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a Applications of New DOE National User Facilities in Biology Workshop May 2011 Convened by U.S. Department of Energy Office of Science Office of Biological and Environmental Research Co-chairs David Eisenberg Dagmar Ringe University of California–Los Angeles Brandeis University Organizers Roland Hirsch Susan Gregurick [email protected] [email protected] 301.903.9009 301.903.7672 This report and more workshop information can be obtained at: genomicscience.energy.gov/userfacilities/structuralbiologyworkshop/ About the Cover Image credits clockwise from top: • Detector array for the TOPAZ instrument, Spallation Neutron Source at Oak Ridge National Laboratory. • Coherent x-ray imaging system, Linac Coherent Light Source at SLAC National Accelerator Laboratory. • Bio x-ray absorption spectrometer, National Synchrotron Light Source at Brookhaven National Laboratory. • BioNanoprobe prototype, Advanced Photon Source at Argonne National Laboratory. • Advanced photoinjector and initial acceleration section, Next Generation Light Source at Lawrence Berkeley National Laboratory. Suggested Citation for this Report U.S. DOE 2012. Applications of New DOE National User Facilities in Biology Workshop Report, DOE/SC-0147, U.S. Department of Energy Office of Science. genomicscience.energy.gov/userfacilities/structuralbiologyworkshop/report.pdf. DOE/SC-0147 Applications of New DOE National User Facilities in Biology Workshop Report Published: February 24, 2012 U.S. Department of Energy Office of Science Office of Biological and Environmental Research i ii U.S. Department of Energy Office of Science • Office of Biological and Environmental Research PREFACE his report represents the discussions and findings of a workshop held in May 2011 to consider the significance for biological science of five major Department of Energy DOE( ) national user facilities that either have recently begun full operations (Linac Coherent Light Source and Spallation Neutron Source), are under construction T(National Synchrotron Light Source-II), or are being designed (Advanced Photon Source Upgrade and Next Generation Light Source). The Office of Biological and Environmental Research (BER), a program office in DOE’s Office of Science, initiated support for researcher access to major user facilities for structural biology in 1990, when DOE was engaged in a similar program for constructing and upgrading these facilities. That initiative was focused on DOE synchrotron light sources and neutron beam facilities. The workshop took place May 9–11 in Rockville, Maryland. Two months before the meeting, leaders from each of the five facilities submitted papers describing the facilities and potential applications in biology (these papers are included in Appendices A–E of this report). A panel of experts in the design, operation, and management of these facilities, as well as in several key nonfacility technologies used in biological research and in major areas of biology supported by BER, read these reports prior to the meeting (see Appendix F for participants list). At the meeting, the entire panel separately heard presentations from and engaged in discussions with representatives of each facility and then developed outlines for the chapters of this report. The Executive Summary and the five chapters were prepared after the meeting by panel members and circulated to the entire panel for comments and editing prior to completion of the report. BER appreciates the involvement of all panel members, especially the co-chairs, Dagmar Ringe of Brandeis University and David Eisenberg of the University of California–Los Angeles. The appendices describing the five facilities were prepared by staff of the respective national laboratories. In some cases, comments from panel members led to revisions of a paper; however, the final version included in this report represents the views of the national laboratory, not the panel members. The efforts of national laboratory staff members to prepare their papers are very much appreciated. All of the written materials in this report were edited and prepared for publication by members of the Biological and Environmental Research Information System group at Oak Ridge National Laboratory. BER is indebted to the members of this group who devoted extensive time and much thought to preparation of all report components for publication. Comments on this report will be welcomed by Roland Hirsch and Susan Gregurick, the BER program managers involved in the workshop. U.S. Department of Energy Office of Science • Office of Biological and Environmental Research iii iv U.S. Department of Energy Office of Science • Office of Biological and Environmental Research TABLE OF CONTENTS Executive Summary ....................................................................................................................................................vii Chapter 1. Advanced Photon Source Upgrade ........................................................................................................1 Chapter 2. Linac Coherent Light Source....................................................................................................................5 Chapter 3. National Synchrotron Light Source-II ..................................................................................................11 Chapter 4. Next Generation Light Source ...............................................................................................................15 Chapter 5. Spallation Neutron Source .....................................................................................................................19 Appendices ...................................................................................................................................................................25 Appendix A: Advanced Photon Source Upgrade ................................................................................................27 Appendix B: Linac Coherent Light Source ............................................................................................................45 Appendix C: National Synchrotron Light Source-II ............................................................................................63 Appendix D: Next Generation Light Source .........................................................................................................81 Appendix E: Spallation Neutron Source ...............................................................................................................99 Appendix F: Workshop Agenda and Participants ............................................................................................ 115 Acronyms and Abbreviations .........................................................................................................Inside back cover U.S. Department of Energy Office of Science • Office of Biological and Environmental Research v vi U.S. Department of Energy Office of Science • Office of Biological and Environmental Research Executive Summary EXECUTIVE SUMMARY iology has benefited greatly from resources enabling life sciences (for example, experiments for development of atomic-level investigations of matter. Biological ques- particle beam therapies). tions that can only be addressed using high-intensity Bphoton and neutron beams are now being explored. Particle BER has played a major role in enabling new capabilities for accelerators developed over decades of research in high- biological research at existing Office of Science facilities. The energy physics have led to synchrotron light sources that primary focus of BER’s Structural Biology activity is to sup- offer very intense beams with tunable energies. Important port specialized instrumentation for biology at synchrotron contributions to the current understanding of a cell’s biologi- light sources and neutron facilities. The light sources produce cal infrastructure and the chemistry underpinning cellular intense beams of x-rays and other wavelengths extending into function are based on results from experiments conducted at the infrared to terahertz region, while particle accelerators these synchrotrons. and nuclear reactors produce neutron beams. These beams are directed into experimental stations housing instruments An estimated 30% to 40% of light source users are from the configured for specific biological investigations. This infra- biological sciences, and Nobel Prizes awarded in 1997, 2003, structure provides user access to beamline instrumentation 2006, and 2009 recognized biochemical discoveries enabled for studies of biological organisms and molecules in all areas by light sources. In fact, the biology community probably rep- of life science research. BER has supported development and resents the largest single user group, even though synchrotron operation of many of the instruments at the facilities, in close facilities in the United States generally were developed to sup- coordination with counterpart programs at other agencies port research in a variety of other fields, particularly materials and in the private sector. science, geoscience, chemistry, and nanoscience. These research facilities enable scientific studies aimed at In the United States, large scientific user facilities relevant understanding the structure and properties of matter at the to biological science are supported by many federal and atomic, molecular, and cellular levels, experiments not pos- state agencies. This report concerns facilities funded by the
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