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ALSNews Features
Notification of General User Proposal Results 2015-1 Print

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 This e-mail address is being protected from spambots. You need JavaScript enabled to view it , the proposal coordinator, and This e-mail address is being protected from spambots. You need JavaScript enabled to view it 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.

gup notifications

Diffraction-Limited Soft X-Ray Workshop Print

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.

ALS User Meeting Highlights Challenges, Accomplishments Print


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 Neaton gave ALS users an overview of the 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."

General User Proposal Timeline for Reviews and Notifications Print

The User Office received 301 new General User Proposals (GUPs) and 260 Beam Time Requests (BTRs) for the 2015-1 running cycle.  All the proposals have now been processed by the User Office. Users submitting new proposals should have received an email inviting them to login to ALSHub and check the proposal PDF which will be sent to reviewers.

The Proposal Study Panels (PSP) and ALS Division Deputy for Science Steve Kevan provide oversight for the review process. We are often asked about the review process and when notifications will be sent. We hope the following timeline and description will be helpful.




Sept 10

Start beamline scientist feasibility checks.

Sept 10-17

Initial automated assignment of reviewers followed by manual adjustments to assign up to four external reviewers per proposal.

Sept 18

Start the external review process.

Sep 25

PSP members emailed to start their reviews.

Oct 13

Deadline for completion of external review process.

Oct 13-17

Checks on review outcomes for score consistency and comments identifying problems.

Oct 20

PSP meeting when the final score is assigned to each proposal and the likely cutoff score is identified for each beamline.

Oct 21-25

User Office uses final scores to produce allocation sheets for each beamline. The allocation sheets list all new GUPs and BTRs sorted by score.

Oct 27-Nov 7

Allocation meetings for each beamline or technique area involving the beamline scientist(s), user office staff and oversight from the ALS Division Deputy for Science. Each proposal, starting from the top of the sorted list, is assigned beam time until no beam time is left. The cutoff score is compared with that from the PSP, to check for consistency.

Nov 10-14

Users will be notified to login to ALSHub to view the outcome of each proposal and the reviewer and PSP comments.

Nov 17-Dec 19

Liaison between beamline scientists and users to produce a schedule for each beamline.


Staff in the user office, including This e-mail address is being protected from spambots. You need JavaScript enabled to view it and This e-mail address is being protected from spambots. You need JavaScript enabled to view it are available throughout this process to answer user queries, and help you. Do not hesitate to contact us for advice, or login to ALSHub to check on the progress of your proposals.

Ptychography: A Fun Word with Big Promise Print


Ptychography has won accolades for the ALS recently, as researchers achieved the highest resolution ever recorded in x-ray microscopy, but what exactly is this technique with the catchy name? (For the record, it’s pronounced “tie-cog-raphee.”) We recently sat down with ALS physicist David Shapiro, lead author on the paper reporting this research in Nature Photonics, to talk about ptychography and why the ALS is uniquely suited to work on this next-generation technique.

(A) Conventional scanning x-ray transmission image of partially delithiated LiFePO4 using a 25 nm focusing optic. (B) Ptychographic image of the same sample using a 60 nm focusing optic.  The improved resolution and contrast elucidate the presence of multiple particles and surface cracks which result in lower absorption (red arrows) and influence the phase transformation from LiFePO4 to FePO4.

Shapiro explains that with a conventional scanning microscope, you focus the beam onto a sample and while scanning it, you record the total transmitted x-ray intensity. Since different chemical species will have different soft x-ray transmission this provides the ability to map chemical composition but is limited in resolution to the smallest spot that you can make.  Focusing is a challenging process with x-rays because x-ray optics are difficult to make, inefficient, and have very short focal lengths.

With ptychography, you can work with a somewhat larger spot and measure a diffraction pattern rather than the total transmission. A specialized two-dimensional imaging detector measures all the scattered x-rays and gives researchers much more information than traditional x-ray microscopy.

“We record information that’s outside of the numerical aperture of the x-ray optic, this information is always present but conventional microscopes can’t measure it.” says Shapiro.  The very large volume of data generated by a ptychographic microscope requires state-of-the-art, high speed imaging detectors developed by the ALS detector group.

The measurement must then be converted into an image, so researchers use high performance computing and phase retrieval algorithms to reconstruct the sample at high spatial resolution from the diffraction information. There are some standard algorithms that are commonly used, but Shapiro and his colleagues are also working with The Center for Applied Mathematics for Energy Research Applications (CAMERA) in Berkeley Lab’s computational research division to develop even faster algorithms and computer code.

“We’re approaching the point where the resolution is comparable to the wavelength of the x-rays,” says Shapiro. “The ultimate goal would be to map chemical composition in three dimensions at that resolution.  The ALS is bringing together the technologies which will make that a reality but the very high brightness x-ray beams from the new ultimate storage ring sources is needed.”

Read more about ALS ptychography in the recent Berkeley Lab news release:

ALSHub: Submit Proposals and Give Us Your Feedback! Print

The ALS User Office rolled out ALSHub, a new user portal, five months ago, but many users will be trying it for the first time when they submit proposals for the September 3 deadline. We encourage you to provide feedback; tell us what you like or anything we could improve or add to the portal.


What will be different?

The login site, and the interface you see when you log in are all new. In order to login the first time, existing ALS users should use their email on file, but will need to request a new password. The landing page will provide a number of options, including the ability to update your contact details, including email,  by changing your profile. ALSHub provides additional information that you have not been able to view before: including all your current and previous proposals, your LBNL ID, your up-to-date basic safety training status and expiry dates, and whether your access badge is currently active.

Please note that since the login uses your email, you will need to contact the This e-mail address is being protected from spambots. You need JavaScript enabled to view it if you have changed your email address and no longer have access to your previous email.


General User Proposals for the ALS 2015-1 cycle

Deadline: September 3, 2014

Please login to ALSHub to submit a new General User Proposal (GUP) or to make a Beam Time Request (BTR) on an existing active proposal.


RAPIDD Proposals

Users requiring limited but rapid access to ALS beam time, may prefer to submit a RAPIDD proposal rather than a GUP. RAPIDD proposals may be submitted at any time and the system includes:

  • Rapid access to structural biology beamlines
  • Rapid access to some general user beamlines (7.3.3, 8.3.2, 9.3.1 and 11.3.1)
  • Industry proposals on most ALS-run beamlines
  • Director's Discretionary beam time on most ALS-run beamlines
Student UEC Member Goes Above and Beyond Print

As a student representative to the ALS Users Executive Committee (UEC) for the past two years, Mahati Chintapalli has gained a better understanding of how the ALS functions as an organization, while the UEC has gained a devoted and outgoing member. This year, Chintapalli led the fundraising drive for the annual User Meeting awards along with UEC member Micky Holcomb, and they raised the monies in record time. She’s currently a PhD student in Materials Science at UC Berkeley and has been conducting research at the ALS since she began her PhD program in 2011.

“Being on the UEC has been really positive,” says Chintapalli. “I’ve had a chance to meet a lot of people and learn about how the organization plans for the future of the synchrotron.”

Two years ago, Chintapalli won the student poster competition at the ALS User Meeting for her poster about carbon monoxide dissociation on cobalt nanoparticles, based on her research into how the size of nanoparticles affected the CO dissociation. These days, her research is focused on block copolymer electrolytes and how they conduct ions for lithium batteries; she’s using the small-angle scattering capabilities at BL 7.3.3 for this work. In the future, she hopes to be able to use spectroscopy to look at how ions are solvated and conducted in polymer electrolytes with the hope of learning how to design polymer electrolyte systems with improved ionic conductivity.

“I am very grateful that I’ve gotten a chance to do different types of research in my time at the ALS,” she says. “With my current work at 7.3.3, I’ve been able to see the correlation between the structure of the polymer and how well or how poorly it conducts ions because of its structure.”

Chintapalli says her involvement in the UEC has given her a broader view of the ALS user community, as she’s gotten to know scientists outside of her own field. She says that these informal connections have opened up wider opportunities for her at the ALS.

September 2014 Call for General User Proposals Print

The User Office is accepting new General User Proposals (GUPs) from scientists who wish to conduct research at the ALS in the January – June 2015 cycle.


Please log in to ALSHub to submit a new GUP or to make a Beam Time Request (BTR) on an existing active proposal.

Users are reminded that they need to have an ALSHub account to submit proposals, and that creating an account may take 1-2 business days. We encourage all users to check their account well before the proposal deadline.

New Proposals

For more information about how to apply for beam time and proposal writing guidelines, follow the link to Apply for Beamtime in the User Guide.

Maintaining an Active Proposal

Proposals for general sciences beamlines are considered active for two years, or until the total shifts requested in the proposal have been used. Users may decide whether to submit a new proposal or make a BTR on an active proposal based on the cutoff score for that beamline. Users are reminded that their proposal score may be improved if they fell below the cutoff in the first cycle, as described on GUP web pages.

RAPIDD proposals

Users requiring limited but rapid access to ALS beam time, may prefer to submit a RAPIDD proposal rather than a GUP. RAPIDD proposals may be submitted at any time and the system includes:

  • Rapid access to structural biology beamlines
  • Rapid access to some general user beamlines (7.3.3, 8.3.2, 9.3.1 and 11.3.1)
  • Industry proposals on most ALS-run beamlines
  • Director's Discretionary beam time on most ALS-run beamlines

All proposal forms include a productivity section with publications from previous ALS work. The publications will be pre-filled automatically from the ALS publication database by searching for the Principal Investigator's name. Please make sure your publications are entered into our database and be sure to select your group’s publication when submitting your proposal.

ALS Data Visualization Lab Serves Up Computing Power Print


Even though the ALS has been in shutdown mode for almost two months, there’s one area of the facility where users have been busy. The new ALS Visualization and Analysis Lab, which opened to users in November 2013, hosts an impressive amount of computing power that’s helping scientists work through data-heavy beamline results much more quickly and efficiently.

Located on the second floor of the ALS (building 6, room 2244), the data visualization lab (or “viz lab,” as ALS folks refer to it) includes two Windows workstations with 64 GB of RAM,high-end graphics cards, and large displays; three top-of-the-line iMacs; a teleconferencing television; and a 55” 3D television. The room that houses all of this was previously a library, available to users and mostly used as a place to work on laptops or make phone calls. The computing capabilities were not previously available to users; they had limited access to computers at the beamline, but once their beamtime was over they had to find other means of accessing and analyzing data.

The viz lab was a dream come to fruition for ALS Beamline Scientists Dula Parkinson and Alex Hexemer. Their effort to create the lab was directed by ALS Deputy for Experimental Systems Howard Padmore and ALS Deputy Division Director for Operations Michael Banda.

“Users at my beamline collect a lot of data, and to be able to do anything with that data they need a lot of computational horsepower,” says Parkinson. “Every data set is about 50 GB, which isn’t going to load too well on a user’s laptop.”

Parkinson says many users don’t even have the software needed to view data on their own computers. Users sometimes weren’t able to finish what they needed to do, because of limited access to computers at the beamline. Parkinson estimates that more than 50 percent of his users are from the Bay Area, so a lot of them can actually drive over and use the viz lab even after they’ve finished with their beamtime. In addition to computing power and software, the viz lab gives users a place to collaborate and trouble-shoot; ALS staff are frequently available to assist users in the viz lab and other users working there often share tips.

“It brings collaboration,” says ALS user Katherine Harry, a graduate student in the Department of Materials Science and Engineering at UC Berkeley who has been doing beamline research on lithium batteries at the ALS for almost three years. “It’s also nice because you’ll often run into other researchers in the lab and they can help you decipher things.”

Before she had access to the viz lab, Harry says she would remotely access beamline computers at off-hours and hope a computer was available. “The data sets we’re collecting are enormous,” she says. “I personally don’t have the computing power to even open a single dataset on my laptop.”

The viz lab is available to anyone at the ALS, and the space has been getting busier and busier since it opened. Parkinson says he’s had a lot of requests from staff and post-docs from other beamlines.

“The great thing about the ALS is that it produces a lot of x-rays,” says Parkinson. “That allows you to collect high-resolution images very quickly, and all those pixels turn into a lot of data.”

2014 Shutdown: Final Update Print

Steve Rossi reports on nearing the end of this year's shutdown:

We're in the final days of our extended shutdown here at the ALS. Our technical staff has accomplished over 7000 hours of scheduled work along with the myriad of small tasks requested of them on an ad hoc basis. Each shutdown I find myself in awe of the overall effort it requires to organize and execute the work, as well as the amazing professionalism and dedication of our staff.

This is the tense, nail-biting portion of the shutdown as we begin to power up and test the various systems that we have modified and installed. So far. things are proceeding very well with the new storage ring radio frequency system high-voltage switch, which was our "critical path" project. All the new water-flow monitoring equipment, for the entire booster and storage ring, has been installed.

The linear accelerator klystron modulator has been replaced and tested, which is dramatically increasing our injection efficiency. The damaged QFA magnet power supply that caused an unexpected outage just prior to this shutdown, has been fully repaired and tested.

Youngest ALS Users Go to the White House Print


Christine Mytko, Patricia Falcone (White House Office of Science and
Technology Policy), Sam Schickler, and Jane Yarnell.

Two seventh graders from Black Pine Circle (BPC) School in Berkeley, who came to the ALS last November on a field trip that included actual beam time earned through peer-reviewed proposals, have now made it all the way to the White House.

Samuel Schickler and Jane Yarnell, along with their science teacher Christine Mytko, were invited to attend the first-ever White House "Maker Faire." The event featured "Makers, innovators, and entrepreneurs of all ages who are using cutting-edge tools to bring their ideas to life."

The White House Maker Faire website describes how the BPC students "used a powerful x-ray beam at the U.S. Department of Energy Office of Science's Advanced Light Source to get high-resolution scans of samples they selected, then used open source visualization software and 3D printing to make enlarged physical models, revealing the samples' internal microstructures."

The first-ever White House Maker Faire was held on Wednesday, June 18, 2014.

The students' presentation of their work had earned them high honors at a regional Maker Faire held May 17–18 in San Mateo, where they won Editor's Choice and Best in Class awards for demonstrating "great creativity, ingenuity and innovation."

At the White House, the students rubbed shoulders with fellow innovators from across the country, whose do-it-yourself projects ranged from a robotic giraffe to a low-cost, non-electric infant warmer that can help save premature babies in rural villages. They were present in the East Room where President Obama, in his remarks, said that the "democratization of manufacturing" exemplified by the Maker Faire "gives you a sense that we are at the dawn of something big," noting that comparisons have been made to where we were with the Internet 25 to 30 years ago.

The President also highlighted the importance of learning by doing and asked how we might redesign high schools so that young people can do more than just sit and listen to a lecture. "So math, science all gets incorporated into the task of actually making something, which the students tell me makes the subject matter that much more interesting."

Left: Microtomographic image of an eggshell. Right: Several 3D prints of the eggshell data.

The journey from BPC to D.C. began last fall with lessons that had been developed by Mytko during a summer internship at ALS Beamline 8.3.2, with Beamline Scientist Dula Parkinson. The lessons culminated last November in a class visit to the ALS, and those whose proposals were scored highest by fellow classmates used Beamline 8.3.2 to scan their samples, including things such as egg shells, snake skin, and duct tape. The students then used the microtomography data to 3D-print blown-up versions of their samples, some of which Jane and Sam carried in their pockets with them to the White House.

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