Looking Forward and Celebrating 20 Years in 2013
We recently sat down with ALS Director Roger Falcone to talk about what 2013 has in store for the ALS. An immediate answer is - a celebration - as the ALS marks its 20th year of operation. We’ll spend some time this year looking back at what we’ve accomplished over the past couple of decades and forward to how we’ll continue to contribute to the future of scientific research.
The next few months at the ALS will be both busy and exciting as we prepare for our annual shutdown in February and for a DOE budget review in March, says Falcone. The shutdown will bring some long-anticipated upgrades and implementations to our facility and the budget review will give the ALS an opportunity to revisit, fine-tune, and prioritize our strategic plan. We continue to improve our accelerator so that we maintain our leadership as one of the brightest soft x-ray synchrotrons in the world — a valuable enabling resource for thousands of users.
“Our strategic plan captures our best ideas about how we will work with users to stay at the forefront of science,” says Falcone. “The roadmap for how we do that will be informed by where the DOE and other agencies are focusing resources.”
One of the DOE’s major focus areas in 2013 will continue to be sustainable energy, says Falcone. The ALS has continually played a role in this arena by partnering with scientists involved in major sustainable energy efforts, including JCAP, an ongoing effort in artificial photosynthesis, and JCSER, a new energy storage initiative.
“We’ve always done world-leading research, and that has put us in a position to contribute directly to these grand-challenge missions that the DOE has taken on,” says Falcone. That also means we need to continue our basic research mission to be prepared for the grand challenges in the future.
New ALS instrumentation plans in 2013 such as our AMBER beamline proposal will build upon existing ALS capabilities for supporting energy research.
Partnerships and collaborations with other divisions at the Lab will also inform our focus and strategy, says Falcone. With Omar Yaghi as the new director of the Molecular Foundry, we are looking more closely at how we can expand our small-molecule crystallography capabilities to provide the best research capabilities for new functional materials including metal-organic frameworks (MOFs), which would also align well with the DOE’s interest in mesoscale research.
More than 6000 people came up the hill to see what is happening at Berkeley Lab during Open House on Saturday, October 13, and more than 1500 of them came even further up the hill to visit the ALS for tours, talks, and hands-on activities, all of which helped them understand how we use electrons, magnets, microscopes, and computers to conduct research at the ALS. At the X-Ray Café, ALS staff and scientists spoke one-on-one with guests about how the ALS works, why and how scientists want to use it, how it is funded, and plans for the future. Inside the ring, visitors heard science stories from beamline scientists. You can see more candid photos of the Open House on the ALS flickr site.
ALS Users’ Executive Committee Chair Brandy Toner launched this year’s User Meeting with a warm welcome to the 417 registered attendees who gathered from around the world to attend plenary sessions, workshops, and social gatherings. Berkeley Lab Deputy Director Horst Simon then extended his own welcome, touching upon the importance of the synergy between the ALS and the Lab as the ALS begins a collaboration with the Lab’s computational research program, which Simon previously led, to solve data management challenges. ALS Division Director Roger Falcone thi(at left) provided a broad overview of the state of the ALS, covering budgets, important research areas, and user demographics. Falcone was pleased to point out the jump in the number of refereed publications last year and notable science highlights, which communicated ALS advances in structural biology, battery research, and fundamental science. Falcone acknowledged the work of Simon Morton and Jeff Dickert at the BCSB beamline this year, which won them an R&D100 Award.
DOE Associate Director of Science for Basic Energy Science (BES), Dr. Harriet Kung, began her presentation with a discussion of new opportunities for mesoscale science, which the DOE sees giving rise to interesting possibilities for integration of computation, characterization, and synthesis. Regardless of uncertainties in funding, which Kung described as “a very challenging situation,” BES is looking forward to continuing its commitment to science with a focused interest on clean energy science and advances in computational power. Kung detailed BES efforts to inform taxpayers about the benefits of facilities and programs through various communications efforts.
Don Medley, Berkeley Lab’s Head of Federal Government Relations, continued Kung’s discussion of communication efforts with a lively talk about building support for science among our elected officials through education and outreach. Monica Metzler, Chair of the Illinois Science Council, followed with an entertaining and informative message about communication techniques that make presentations most effective.
The Molecular Foundry’s Director, Omar Yaghi, then took the stage to discuss his groundbreaking work on metal-organic frameworks (MOFs), which show great promise for natural gas storage and carbon gas capture. Yaghi articulated the vast opportunities available to scientists who want to help move MOF research forward and his hopes for collaboration between the Foundry and the ALS.
ALS staff updates included User Services group lead Sue Bailey, who introduced plans for a new ALS user portal and an updated registration and proposal system. David Robin, Division Deputy for Accelerator Operation and Development, reviewed planned accelerator, instrumentation, and controls upgrades and a new operational mode.
Pupa Gilbert of the University of Wisconsin discussed her work on mapping the amorphous-to-crystalline transitions in sea urchin biominerals using the PEEM microscope at Beamline 11.0.1. Steve Kevan, newly appointed Deputy Division Director for Science at the ALS, discussed his work on hidden symmetries in magnetic domains.
Twenty-one students from around the world then stepped up to present their research for the third annual student poster slam (at right). They were followed by Nate Lewis, Director of the Joint Center for Artificial Photosynthesis (JCAP) at Caltech, a program dedicated to the development of an artificial solar-fuel generation technology. JCAP aims to find a cost-effective method to produce fuels using only sunlight, water, and carbon-dioxide as inputs.
At the poster competition (below) and reception that evening, students fielded questions about their work, with first prize going to Mahati Chintapalli of the Materials Science Department at UC Berkeley for her research on size-dependent dissociation of CO on cobalt nanocatalysts.
Tuesday morning began with award winners speaking about their work – first up was Shirley Award winner Carl Percival, an atmospheric chemist from the University of Manchester, whose team made the first direct measurements of the reaction rates of Criegee intermediates and thus showed that their impact on tropospheric chemistry and climate may be substantially greater than previously assumed. Student poster award winner Mahati Chintapalli also had a chance to present and field questions about her research.
Tuesday progressed with presentations by ALS users working in a variety of research areas. Berkeley Lab senior materials scientist Rob Ritchie talked about his research on the fracture behavior of human bone and ceramic composites using x-ray synchrotron microtomography. Wanli Yang, an ALS staff scientist working on battery research, spoke about using soft x-rays to probe electronic states key to battery performance. Andrew McElrone, an ALS user and Research Scientist with the USDA-Agricultural Research Service, spoke about his use of high-resolution computed tomography to gain a better understanding of a grapevine’s water transport system and reactions to drought pressure.
ALS staff scientist Eli Rotenberg rounded out Tuesday’s session with an entertaining and enlightening retrospective on the past 19 years of photoemission at Beamline 7. The beamline was retired recently and is currently undergoing a complete rebuild.
Tuesday’s awards dinner brought the ALS user community together to recognize some of their own distinguished accomplishments. The Klaus Halbach Award for Innovative Instrumentation went to Simon Morton and Jeff Dickert of Berkeley Lab’s Physical Biosciences Division for the invention and implementation of the Compact Variable Collimator, which has led to a dramatic increase in productivity in protein crystallography at the Berkeley Center for Structural Biology beamlines. The Tim Renner User Services Award for Outstanding Support to the ALS User Community was awarded to Tolek Tyliszczak, beamline scientist at the Molecular Environmental Sciences beamline, a leading national resource in the field of soft x-ray synchrotron radiation research. Descriptions of the awards and photos of the recipients are available on the 2012 ALS User Meeting Awards Web page.
Thirteen workshops took up the remainder of the meeting; see the complete list of workshop speakers and agendas.
Although it’s defined by DOE as a national user facility just as the ALS is, the Energy Sciences Network (ESnet) doesn’t quite fit the image of a centrally located facility serving a specific set of users. Rather, ESnet is a nationwide network that provides high-bandwidth, reliable connectivity linking tens of thousands of scientists at more than 40 DOE labs and facilities. The systems and services provided by ESnet staff advance research by helping scientists share their ideas, their data and their discoveries with collaborators and peers around the world.
Managed by Lawrence Berkeley National Laboratory (LBNL), ESnet will soon take bandwidth to the next level as it rolls out the world’s first 100 gigabits per second (100 Gbps) network by the end of 2012. According to ESnet Director Greg Bell, the scientific data resulting from experiments at DOE’s particle accelerators, light sources and genome sequencing facilities are push the limits of ESnet’s current 10 Gbps network.
“We never want the network to be a gating function for scientific discovery,” Bell said.
According to ALS Scientist Dula Parkinson, a new fast camera installed at the hard x-ray tomography Beamline 8.3.2 at the ALS last year allows scientists to study a variety of structures as a function of time—from bones to rocks, and even metallic alloys—in unprecedented detail. The new camera produces data at a rate of 300 megabytes per second, which is 50 times faster than the one it replaced.
“Two years ago the hard x-ray tomography beamline at Berkeley Lab’s ALS generated about 100 gigabytes of data per week, but we got a faster camera and now we are generating anywhere from 2 to 5 terabytes of data per week,” says Parkinson. “This is pushing the limit of what our current infrastructure can handle.”
According to Parkinson, in the current system, a typical ALS user will create a folder on a data storage server connected to the instrument, and save their raw data to this folder. In many cases, users may do some initial processing on desktop computers at the ALS and save these files on the facility’s storage server. Upon leaving the facility, researchers will copy their data on an external hard drive and carry it home for further analysis. The files and raw data initially saved on the ALS storage server are typically left behind for the facility’s staff to manage. Keeping up with the torrent of data requires new methods for moving, storing, and analyzing data.
For the first step, ESnet staff helped Parkinson set up a data transfer node (tuned for optimal performance) and LBNL networking staff helped deploy a 10 Gigabits-per-second switch, giving Parkinson’s data a high-performance path through the LBNL network (LBLnet) to ESnet. This approach is an example of ESnet’s “Science DMZ” model, where data-intensive science applications are run on dedicated infrastructure configured for high performance.
ESnet carries the ALS data to DOE’s National Energy Research Scientific Computing Center (NERSC) in Oakland, where the data is stored, managed and shared with other researchers. To pave the way, NERSC staff helped Parkinson with his data acquisition and data transfer workflow. Future plans include tapping into NERSC’s supercomputing resources to improve data analysis.
“This is a success story for the ALS, for LBLnet, for ESnet and for NERSC,” said ESnet network engineer Eli Dart, who worked with Parkinson. “This is a working example of the science infrastructure needed to support a new generation of data-intensive science experiments at X-ray light sources, neutron sources, and free-electron lasers.”
ALS users interested in using the network for data-intensive workflows can contact ESnet at
or learn more at the October user meeting poster session.
Lots of changes have been happening in the ALS User Office over the last couple of months: users will find that a familiar face is gone and new ones are there to welcome them and help complete their registration.
Sharon Fujimura, who has worked in the ALS User Office since the start of ALS operations, retires at the end of June. Sharon manned the Reception Desk in the mezzanine and was renowned for her sense of humor and efficient user registration technique. Staff and users would like to thank Sharon for her dedication to supporting users over the years and wish her a long and happy retirement.
The User Office is happy to welcome Giselle Jiles, who began in early June as Sharon's replacement. Giselle was previously admissions director at St. Joseph's High School in the Bay area.
We are also very proud of Deborah Smith, supervisor of the User Office, who has recently graduated with a liberal arts associate degree from Berkeley City College, and who is progressing to her Bachelor's degree at JFK University.
ALS Beamline Scientist Kate Jenkins recently spent an afternoon discussing the scientific vailidity of The Avengers with 16- and 17-year-old high school students. It was all in the name of promoting science as cool, relevant, and something to consider as a future career.
Jenkins visited with AP and college prep physics students at Albany High School as part of the Institute of Electrical and Electronics Engineers (IEEE) program “Day with an Engineer.” She talked about her educational path and her job as a materials scientist and then took questions from the teens, the most common one being: “Is what I saw in the movie The Avengers real?” Luckily, Jenkins had seen the movie and anticipated the question.
“I had printed out a screen shot of this thing from the movie called a tesseract, which is the ‘source of ultimate potential energy,’” says Jenkins. “In the movie they control the tesseract with a septapole magnet, so I was able to say ‘actually, I work on a machine that uses the same thing as the tesseract… and here’s what I do with it.’”
With the help of LBNL’s Center for Science and Engineering Education (CSEE), Jenkins also presented the students with a series of models that helped her explain magnetism and superconductivity. The students were suitably impressed with her superconducting magnetic levitation train and oxygen liquefying cone, Jenkins says. Following her visit with students, Kate received several letters from the students thanking her for her efforts and enthusiastically promising to keep up their studies in physics.
When she’s not acting as an ALS ambassador to local students, Jenkins can be found conducting magnetic spectroscopy and scattering research at Beamline 6.3.1 .
Corie Ralston’s appointment as Head of the Berkeley Center for Structural Biology (BCSB) has her busy looking at budgets, funding, and big-picture goals. The biophysicist staff scientist has been with BCSB for more than 10 years, so much of what she’s considering comes from an intimate familiarity with the day-to-day operations and challenges of the facility.
Ralston joined BCSB, which runs five of the crystallography beamlines at the ALS, as a staff scientist in 2002 and took on the larger role of operations manager about five years ago. While Ralston will definitely keep a hand in the crystallography research she’s been doing, her work balance will shift more toward user relations and funding development. Her new position entails managing a group of 12 employees and a budget of $3 million.
In her beamline research, Ralston studies chaperonin protein structures, which she describes as “the really important medics in our cells” that can fix mis-folded proteins. Since mis-folded proteins may cause many diseases, such as Alzheimer's and Parkinson's, a better understanding of chaperonins could lead to breakthrough drug developments. Ralston’s research is part of a collaboration with Stanford that was organized by former BCSB Head Paul Adams.
“The thing about keeping my hand in crystallography is that it gives me a sense of what’s needed at the beamlines,” says Ralston. “Especially because I work on a hard project – it’s not easy to crystallize; it’s not easy to solve; the data is always sub-optimal, so I have to have the best tools at the beamline.”
Beamline engineering developments are what keep Ralston’s crystallography work moving forward, and managing this process will be key to her new position as Head of BCSB. From software tools that advance data processing and collection to hardware tools like beamline optics and robotic controls, engineering development is what keeps the ALS crystallography beamlines at the forefront.
“It’s a challenge because whenever you’re doing something new that increases the flux of the beamline, you’re in danger of making it less stable,” says Ralston. “Maintaining this balance between stability and technological advancement is one of our biggest challenges.”
Besides maintaining existing BCSB funding – the majority of which comes from contracts with participating research teams (PRT), Howard Hughes Medical Institute, and an NIH grant – Ralston hopes to develop new funding sources by restructuring beamline contracts. She’d like to be able to offer smaller amounts of guaranteed beamtime to PRT users with smaller budgets, which is a more common situation in today’s economy. Ralston would then launch an aggressive PR campaign, travelling to present the new option to companies and academic institutions nationwide.
“I would really love BCSB to be the first thing someone thinks of when they need to solve a structure in order to move forward with their research,” says Ralston.
In Her Spare Time: Award-Winning Science Fiction Writer
In addition to her new appointment at BCSB, Ralston has recently been recognized for her science fiction writing achievements, winning first prize in an international competition organized by the UK’s national synchrotron facility, Diamond Light Source. Her short story “The Sound of Science” follows a series of interactions between a beamline scientist and an alien as the scientist leads a group tour of a synchrotron. While the scientist begins the tour feeling frustrated with the inconvenience of taking time away from her work, her interactions with the curious alien lead her to some new realizations about science and our species’ interconnectedness.
“We all depend on each other for various areas of expertise,” Ralston muses. “I don’t really know how my car works and I can’t build a coffeemaker, but I can fix the beamline.”
The inspiration for her story came partly from Ralston’s personal experience at the ALS. “I do give a lot of tours and often I’m not initially enthusiastic about doing it, but then the people on my tours are so amazed by everything that it serves as a nice reminder of why I like this place so much,” says Ralston. “I thought to include an alien maybe because some of the people on my tour seem alien to me.”
Ralston has been writing science fiction since she was a teenager, becoming serious about her pursuit about 10 years ago. She now has more than a dozen published stories at the professional level. She recently finished a draft of her first novel, which is set in post-apocalyptic Bay Area.
Read Corie's winning entry "The Sound of Silence" and see her describing her work on Beamline Highlight 8.3.2: Structural Biology.
View the PBD announcement of her appointment here.
Berkeley Lab Scientists Kevin Wilson and Oliver Gessner have been selected from a nationwide pool of more than 800 applicants to receive research awards from the DOE’s Early Career Research Program. Wilson and Gessner join 66 other U.S. university- and laboratory-based researchers who were selected for the five-year awards.
Overseen by the DOE’s Office of Science, the Early Career Research Program provides crucial financial support to top researchers in their formative career stages. With these awards, the DOE specifically targeted research areas that are high priority to the department and the nation as a whole.
Wilson, Beamline Scientist on the Chemical Dynamics Beamline 9.0.2, plans to focus his Early Career research on the fate of hydrocarbons in the environment. His research will use new experimental techniques to look at how hydrocarbons at the liquid-water interface react with gas-phase free radicals. “It was my beamline work here at the ALS that led to some of these questions about how chemical reactions occur on the surface of organic aerosol particles,” says Wilson.
Gessner, also associated with the Chemical Sciences Division, will concentrate his Early Career research on molecular electronic function. Gessner’s work will use intense, ultrashort x-ray pulses to monitor the light‐induced creation and transport of charges in complex molecular systems. Some important proof-of-principle work that went into Gessner’s proposal was conducted at the ALS, exploring the unique capabilities of the light source in combination with pulsed optical lasers. “There’s so much expertise here in the fields of x-ray spectrometry and the physics of condensed phase systems,” says Gessner. “Our work at the ALS provided a great base to build on as I crafted my proposal.”
The awards serve as a rare opportunity for both scientists to delve deeper into their work and craft well-rounded research programs. “It’s a rare opportunity to really focus on a single problem and to put together a scientific program around it,” says Wilson.
“This early career award will allow me to grow this work into an actual program,” says Gessner. “It’s very gratifying to see the DOE acknowledging our work in this manner.”
A list of Early Career Research Program selectees, their institutions, and abstracts of their research projects is available at http://science.energy.gov/early-career/
September 28, 2011
Twice this month, the ALS achieved a 12-week running average reliability of over 99%--something without precedent according to Dave Richardson. The most recent 12-week running average for MTBF was above 78.5 hours, and the MTTR was 38 minutes. See charts below for detailed information. Congratulations to all who helped achieve these successes!
The 2011 ALS summer shutdown is turning out to be quite productive. Read updates of shutdown activities and see pictures here. This page will be updated, so check back regularly!
THE DOME of the Building 6 roof is in need of repair both inside and out
The exterior of the roof is nearly re-shingled! See the newest images here, taken from atop the dome!
Construction crews built scaffolding around the outside of the dome's roof so they could access the whole dome safely.
Asphalt shingles that used to leak during heavy rains will be replaced with "cool roof" technology.
The dome is half done in this photograph. You can clearly see the old (bottom) and new (top) shingles!
Construction crews have been hard at work all month reroofing the ALS dome! What a gorgeous view they get from the office!
It's nearly complete. The ALS's new "cool roof" will be complete soon!
No update on the dome's interior. The plastic sheeting is still in place. Stay tuned to see the final result...
Scaffolding was built on top of the large crane in the ALS building. Workers will be scraping lead paint away from 30% of the dome's interior. A "lead lock" coating will then be applied to protect occupants from exposure to the remaining lead paint.
A plastic sheet now hangs between the interior of the dome roof and the delicate controls below. This will prevent stray pieces of hardware or lead paint chips from falling.
Super Bend Magnets get new cold heads - every year
This is one of the ALS's three super bend magnets (super conducting center bend in SR 4, 8, and 12). The cold heads (helium compressors) on the magnets must be swapped out every year. This involves warming the magnets up from their sub five kelvin operating temperature, breaking the vacuum, swapping the cold head, reestablishing the vacuum and cooling the magnet back down. This process takes a minimum of three weeks and is one of the things that drives our need for an annual extended shutdown.
Sector 6 gets ready for a new Elliptically Polarizing Undulator
This EPU has been undergoing magnetic testing in the building 15 high bay for several months. It's final location is expected to be in sector 6.
This new vacuum chamber was installed during the shutdown, as well as a new chicane magnet. These preparations have prepared this downstream section of straight 6 for the new EPU, which will be installed over several 2-day shutdowns in the coming months.
POWER SUPPLIES are also being replaced during this shutdown. An old QFA and an old SD power supply were both removed in preparation for newer models.
Crews remove the old sextupole power supply using a counter weight and a 4-ton crane. Two new sextupole power supplies will replace this old one, providing a tested backup should it ever be needed.
The old QFA power supply was also removed in preparation of a new one. The new QFA will be less sensitive to line voltage sags that cause beam dumps. Both power supply upgrade projects will aid in more reliable beam delivery, but are mainly to replace aging equipment and keep the ALS running smoothly.
The Institut Pasteur de Montevideo (IPM) in Uruguay introduced students to remote protein crystallography data collection with the help of Peter Zwart at Beamline 5.0.2. A two-week, international workshop on macromolecular crystallography (MX) and its applications instructed 20 PhD students, postdocs and research assistants on the complete MX process.