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Ring Leaders
Ringleader: Musa Ahmed Print

In his 19 years at the ALS, senior scientist Musa Ahmed has seen chemistry grow from a somewhat obscure synchrotron science focus area to a cornerstone, award-winning ALS program. Ahmed was recently charged with leading the chemical sciences program for both ALS chemical dynamics beamlines, 9.0.1 and 11.0.2, which befits his long-standing enthusiasm and leadership in advancing chemistry research at the ALS.

“Our hallmark for the last 20 years has been fundamental chemical physics,” says Ahmed. “We do chemistry with a very big C, focusing on building up our knowledge base.”

The two chemical dynamics beamlines cover a broad range of science, including combustion, environmental chemistry, energy science, astrochemistry and astrophysics, fundamental chemical physics, and chemical dynamics. From biofuels to soot formation, the facilities and capabilities available at Beamlines 9.0.2 and 11.0.2 give scientists at molecular-level understanding of fundamental chemical processes. Ahmed notes that both the 2011 and 2012 David Shirley Awards for Outstanding Scientific Achievement at the ALS went to chemical dynamics beamline scientists, a testament to the excellence of the program.

Ahmed’s own research focus is on understanding and mapping the physical and chemical principles that govern complicated phenomena in nature. “My goal is to gain a molecular-level understanding of alternative carbon neutral energy sources and global climate change using imaging and biological mass spectrometry, atmospheric and environmental chemistry, and dynamics of combustion processes,” he says.

Ahmed’s scope reaches beyond the two beamlines in his latest endeavor, which is to create an umbrella group focused on chemistry at the ALS in general. He hopes it will be an opportunity for collaboration among beamline scientists and users from around the ring. Recent LDRD funding will also allow Ahmed to push the chemical science beamlines beyond the static regime into probe dynamics and more laser synchrotron experiments. Beamline 9.0.2  will soon gain some extra space, as BL 9.0.1 is moving, which will give Ahmed and his group greater flexibility in the layout of their many roll-out endstations.

“I’ve stayed at the ALS all this time because I feel I’ve been able to help create a unique research environment that other synchrotrons actually try to emulate, and the ALS has allowed this to evolve,” says Ahmed. “There’s also a lot of intellectual satisfaction in working with a beamline that produces some of the brightest vacuum ultraviolet photons in the world.”

October 2013 Print

Greta Toncheva and Robert Fairchild, Laser Safety Officers

“Safety is elemental” is the latest safety tagline for the ALS, and it also pretty much sums up the mission of laser safety officers Greta Toncheva and Robert Fairchild. Toncheva and Fairchild share the responsibility of ensuring laser safety lab-wide, with Toncheva responsible for overseeing laser safety operations at the ALS. Fairchild has been at the Lab for the past 16 years. Toncheva started last year after spending the past 10 years at Duke University in radiation hazard protection. The excellent safety record that the ALS holds speaks volumes to their efforts.

In addition to lasers, Toncheva supports ionizing radiation, with a heavy focus on supporting accelerators. Fairchild supports lasers and all nonionizing radiation, which means his work is spread throughout the Lab campus and other facilities, including JCAP and JGI. Their work at the Lab and the ALS involves a unique combination of highly technical knowledge, excellent communications skills, and multi-tasking finesse.

“Being on top of the game is important,” says Toncheva. “There’s a huge volume and diversity of lasers to keep track of.”

In addition to a diversity of lasers, Toncheva and Fairchild deal with a huge array of personnel, including users new to the ALS setting up their experiments.  Educating users about our safety culture and process can be challenging, but it’s one of the job duties that both Toncheva and Fairchild enjoy. They work closely with Doug Taube, ALS chemical safety specialist, to ensure that new experiments go through the correct safety channels and laser hazard evaluations are underway where necessary.

“We are required to constantly be learning while on the job, keeping up with advancing laser technology,” says Toncheva. “It’s challenging and I like it.”

September 2013 Print

Deborah Smith, ALS User Office Senior Administrative Supervisor


Deborah Smith, senior administrative supervisor in the ALS User Office, plans much of work life around the annual ALS User Meeting, which is fast approaching October 7-9. Smith and her team have been hard at work creating an amazing event for the 400-plus attendees that flock to the hill each year to attend workshops, listen to distinguished speakers, and take part in the active social program.

It’s a representation of what Smith says she loves most about her job: having a chance to interact with so many different people. The day after this year’s User Meeting activities end, Smith will be right back on track planning for next year. “I literally start booking conference rooms for the next one the day that the previous one ends,” she says.

Smith is quick to acknowledge that she’s not alone in pulling off the ALS’s biggest annual event – she credits her User Office staff first and foremost, as well as ALS Communications, the Users’ Executive Committee, and the warehouse crew as key to making her meeting planning successful. “We all come together and pull it off,” she says.

This year’s User Meeting highlights include 13 workshops that represent the great science that’s happening at the ALS, Smith says. The UEC collaborates with senior management to put the workshops together, while Smith and her staff handle the logistics. Smith envisions the User Meeting growing large enough that it warrants being held off-site, which would be a well-earned challenge for her and her team.

When she’s not working on the next User Meeting, Smith might be found managing ALS user statistics for the DOE Questionnaire annual report, providing user statistics for ALS staff, monitoring security and safety training for ALS users, acting as host for the majority of ALS users, verifying publications that the DOE uses to measure the ALS, and overseeing the User Office. “Publications are the major metric of how the DOE measures the ALS,” Smith says.

Since she started in the User Office in 2008, Deborah has seen customer service as her main focus, “We want the users to keep coming back and we feel like we can do that if we make the processes as easy as possible,” she says. “We try to get them down on the floor to do their magnificent science as quickly as possible.”



ALS User Office staff make the User Meeting happen each year: From left: Clyde Lewis, Deborah Smith, Giselle Jiles, Angel Hernandez.

August 2013 Print

Sue Bailey, User Services Group Leader

baileyAs head of ALS User Services for the past six years, my goal has been to make the ALS user experience as smooth and efficient  as possible. I am constantly looking for ways to improve the processes for users to apply for beam time, register, complete their training, and coordinate experiments. I am a primary liaison with the ALS Users’ Executive Committee (UEC) and we work together to ensure the success of the annual ALS User Meeting , which attracts more than 400 participants each year.

ALS User Services is currently transitioning from a dated software and database system to a new user portal, which will provide a much more interactive environment. The transition will be evolutionary, so users will notice many small changes over the next two years.  We have already implemented some components, including the RAPIDD Proposals system, which complements the existing General User Proposal process. RAPIDD is a flexible system that allows users to obtain relatively short beam time allowances to perform single experiments. It provides rapid access to structural biology, small molecule crystallography, SAXS/WAXS, and tomography facilities. It is also the formal mechanism for applying for Director’s discretionary beamtime and for submitting industry proposals. We will soon be rolling out an online user interface that will provide more intuitive ALS access. We are also working on software for an experiment tracking system, which will replace the current Experiment Safety Sheet.

Explaining and promoting science to the wider community is an essential role for all of us who work in science and at user facilities. This year I was fortunate to be elected to the National User Facility Organization (NUFO) steering committee and to help run a science exhibition to educate our elected representatives on the wide range of science and innovation happening at the ALS. I organized this year’s NUFO meeting, which was held at LBNL, and it provided an excellent opportunity for ALS staff to contribute to discussions of new outreach ideas and best practices across national facilities.

The ALS values user input and ideas and there are both formal and informal ways for users to make their voices heard. The UEC is a very important link between ALS management and users; I encourage users interested in learning more about and helping to determine how the ALS operates  to talk to current UEC members and consider running for election. The UEC will be looking for new members within the next few months. ALS also solicits input from users on our user satisfaction form—we like to hear what went well and where there is room for improvement. My door is always open and I encourage users to talk to me or other ALS staff so that we can help support their science.

Contact: Sue Bailey, 510-486-7727, This e-mail address is being protected from spambots. You need JavaScript enabled to view it

July 2013 Print

Interim EHS Program Management

Since 2006, Jim Floyd has served as the Environment/Health/Safety (EHS) program manager for the ALS. July 8 he assumed a new position as director of the Lab's EHS Division. While the ALS is recruiting for a permanent replacement, two EHS Division staff will provide interim support.






In the area of accelerator and radiation safety, Jeff Bramble will be here approximately 50% to coordinate this important function. Jeff is an experienced health physicist (HP) with a very broad background, providing backup radiological control technician support here at the ALS and HP support at the 88” cyclotron. Among his duties will be assistance on:

  • Procedures
  • Interlock design, installation and documentation
  • Floor operator support
  • Shielding and ALARA studies
  • Incident corrective actions
  • Rad material RWA for users
  • Accelerator Safety Order implementation tasks
  • Work permits and shut-down work planning

Interim Division Safety Coordinator support will be provided, also at approximately 50% effort, by Andrew Peterson. Currently the assurance manager at EHS as well as the division liaison for ALS. Andrew served as the safety coordinator for the Life Sciences Division and is very familiar with our on-going staff safety functions. He’ll be providing assistance on:

  • JHA
  • Activity hazard documents (AHD) and other task-based authorizations
  • Self assessment
  • First-aid/Injury investigations
  • ALS representation to LBNL and DOE


User Safety will continue to receive strong support from Doug Taube, David Malone (pictured at left) and the rest of the team. You can find a list of safety contacts on our Safety Organization and Contact Information page.

June 2013 Print

Alastair MacDowell, Beamline Scientist, Experimental Systems Group


Alastair MacDowellBeamline scientist Alastair MacDowell has pioneered several hard x-ray science programs in his 17 years at the ALS. MacDowell began his career here with a directive to prove the viability of providing hard x-ray capabilities. Early in his tenure he did just that, working to establish the micro-XAS program at Beamline 10.3.2 and the x-ray microdiffraction program that ended up at Beamline 12.3.2, both of which are still in operation today.

MacDowell went on to develop many other ALS hard x-ray programs. He also proved that protein crystallography was tenable on bend-magnet beamlines, which lent vital support to the ALS superbend project and the five protein crystallography beamlines subsequently established at the ALS. MacDowell conducted the initial tomographic experiments on Beamline 7.3.3, establishing a program that moved to Beamline 8.3.2, and high-pressure x-ray diffraction experiments that led to an endstation at Beamline 12.2.2. He also implemented small-angle x-ray scattering (SAXS) at the ALS, which has remained at Beamline 7.3.3. Being involved in so many programs has its pros and cons, says MacDowell.

“If you build the equipment, then bring people in to use it, they come to you when something is broken,” he says.

MacDowell cites the “village” that makes up the ALS as key to establishing all of these programs. “They all require multiple people, from the techs to assemble, engineers to design, the ALS management and support to provide the environment, and the local scientists to provide the scientific motivation,” he says.

These days, MacDowell is in charge of the ALS tomography program at Beamline 8.3.2 and the high-pressure x-ray diffraction station at Beamline 12.2.2. At Beamline 8.3.2 MacDowell and ALS Postdoctoral Fellow Abdel Haboub are currently working on a Laboratory Directed Research and Development (LDRD) program on coded-aperture detectors and an x-ray microtomographic hot cell that allows users to research the failure of materials at very high temperatures. MacDowell and his team built the instrumentation for the hot-cell technique, which is already enabling exciting research. Notably, Berkeley Lab senior materials scientist Rob Ritchie and his team have made headlines with the research they’ve conducted at Beamline 8.3.2 using the hot-cell facility to study the heat-resistant properties of advanced ceramic composites, which show promise as next-generation jet engine materials (see a video about their research).

The hot cell, which MacDowell calls “totally novel,” is currently not available at any other synchrotron facility. Researchers are using it for a variety of research topics, including

  • Gaining a better understanding of volcanoes by monitoring the cracking of magma,
  • Studying how concrete behaves at high temperatures in order to monitor the stability of burning buildings, and
  • NASA research on heat shields for space reentry vehicles.
May 2013 Print

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.”

Recent research from the BSISB includes Molecular Measurements of the Deep-Sea Oil Plume in the Gulf of Mexico following the Deepwater Horizon blowout in the Gulf of Mexico. They have also monitored protein phosphorylation inside single living cells, following live chemical changes without bias and without harming the cells (Tracking Living Cells as They Differentiate in Real Time). Most recently, they helped a team of Germany scientists examine the function of a mysterious microbial community in a cold sulfur spring (Synchrotron Infrared Unveils a Mysterious Microbial Community).

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.



April 2013 Print

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.”

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