Carolyn Larabell, Director, National Center for X-ray Tomography
The National Center for X-ray Tomography (NCXT) soft x-ray microscope, Beamline 2.1, is now in its third year of operation. This was the world’s first soft x-ray microscope to be designed specifically for biological and biomedical imaging, and as such has set the pace on developing this modality for imaging biological cells. Under DOE-BER and NIH funding, the NCXT has taken a somewhat esoteric synchrotron-based imaging technique and turned it into an increasingly mainstream biological tool [for example, a recent issue of the Journal of Structural Biology was dedicated in entirety to x-ray microscopy of biological materials (Carrascosa, 2012 #3)]. Consequently, this beamline is following a common trajectory in terms of increases in both requests for access to beamtime, and publications. To a great extent this growth in interest from the biological community can be attributed to the uniqueness of the data and information produced by this type of microscopy. No other technique can image an intact, fully hydrated eukaryotic cell with such high fidelity and spatial resolution.
The NCXT is no by means a one-trick pony. In laboratories near Beamline 2.1 staff have been working on further developing "High Numerical Aperture Cryo-Fluorescence Microscopy."* . Again, this breakthrough microscope was the first in the world, and represents an enormous coup for the ALS in terms of a light source impacting cell biology. This new light microscopy has a number of unique features that make it exciting as a stand-alone instrument for determining the location of labeled molecules inside a cell. However, when it is coupled with soft x-ray tomography – on the same cell – it becomes a veritable powerhouse technique. Soft x-ray tomography produces quantitative, high-resolution, 3D images of the cellular and sub-cellular architecture of fully hydrated, unstained cells, including eukaryotic cells. Currently, this microscope operates with optics that produce images with a spatial resolution of 50 nm, with the prospect of achieving 10nm resolution in the near future with the installation of the latest generation of zone plates developed by the Center for X-Ray Optics. High NA cryogenic fluorescence microscopy generates 3D maps—with isotropic precision—that detail the position of fluorescently labeled molecules inside the cell. Both of these techniques are closely matched in terms of resolution/precision, and therefore optimally suited to the generation of a correlated view of a cell, and answering questions important in fields as diverse as medicine and biofuel production.
*Larabell, C. A. & Nugent, K. A., "Imaging cellular architecture with X-rays,". Curr Opin Struc Biol 20, 623-631, (2010)
McDermott, G., Le Gros, M. A. & Larabell, C. A., "Visualizing cell architecture and molecular location using soft x-ray tomography and correlated cryo-light microscopy," Annual review of physical chemistry 63, 225-239, (2012).
McDermott, G., Le Gros, M. A., Knoechel, C. G., Uchida, M. & Larabell, C. A., "Soft X-ray tomography and cryogenic light microscopy: the cool combination in cellular imaging," Trends Cell Biol 19, 587-595, (2009)
Howard Padmore, Division Deputy for Experimental Systems
As the ALS Deputy for Experimental Systems, I oversee the Experimental Systems Group (ESG) with the help of the group deputies, Alastair MacDowell and Tony Warwick. The mission of the ESG is to assist researchers working on ESG-supported beamlines, to develop the technical infrastructure needed to carry out this work, and to help develop new applications of synchrotron radiation primarily through the development of new techniques. A particular focus of the group’s work is in x-ray microscopy and in the application of many techniques to the challenges in energy sciences.
In addition to maintaining and improving the performance of our present suite of beamlines, we have active programs that will add new capabilities in the next few years.
- COSMIC: This will be an EPU powered soft x-ray beamline, in the soon to be chicaned sector 7, that will support two endstations: one for coherent scattering and one for coherent imaging. The optical design is complete and we are about to start working with the engineering group on realization of this new state-of-the-art system for coherent soft x-ray experiments.
- Nanosurveyor: This is a new ptychographic microscope that will be on COSMIC and should give a resolution well beyond that achievable with conventional x-ray microscopy. In this system, a diffraction pattern is recorded from two overlapping spots on the sample; the overlap provides a robust way to phase the diffraction pattern and recover a real-space image. A prototype of the microscope is now undergoing testing on BL 9.0.1, and using the BL 11 and 18.104.22.168 STXMs, testing of this modality is underway using present microscopes. Initial results indicate that sub-10 nm resolution will be achieved.
- Optical metrology: Beamlines depend on good optics, and for this we must qualify and adjust all optics we receive. This is done in our optical metrology lab. A new lab with temperature-controlled and clean conditions is under construction in the USB and should give us a major improvement in capability.
- Improvement to existing beamlines: We have a medium-term plan to upgrade some of our older beamlines using state of the art optics (LUXOR project). This is a similar program to that successfully carried out on the protein crystallography beamlines a couple of years ago. We are awaiting funding so that a start can be made in this area.
- Beamline upgrades and moves: We plan to move and upgrade beamline 11.3.1, the Chemical Crystallography Beamline. This is ALS’s most productive beamline in terms of published output, but it is on a non-optimum source. Moving it to a superbend magnet will mean a factor of 1000 increase in flux density at the sample for small crystals. In collaboration with the Chemical Sciences Division, we are also examining the opportunities for moving the existing BL 7.0 beamline to sector 9, to replace the coherent optics beamline. This will give new soft x-ray capabilities to the chemical dynamics group.
This is a small glimpse into the work of the Experimental Systems Group. The work of the group is only possible through the hard work and dedication of the group members who play a central role in keeping the ALS at the leading edge of synchrotron science.
Zahid Hussain, Division Deputy for Scientific Support
As the ALS Division Deputy for Scientific Support, I oversee the Scientific Support Group (SSG), with the help of deputies Eli Rotenberg and Michael Martin. The SSG's primary mission is to support the efforts of researchers at the ALS through scientific and technical collaboration and scientific outreach. Depending on the needs of ALS users, the degree of collaboration can range from technical assistance with a beamline to full partnership in developing new research programs and experiment endstations. The SSG also strives to expand ALS scientific programs and broaden its user base through presentations, demonstration experiments, and publications.
The group organizes a variety of seminars, including a weekly ALS Center for X-Ray Optics (CXRO) x-ray science and technology seminar series: a targeted weekly lecture series with talks given by leading researchers on various topics.
The ALS Doctoral Fellowship in Residence program, established in 2001, enables students to acquire hands-on scientific training and develop professional maturity for independent research. In 2007, we initiated an ALS Postdoctoral Fellowship Program that identifies outstanding individuals in new and emerging scientific fields and provides them with advanced training. Both programs lead the way in establishing a pipeline of future beamline scientists to U.S. Department of Energy Basic Energy Sciences user facilities.
The SSG played a very active role in creating the "Advanced Light Source Strategic Plan: 2009–2016, Addressing the Scientific Grand Challenges and Our Energy Future" and the "Photon Science for Renewable Energy" brochure, which is currently being updated.
The SSG has pioneered unique techniques that enable novel science, particularly using soft x rays. Some of these are listed below:
- Development of ambient-pressure x-ray photoemission spectroscopy (APXPS) that enables XPS experiments at pressures of up to 10 torr, bridging a gap between ultrahigh vacuum and real-world industrial manufacturing conditions. This instrument received a 2010 R&D 100 Award.
- Development of time-of-flight (TOF)–based electron-energy analyzers that provide unique advantages over dispersive analyzers. Recently, spin-resolved TOF achieved a world-record energy resolution of better than 20 meV and an overall figure of merit that is 1000 times better than state-of-the-art commercial systems.
- Development of a scattering chamber that has been used both at the ALS for static measurements and at the LCLS for dynamic studies of charge ordering.
- Development of a new generation of both high-resolution and high-throughput spectrographs for photon-in/photon-out spectroscopy. Both of these perform at orders of magnitude higher than previous generations. The high-resolution RIXS spectrograph has the world’s best resolving resolution of 10 meV.
- Achieved a spatial resolution of better than 10 nm from a scanning transmission x-ray microscope.
The SSG has recently developed a new, higher-flux infrared beamline (Beamline 5.4), the meV-resolution beamline (MERLIN), and has begun construction of the MAESTRO beamline that will allow for nano-ARPES studies. Progress has also been made in the development of a coherent scattering chamber for the COSMIC beamline. We plan to submit a proposal for the construction of the Advanced Materials Beamline for Energy Research (AMBER), which will study energy related problems under in-situ and operando conditions.
I am very proud of the work done by the members of the SSG. They play a pivotal role in keeping ALS science at the forefront of its fields and making the ALS an outstanding user facility.
Jim Floyd, Environment, Health and Safety
The Advanced Light Source’s Environmental Health and Safety program is responsible for both staff and user safety. As always, there are many different issues and opportunities to work on. Following are some of the current highlights:
We have instituted a more efficient beamline review process for smaller projects. Called Abbreviated Beamline Reviews, these have fewer steps and reviews than previous procedures, though they cover the same design and readiness review steps. This was finalized in ALS Procedure BL 08-16, which can be found at https://sites.google.com/a/lbl.gov/procedures/, and we have successfully used this new process in six reviews.
We are also in the process of combining the annual beamline inspections with the annual permanent end-station inspections. By combining these inspections, our goal is to provide clearer guidance for beamline staff, more consistency, better follow-up on open items, and fewer overall inspections. We expect to start trial runs of these in the next month.
Lastly, we are preparing for upcoming lab-wide efforts to replace the Job Hazards Analysis (JHA) with a new work planning and control system. Our focus is on work planning at the beamlines, and, in particular, how we train and qualify new staff to work on them. We’re starting with a few individual beamlines to learn about issues that might be specific to the ALS. Eventually, we will develop ALS-wide models that can be incorporated into the lab-wide system. If you’d like more information on this, please
There are two main user safety initiatives. We’re working with User Services on the design of a new User Portal and have already done extensive analysis of, and comparison with, other DOE light source user safety systems. Generally, we want to model our system after the one used at Argonne’s Advanced Photon Source, and are in the process of identifying current software that might accomplish this. We hope that this might be done in conjunction with the Berkeley Lab work planning and control efforts.
Shraddha Ravani is continuing her efforts to help us provide better biosafety support to our users. Most users can now take advantage of a division-wide Bio Use Notification (BUN) without having to create their own. Its scope is steadily expanding and we are now working to get a USDA soil permit. This should allow us to accept an even broader range of samples. Use of the User Support Building’s biology labs continues to expand. If you have an interest in the capabilities of these labs, please
Overall, we continue to push pro-active efforts to identify vulnerabilities and address them before they become incidents. An update on some of the items raised by staff:
- After one year of experience using the new User Machine Shop system, users now take a brief annual refresher to keep everyone aware of the system.
- We have a more standard and thorough orientation package for new affiliates.
- The ALS1001 training is now linked to the card-key access system.
- The control room staff now have emergency guides to assist them in the event of an emergency.
- An online Lockout/Tagout (LOTO) awareness course that will be more tailored to the needs of our staff is in the works.
We are always looking for ways to improve. Please let us know if you have any questions or ideas.
Sue Bailey, User Services Group Leader
As head of User Services I am responsible for the User Office, the Communications Group, and experiment safety coordination at the ALS. I am available to users to discuss any aspect of your interactions with the ALS: from obtaining access to the facility, to conducting your experiment safely, to ensuring you get proper recognition for your research results and publications. So please, drop by my office (6-2212D), give me a call (x7727), or send an email (
) if you have questions.
The ALS User Office has been reviewing and updating many of its procedures following a detailed analysis of our software and database. Most of the changes are intended to make life easier for ALS users or to improve efficiency. One change that you will see at the start of the next General User proposal cycle is the shift in submission deadlines from July and January to the first Wednesdays in September and March, thus shortening the lead time between proposal and beam time cycle to 4 months. We recently simplified the Score Adjustment Mechanism for active proposals with the aim of reducing user workload while still retaining fairness in the system. We are always happy to receive feedback about our processes, either by direct contact or in the User Satisfaction Survey, which all ALS users are invited to complete after their beam time.
We are also working on developing a modern Web portal for users that will include new user registration, safety systems, and centralized scheduling. Experiment safety coordination is critical to the mission of the ALS: "Support users in doing outstanding science in a safe environment.” We use the LBNL Integrated Safety Management (ISM) system, which follows these 5 core steps: define the scope of work, analyze the hazards, develop and implement controls, perform work within the controls, and provide feedback and improve. We particularly ask users to help with steps 1 and 4. We need your support for a detailed description of the scope of work, which you submit to us online, either when you complete your proposal or when you complete or update your Experiment Safety Documentation. We also need your commitment to performing your experiments within the controls developed for your safety. If you need additional support, do not hesitate to
The ALS Communications Group constantly finds creative new ideas to advertize the exciting science that results from experiments done at the ALS. See our selection of articles and PowerPoint slides focusing on recent Science Highlights, submit a Science Brief to tell us about your work, or attend the next lunchtime Science Café to hear the latest from selected users and staff. If you are a social media fan, be sure to “like” us on Facebook and to view our short ALS videos on You Tube.
The ALS User Executive Committee (UEC), with the support of the User Office and communications staff, are already planning the next annual User Meeting (8-10 Oct, 2012-save the date!). If you have good ideas for speakers or want to contact the UEC about any aspect of your experience at the ALS, please email the UEC.
Contact: Sue Bailey, 510-486-7727,
Roger Falcone, Director's Address
I welcome all members of the ALS community back for a new year. We had a fine 2011 that included an excellent review by the Department of Energy as well as the launching of a number of new activities. We are starting 2012 with the promise of healthy funding for both user operations and machine and beamline projects.
One of our primary jobs is to keep the ALS machine both reliable and at the forefront of synchrotron brightness. To accomplish this, we are upgrading our RF system with new klystrons, modernizing our control systems, and building new sextupole magnets to tighten the electron beam in the storage ring. These are long-term projects, some began under the stimulus funding in 2009, but all are on track, and those that require on-going funding have seen consistent support from DOE.
Another job we have is to work with users to develop new photon science capabilities that are needed for world-leading science. We are progressing well on beamline projects including MAESTRO (for nanoscale resolution photoemission studies), COSMIC (for advanced coherent scattering measurements and high-resolution diffractive imaging), and the SEMATECH EUV Project (supporting the industrial consortium that is developing the next generation of computer chips).
Many beamlines, including those supporting the basic science of sustainable energy technologies, benefit from partnerships with other divisions at LBNL. These include combustion studies with the Chemical Sciences Division (see this month's science highlight on Criegee intermediates), battery studies with the Material Sciences Division, and carbon capture and sequestration studies with the Earth Sciences Division. These collaborations build on other activities, such as working on advanced data handling with the Computing Division, studying new systems for artificial photosynthesis with the Joint Center for Artificial Photosynthesis (JCAP Energy Hub), and of course our strong history of collaboration with the Engineering and Accelerator, and Fusion Research Divisions.
User demand continues to grow, but with anticipated flattening of funding in coming years, we may see a stabilization in total research output (for example the number of papers) from ALS users, as our capabilities to serve increasing numbers of users depends on our total number of staff. Of course, we work to be more efficient and we make trade offs in the capabilities we offer, as new and important activities grow.
To help our users better connect with the ALS, this year we are working on a new Web portal where users can submit proposals, arrange visits, learn about safety, communicate regarding experimental setup, and post publications.
Additional priorities for this year include bringing our construction projects to completion on time and on budget. We are working with partners to propose new beamlines, including AMBER, which will address the basic science of energy technologies under real, operational (in situ) conditions, a capability necessary for greater understanding of processes like catalysis or components such as fuel cells. We are continuing to explore ways of having more theoretical support for photon sciences, fielding high data rate x-ray detectors, and processing data in real time so that feedback to users doing experiments can help them be more productive.
There is a lot to learn about our activities at ALS, and I urge you to take a look at our website, especially if you haven’t recently (http://www-als.lbl.gov/). There we highlight our science, point toward fun activities such as our bi-monthly Science Cafés, and provide links to helpful information, encouraging all of you to participate in ALS planning.
Michael Banda, Deputy Division Director for Operations
As the relatively new Deputy Division Director for Operations, I have found that there is never a dull moment at the ALS. While we have many challenges in these difficult political times that are wrought with uncertainty, we enjoy strong support from our users and from the Office of Basic Energy Sciences. This shows in the investments being made in us: beamlines are being improved, and new ones (MAESTRO and COSMIC) are being constructed. In addition, we are in the process of completing several upgrades to the synchrotron that will increase our brightness and reliability. These upgrades include an improved storage ring RF ,a controls upgrade, new power supplies, and new sextupole magnets to decrease horizontal emittance and thus increase brightness. Curiously, I have become quite enamored of the machine. It is probably due to my training as a biologist that makes me occasionally think of our synchrotron as a living organism. It seems alive and I am convinced that sometimes it expresses an attitude, good and annoying – fascinating.
It has been a year-and-a-half since I joined the ALS, and I have had the benefit of moving into a great organization with an outstanding staff. I came to particularly appreciate the quality of ALS and our staff when Roger asked me to help shepherd the BES triennial review that took place in March of this year. I will never describe such an event as fun, but it was, however, a wonderful opportunity for me to learn and experience the skill and dedication of the people that work at the ALS. Yes, our machine and beamlines are first rate, but our people are even better. It was remarkable for me to see how everyone pulled together to achieve the best review possible, truly befitting of an organization that epitomizes the “Big Science” concept advanced by E.O. Lawrence. I am struck by all the skill sets that are necessary to keep us making and using light. The pride in being from, or associated with, the ALS is palpable. Through enabling and doing cutting-edge science that result in more than 600 publications per year, to keeping the machine in top form, all members of the ALS have much to be proud of. A member of one of our advisory boards introduced herself to me shortly after I joined ALS. She told me that she uses many synchrotrons but that ALS is her favorite, and she likes coming here the best. I can understand why. I am very pleased to be working for you.
I wish you a safe and happy holiday season.
Peter Denes, Head, Photon Sciences Initiative
I joined the ALS family in 2007, filling the newly created position of ALS Division Deputy for Engineering. Because a large percentage of ALS staff are part of the Engineering Division, this position was created to establish shared management in the two divisions to ensure better integration and coordination between engineering and non-engineering ALS staff.
My natural connection to the ALS is as a detector developer—after all, what you get is what you see. A 2005 strategic LDRD-funded initiative nucleated a virtual detector group, consisting of members of the Integrated Circuit Design and Electronic Systems groups in the Engineering Division, in collaboration with the Microsystems Lab with support from members of the Physics Division. This team developed a prototype fast direct-detection CCD that has been used both to explore new concepts and to enable experiments at the ALS, APS, and LCLS. Based on that work, we received ARRA funds to develop megapixel frame-store (electronic shutter) detectors reading out at 200 frames/second. Eight of those systems, as seen in the photo on the right, will be delivered to the ALS next year.
This virtual detector group has continued to grow, and in addition to the detector itself, we have also developed high-speed data acquisition and processing electronics capable of in-line firmware data processing. High-speed readout enables dynamics, simultaneous position/energy detection, and simple efficiency, but it generates huge volumes of data. A growing challenge will be to develop effective strategies for dealing with the massive amount of data resulting from high-speed readout.
With funds from the BES Accelerator and Detector R&D program, the team is developing even faster detectors (approaching 10,000 megapixel frames/second) while improving direct detection soft x-ray (and electron) performance.
Presently, my time is spent helping to plan for a Next Generation Light Source. The scientific and technical case that Berkeley Lab put forward for a high-repetition-rate x-ray free-electron laser array has resulted in a broad national consensus on the need for such a facility, and many of us continue to vigorously pursue R&D on key technical challenges in order to be ready as soon as a project is formalized.