Recent research at ALS Beamline 5.3.1, detailed in this month’s Science Highlight, revealed that an important photosynthetic mechanism called “nonphotochemical quenching” is triggered by the translocation of the carotenoid pigment within a critical light-sensitive protein called the Orange Carotenoid Protein (OCP). The x-ray footprinting (XFP) technique developed at 5.3.1 allowed researchers to confirm that this translocation actually occurs when OCP is in its natural solution environment and was not due to structural changes that the protein undergoes during crystal formation.
The ALS XFP experts at Beamline 5.3.1. From left: Research Scientist Sayan Gupta, Beamline 5.3.1 Scientist Rich Celestre, and BCSB Head Corie Ralston.
XFP, a powerful technique for the study of macromolecular structures and dynamics of proteins and nucleic acids in solution, is relatively new to the ALS, though it was first developed more than 10 years ago by scientist Mark Chance at the NSLS. Two years ago, Head of the Berkeley Center for Structural Biology (BCSB) Corie Ralston obtained LDRD funding to bring the technique to the ALS, partly based on the fact that the only other XFP capability available in the U.S. was at the NSLS, and soon to be unavailable due to NSLS closure. The ALS is currently supporting NSLS users while they recommission their own XFP beamline.
“The user base is also big enough that we need more than one beamline with XFP capability,” says Ralston. “Even once NSLS is back up in 2016, we plan to continue to offer the technique.”
Ralston describes XFP as being “highly complementary to crystallography,” though one of its main advantages happens to be that it doesn’t require a crystal. Using XFP, researchers can look at proteins in solution and see where the protein is solvent-accessible. “So if you want to look at a protein-protein interaction, for example, where the proteins meet they exclude solvent and you get a protected patch that can be detected,” says Ralston.
During XFP, the x-rays traveling through a solution generate hydroxyl radicals, which then modify the amino acids in the protein that are solvent accessible. They don’t modify the ones that aren’t solvent accessible, which then basically creates a map of all the solvent-accessible areas on a protein. “You can look at huge complexes; the size of the protein doesn’t matter,” says Ralston. “Whereas, in crystallography, trying to crystallize large complexes is very challenging.”
Another benefit of XFP is that it can be done at close to physiological conditions, which gives researchers a more real-life representation of the protein. “XFP is really useful for looking at a protein changing in solution as a function of pH or salt concentration, for instance, or to watch protein-protein interactions and see where they are binding,” says Ralston. “Having this other technique that can give us more information is just really helpful.”
XFP has been a team effort at the ALS, with research scientist Dr. Sayan Gupta, previously employed at NSLS, working out the kinks of the ALS XFP system on the beamline floor. Beamline 5.3.1 scientist Rich Celestre has also been heavily involved, especially with working out a way to focus the high brightness beam at 5.3.1, allowing researchers to utilize microsecond exposures, which opens up the possibility for time-resolved studies on proteins. XFP has also been deployed at Beamline 3.2.1, which offers high flux but not high brightness.
The ALS is updating the User Experiment Safety Process. The main change that will affect users is a new requirement to complete an Experiment Safety Sheet (ESS) for each visit and for each beamline. This is a change from current procedure where an ESS can be valid for up to one year and may cover more than one beamline.
We want this to work well and to help you, so if you have feedback on these changes, I encourage you to
. Your primary point of contact during the change, for submitting and handling ESSs, will be the ALS Experiment Coordinator,
, with other members of the safety team and user services as back up.
Summary of Changes
In general, we will require your ESS submission a minimum of 1–2 weeks before the experiment (earlier is also good). But see below for more hazardous experiments.
An ESS will be required for each visit and will include the experiment date.
The ESS will only cover work at a single beamline; a group working on two beamlines at the same time will require two separate ESSs.
The ESS should only cover the work of a single group.
To simplify submitting each ESS, we are making it easy to use a previous ESS as a template.
Automated emails will be sent to remind users to submit an ESS, starting 3 weeks before the expected start of the experiment. Since schedules sometimes change, we may miss occasional reminders—this does not prevent you submitting an ESS—you know when your experiment will happen.
Very early submission of an ESS is needed for experiments requiring additional review.
Some experiments require additional safety documents and review by subject matter experts. These include:
All biological materials
Electrical equipment the user is bringing (anything with a plug)
For such experiments, please submit your ESS in good time to allow our staff to help you get ready. If the final details of every sample and experimenter will not be known until later, just give us what you have. An initial submission several weeks before the experiments alerts us to start a dialogue on handling the samples and equipment.
Søren Ulstrup, an ALS postdoc who received his Ph.D. from Aarhus University in Denmark last year, was selected by the Aarhus University Research Foundation as one of five promising young scientists to receive its prize for outstanding doctoral thesis. The title of Søren's thesis was "A Direct Study of the Electronic Structure of Graphene."
With these awards, the Aarhus University Research Foundation recognizes work that includes a significant amount of new and important results that have been communicated extensively to both peers in the scientific field and to a broader audience via public media. The official Aarhus University Research Foundation video of Søren describing his work is posted below with English subtitles:
Søren's full award citation (in Danish) can be found at the Aarhus University Research Foundation site. In translation, it says, in part:
Laser Pulses Reveal Huge Potential in 2D Fabric
With his studies of graphene, Søren Ulstrup, among others, showed how to manipulate the substance's electronic properties and its quality in the manufacturing process. And these factors are also crucial.
"Graphene has some really wonderful features that you want to use in combination with other materials. It can be used for enhancing surfaces and protection against corrosion, but because of its ability to conduct electricity and heat, it is particularly relevant to electronic components and energy storage in solar cells, for example," he says.
"We exposed the graphene to some ultrafast laser pulses. And it turned out that with the laser light we could bring many of the material's electrons out of their ground state. The energy the free electrons create inside the graphene could be 'harvested' in a solar cell," says Søren.
The consequence is that a graphene-based solar cell has the potential to be extremely effective. Whether it works in practice remains to be seen. But the international attention on Søren Ulstrup's result is beyond doubt—and he leaves it to others to build the solar cell.
Søren is currently investigating the electronic properties of new low-dimensional material systems with the MAESTRO group at Beamline 7.0.2. The goal is to use state-of-the-art photoemission experiments with nanoscale spatial resolution in addition to energy and momentum resolution to uncover the electronic texture of complex nano- and micron-sized materials.
His postdoc project at the ALS is funded by the Sapere Aude program of the Danish Council for Independent Research and has a duration of 2 years and 3 months.
A novel x-ray scattering concept by researchers at Lawrence Berkeley National Laboratory’s (Berkeley Lab) Advanced Light Source (ALS) is receiving support from the Gordon and Betty Moore Foundation in the amount of $2.4 million. The grant was in April by the foundation. The lead investigator on the effort will be ALS Division Deputy Zahid Hussain with ALS Director Roger Falcone acting as co-PI on the project.
The Moore Foundation awarded the funding for the development of a new spectrometer for studying materials using X-ray scattering. The citation reads: “In support of research targeting the development of novel x-ray scattering instrumentation for probing quantum materials.”
The grant is part of the Moore Foundation’s Emergent Phenomena in Quantum Systems (EPiQS) Initiative, which “strives to deepen our understanding of the complex collective behavior electrons exhibit in materials and engineered structures.”
The $2.4M will be over a 5-year period.
To understand the emergent physical rules that quantum materials follow, one needs powerful tools to manipulate the entangled structures. This newly designed instrument will make far more efficient use of synchrotron X-rays and advance the state of the art in energy resolution. It will also increase the number of material systems that can be studied.
“The Gordon and Betty Moore Foundation has recognized that the field of quantum materials is of increasing importance for both fundamental science and new technologies,” said ALS Director Falcone. “At the ALS we’re very pleased that the Foundation is supporting the development of a globally unique instrument for inelastic x-ray scattering, which will provide extraordinary new insight into these materials, allow tailoring of functional properties, and support leading scientists from around the nation and the world in their work in this field. I have no doubt that amazing and important discoveries will result from this partnership between Berkeley Lab and the Moore Foundation.”
This research is funded in part by the Gordon and Betty Moore Foundation EPiQS Initiative, Grant 4630 to Berkeley Lab. Support also comes from the Department of Energy’s Office of Science.
(Initially issued as news release from Berkeley Lab Public Affairs)
In an ongoing effort to build closer working relationships between Berkeley Lab’s light source and nanoscale science research center, Elaine Chan has recently been appointed by the ALS and the Molecular Foundry to a new role as joint ALS/Foundry project scientist. Chan’s mission will be to foster collaborations between the two facility’s users and to communicate a wider understanding about how the two research centers are mutually scientifically beneficial.
Chan has a background in nanoscale science and has worked for four years at ALS Beamline 7.3.3, a beamline that’s hosted many Foundry users and is uniquely suited to serve the needs of ALS/Foundry research. One of the capabilities of Beamline 7.3.3 is high-throughput x-ray scattering characterization of materials, which complements the high-throughput chemical syntheses of the novel materials produced by the Foundry.
Chan’s efforts will be focused on communicating with users and coordinating scientific collaboration. To that end, she’ll begin with the launch of a seminar series at the Molecular Foundry called ALS School, which will bring ALS scientists to the Foundry user community on a regular basis to “teach” them about how various ALS capabilities can advance their science. Likewise, a similar seminar series for Foundry scientists to teach the ALS user community about their materials characterization challenges is in the works. Chan has also envisioned a new joint ALS–Foundry user highlight series that would showcase the work of ALS and Foundry users. A joint webpage that would disseminate information and showcase the highlights and the seminars is also in the works.
“The seminar series will really be our first push,” Chan says. “We’d like to sort of do away with some of the mystery of what happens at the ALS; really communicate at a basic level how the facility can serve both sets of users.”
Chan will also be working closely with Foundry users at ALS Beamline 7.3.3 to make photon science experiments more user-friendly and productive. She will be assisting Foundry users with high-throughput scattering measurements of their materials. Chan is also developing software interfaces for the beamline endstation in order to better streamline the high-throughput experimental set-ups and to facilitate the interpretation of the scattering data.
Chan notes that joint ALS/Foundry publications have been increasing steadily for the past four years, with about 25 percent of those publications coming from Beamline 7.3.3 on the ALS side. Over the last year, 16 percent of all Foundry user publications involve joint work with a variety of beamlines at the ALS. Chan believes that there are even more potential opportunities for the two user facilities to partner, and she’s excited to help them become realized.
The upcoming long-term operating schedule has been published and users will note that it includes an extended shutdown period (October 26, 2015-January 13, 2016) for the ALS. The lengthy shutdown is in part because it spans the Thanksgiving and Holiday shutdown periods, as well as being indicative of the amount of time required to implement major upgrades. The main project for this shutdown is the Storage Ring Radio Frequency (SRRF) Upgrade. This is the final phase of this many-year effort to provide more RF power that will be required for the use of additional insertion devices, and to create a robust back-up system. We have already replaced our long-lived klystron, the RF high-voltage power supply, and the high-voltage RF switch in prior shutdowns. While the ALS reliably operated on this new equipment, a second klystron was also installed. This last phase installs a "switch matrix" RF wave guide, which in its nominal state will provide each ALS storage ring RF cavity with RF from a single klystron. In the event of a klystron failure in the future, we will be able to redirect RF from either klystron to either cavity in the matter of hours rather than the many days it would take to swap out and commission a spare klystron.
The other major activity planned for this shutdown is installing the very first non-evaporable-getter(NEG)-coated vacuum chamber in the ALS. This is new technology for the ALS, and is very exciting since it will enable the small gap insertion device required to meet the carbon edge on the new COSMIC beamline in sector 7. While there are many other accelerator activities planned, these are the major shutdown projects.
In order to maintain and expand ALS capabilities for users, the last couple of years have been an extensive period of renewal and upgrades including Top Off, the Sextupole Upgrade (low-emittance lattice), the RF Upgrade, the Instrumentation and Controls Upgrade, and the chicaning of sector 7 for the MAESTRO and COSMIC beamlines. The next couple of major shutdowns will focus on changes required to create the space needed in sector 2 of the accelerator for the Howard Hughes Medical Institute funded Gemini insertion device and the installation of the Gemini beamline front-end.
Beamline work for this upcoming shutdown has not yet been detailed, but work requests are already being submitted. Staff and users are asked to contact
as soon as possible with work requests planned for the shutdown.
Reflecting on 2014, I’d first point to our impressive science (see many highlights on the webpage http://www-als.lbl.gov/index.php/science-highlights/science-highlights.html), and a record number of users and publications: the ALS supported over 2,400 users and we expect to exceed our 2013 record of more than 800 publications. Of course, the past year was also a challenging one for us; together with other national facilities, we had to reduce staff due to reduced government funding. While there is still uncertainty about what the next few years hold for broad government support of science, funding for us this year is now secure and we are well positioned to take advantage of resources as we go forward.
After visiting the ALS and talking with beamline scientists, DOE Secretary Ernest Moniz toured the facility with ALS Director Roger Falcone.
This year is a good time for ALS to both focus on its core strengths and expand partnerships—with other divisions at LBNL, new research programs, other national laboratories, and new funding sources, including foundations. We have an ambitious set of beamline and instrument projects planned for the next few years, and we’ll be able to accomplish our goals with support from those new funding sources.
This year will see the completion of the MAESTRO nano-ARPES beamline, and the COSMIC imaging and scattering project will move forward towards a 2016 completion date. Two new beamlines—AMBER and QERLIN—are in early-stage development and should be completed within the next few years. These projects are key to the future of the ALS in various research areas, including renewable energy sciences and quantum materials. Additional projects include the upgrade of existing beamlines—SAX-WAX (together with the Molecular Foundry), small molecule crystallography, spin-ARPES, ambient pressure photoemission (in support of the energy hubs JCAP and JCESR), and scattering in the so-called “tender” x-ray regime (supported by LDRD funds). Beyond that, we’re also working with Howard Hughes Medical Foundation to complete a world-leading micro-focus beamline for structural biology.
In the next few years, we look forward to supporting users with these new capabilities, which will keep us on the cutting edge of science. Also, these projects are consistent with our long-term desire to upgrade the ALS storage ring to fully utilize diffraction-limited or highly coherent x-rays. Together with our community, we’re continuing to examine the opportunities that would be made available with such a brightness upgrade. Also, it is important that instruments we build over the next few years be upgradable for “ALS-U” operations, since we see that as the future for our facility.
Support from Basic Energy Sciences at DOE, together with contributions from our partners, is helping us to operate optimally for users and move forward with our project priorities. We will continue to demonstrate how ALS can increase scientific productivity across a broad spectrum of science and technology, and contribute to the technical and economic vibrancy of the nation.
ALS Director Roger Falcone talked about the power of new nanoscale imaging techniques at the 2014 User Meeting.
I am very proud that in the past year we significantly expanded our relationship with the computing divisions at the Lab. As the brightness of our storage ring and the number of ALS instruments has increased over more than 20 years of operation, so have the number of users, experiments, and rate of data generation. Dealing with enormous amounts of data has become increasingly important to the future of the ALS and the Lab as a whole. The Computing Research Division and NERSC computing facility are playing a key role in helping us manage this data, and together we have developed a nationally recognized capability and reputation for rapidly processing huge amounts of data, benefiting users both at the ALS and related facilities.
People at ALS are of course the reason for our success, and I’m pleased to welcome Scott Taylor as safety coordinator and newest member of our ALS family. With Scott’s past experience here at LBNL, and ALS’s Jim Floyd’s promotion to director of the Lab’s EHS Division, we’re well positioned to continue as a model for a great safety culture.
It’s going to be a fun and productive year!
On October 1-3, 2014, the ALS hosted a workshop on Soft X-Ray Science Opportunities Using Diffraction-Limited Storage Rings. The workshop charge was to elaborate transformational research opportunities that would be enabled by emerging storage-ring-based ultrahigh brightness soft and intermediate x-ray beams, and to examine the primary challenges needed to accomplish these opportunities. More than scientists from around the world attended the workshop and set a very enthusiastic tone throughout the three-day period.
The first morning of the workshop started off with plenary talks covering material and biological science opportunities as well as the potential capabilities of high-brightness accelerators. These talks were followed by nine energetic short talks by staff from facilities around the world that described techniques and research opportunities enabled by high-source brightness and the resulting diffraction-limited beams. These talks formed the basis for 13 separate breakout sessions over the following two days that focused on quantum materials, magnetic materials, low power information processing, energy science and catalysis, chemical and materials excitations, fluctuations, and dynamics, biological science, soft condensed matter, and environmental science. These were scheduled so that attendees could move from one subject thread to another to gain a wider appreciation of scientific opportunities. Much time for discussion of science ideas was provided, both during the breakouts and also after each session, ensuing a healthy "flux" of ideas among attendees. This cross-fertilization was both fun and challenging, inspiring outside-the-box thinking and new collaborations.
Leaders of the breakout sessions, facilitated by ALS staff, are already drafting a workshop report with chapters on the various subjects noted above. The document should be available to the broad community by the end of 2014.
The Proposal Study Panel met on October 20 to oversee and finalize the scoring of all General User Proposals for the 2015-1 (January–June) operating cycle. Allocation meetings for each beamline are now taking place, and the results of the review are expected to be released to ALS users around mid-November.
The mechanism for notifying users of their proposal results will be different from previous cycles. Each principal investigator and experiment leader, who have submitted one or more proposals, will be sent a single email inviting them to login to ALSHub, the ALS user portal, to view the outcome of the review and allocation of beam time. This replaces the previous mechanism of sending a separate email for each proposal.
What will you see in ALSHub?
Users will be able to see their proposals submitted this cycle as well as submissions from previous cycles. The status will indicate ‘Review completed’ for the new proposals submitted for this cycle. Proposals from previous cycles will have a status of ‘Active’ or ‘Expired’.
To view the results of the review for each proposal, users will need to click on the Experiment ID. An example of what is displayed is shown below.
Staff in the user office, particularly
, the proposal coordinator, and
are available throughout this process to answer user queries, and help you. Do not hesitate to contact them for advice, or login to ALSHub to check on the progress of your proposals.
On October 1–3, 2014, the ALS hosted a workshop entitled Soft X-Ray Science Opportunities Using Diffraction-Limited Storage Rings. The workshop charge was to determine transformational research opportunities enabled by emerging storage-ring-based ultrahigh brightness soft and intermediate x-ray beams, and to examine the primary challenges to accomplish these opportunities. More than 80 scientists from around the world attended the workshop and set a very enthusiastic tone throughout the entire three-day period.
The first morning of the workshop started off with three plenary talks on material and biological science opportunities, and on the capabilities of high- brightness accelerators. These presentations were followed by nine energetic short talks by staff from facilities around the world, which described techniques and research opportunities enabled by high source brightness and the resulting diffraction-limited beams. These talks formed the basis for 13 separate breakouts over the following two days focused on quantum materials, magnetic materials, low power information processing, energy science and catalysis, chemical and materials excitations, fluctuations, and dynamics, biological science, soft condensed matter, and environmental science. These were scheduled so that attendees could move from one subject thread to another. Much time for discussion of science ideas was provided, both during the breakouts and also after each session, to ensure a healthy flux of ideas among all attendees. This cross-fertilization was fun and led to a healthy cross-fertilization and outside-the-box thinking.
Breakout leads, facilitated by ALS staff, are already drafting a workshop report with chapters on the various subjects noted above. This should be available to the broad community by the end of 2014.
The 2014 ALS User Meeting launched with 422 attendees and a welcome from UEC Chair Peter Nico. Don DePaolo, Associate Lab Director for Energy and Environmental Sciences,followed with his own welcome and then spoke about the pivotal role of the ALS in the future of the Lab. DePaolo highlighted the synergies between the Molecular Foundry and NERSC and the ALS, and encouraged users to take advantage of those.
ALS Director Roger Falcone was up next and he began with a sad acknowledgement of the passing of a veteran ALS user, Dennis Lindle. While the past year has been a tough one in terms of funding realities for the ALS, Falcone pointed to highlights in scientific achievements. The ALS had a record number of users in 2014, with an impressive number of publications to accompany that trend. Falcone also stressed the synergistic capabilities of the ALS and Molecular Foundry.
DOE Associate Director of Science for Basic Energy Science, Dr. Harriet Kung, spoke about federal budget realities.
DOE Associate Director of Science for Basic Energy Science (BES), Dr. Harriet Kung, took the stage to give users a Washington update, acknowledging that the past year and future year’s budgets are quite challenging for the department. She said her department has been “heartened by the proactive steps that facilities have taken to align with our funding realities.” The next step, as she sees it, is to figure out how to survive and grow in today’s economic environment. As an upgrade project is in the early planning stages for the ALS, Kung encouraged users to think about making wise scientific and technical choices to remain competitive in the midst of a potentially lengthy upgrade process. Kung ended with a nod to funding situation once again, encouraging users to lend their support in the effort to “strongly defend the level of funding needed.”
John Hill, X-Ray Scattering Group Leader Brookhaven National Lab, spoke about high temperature superconductivity and charge correlations, which he describes as “a complicated problem led by the discovery of the products and also the promise of the materials.” The driving force behind this research area is the promise of superior electricity generation. Researchers have been trying to understand superconductors for more than 30 years, and the ALS has allowed them to understand more.
Sam Bader, Chief Scientist for Argonne’s National Lab’s Center for Nanoscale Materials, followed up with how the ALS has enhanced the scientific community’s understanding of spintronics. He described nanomagnetism as the oldest field in science, but at the forefront of new materials. His studies in vortex physics and medical applications marry biology and physics to address promising new brain cancer treatments.
Next up was UC Berkeley’s Jim Hurley, a cell biologist who spoke about “cellular self cannibalism,” a topic with a catchy title and an intriguing story. The self cannibalism refers to the autophagy process whereby cells cannibalize themselves, which is a process of survival involved in most diseases. As we age, Hurley explained, autophagy slows down and the rate of damage is no longer offset by self cannibalism, which is not always a good thing (take cancer cells, for example). Crystallography at the ALS is helping Hurley and his colleagues discover more about the process of autophagy.
Afternoon speakers included Yayoi Takamura from UC Davis, who spoke about the usefulness of complex oxide nanostructures, and William Chueh from Stanford University, who spoke about nano spectromicroscopy and battery kinetics.
ALS staff updates included User Services group lead Sue Bailey, who gave users an update on the new ALSHub process, and David Robin, ALS Division Deputy for Accelerator Operations, who reviewed accelerator, instrumentation, and controls upgrades.
Students from across the country and around the world then took the stage to briefly present their research for the annual student poster slam. At the poster session and reception that evening, the students fielded questions about their work, with first prize going to Kamran Ghiossi from UC Davis, whose poster focused on progress in fullerene x-ray crystallography.
Day two featured Berkeley Lab’s Mayram Farmand speaking on ptychographic imaging of nanomaterials, followed by the student poster award winner Kamran Ghiassi who discussed his poster "Progress in Fullerene X-Ray Crytallography.". Chuck Fadley, Shirley Award Winner, talked about depth-resolved ARPES. Molecular Foundry Director Jeff Neatongave ALS users an overview ofthe Foundry and potential opportunities for ALS users.James Sethian from the Center for Applied Mathematics for Energy Related Applications (CAMERA) spoke to users about CAMERA and senior scientist Musa Ahmed, Chemical Sciences Division,spoke about new insights into soot formation.
The final speaker of the afternoon, Scripps Research Institute’s Erica Saphire, brought some audience members to tears with her discussion of the current Ebola virus outbreak and the race for a cure. Saphire is an ALS user whose x-ray crystallography work contributed to the development of a promising Ebola treatment.
UEC Chair Peter Nico (at left) with 2014 Klaus Halbach Award winners (from left): Alastair MacDowell, James Nasiatka, Dula Parkinson, Abdel Haboub, and Hrishikesh Bale.
Afternoon workshops and the evening awards dinner were well-attended, with the following awards given out:
David A. Shirley Award for Outstanding Scientific Achievement at the ALS to Charles (Chuck) Fadley for "for significant contributions to a better understanding of surfaces and interfaces through the development of novel x-ray photoemission spectroscopy techniques."
Klaus Halbach Award for Innovative Instrumentation at the ALS to Alastair MacDowell, Hrishikesh Bale, Abdel Haboub. James Nasiatka, Dilworth (Dula) Parkinson and Robert (Rob) Ritchie for "for the development of tomography of composite materials at ultra-high temperatures resulting in unique new capabilities in materials science."
Tim Renner User Services Award for Outstanding Support to the ALS User Community to Tony Warwick "for reforming, formalizing, streamlining and documenting the Beamline Review Committee (BRC) over a ten year chairmanship for the benefit of those that follow."
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