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ALSNews Vol. 272 Print


Continuing Resolution update

The initiation of bacterial DNA replication

Top-off upgrade and operation status

SAC reviews the year and looks ahead

UEC Corner: Notes from the Users' Executive Committee

Safety First: ALS Radiological Work Authorization approved

Coherence 2007 Workshop to take place in June

Julie McCullough joins the ALS editorial team

Please report ALS publications by Friday, February 9

News Links

A comet comes to the Advanced Light Source

Synchrotrons help reveal the nature of comets

UC Berkeley researchers developed techniques to pluck comet dust from Stardust collectors

Discovery of new possibilities for magnetic storage

A boost for hydrogen fuel cell research

Zooming in on a molecular relay

New "chemical factory" will help scientists understand red wine's beneficial effects

Online class, Synchrotron Radiation for Materials Science Applications, taught by David Attwood




For the user runs from
January 17–28:

Beam reliability*: 89.9%

Completion**: 76.3%

Multiple problems with the injection system were the cause of most of the beam time lost.

*Time delivered/time scheduled
**Percent of scheduled beam delivered without interruption

Questions about beam reliability should be sent to Dave Richardson ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ).

Requests for special operations use of the "scrubbing" shift should be sent to Rick Bloemhard ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it , x4738) by 1:00 p.m. Friday.

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Julie McCullough
Lori Tamura
Liz Moxon

Greg Vierra

LBNL/PUB-948 (2007)

This work was supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Disclaimer.

Continuing resolution update

Contact: Roger Falcone, This e-mail address is being protected from spambots. You need JavaScript enabled to view it

This e-mail address is being protected from spambots. You need JavaScript enabled to view it The ALS and other Department of Energy (DOE) user facilities continue to view with concern the current state of the budget for DOE's Office of Science. New congressional leaders have indicated that fiscal year (FY) 2007 budgets, in which the Office of Science was expected to receive a major increase, may be held at FY06 levels. As you probably have heard, at the ALS this will mean foregoing the hiring of new beamline scientists and other personnel, together with major delays in new projects and lower than needed expenditures on maintenance; other DOE laboratories and facilities are looking at similar or worse scenarios. We are keeping our leadership in Washington informed about the impact of this so-called Continuing Budget Resolution on the user programs at the ALS. Importantly, users have also been communicating with their congressional representatives in the hope that Congress will pass a FY07 budget that reflects the intent of both the executive and congressional branches, expressed last year, to fully fund the Office of Science.

Editors' Note: Developments occurring at press time in the House of Representatives ("U.S. House Throws Science a Lifeline") can be viewed online.

The initiation of bacterial DNA replication

Contact: James Berger, This e-mail address is being protected from spambots. You need JavaScript enabled to view it

For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates that this AAA+ superhelix will wrap coils of the DNA around its exterior, causing the DNA double helix to deform as a first step in the separation and unwinding of its strands. Eukaryotic and archaeal initiators also have the structural elements that promote open-helix formation, indicating that a spiral, open-ring AAA+ assembly is a conserved element from a common evolutionary ancestor of Archaea, Bacteria, and Eukarya. Read more...

ATP-DnaA Structure

Publication about this research: J.P. Erzberger, M.L. Mott, and J.M. Berger, "Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling," Nat. Struct. Mol. Biol. 13, 665 (2006).

Top-off upgrade and operation status

Contacts: Steve Rossi, This e-mail address is being protected from spambots. You need JavaScript enabled to view it ; Christoph Steier This e-mail address is being protected from spambots. You need JavaScript enabled to view it

This was the longest shutdown for the ALS since it began operations in 1993. The focus was on completion of the installations necessary for the upgrade to top-off injection. However, there were many other significant tasks accomplished as well—replacement of the front end optics at the protein crystallography beamlines in Sector 5, installation of a higher-order-mode damper in one of the storage-ring radio frequency (rf) cavities, and preparations for the installation of an experimental camshaft bunch kicker, to name a few. This long shutdown also allowed us to make tremendous progress on less glamorous maintenance items such as replacement of the nearly four miles of low-conductivity water lines in the accelerator.

The most significant work was associated with the top-off upgrade. This included a complete replacement of the booster rf transmitter and waveguides, replacement of the four booster-to-storage ring dipole magnet power supplies, replacement of the two booster quadrupole magnet power supplies, replacement of the booster dipole magnet power supply, new pulsers and upgrades to the pulsed magnet systems, additions to the timing system, a new control system for the new equipment as well as for the many existing power supplies, new interlock systems, and new collimators for radiation safety. Largely the work went well and was completed on time. However, on December 15th there was a serious failure in the booster dipole power supply during testing by the power supply vendor. The power supply had been delivered late, this was the last day of testing, and it was right before recommissioning of the booster synchrotron with beam was to begin.

Parallel Power Supply

Old bend power supply (far left) working in parallel with new undamaged power supply (tall unit on far right).

The power supply comprises two separate units that work in unison to supply the needed power. One of these units was damaged, and it was clear it would not be in working condition in time to begin user operations. We therefore implemented several contingency plans. We determined that the two units of the power supply could operate independently and that one half would be sufficient to inject beam, albeit at a lower energy. We reinstalled the old bend power supply in parallel with the new undamaged unit. We then fully commissioned the booster with each of these power supplies. This setup allows us to switch back and forth between the power supplies in a matter of hours, allowing for the repair, completion, and full commissioning of the new supply and is an option should the new supply experience another failure. Operations had been scheduled to begin on January 5th. Despite this setback, operations began on January 17th.

The near-term plan is to continue to use half of the new bend-magnet supply to inject at 1.23 GeV (instead of 1.9), then migrate to full-energy injection (1.9 GeV) within the next few months. We are currently working with the vendor to develop a path forward and hope that we will be able to migrate to full-energy injection (1.9 GeV) during May shutdown, at the latest.

With the completion of this shutdown and commissioning period, the major hardware work for the top-off upgrade is complete. Remaining hardware work is relatively limited and consists of some additional radiation safety interlock systems and the gating signal distribution chassis, which can be installed anytime outside of major shutdowns. Our main focus before starting operation in top-off mode will be completion of the very extensive radiation safety studies. There has been good progress recently, and we hope to receive regulatory approval for top-off operation this summer or fall and begin top-off operation immediately thereafter.

SAC reviews the year and looks ahead

Contact: Roger Falcone, This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Members of the ALS Scientific Advisory Committee (SAC) met at Berkeley Lab on December 14 and 15 to hear about the latest ALS initiatives, projects and upgrades and to advise management on a variety of issues, including recommendations of the Program Study Panel, plans for accelerator renewal, and progress on a next-generation light source. Berkeley Lab Associate Laboratory Director Paul Alivisatos welcomed the attendees, and introduced the new ALS director, Roger Falcone, who acknowledged that the year had brought several organizational changes, among them, sadly, the sudden loss of our colleague Neville Smith. He then brought the committee up to date on recent developments, including the ALS Users' Meeting, safety issues, optimizing beamline staffing, and progress toward facility improvements and beamline development. He also stressed that the ALS presence continues to increase—publications are up, there are more general user proposals, and there are more users.

SAC members 2007

Scientific Advisory Committee, 2007. From left: Friso van der Veen, Linda Young, John Parise, Carolyn Larabell, Clemens Heske, Peter Johnson, Phil Bucksbaum, Roger Falcone, Steve Kevan, Erwin Poliakoff, Jeff Bokor, and Sam Bader.

Ben Feinberg (ALS Deputy Division Director) then introduced three Laboratory Directed Research and Development (LDRD)-funded ALS projects. Principal Investigators Andreas Bartel, Michael Martin, and Alexander Hexemer provided brief overviews. This was followed by a short presentation and discussion on the Program Study Panel report by Peter Johnson of Brookhaven National Laboratory. After lunch, the meeting focused on accelerator renewal issues. David Robin (Accelerator and Fusion Research Division, AFRD) provided the overview, Christoph Steier (AFRD) gave the top-off upgrade status; Greg Portmann (Engineering) discussed single-bunch kicking, Ken Baptiste (Engineering) focused on klystron replacement, and David Robin (AFRD) concluded with a presentation on a higher-brightness lattice.

The afternoon ended with an overview and discussion of the next generation light source by Roger Falcone and an accelerator research and development proposal by John Corlett (AFRD). The second day's session focused on the proposed environmental science infrared beamline (Michael Martin, ALS, and Peter Nico, Earth Sciences Division), the QERLIN momentum-resolved spectroscopy technique (Zahid Hussain, ALS, and Zahid Hasan, Princeton University), and a summary of a recent review of the protein crystallography beamlines (Keith Moffat, University of Chicago). Gary Krebs and Janos Kirz (ALS) then concluded the meeting with a presentation on upcoming beamline reviews. Presentations and a listing of current SAC members are available online.

UEC Corner: Notes from the Users' Executive Committee

Contact: Tony van Buuren, This e-mail address is being protected from spambots. You need JavaScript enabled to view it

This e-mail address is being protected from spambots. You need JavaScript enabled to view it The ALS Users' Executive Committee (UEC) conveys the concerns and interests of users to ALS management. Members are elected annually by ALS users. The UEC also facilitates communication between the ALS and other synchrotrons and between users and federal funding agencies.

As Roger mentions above, a $500 million increase for the Office of Science proposed by the President and approved by the House of Representatives could very well be lost when Congress adopts a Continuing Resolution for the entire 2007 fiscal year. This budget scenario will have a significant effect on efforts to appropriately support users with scientific and engineering staff, plans to replace aging instruments, and the ALS strategy to develop and implement new scientific capabilities.

As the new chair of the Users' Executive Committee, I want to extend an invitation to all users to contact the members of the UEC with concerns or questions regarding the ALS Users' Group. We are here to support your needs, so please contact me ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ) or anyone else on the UEC with any questions.

The current members of the committee (with terms) are listed below:

  • Tony van Buuren (chair), Lawrence Livermore National Laboratory (2005-07)
  • Elke Arenholz, Advanced Light Source, Berkeley Lab (2006-08)
  • Peter Fischer, Center for X-Ray Optics, Berkeley Lab (2007-09)
  • Kenneth Goldberg, Center for X-Ray Optics, Berkeley Lab (2007-09)
  • Jinghua Guo, Advanced Light Source, Berkeley Lab (2005-07)
  • Clemens Heske (past chair), Univ. of Nevada, Las Vegas (2004-06)
  • Franz Himpsel, Univ. of Wisconsin, Madison (2007-09)
  • Amanda Hudson, Univ. of Nevada, Las Vegas (2005-07)
  • Alessandra Lanzara, Univ. of California, Berkeley; Materials Sciences Division, Berkeley Lab (2006-08)
  • Simon Morton, Physical Biosciences Division, Berkeley Lab (2005-07)
  • Hendrik Ohldag (vice chair), Stanford Synchrotron Radiation Laboratory (2006-08)

Contact information for all UEC members can be found online.

The Users' Associations at the light sources across the country have formed a group to work on outreach and education to help ensure that people understand the importance of these facilities, and Corie Ralston is representing the ALS UEC in this activity. Please contact her at This e-mail address is being protected from spambots. You need JavaScript enabled to view it with any questions or suggestions.

We would very much like to thank Clemens Heske, who was Chair of the UEC last year, for all of his efforts, and Ed Westbrook and Greg Denbeaux, who rotated off the UEC this year.

Again, please don’t hesitate to contact me with any questions or concerns. I look forward to meeting you and a productive and interesting year at the Advanced Light Source!

Safety First: ALS Radiological Work Authorization approved

Contact: Jim Floyd, This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Safety First logoA revised Radiological Work Authorization (RWA) for the ALS has been reviewed, approved, and is now in effect. Careful controls are still in place for reviewing and implementing beamline shielding changes. Please contact John Pruyn at This e-mail address is being protected from spambots. You need JavaScript enabled to view it if you have any questions regarding shielding or shielding changes at the beamlines. Following the fire at Sector 5, almost all of the affected light fixtures have either been removed or had new bulbs installed as an interim measure. The final plan is to replace all of the fixtures during our next shutdown.

With the upcoming demolition of Building 10, the User Chemistry Lab is relocating to 6-2233 on an interim basis. As this space is much smaller and is being generously shared by the Molecular Environmental Science program, work there will have to be coordinated and done more carefully. Donna Hamamoto is leading this effort, which will include more thorough training, orientation, scheduling, chemical inventory and waste management. A new orientation packet has been prepared for users of that space that gives an overview of their responsibilities. Work involving waste generation, prolonged use of the hood, hazardous gases, etc., will need to be reviewed and scheduled.

The ALS received its MESH (Management of Environment, Health, and Safety) review from the Safety Review Committee (SRC), and Roger Falcone gave the ALS response at the Committee's January meeting. All responses were accepted by the SRC. The ALS Staff Safety Committee has finished its investigation of the Beamline 5.3 radiation safety shutter issue and presented its findings to management. Although no definitive cause could be determined, a number of recommendations were made. Final corrective actions are still being decided upon.

Coherence 2007 Workshop to take place in June

Contact: Janos Kirz, This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Coherence 2007The fourth International Workshop on Phase Retrieval and Coherent Scattering will take place June 25–28, 2007, at the Asilomar Conference Center in Pacific Grove, California. This year’s workshop, Coherence 2007, will focus on how coherent x rays from third-generation light sources and free-electron lasers are providing exciting opportunities for microscopy based on recording and reconstruction of diffraction patterns, and for extending speckle correlation spectroscopy to the x-ray range. The workshop offers the chance to review recent progress and exchange ideas for future initiatives in these areas.

Previous workshops were held in Berkeley, France, and Australia. Sponsors for this year’s meeting include Berkeley Lab’s Advanced Light Source and Center for X-Ray Optics; Lawrence Livermore National Laboratory; XRADIA; and the University of California, Davis, Center for Biophotonics.

The deadline for abstract submissions is March 1, 2007. Information about abstract submissions, meeting registration, accommodations, and Monterey/Pacific Grove tourist activities is available online.

Julie McCullough joins the ALS Editorial Team

This e-mail address is being protected from spambots. You need JavaScript enabled to view it In December 2006, Julie McCullough joined the ALS Technical Information Section staff, where her main beat is ALSNews. Although new to the ALS, she was lead writer and editor in the LBNL Public Affairs' Creative Services Office (formerly the Technical and Electronic Information Department) before taking time off to write her coming-of-age novel about a girl growing up in New Orleans. Julie welcomes your feedback and suggestions for ALSNews. You can reach her at This e-mail address is being protected from spambots. You need JavaScript enabled to view it or x6838. Her office is in Building 4, Room 221.

Please report ALS publications by Friday, February 9

Contact: This e-mail address is being protected from spambots. You need JavaScript enabled to view it

If you have recently published any ALS-related work in a scientific journal, conference proceedings, or book chapter, completed a Ph.D. thesis, or received a patent based on work done at the ALS, please let us know by February 9th.

Simply go to the User Services Publications Web page. From there, it is an easy two-step process: (1) Do a "Search for Publications" to see if your publications were previously entered into our database by a collaborator. If you are one of our more prolific publishers or have a common last name, you can limit the search by initials, beamline, year published, or journal name. (2) For your publications that are not reported in our database, fill out the "ALS Publications Submission" form. This works best if you use Netscape 6 or 7, Microsoft Internet Explorer version 5.0 or greater, or Safari 2.0 (Macs only) or greater; otherwise, you will lose data if you hit the "Back" key. Most of the mandatory fields are required by DOE. The most important fields are "Title" and "Journal or Publication Name." If you are missing information, such as the specific page or month published, please type "n/a" in the field; we will attempt to track it down.

Your timely response will be greatly appreciated, as it is imperative that we accurately track the publications we generate. Remember, if it's on your CV, and all or part of the work was done at the ALS, it should be in our database!