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ALSNews Vol. 297 Print
Wednesday, 29 April 2009 00:00

In This Issue

Preservation of Fe(II) by Carbon-Rich Matrices in Hydrothermal Plumes

How Dynein Binds to Microtubules

Top-Off Mode Now at Full Current; Congratulations Team!

Meet Our New Deputy Director For Science: Bob Schoenlein

Funding and User Support Building Updates

Guest House Takes Shape on Hillside


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Scripps Research Scientists Model 3-D Structures of Proteins that Control Human Clock

A Research Center for Understanding How to Store CO2 Underground

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Preservation of Fe(II) by Carbon-Rich Matrices in Hydrothermal Plumes

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Despite the considerable amount of iron that enters the oceans from the continents and from hydrothermal vents at mid-ocean ridges on the seafloor, there are large regions of the global ocean where iron availability is so low that it limits life. Oceanographers have long explained this anomaly by assuming that the iron in the sea is primarily incorporated as Fe(III) into inorganic minerals that lack both the mobility to circulate over long distance and bioavailability to sea life as an essential nutrient. Now, a collaboration led by researchers from the Woods Hole Oceanographic Institution has reported that the hydrothermal plumes emerging from the vents actually contain iron in both Fe(II) and Fe(III) oxidation states associated with organic material from nearby flora and fauna. The collaboration suggests that the organic matrices prevent oxidation and precipitation of the Fe(II), perhaps increasing both its circulation through the world's oceans and its bioavailability as a deep-sea nutrient. Read more...

Fertizlizing the Ocean

Publication about this research: B.M. Toner, S.C. Fakra, S.J. Manganini, C.M. Santelli, M.A. Marcus, J.W. Moffett, O. Rouxel, C.R. German, and K.J. Edwards, "Preservation of iron(II) by carbon-rich matrices in a hydrothermal plume," Nature Geoscience 2, 197 (2009).

How Dynein Binds to Microtubules

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Cytoplasmic dynein is a protein complex responsible for the transport of a large variety of cargoes, from specific RNAs and proteins to whole organelles, in a directional fashion along microtubules that serve as cellular conveyor belts. Consistent with this central role, cytoplasmic dynein is associated with a number of disease-related processes, including the transport of viruses, neurodegeneration, and the mitotic checkpoint malfunctions that lead to cancer. A team of researchers from the University of California's San Francisco and Berkeley campuses has recently solved the structure of dynein's microtubule-binding domain (MTBD) and part of the stalk structure that connects MTBD to the rest of the dynein complex. This first look at any part of the dynein motor domain identifies how it binds to microtubules and gives some hints into the fascinating question of how communication passes along the stalk from the MTBD to the rest of the motor. Read more...

A Motor Protein's Moving Parts

Publication about this research: A.P. Carter, J.E. Garbarino, E.M. Wilson-Kubalek, W.E. Shipley, C. Cho, R.A. Milligan, R.D. Vale, and I.R. Gibbons, "Structure and functional role of dynein's microtubule-binding domain," Science 322, 1691 (2009).

Top-Off Mode Now at Full Current; Congratulations Team!

This month, the ALS ramped up to its target of 500 mA of average storage-ring current in top-off mode. According to David Robin, ALS Division Deputy for Operations and Accelerator Development, top-off is exceeding expectations, with less of a "teething period" than anticipated. As expected, he said, we have improved thermal stability, we increased the flux, and we've increased the usable beam time. Furthermore, reliability [(time scheduled – time lost)/time scheduled)] has actually improved: we're getting close to our best operation since the ALS was commissioned.

The top-off project has been the largest upgrade to the accelerator since the ALS was commissioned in 1993. Similar to the superbend upgrade in 2001, it was major surgery, with a lot of risks and breaking new ground in many areas. For example, bunch cleaning for two-bunch mode was a requirement for which there wasn't a solution when the project began. The method ultimately devised by the team proved to work extremely well, resulting in greater bunch purity than before and an increase in average two-bunch current by nearly a factor of three.

Top-off project team

Top-off team members (listed in diagonal rows running from back left to right front). Row 1: Bill Kenney, Jin-Young Jung, Mike Fahmie, Ron Gervasoni. Row 2: Barry Bailey, Steve Cooper, Christoph Steier, Alexis Smith-Baumann, Ken Baptiste. Row 3: Greg Portmann, Tony Warwick, Weishi Wan, Alex Gavidia, Walter Barry, Helen Chen. Row 4: Chris Hernikl, Steve Rossi, Pat McKean, Hiroshi Nishimura, Bill Kelius. Row 5: Ryan Sprague, Tom Scarvie, Mike Kritscher, Max Vinco, Fernando Sannibale. Row 6: Warren Byrne, Mike Chin. Row 7: Jonathan Elkins, David Robin. Row 8: Pat Casey, Jonah Weber. Row 9: Moises Balagot. Row 10: Bob Mueller. Not pictured: Alan Biocca, Richard Donahue, James Dougherty, Bill Gath, Susanna Jacobson, James John Julian, Slawomir Kwiatkowski, Steve Marks, Jim Oneill, Ross Schlueter, Derek Shuman, Greg Stover, Chris Timossi, Eric Williams, Russell Wells.

"It was a terrific feeling to be able to pull up the ALS ring status on my laptop computer, at any hour of the day, even when I was back at DOE in Washington, and see the high and flat beam current," said ALS Director Roger Falcone. "And then the emails started coming in from the users, highly laudatory and very grateful... We told people at DOE we were capable of doing it; we did it. We told our users we could do it; and we did it."

Many thanks and congratulations to Christoph Steier, top-off project manager, and all ALS, engineering, accelerator operations, and EH&S staff for all your help in making this project a success.

Meet Our New Deputy Director For Science: Bob Schoenlein

Last month we briefly announced that Robert (Bob) Schoenlein (pronounced "Shane-line") would join the ALS as Deputy Director for Science. Here is a more detailed account of Bob's past involvement with the ALS and his goals for the future.

Bob SchoenleinBob's research is in the area of ultrafast science, with programs in Berkeley Lab's Materials Sciences and Chemical Sciences Divisions (MSD and CSD, respectively). His involvement with the ALS dates back more than 15 years, beginning as a somewhat unconventional "ALS user"—first joining with an interdisciplinary team of colleagues from the Lab's Accelerator and Fusion Research Division (AFRD) and the ALS to develop laser-based techniques for manipulating electron beams to generate ultrafast x-rays, and then applying these unique sources to studies of structural dynamics in matter.

In the mid 1990s, Schoenlein, W. Leemans, and colleagues used Thomson scattering with the ALS linac injector to generate femtosecond hard x-ray pulses for some of the earliest subpicosecond diffraction studies. Even newer ideas from AFRD colleagues A. Zholents and M. Zolotorev, based on injecting femtosecond laser pulses into the storage ring, were demonstrated on Beamline 6.3.2 and further developed at the prototype femtosecond x-ray Beamline 5.3.1 with ALS Scientists P. Heimann and E. Glover. This approach is the basis for the new Ultrafast Slicing Beamlines 6.0.1 and 6.0.2, which support Bob's current research (on dynamics in complex materials and condensed-phase molecular dynamics) as well as that of many other ALS users in the growing field of ultrafast x-ray science.

In addition to his new role as Deputy Director for Science, Bob plans to remain active as a researcher within MSD, CSD, and at the ALS. Of course his first priority will be to support the world-class science program of the ALS, which he believes is a testament to the outstanding scientific staff, technical staff, and user community of the ALS. His major goals are to maintain and build on this record of excellence—fostering the development of new research directions and exploiting new scientific opportunities. He is looking forward to working closely with ALS scientific staff, users, and advisory committees to meet these challenges and to helping Roger and his team implement the ALS Strategic Plan that will serve as a roadmap for the facility into the next decade and beyond. Bob is fortunate to have the opportunity to work with ALS Science Advisor and former Director Janos Kirz during a transition period. This leaves only one grand challenge standing between Janos and retirement from management responsibilities—passing along his extensive knowledge, expertise, and scientific judgment that has served the ALS so well.

Funding and User Support Building Updates

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After a series of ups and downs, we have excellent news about the ALS budget for fiscal year 2009 (October 2008–September 2009). In brief, the ALS will receive an increase of about 10% over the continuing resolution funding under which we've been operating. In addition, we will receive a supplement to allow us to complete both the seismic work on Building 6 and the klystron replacement project.

The four Department of Energy (DOE) light sources have also been asked to submit a substantial number of additional projects under the stimulus legislation. The ALS and DOE intend to use this funding to jump start the ALS Strategic Plan. Stay tuned for results of this exciting submittal.

The User Support Building (USB) project has faced many funding challenges to date, but it appears that those days are now behind us. The anticipated FY09 funding of $11.5M is in the recently signed omnibus spending bill. Additionally, the FY10 funding of $14.5M has been forward funded to the project as a part of the stimulus bill. Construction activities can now proceed uninterrupted and be completed in the most efficient way possible.

On April 22, the USB project underwent an extremely successful and positive DOE Lehman review led by Steve Tkaczyk of the DOE's Office of Engineering and Construction Management, with Pedro Montano, Director of the Scientific User Facilities Division of the DOE's Office of Basic Energy Sciences (BES), and Tom Brown, Program Manager in BES for the USB project, observing. Lehman reviews are independent technical, cost, schedule, and management peer reviews of DOE Office of Science construction projects.

Lehman review of USB

Pedro Montano (center, with arms crossed), Tom Brown (to Montano's immediate right, in light brown jacket), and Steve Tkaczyk (to Montano's left, in light tan jacket) pose at the USB construction site with members of the Lehman review committee, DOE representatives, and members of the USB project team.

Structural steel erection began on Monday, April 27. The structural steel activity will be one of the most challenging phases of the project due to crane needs, the large quantity of material to be delivered and staged, and the constricted construction site. Each time construction begins on the site it takes weeks for personnel to adjust and respect the new boundaries. This time we do not have that luxury so we ask for your immediate cooperation and assistance.

The current forecast construction completion date is in June 2010. We anticipate taking occupancy of the building in August or September 2010.

Guest House Takes Shape on Hillside

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Construction of the Berkeley Lab Guest House is proceeding nicely, and we are on schedule for an August 2009 completion date. Located within a short walk of the ALS and the cafeteria, the 57-room Guest House will provide 70 beds in single- and double-occupancy rooms, and will include a main lobby, lounge/kitchenette area, laundry facilities, vending areas, and an outdoor patio. All rooms will have a refrigerator and free wireless Internet access. As finish work on the exterior progresses in earnest, and with the removal of the scaffolding that was cloaking the building's facades, the structure is now recognizable as the guest house depicted in the architectural drawings. Interior rough-in work is nearly complete and finish sheet-rock work is getting underway. Although we had hoped to have set rates available at this point in time, various challenges have arisen, precluding this for now. As soon as we are confident of an opening date and operations plan, reservations will be accepted and rates will be announced.

Guest House drawing and current status

Berkeley Lab Guest House. Left: Architectural drawing. Right: Current construction.


For the user runs from March 18 to April 12, 2009, the beam reliability [(time scheduled – time lost)/time scheduled)] was 95.4%. For this period, the mean time between failures (MTBF) was 22.2 hours, and the mean time to recovery (MTTR) was 64 minutes. There were no significant interruptions.

Note that the previously reported metric, "percent of scheduled beam delivered to completion," depended on the practice of periodically refilling the storage ring. With the advent of top-off mode, there is only one storage ring refill—at the beginning of each week. Therefore, we are reporting instead MTBF and MTTR, two standard reliability metrics often requested by users that will provide something like the "delivered to completion" number of the previous mode of operation.

Questions about beam reliability should be sent to 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).

Long-term and weekly operations schedules are available here. View the ring status in real time here.

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