Hoi-Ying Holman, Director of the Berkeley Synchrotron Infrared Structural Biology Program
Hoi-Ying Holman, head of the Chemical Ecology Group in Berkeley Lab’s Earth Sciences Division (ESD), is the director of the Berkeley Synchrotron Infrared Structural Biology (BSISB) Program (website) at ALS Beamlines 1.4 and 5.4. The ALS and ESD built the BSISB together with funding from the Department of Energy's Office of Biological and Environmental Research. ALS Infrared Group Leader Mike Martin and Beamline Scientist Hans Bechtel are part of the BSISB, which focuses on developing new technologies that draw from multiple scientific areas to address challenges in environmental sustainability, renewable energy and biomedicine.
One of the great advantages of synchrotron infrared spectromicroscopy is that it doesn’t (necessarily) kill its living subjects, as Holman explains. "In 1997 I was looking for a way to study the chemistry of microbes on rock surfaces noninvasively and in real time. On my first visit to the ALS I ran into Wayne McKinney, who told me the good news and the bad news: There was an infrared beamline, but the equipment was still in the boxes. So I became the first user of Beamline 1.4 by helping to unpack the boxes."
Holman published her first paper on real-time synchrotron IR spectromicroscopy in 1999 (PDF). By the mid 2000s, she found that in order for synchrotron IR to become a truly non-invasive molecular technique for studying the real-time biological processes in living cells, she needed to expand the current supporting capabilities to include a microfluidic platform.
Aqueous environments hinder SR-FTIR’s sensitivity to biological activity. She applied for DOE funding to develop an infrared-compatible microfluidic system, which was at that time the bottleneck of the synchrotron IR technology (see Real-Time Chemical Imaging of Bacterial Biofilm Development). This progress towards establishing IR spectromicroscopy eventually led to the BSISB ribbon cutting in 2010.
Holman earned the 2010 David A. Shirley Award for Outstanding Scientific Achievement at the ALS “for her pioneering study of living cells and their response to environmental stimuli using synchrotron-based FTIR spectromicroscopy.”
Complementary imaging technologies at the BSISB include a hyper-spectral imager that allows researchers to study specimens using IR as well as visible light on the same sample. In July, the BSISB expects to install a full-field IR system that will allow researchers to do 2D spectral imaging and 3D spectral tomography.
They are also developing an instrument that will combine the microfluidic IR spectromicroscopy platform (see highlight link) with Raman microscopy and mass-spectrometry imaging. A new near-field imaging capability called nanoscopy is also in development by Bechtel and Martin, and is expected to overcome the current diffraction limit by combining atomic force microscopy with broadband IR spectroscopy.
Simon Morton, Instrumentation Manager for the Berkeley Center for Structural Biology
Simon Morton, Instrumentation Manager for the Berkeley Center for Structural Biology (BCSB) and member of the Experimental Systems Group (ESG), is responsible for developing new hardware and systems to improve ALS beamlines. “We have a very aggressive program of continuous upgrades so that we’re always on the cutting edge,” says Morton. “One of the first jobs I had in coming to BCSB was evaluating the performance of the Sector 5 beamlines and developing new optics upgrades for them, which increased the flux about 30 times from 2004-2007.”
Morton has been a member of the Physical Biosciences Division, but he is now transitioning to work 60% time for the ALS, developing beamline upgrades as part of ESG. An example of one such project is the planned relocation of the ALS Small Molecule Beamline 11.3.1. One of the most productive beamlines at the ALS, “this very simple beamline design was put together very economically, but it no longer yields optimal performance using its current bend magnet source,” says Morton, so he hopes to move it to a stretch of the ring with a superbend magnet.
He is looking at lessons learned from previous upgrades to ALS protein crystallography beamlines, applying them to other existing beamlines to cost-effectively upgrade the optics, improve performance, and make use of already-developed, proven designs. “Because of the aggressive upgrades we’ve been doing to our beamlines, the performance is as good as it can be. Smaller protein crystals require a smaller and more intense x-ray beam, but we are already capturing all the x-rays and focusing them down to the smallest spot we can. So to get to the next level we need a new source of x-rays, which would be an undulator,” Morton says.
Last year Morton and Jeff Dickert (at left in photo above) developed the Compact Variable Collimator (CVC), winning them the Halbach Award for Innovative Instrumentation at the last ALS User Meeting, as well as an R&D 100 award. Morton explains his invention “To get the best data quality, it’s very important that the size of the x-ray beam is matched exactly to the size of the crystal, or even to a particular portion of the crystal that you are studying. The CVC allows users to type the size of the beam they want and have it matched instantly. They can do it remotely, there’s no realignment required, which is really the unique feature here.” Now, all BCSB beamlines have a CVC. Morton is working with other synchrotrons to install the technology and is also seeking a commercial partner.
Until recently, Morton has focused his instrumentation talents on the BCSB, which is always looking to increase the performance of its beamlines by upgrading optics, increasing capacity and throughput, and improving automation to stay competitive in the protein crystallography market. “We’re all in competition with each other, but the ALS beamlines do very well,” Morton says. He and his colleagues do a lot of outreach because users apply to multiple synchrotrons. Hosting a booth at conferences—like the upcoming American Crystallographic Association’s Annual Meeting (to be held June 20-24 in Honolulu, Hawaii)—allows them to actively promote ALS capabilities and beamlines amongst tough competition.
That’s because most BCSB users don’t come to the beamlines to do their research, but instead rely on highly automated, robust tools to get measurements at the synchrotron of their choice. “A lot of our users are proprietary users paying for beam time. We’re providing a commercial service, so things just have to work. We have to have automation, reliability, and support,” Morton says. “Our users are biologists, not synchrotron scientists. We run in full remote control, so we have a lot of integrated robotics, software, and hardware.”
During the most recent ALS shutdown, a number of upgrades were done to the optics, robotics, and sample-positioning systems to improve the capacity and performance of BCSB beamlines. Most significantly, the cooling system and the focus adjustment system were improved on the Sector 5 mirrors, which should tighten their focus. The capacity of the 5.0.2 robot was doubled as well, eliminating the need for staff to reload the machine on the weekends when beamlines are running fully remote users.
In addition to 35% academic and general users, about 65% of users on Sector 5 come from industry, primarily pharmaceutical companies doing drug development research through a participating research team. In Sector 8, 70% are from the Howard Hughes Medical Institute (HHMI), which funds the beamlines. “HHMI users tend to work on a small number of extremely challenging, multi-year projects. I don’t always keep track of the research projects,” Morton jokes. “I’m more into the hardware, myself.”
After 20 years of photoemission research at Beamline 7, ALS Senior Scientist Eli Rotenberg has taken on a new role in overseeing a complete rebuild of the beamline and its endstations. The project will expand Beamline 7’s footprint to include three endstations, three preparation chambers, and space to expand. The new setup will offer 1000-times better spatial resolution and at least 10-times better energy resolution.
“Beamline 7 wasn’t initially built for very high energy resolution,” says Rotenberg. “When it was built it was very good in other regards – high brightness and small spot size – but after 20 years the beamline and endstations were a bit mismatched.”
The endstations at Beamline 7 had evolved over the years to be pretty state-of-the-art; users come from around the world to do electronic structure research here. Rotenberg has always seen the potential for improving the 50-micron beamline resolution. About 10 years ago, he began building support for a proposal to get the resolution to less than a micron and bring the energy resolution up to current standards at the same time.
“We’re always trying to keep up with the state-of-the-art,” says Rotenberg. “At the time our proposal was submitted, it was revolutionary.”
Users have come to rely on Beamline 7 as a top-of-the-line facility for growing their own crystals and measuring them in place, a capability that Rotenberg says has been perfected in large part because of close collaboration with users. The rebuild will expand these capabilities with advanced spatial resolution, which will benefit users and Rotenberg’s own graphene research.
“There won’t be anything in the world this comprehensive,” says Rotenberg. “We’ll be able to grow anything and look at non-homogeneous samples in amazing detail.”
Rotenberg also sees the renovated Beamline 7 (modeled at right) fitting in really well with the Lab’s new mesoscale science initiative because it will offer the spatial resolution necessary to study emerging phenomenon.
“We know a lot about what electrons and materials do at the atomic scale and large scale,” says Rotenberg. “This would be the first time that we’d be able to look at complex materials at the medium scale and understand what’s happening.”
If everything falls into place as planned, Rotenberg says the ALS should see the first light down the new Beamline 7 this summer, and light to the endstations in the fall. See some photos of Sector 7 upgrade on the Shutdown 2013 Update page.
Steve Kevan, ALS Deputy Division Director for Science
ALS Deputy Division Director of Science Steve Kevan has a long and collaborative history with the ALS – he’s been involved with the facility since its planning stages, is a veteran user, a longtime member of the ALS Scientific Advisory Council, and was the first chair of the Users' Executive Committee.
It’s fitting then that Kevan joined the ALS in July shortly before our historically significant 20th anniversary. He brings insights drawn from his many years working with the ALS, his experience as a professor of physics at University of Oregon since 1986, and his own research, which is focused on undulator radiation. Kevan worked on the team that built the first beamline at the ALS and led the construction of Beamline 12.0.2 in 2001, which was a first step toward a dedicated and flexible coherent soft x-ray scattering and imaging beamline and has led to the construction of the COSMIC beamline.
In his new role at the ALS, one of Kevan’s primary directives has been to explore career development opportunities for beamline scientists and graduate students. Kevan says he started looking into professional development for scientists even before he joined the ALS – he describes it as an area that’s difficult to define at a facility devoted to serving users.
“As the ALS approaches middle age, many of our beamline scientists are approaching middle age as well,” says Kevan. “We need to make sure we are fostering an entrepreneurial, collaborative approach that serves them well.”
Kevan sees the ALS scientists as an integral part of the user experience. “We offer tools, but our beamline scientists are the experts in using those tools,” he says. “People need help using our tools and analyzing data, and our people are the keys to providing that service.”
Kevan is also focusing his initial efforts on building collaboration and community among scientific staff. At the urging of senior scientist Elke Arenholz, Kevan has created collaborative groups of beamline scientists organized by interest areas rather than management structure. Many of the scientists in these groups came together recently for a brainstorming workshop to discuss how the ALS might contribute to the DOE’s recent mesoscale research initiative.
“I’ve already seen beamline scientists discovering through these groups that some of their colleagues were doing things that they didn’t know about but found interesting,” Kevan says.
This collaborative approach focused on research areas will guide some of Kevan’s other big-picture projects this year as well. Most immediately, he’s working on the ALS strategic plan, which he’s organizing by scientific subject areas that will align with internal “cross-cut” reviews, which are focused on subject areas rather than beamlines. Kevan hopes to have cross-cut reviews for each subject area every three years.
“Our goal is to be a ‘collaboratory,’ not just a user facility,” says Kevan. “We want to help people solve problems, use our facility better, make progress, and collaborate with them.”
As a chemical safety specialist, Doug Taube oversees chemical safety and experiment review for both ALS scientists and users. A natural result of his job description is his broad knowledge of all the techniques and experiments taking place around the experiment floor. Because of this and his affable and enthusiastic demeanor, Taube has become a go-to ALS tour guide. It’s a role he enjoys and views as an opportunity to enlighten others about the amazing and important scientific research underway here.
Taube, who holds a PhD in chemistry and worked as a catalyst chemist for ten years, joined the ranks of the ALS two and a half years ago. He estimates he’s given more than 150 tours since then, with groups ranging from distinguished guests from the Office of the UC President to fifth graders. He enjoys them all, but says that the best tours are really those with people who engage with him. “Regardless of their knowledge, it’s more interesting when there’s some give and take,” says Taube.
When he’s not entertaining tour groups with ALS history quizzes and accelerator science trivia, Taube is busy ensuring experiment safety at the ALS. The signs posted around the facility that inform users wondering about experimental procedure: “Better Call Doug!” pretty much say it all. Before users can access the ALS User Chemistry Labs or proceed with experiments on the beamline floor, they need Doug’s approval.
“I get the rare treat of visiting with just about every user who comes through the ALS. I make sure they’re doing their experiment safely then I get to ask them the big-picture questions about why they are doing their work” says Taube.
Taube earned his PhD in inorganic chemistry at UC Santa Barbaraand then spent three and a half years at UC San Diego doing post-doc work before moving into industry. He worked as a catalyst chemist for ten years and another ten years in safety at Catalytica in Mountain View before coming to the ALS. Taube also taught freshman chemistry at Cal State Hayward for several years. His broad background has given him the ability to appreciate the many types of scientific research at the ALS, and to explain and elaborate upon it for his tour groups.
Around this time of year, Steve Rossi, project and facility management group leader at ALS, shifts his focus to shutdown mode. Preparation and planning for the weeks that the ALS is out of commission is a huge part of Rossi’s job. While much of this is invisible to users, all of it is absolutely essential to the maintenance and growth of the ALS.
“This is a pivotal shutdown,” says Rossi. “We have many multi-year projects that are finally coming to fruition.”
The ALS shutdown is scheduled for February 4 through April 8, 2013, which is slightly longer than usual to accommodate this year’s to-do list. Rossi’s list includes work on the ALS controls upgrade, sextupole magnet installations, MAESTRO front-end and beamline installation, an RF power supply upgrade and replacement of the storage ring bend magnet power supply.
“At the ALS we’re always chasing an increase in performance and reliability,” says Rossi. “And shutdown is when we work towards reaching those goals.”
The RF upgrade, a $4.8 million project, and the controls upgrade, a $7.6 million project, have been many years in the planning stage, says Rossi. The work on these two projects will largely be transparent to users, but they are essential to the future of the ALS – the controls upgrade will update and replace an aging controls system and the RF upgrade will give the ALS vastly improved backup capabilities in addition to the ability to provide more RF power to the storage ring.
“We’re doing our job right if users never notice the work we’ve done,” says Rossi, “because that means we’re identifying our vulnerabilities and investing in them before our users see them.”
This forward-looking viewpoint is what much of Rossi’s work is based on. He describes his position as “an inch deep and a mile wide,” which is apt when taking into consideration what he’s responsible for – the overall project portfolio of the ALS and the oversight and coordination of maintenance and facility projects. As such, Rossi often serves as a bridge between operations and technical staff – coordinating projects and the players involved in carrying them through to fruition. He describes his management philosophy as “not looking into the past, but projecting into the future.”
Elke Arenholz, Senior Scientist, Scientific Support Group
Senior scientist Elke Arenholz has seen a lot of changes at Beamlines 4.0.2 and 6.3.1 since she arrived at the ALS in 2000, but what brought her here initially is still what keeps her passionate about her work – designing new instrumentation and working with the user community to optimize research capabilities.
Arenholz’s first big project at the ALS ended up becoming her “claim to fame” – an eight-pole electromagnet that provides magnetic fields up to 0.8 T in arbitrary directions relative to the incoming x-ray beam.
“It was really exciting to build and it had a huge impact right away because we were able to use it characterize materials in a way that no one had before,” says Arenholz. “It was the first device installed at a synchrotron that could apply the magnetic field in any direction, instead of just having it parallel to the x ray beam.”
Arenholz has continued with this theme ever since, always asking: “How can we extract some new information?” Typically, the answer involves working with engineering to create a new experimental configuration.
“I want to understand very fundamentally the interaction of x-rays with magnetic materials, and to do that I build new systems that people haven’t used before,” says Arenholz. “It’s a lot of fun, and we are really lucky to have a wonderful engineering department here at the Lab with lots of experts.”
In 2011, her group, which includes Beamline Scientists Catherine Jenkins and Padraic Shafer, completed work on a first-of-its-kind, ARRA-funded superconducting vector magnet. The magnet, which is a superconducting version of Arenholz’s eight-pole electromagnet, provides fields up to 5 T in arbitrary directions.
Arenholz has focused on spectroscopy for much of her career, but she has recently turned her attention to scattering—studying x ray diffraction patterns from periodic structures on the nanoscale. Once again, this shift required building a new endstation. The LDRD-funded system that was installed at Beamline 4.0.2 last fall uses a superconducting disc of 0.8” diameter to generate 4T at the sample while still allowing maximum flexibility for the scattering geometry.
While Arenholz enjoys her own research and the continual process of advancing beamline and endstation capabilities, she also finds her interactions with users at the beamline very rewarding. She describes her work life as consisting of two experiments: the scientific ones and the anthropological experiment of working with users.
“There’s a lot of teaching involved,” says Arenholz. “I am constantly thinking ‘How can I explain things better to users and make the system operation easier so that they make the best use of the experimental capabilities and beamtime?’”
In addition to her work at the ALS, Arenholz is an academic editor for AIP Advances, on the editorial board of the Journal of Magnetism and Magnetic Materials (JMMM), and program co-chair for the 2013 Joint MMM/Intermag Conference.
David Shuh, Senior Scientist, Chemical Sciences Division
For the past decade, David Shuh has led one of the most in-demand beamlines at the ALS. In addition to his position as a Senior Scientist in Berkeley Lab’s Chemical Sciences Division (CSD), Shuh is Project Leader at ALS Beamline 11.0.2 , the Molecular Environmental Sciences (MES) Beamline, a leading national resource in the field of soft x-ray synchrotron radiation research. Research at the MES Beamline has provided some of the first significant molecular-level understandings of important chemical and physical processes taking place at interfaces under real or more realistic conditions than ever before possible.
Run by the LBNL CSD in partnership with the ALS, Shuh credits the MES Beamline’s popularity and success to multiple factors, a primary one being its initiation with a strong, innovative, and sufficiently developed scientific program proposed by the initial core research team members (Hendrik Bluhm-CSD, Mary K. Gilles-CSD, and Tolek Tyliszczak-ALS). Secondly, the needs of the scientific programs were expertly translated into a revolutionary general-purpose beamline operating from 75 eV to about 2100 eV downstream of an elliptical polarization undulator (EPU) and flagship endstations. The beamline construction team was led by Tony Warwick and they did a fabulous job including the development of a fantastic monochromator.
“The contributions and dedication of the core research team and the scientists at the MES Beamline have been key to the development of scientific programs, endstations, support of general users, and general user scientific programs,” says Shuh.
Shuh also notes that it was the strong and unwavering support of the U. S. Department of Energy (DOE), Office of Science, Basic Energy Sciences, through the Divisions of Materials Science and Chemical Sciences, Geosciences, and Biosciences, that enabled the construction of the MES Beamline.
“The strong operational support provided early on from of the DOE’s Division of Chemical Sciences, Geosciences, and Biosciences served as a solid foundation for all the developments that have followed at the MES Beamline,” says Shuh. “And the partnership and support we’ve received from the ALS has also been key to our success.”
The MES Beamline Scanning Transmission X-Ray Microscope (STXM) endstation is a top worldwide resource for a diverse set of scientific investigations utilizing soft x-ray STXM. The endstation pair – the MES Ambient Pressure X-ray Photoelectron Spectroscopy (APXPS) endstations are leaders in surface studies of interfaces at pressures approaching 10 Torr for a wide range of energy research. Shuh notes that several other synchrotron radiation facilities have built similar beamlines and endstations, adding that “imitation is the highest form of flattery.”
The MES research team’s significant scientific diversity and history has also been a major contributor to the success of the beamline, says Shuh. Physicists Tolek Tyliszczak and Hendrik Bluhm, as well as chemist Mary K. Gilles, were all involved early on in the MES Beamline effort.
“The scientific diversity of the staff, their expertise, dedication, and years of experience are invaluable to the wide range of users at the MES Beamline and in general to the ALS as well,” says Shuh.
The MES Beamline scientists have been recognized over the years for their development of beamline endstation instrumentation. Tolek Tyliszczak has been awarded two ALS Klaus Halbach Awards for Innovative Instrumentation as part of two teams for STXM developments in 2002 and 2010. Similarly, Hendrik Bluhm was part of a team awarded a Halbach Award in 2004 and an R&D 100 Award in 2010 for the development of ambient pressure photoelectron spectroscopy.
Shuh and the MES team have seen many accomplishments over the years at the MES Beamline – he notes that they’ve had a tremendous impact in magnetic dynamics, the development and use of in-situ reaction cells for science in the soft x-ray regime, environmental science, and a significant impact on realistic catalysis and interfacial science across the board.
In addition to his role at the MES Beamline, Shuh is the Director of the Glenn T. Seaborg Center and is a co-lead on the Berkeley Lab Critical Materials Initiative. Shuh, along with Frances Houle (CSD), will work toward reducing current shortages and preventing future shortages through advances in nanoscience, chemistry, materials science, computation and theory, physics, materials genomics, and energy analysis techniques. The project will make use of Department of Energy national user facilities located throughout the country.
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