LBNL-103E Laboratory Directed Research and Development Program FY 2013 June 2014 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, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or The Regents of the University of California. 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Report on Ernest Orlando Lawrence Berkeley National Laboratory Laboratory Directed Research and Development Program FY 2013 Ernest Orlando Lawrence Berkeley National Laboratory Berkeley, CA 94720 FEBRUARY 2014 Prepared for the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 Table of Contents Introduction................................................................................................................................................... viii Accelerator and Fusion Research Division.................................................................................................... 1 Paul Emma, Free Electron Laser Soft X-ray Self-Seeding ................................................................ 1 ....... Marco Venturini Thomas Schenkel Probing Point Defect Dynamics in Solids with Short Ion Beam Pulses ................................................................................................ ................................2 .... Jeroen van Tilborg Experimental Realization of a High-Harmonics-Seeded, Laser- Plasma-Accelerator Driven Free-Electron Laser................................ ................................3 ... Advanced Light Source Division .................................................................................................................... 4 Elke Arenholz, Magnetic-Field-Induced and Transient Quantum Phases in Ramamoorthy Ramesh Correlated Materials ................................................................................................ 4 .............. Yi-De Chuang Studying the emergence of electronic correlations with time- and momentum-resolved RIXS ................................................................ 5 ............................. Jinghua Guo Soft X-Ray Spectroscopy for In-situ Electronic Structure Study of Artificial Photosynthesis ................................................................ ................................6 .. Alastair MacDowell, New Opportunities in Hard X-Ray Tomography – High et al. Temperature and Elemental Imaging ................................................................ 7 .................... David Shapiro Ultra-high Resolution Microscopy of Nano-materials by Scanning X-ray Diffraction Microscopy ................................................................ 8 ............... Dimitriy Voronov Next Generation Grating for Spectroscopy and Pulse 9 Compression .......................................................................................................................... Cheng Wang, et al. Soft X-Ray Spectroscopy of Lithium and Conductive Polymers for Li-Ion Batteries ................................................................................................ 10 ................ Chemical Sciences Division ........................................................................................................................... 11 Rebecca Abergel Global Transcriptome, Deletome and Proteome Profiling of Yeast Exposed to Radioactive Metal Ions: a Tool to Distinguish Radiation-Induced Damage From Chemical-Toxicity ................................ 11 .......................... Ali Belkacem, et al. Scientific Tools in Multi-Dimensional X-ray Spectroscopy and Coherent Diffractive Imaging................................................................ 12................................ David Chandler Asymetric Responses of Systems Far From Equilibrium................................ 13 ...................... Oliver Gessner, et al. Ultrafast X-ray Studies of Interfacial Charge Transfer Processes................................ 14 ......... Mary Gilles Photo-switchable Metal Organic Frameworks for CO2 Sequestration ................................................................................................ 15 ........................ John Hartwig Elementary Organometallic Reactions in a Protein Matrix................................ 16 ................... Martin Head-Gordon New Algorithms for Performing and Analyzing Large Scale Electronic Structure Calculations................................................................ 17 .......................... Teresa Head-Gordon Electrostatic Nanoscale-mesoscale Coupling to Discover Design Rules for Energy Materials ................................................................ 18 ....................... iii David Shuh, Developing f-electron Soft X-ray Spectroscopy Simulation, David Pendergast, Theory, and Experiment for Clean Energy Materials ................................ 19 .......................... Andrew Canning F. Dean Toste, A Multi-Investigator Approach Towards Chemoenzymatic Kenneth Raymond, Catalysis ................................................................................................ 20............................... Robert Bergman Kevin Wilson, Oxidative Transformations of Organic Aerosol ................................ ................................21 ... Allen Goldstein Computing Sciences (National Energy Research Scientific Computing Center, and Computational Research Divisions).. 22 Maciej Haranczyk An Optimization-based Strategy for Computational Design of Nanoporous Carbon-Zero Materials ................................................................ 22 ..................... Xiaoye S. Li Next Generation Computing for X-ray Science ................................ ................................23 ... Peter Nugent Nyx: The Lyman Alpha Forest Cosmology Simulator................................ 24 .......................... Leonid Oliker High-Performance Parallel Graph-Analysis for Key Genomics 25 Computations......................................................................................................................... Jamie Sethian, et al. Interlinkage of Cross-Disciplinary Mathematical Technologies................................ 26 ........... David Trebotich Modeling Subsurface Reactive Transport Processes from Mineral Surface-to-Pore-to-Continuum ................................................................ 27 ................ Craig Tull Towards an End-to-End Solution for Light Source Data ................................ 28 ...................... Daniela Ushizima Quantitative Image Analysis for Computational Modeling ................................ 29 .................. Chao Yang Computational Approaches to Understanding Ultrafast Science ................................ 30 .......... Chao Yang, Lin Lin Computational Algorithms and Mathematical Software Tools for Material Science and Chemistry ................................................................ 31 ...................... Shane Canon Defining an Ecosystem to Support Data-Intensive Science ................................ 32 ................. David Skinner Integrated Tools for Next Generation Bioimaging................................ 33................................ Earth Sciences Division ................................................................................................................................. 34 Nathan Bouskill Developing a Mechanistic High-Latitude Soil Carbon and Nitrogen cycle Model in TOUGHREACT................................................................ 34 ............ Eoin Brodie, et al Integrative Mapping of Soil Heterogeneity at the Microbial Scale ................................................................................................................................ 35 ...... Romy Chakraborty High-throughput Isolation and Functional Screening (HIFS) of Microbes Relevant to Today's Carbon Cycling and Bioenergy Needs................................................................................................ ................................36 ..... Jeffery Chambers Tropical Forest Ecosystems Under a Changing Climate................................ ....................... 37 John Christensen, Isotopic Probe of Ion Migration Processes in Li-ion Batteries ................................ 38 ............. Ian Bourg, Vincent Battaglia James A. Davis Effect of Mineral Coatings on Biogeochemical Processes................................ 39 .................... Christer Jansson CyanoAlkenes: Engineering Cyanobacteria for Phototrophic Production of Advanced Biofuels ................................................................ 40 ......................... iv Lara Kueppers Using Experiments and