User Access

EMSL's Response

EMSL is the process of a major rewrite of its web sites with one of the goal to make the proposal process less confusing. In response to EMSL review committees' recommendations, additional processes have been or will be implemented to improve the administration and better assess the effectiveness of our research programs. EMSL is working hard to streamline these processes to make it as easy as possible for our users to get their science done.

EMSL processes hundreds of proposals each year:

• In February 2007, the second annual EMSL Science Theme Call for Proposals was sent out to users. The call resulted in nearly three times the proposal submissions of the first year, with 279 proposals submitted: 29 for Atmospheric Aerosol Chemistry, 74 for Biological Interactions and Dynamics, 51 for Geochemistry/Biogeochemistry and Subsurface Science, and 125 in Science of Interfacial Phenomena. Based on instrument availability and scientific merit, 202 of the proposals were selected as full Science Theme Proposals, and 50 as limited proposals.
• In April 2007, a Capability-based call was issued seeking proposals in four areas: Single Crystal and Microbeam X-ray Diffraction (XRD); Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM); Transmission Electron Microscopy with Cryo Stage and Tomography (Cryo-TEM) and Bio-solids Capability on the 900-MHz nuclear magnetic resonance (NMR) spectrometer. The call resulted in 19 proposals submitted, with 7 accepted for the FIB/SEM; none accepted for XRD; 3 accepted for Cryo-TEM; and 4 accepted for the 900-MHz NMR bio-solids.
• Under the Open call, 95 proposals were submitted, of which 89 were accepted. An additional 21 Rapid Access requests were approved.

EMSL's Response

EMSL strives to balance effective training while adhering to U.S. Department of Energy (DOE) and Pacific Northwest National Laboratory (PNNL) training requirements. Within the last year, training requirements at PNNL have changed, resulting in many users having to take the same training as staff or vendors. EMSL is still working with PNNL to reassess and revise the training required by EMSL users.

EMSL's Response

All proposals are submitted against one of several Calls (e.g. Open, Science Theme, Capability-based, etc). Depending on the Call type, a proposal may be extended annually until the maximum total period has been reached. For example, Science Theme proposals are valid for 1 year and can be extended twice for a total period of 3 years. Two months before a proposal's annual end date, the user will receive an email requesting a summary and justification for extension. Extension is not guaranteed and is considered based on the progress and justification for future work. A proposal that is closed or will be forced to close soon due to time limits may be renewed via the User Portal. Renewal essentially brings up the old proposal in the system, which the user updates and then submits for review.

EMSL's Response

EMSL strongly encourages its users to continue to provide feedback through the bi-annual survey, email, and conversations with staff. We would like to remind users that EMSL has a User Advisory Committee. This committee, an independent body of experts from academia, industry, and national laboratories, is charged with providing objective, timely advice and recommendations to EMSL leadership. The UAC is open to suggestions from the user community.

EMSL's Response

Quotes for DOSY (Diffusion Ordered Spectroscopy) capability, 13C - cryoprobe and carbon observe capabilities on medium and higher field spectrometers are being sought and considered.

A broad-band liquids probe for a 600-MHz system has just been installed and is being tested. This capability will allow direct observation for a range of liquid-state NMR study including ¹⁹F, ³¹P, ¹³C, ¹⁵N. This is now the highest field system with this capability.

Solid-state spin controllers are aging and have been a problem on some systems (750-MHz) from time to time as noted by some of our users. We will transfer and schedule carefully the use of a few newer systems as we seek to update our older spin controllers.

The circular dichroism spectrometer has had several issues in operation in recent years and a new system has been ordered and is expected in early spring 2008. This will replace its 13-year-old predecessor.

A high-temperature, large sample volume, constant flow magic-angle spinning NMR probe for the 11.7-Tesla magnet was constructed and is being tested. This probe will allow the study of catalytic reactions in the steady state at temperatures up to 400°C. Besides working at temperatures much higher than normal for NMR probes, this probe can flow reactants across a catalyst bed while the sample is spinning at several kilohertz. The combination makes this probe uniquely capable of studying reactions that could not have been studied before.

EMSL's Response

Staffing availability between multiple projects and visitors with our hosts/operators are sometimes problematic in terms of last-minute schedule changes. Keeping the throughput of user projects at a high level means we may need to change who is available to work with users from one visit to the next. We will continue to strive to keep the quality of the user visit and interaction with our resources and staff at a high level.

EMSL's Response

The following new capabilities were installed in fiscal year 2007:

• Electron transfer dissociation-linear ion trap quadrupole (LTQ) mass spectrometer: This new system provides important new peptide structural information not available from conventional collisionally induced dissociation methods. The electron transfer dissociation upgrade greatly enhances the mapping of phosphorylation sites and characterization of other proteins' posttranslational modifications.
• Triversa NanoMate: This system has been incorporated into EMSL's novel integrated top-down and bottom-up approaches to enable concurrent liquid chromatography-mass spectrometry analysis and fraction collection for comprehensive high-throughput intact protein profiling. The approach employs high-resolution, reversed-phase liquid chromatography separations coupled online with a 12-Tesla Fourier transform ion cyclotron resonance (FTICR) spectrometer to profile and tentatively identify modified proteins.
• BD™ free flow electrophoresis system: This system provides new opportunities for characterizing proteins, functional protein complexes, subcellular components, and whole cells.

Also, a workshop, "Science Challenges and Design Concepts for Deploying a High Magnetic Field High Performance FTICR Mass Spectrometer System," was jointly sponsored by EMSL and the National Science Foundation's and the National High Magnetic Field Laboratory at Florida State University. Held January 16-17, 2008, at the NHMFL, the workshop identified science drivers that could justify investment in FTICR mass spectrometry at magnetic fields significantly higher than 15 Tesla. The workshop will bring together the principal technologists developing cutting-edge FTICR instrumentation and a select group of major users of FTICR technology to define the recommended direction.

EMSL's Response

EMSL emphasizes complex large-scale problems in science and engineering where computation is integrated with theory and experiment. Our current queuing policy for MPP2 is to give priority to jobs using large numbers of processors that cannot be run on readily available small computer clusters. Smaller jobs that require long execution times tend to wait longer in the queue.

We will revisit the queuing issue to provide our users with balanced support for large- and small-scale jobs associated with multi-facility EMSL science theme projects in summer 2008 when our new $24M supercomputer (codenamed Chinook) will start to be available. The new supercomputer will include 4620 quad-core AMD Barcelona processors, 37 terabytes of memory, and an expected peak performance of about 163 teraflops. The supercomputer will be delivered and tested in two phases starting in March 2008, and is expected to be fully operational in September 2008. It will replace the MPP2 supercomputer, which went online in 2003.

EMSL's Response

EMSL is in the process of replacing the current supercomputer (MPP2) with a new one (Chinook) with greater capacity but a similar balance of processor speed, memory bandwidth, and local scratch. Hardware will start arriving in early 2008. The new supercomputer will have about 10 times the current capacity of MPP2.

EMSL's Response

NWChem is provided to all users. Because of the relative expense, JAGUAR is not provided to all users; however, a user can install their own copy of the software and the consulting group will assist as necessary to get the code running. Molecular dynamics codes such as NAMD and AMBER are provided to users on an "as is" basis. We get the code running as best we can but if code modifications are necessary, these need to be done by the software developer and turn-around time can be slower than we would like. Because the Molecular Science Computing Facility does not do development on VASP, additional functionality must come from the VASP group in Vienna, Austria.

EMSL's Response

In 2008, EMSL will assemble the equipment and capabilities to perform STORM (stochastic optical reconstruction microscopy) imaging of fluorescent samples. This new technology has a resolving power more than 10 times better than conventional optical microscopy. The STORM imaging process consists of a series of imaging cycles in which only a fraction of fluorophores are switched on, such that each of the active fluorophores is optically resolvable from the rest. This allows the position of these fluorophores to be determined with high accuracy. Repeating this process multiple cycles causes a stochastically different subset of fluorophores to be turned on, eventually leading to the reconstruction of an overall image. Work is also proceeding on improving the fluorescent probes necessary for the process and developing automation software.

Other capabilities that EMSL has recently deployed or are developing include:

• A micro-XRD capability was installed with an x-ray beam that can be focused to a 10-micron spot size and has the capability for investigating samples using either an automated x-y stage for planar samples such as petrographic thin sections, sealed capillary tubes for air-sensitive powders, or fiber-mounted particulate samples. The detector is a curved image plate that is capable of measuring a large portion of the Ewald diffraction volume at one time. This detector, coupled with the bright rotating anode x-ray source, allows rapid data acquisition and can be used on even minute samples. Both copper and chromium x-ray wavelengths are available.
• A microfluidics capability is being developed to investigate the effects of fluid flow and transport at the microscale. This new capability will address fundamental scaling issues associated with fluid flow and reactive transport from both a combined experimental and theoretical approach at the micron scale. This capability will bridge the gap in experimental capabilities from the molecular scale within EMSL to the laboratory scales currently available in EMSL's Subsurface Flow and Transport Lab and permit simultaneous spatially and time-resolved spectroscopic examination of geochemical and/or biogeochemical processes. Eventually, EMSL is targeting creation of in-house facilities for the fabrication of microfluidic cells.

EMSL's Response

Recent upgrades and new capabilities in the INSF include the following:

• TEM: We are plan on having a state-of-the-art aberration-corrected TEM with an environmental cell established within 1-2 years. The configuration of the new high-resolution TEM will be optimized (and customized) to enable microscopy and other measurements to be performed in the microscope. This instrument will be designed to allow microscopy and some chemical measurements relevant to catalytic and geochemical studies of importance to fuel cells, emission control, and contaminant migration in the environment. Measurements will be able to be made with samples heated up to at least 800°C. The microscope will be configured with an "open" environmental cell that enables the specimens to be maintained in gaseous environments up to pressures of 20 mbar. It will also be possible to observe specimens exposed to liquid environments in a closed cell, but only at temperatures up to about 200°C.
• FIB/SEM: The new dual-beam system has an electron-backscattering detector.
• VersaProbe - Multi-technique surface analysis system: Current capabilities of the flexible, multi-technique surface analysis system include x-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy, and a new capability for extracting chemical information from organic layers using a C-60 ion beam.
• XPS: We are building the catalysis side chamber for Quantum XPS system. This capability is expected to be operational during summer 2008.
• Time-of-flight, secondary ion mass spectrometer: The latest version of a rapidly evolving method for determining chemical functionality of organic and inorganic surfaces was installed. This instrument also includes a C-60 ion beam as well as a bismuth ion cluster sputter source and a Cs/O2 dual-beam sputtering source. An expanded temperature control increases the ability to conduct novel experiments on organic samples, bio-samples, new catalysts, and materials for new energy research.

EMSL's Response

During FY07, a Zeiss Incubator, QuadView System, and Large-chip Cooled Charge Coupled Device Camera were purchased and installed supporting cell growth and protein imaging studies plus identifying membrane protein interactions/functions. Plans for new capital investments for major instrument systems supporting biological sciences research are under review.