated Brillouin Scattering,” Phys. Plasmas, 11, 2004, pp. 231-244. UCRL-JC-152243.
• Wolford, J. K., “Needs Differing: Personality Dynamics for Peer Ombuds in a Research Setting,” J. California Caucus of College and University Ombuds, 6(1), 2004, (in press). UCRL-JRNL-207131.
• Yang, U.M., On the Use of Relaxation Parameters in Hybrid Smoothers, Numerical Linear Algebra With Applications,  11, (2004), pp. 155-172. UCRL-JC-151575.
• Yang, U.M., Parallel Algebraic Multigrid Methods High Performance Preconditioners, chapter in Numerical Solutions of PDEs on Parallel Computers, Springer-Verlag, 2005, to appear. UCRL-BOOK-208032.