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Laboratory Directed Research and Development Program FY 2000 LBNL/PUB-5464 Laboratory Directed Research and Development Program FY 2000 February 2001 DISCLAIMER This document was prepared as an account of work sponsored by the United States Government. While this document Is believed to contain correct Information, neither the United States Government nor any agency thereof, nor The Regents of the University of California, nor any of their employees, makes any warranty, express or Implied, or assumes any legal responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by its trade name, trademark, manufacturer, or otherwise, dees not necessarily constitute or Imply lis endorsement, recommendation, or favoring by the United States Government or any agency thereof, or The Regents of the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof, or The Regents of the University of California. Ernest Orlando Lawrence Berkeley National Laboratory is an equal opportunity employer. PUB-5464 Report on Ernest Orlando Lawrence Berkeley National Laboratory Laboratory Directed Research and Development Program FY 2000 Ernest Orlando Lawrence Berkeley National Laboratory Berkeley, California 94720 Office of Science U.S. Department of Energy Prepared for the U.S. Department of Energy under Contract No. DE-AC03-76SF00098 Table of Contents Introduction ix Accelerator and Fusion Research Division 1 Swapan Chattopadhyay Innovative Source Technologies for me Generation of Femtosecond-Scale Alexander Zholents Pulses of X-Rays 1 Max Zolotorev John Corlett Dynamics of Low-Emittance Electron Rings with Applications to High Energy Physics Colliders 2 Wim Leemans Computational Studies of Atomic Medium Interactions with Attosecond Eric Esarey Electron Bunches 3 Alexander Zholents Max Zolotorev Swapan Chattopadhyay Ka-Ngo Leung Compact D-D or D-T Neutron Generator for Moderator Design and Biological Gordon Wozniak Research 5 Eleanor Blakely GianLuca Sabbi Next Generation Superconducting Magnets 7 Advanced Light Source Division 9 Thornton Glover Ultrafast X-Ray Spectroscopy via Optical Gating 9 Philip Hermann Howard Padmore Malcolm Howells Phase- and Amplitude-Contrast Tomography using Intermediate-Energy Alastair MacDowell X-Rays 11 Howard Padmore Robert Ritchie Wenbing Yun Howard Padmore Micro X-Ray Absorption Spectroscopy at the Advanced Light Source 12 Alastair MacDowell Geraldine Lamble Richard Celestre Albert Thompson Chemical Sciences Division 15 Ali Belkacem Laser-Assisted Photoabsorption of X-Rays by Atoms and Feasibility of a Thornton Glover Femtosecond X-Ray Source 15 Wim Leemans C. Bradley Moore Selective Chemistry with Femtosecond Infrared Laser Pulses 16 Heino Nitsche Study of Radionuclide-Bacterial Interaction Mechanisms 17 Petra Panalc iii Computing Sciences (Information and Computing Sciences Division, National Energy Research Scientific Computing Division, and Mathematics Department) 21 David Bailey High-Precision Arithmetic with Applications in Mathematics and Physics 21 Grigory Barenblatt Numerical Methods for Time-Dependent Viscoelastic Flows 23 Alexandre Chorin John Bell Science-Based Subgrid Scale Modeling in Fluid Turbulence 24 Phillip Colella Alexandre Chorin Nancy Brown Michael Frenklach Andrew Canning Computational Methods for Electronic Structure Codes in Materials Science: Steven Louie Ground-State and Excited-State Properties 25 C. William McCurdy Electron Collision Processes above the Ionization Threshold 27 Thomas Rescigno Bahrain Parvin Feature-Based Representation and Reconstruction of Geophysical Data 29 Qing Yang Paul Hargrove Berkeley Lab Distribution (BLD): Software for Scalable Linux Clusters .-. 30 William Saphir Robert Lucas Horst Simon Sparse Linear Algebra Algorithms and Applications for Text Classification in Chris Ding Large Databases 31 Parry Husbands Earth Sciences Division 33 Sally Benson Geologic Sequestration of C02 Through Hydrodynamic Trapping Larry Myer Mechanisms 33 Curtis Oldenbury Karsten Pruess G. Michael Hoversten Jim Bishop Ocean Particulate Carbon Dynamics 34 Inez Fung Carbon-Climate Interactions 37 Horst Simon Jim Bishop Terry Hazen Aerobic Bioremediation of Landfills 39 Curtis Oldenburg Sharon Borglin Peter Zawislanski Jinwon Kim Effects of 2xC02 Climate Forcing on the Western U.S. Hych-oclimate using the Norman L. Miller Higb-Performance Regional Climate System Model 41 Chris Ding iv Margaret Torn Isotopic Analysis of Carbon Sequestration in Terrestrial Ecosystems and Global Change Impacts 43 Yu-Shu Wu Development of the High-Performance TOUGH2 codes 44 Karsten Pruess Chris Ding Engineering Division 47 Henry Benner Instrumentation for Sorting Individual DNA Molecules 47 Environmental Energy Technologies Division 49 Melissa Lunden Transformation Pathways of Biogenic Organic Emissions in the Formation Laurent Vuilleumier of Secondary Organic Aerosol 49 Nancy Brown Mark Levine Ronald Cohen Atmospheric Chemistry: Changes at the Interface Between Urban and Nancy Brown Regional Scales 53 Allen Goldstein Robert Harley Haider Taha Donald Lucas Diesel Particle Detection and Control 54 Arlon Hunt Ron Reade Ion-Beam Thin-Film Texturing: Enabling Future Energy Technologies 55 Paul Berdahl Life Sciences Division 57 David Chen Transgenic Mouse Models for DNA Damage Sensing, Repair and Aging 57 Priscilla Cooper Structural Cell Biology of Multi-Component Protein Complexes Essential John Tainer for Genomic Stability 58 Michael Eisen Analytical Tools for Gene Expression and Genome Sequence 60 Robert Glaeser Teraflop Challenges in Single-Particle Election Crystallography 62 Esmond Ng Ravi Malladi Ronald Krauss DNA Microarray Analysis of Metabolic Regulatory Genes in the Mouse 63 Carolyn Larabell Cryo X-Ray Microscopy And Protein Localization 64 Eva Nogales Cryo-Electron Microscopy Studies of the Eukaryotic Transcriptional Basal Factor TFITD 65 Materials Sciences Division 67 Michael Crommie Nanoscale Transport in Ultra-Thin Films 67 v J.C. Seamus Davis Atomically Resolved Spin-Polarized Imaging with Superconducting STM Tips 68 Charles Fadley Holographic Imaging wifhX-Rays: Fluorescence and Fourier Transform Malcolm Howells Holography 70 Andreas Glaeser Novel Routes to the Fabrication of Microdesigned Grain Boundaries via Ronald Gronsky Solid-State Methods 71 Paul McEuen Graphite: The Rosetta Stone of Current Two-Dimensional Condensed Dung-hai Lee Matter Physics 74 Joseph Orenstein Infrared Spectroscopy of Complex Materials 75 Zi Q. Qiu Investigation of the Quantum Well States in Magnetic Nanostmctures 76 Robert Ritchie Spatially-Resolved Residual Stress Characterization at Microstructural Howard Padmore Dimensions 77 Miquel Salmeron Electron Spectroscopy of Surfaces under High-Pressure Conditions 79 Zahid Hussain Charles Fadley Shimon Weiss Single-Molecule Protein Dynamics 81 Robert Schoenlein Improved Temporal Resolution Femtosecond X-Ray Spectroscopy 82 Alexander Zholents Max Zolotorev Phillip Heimann T. Glover Nuclear Science Division 85 Joseph Cemy New Exotic Nuclear Beams by Implementation of the "Recyclotron Concept" 85 I-Yang Lee Gamma Ray Studies using the 8TT Spectrometer Array 85 Lee Schioeder David Ward Claude Lyneis Vacuum, Radio Frequency (RF), and Injection Systems for High-Intensity Stable I-Yang Lee Beams 87 Heino Nitsche First Chemical Study of Element 108, Hassium 88 Uwe Kirbach Physical Biosciences Division 91 Adam Arkin Integrated Physiome Analysis 91 Inna Dubchak Teresa Head-Gordon Stephen Holbrook Saira Mian vi Adam Arkin Structural/Functional Genomics and Pathways: D. radiodurans and Teresa Head-Gordon B. subtilis 92 Stephen Holbrook Daniel Rokhsar David Chandler Development and Application of the General Theory of Hydrophobicity to Interpret Stability and Dynamics of Biological Assemblies 95 Thomas Earnest Structural Biology of Large Biomolecular Complexes 96 "~~ Jay Groves Novel Approaches to the Study of Molecular Organization in Living Cells... 98 Stephen Holbrook Identification of Novel Functional RNA Genes in Genomic DNA Inna Dubchak Sequences 100 Ehud Isacoff Transgenic Optical Sensors for Live Imaging of Neural Activity 103 Daniel Rokhsar Computational Modeling of Protein Folding and Unfolding using Lattice Models and All-Atom Molecular Dynamics 104 Physics Division.. 107 Kevin Einsweiler Silicon-on-lnsulator Technology for Ultra-Radiation Hard Sensors 107 Naimisaranya Busek Roberto Marchesini Gerrif Meddeler Oren Milgrome Helmuth Spieler George Zizka Michael Levi Foundations for a SuperNova Acceleration Probe (SNAP) 109 Saul Perlmutter Sub-Project 00026: Development of an Advanced Imaging Array 109 Sub-Project 00027: Nearby Supernova Search with Ten-Fold Increase in Efficiency 110 David Quarrie Solutions to Data Handling Constraints for Large High Energy and Nuclear Physics Experiments 112 James Siegrist Research on High-LrrminDsity Tracking Sensors 114 George Smoot Extraction of Fundamental Parameters from the Cosmic Microwave Background Data 115 George Smoot Large Astrophysical Data Sets.... 117 Acronyms and Abbreviations 119 vii Introduction capabilities toward vital, excellent, and emerging scientific The Ernest Orlando Lawrence Berkeley National challenges. The program provides the resources for Laboratory (Berkeley Lab or LBNL) is a multi-program Berkeley Lab scientists to make rapid and significant national research
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