User Access

EMSL's Response

Training of staff by a solid state applications chemist is scheduled with an upgraded console installation. This training will allow for staff to have two weeks of on-site training on the state of the art console and two probes associated with the improvements to the 500 MHz WB NMR system.

Improvements to cryogenics support of the magnets are being considered and investments in this area will potentially make two RF trained technical staff more available for probe development projects and repairs.

EMSL's Response

Further development is underway for several solid-state NMR probes. Requests for commercial probes where available are rolled up for consideration as part of the EMSL capital improvement process. We have recently added capabilities specific to in situ chemistry creating innovations specific to PNNL, which produced working prototypes available for user use. Further developments of in situ probes with wider temperature ranges and spinning speeds are underway or under consideration. A first generation high temperature (400 C ) solid-state HX probe for the 900 MHz NMR is nearing completion and should be available for users by summer.

EMSL's Response

Space is tight in the EMSL so some sharing of the lab space among users is needed. However, bench space for user sample prep into tubes and rotors is available in labs 1425, 1514, and 1518 as well as access to hoods and a cold room (1514). Some space is better set up for biological samples and others provide space for inorganic solid-state NMR samples.

EMSL's Response

The primary objective of the MSCF is to provide teraflop computing resources for grand-challenge computational problems. The job scheduling policy has been established to provide a higher priority on effective throughput and turnaround of large jobs. Smaller jobs using 32 processors or less are used for backfill. We encourage users who use small numbers of processors for extended times to use a small local cluster.

EMSL's Response

EMSL is in the process of replacing the supercomputer (mpp2). We expect new hardware to start arriving Fall 2007. MSCF staff will help scientists to start transitioning to the new computer near the end of 2007 after a trial and burn in period. We anticipate the replacement computer to be at least 5 times the total capacity of mpp2.

EMSL's Response

The queue tends to be very long because there are many researchers running calculations. Queues are shorter on weekends and extended holidays.

EMSL's Response

Recent upgrades and new capabilities in the ES&B Facility include:

A confocal Raman microscope for the analysis of radiological samples was added to the facility in Fiscal Year 2006. The research-grade Dilor XY 800 Raman spectrometer is a high-resolution, modular triple spectrometer that can be operated in high-resolution or high-throughput modes, with both bulk sample and confocal microscopic capability for spatially revolved analysis. In its current location at PNNL's 331 Building, significant quantities of radioactive materials and diverse radionuclides can be investigated. Research of this type has included the investigation of the effects of radiation damage in 238P-substituted silicates as potential radioactive waste storage materials, characterization of novel uranium mineral phases, characterization of contaminated soils from the Hanford Site, and identification of technetium-carboxylate solution species. Raman FTIR is available.

A single-crystal x-ray diffraction capability is now operational. The single crystal diffractometer is a Bruker Proteum rotating annode instrument that supplies brilliant copper radiation. Detection is by a large-format charged-coupled device. This combination of source and detector makes it ideal for determining the structure of very large biological molecules. Recently, the software was upgraded so that "small molecule" research such as inorganic compounds can be accommodated. For the "small molecule" application, in addition to de novo structural determinations, this instrument can provide extremely high-resolution measurements of defect structures and lattice strain as a function of composition that would not be possible on a diffractometer with molybdenum radiation. It also is equipped with a liquid nitrogen cooling stage for temperature-dependent measurements.

A capability in microfluidics will serve to bridge the gap between the laboratory-scale flow capabilities currently available in the Subsurface Flow and Transport Laboratory and the spectroscopic and modeling efforts on the molecular scale at interfaces that dominate research in EMSL. This capability is under development — flow experiments in intricately patterned wafers were conducted last year using fluorescent imaging to monitor mixing of various chemical and biochemical reactants. These experiments involved use of two-dimensional flow cells less than 1 cm long and allowed researchers to investigate how mixing occurs with ion-milled pillars of different diameter, shape, and packing density. These experiments could be extended so that the silicon surface itself is functionalized.

Continued investments have been made in an applied-field Mossbauer spectrometer, which is targeted for demonstration in Fiscal Year 2007.

The following capabilities are under consideration for future purchase: confocal microscope capable of FLIM and FRET, Surface enhanced Raman spectroscopy.

EMSL's Response

Recent upgrades and new capabilities in the INS Facility include:

Time-of-Flight Secondary Ion Mass Spectroscopy (ToF SIMS) : ToF SIMS uses a pulsed ion beam to remove molecules from the very outermost surface. The new time of flight secondary ion mass spectrometer (ToF SIMS) is an upgrade for the instrument existing at EMSL. This ultra high vacuum surface analytical system is designed to examine surface structure, composition and chemical state by means of secondary ion detection during ion sputtering. The instrument will be furnished with a C₆₀ ion gun, a liquid metal ion gun with Au or Bi sources, and a Cs⁺/O₂⁺ sputter ion gun with emission current stabilizers. The capabilities include surface spectroscopy with high sensitivity and mass resolution, surface imaging with high lateral resolution, depth profiling with high depth resolution and 3-D analysis. Low primary energy and low ion dose densities provide surface analysis without significantly altering surface. High primary ion energies and currents allow 'dynamic' analysis of the near surface region. The system is equipped with an introduction chamber and a glove box for sample transfer under controlled environment. In addition, we have plans to build a side chamber with limited processing capabilities and the existing transfer technology so that the portable transfer systems including vacuum suitcases can be attached to the main system through the side chamber. This system will be installed in October, 2007 and it is expected to be available for users in November/December 2007.

Dual Beam - Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM): The dual-beam focused ion beam/scanning electron microscopy (FIB/SEM) microscope combines two important high resolution microscopy tools that jointly enable important nanoscale measurements and the unique preparation of samples and materials for other uses or analysis. This instrument will provide rapid and selected region preparation of samples for transmission electron microscopy (TEM) and other spectroscopies; three dimensional analyses of nanoscale materials and other small objects; and the capability for nanoscale lithography. Functionally, the instrument includes computer-controlled ion-beam micromachining based on a liquid-metal ion source and high-resolution SEM imaging based on a field-emission-gun (FEG) electron source. Full functionality incorporates automated sample sectioning with access to electron beam, ion beam, stage positioning (allowing patterning or lithography) and gas injector control (allowing in situ etching or material deposition [beam induced CVD]). The instrument is configured to perform these operations either simultaneously or independently, attended or unattended, at the operator's will. Energy dispersive x-ray spectroscopy (EDXS) and electron backscattering diffractions (EBSD) systems including all necessary hardware and software for quantitative and qualitative analysis are incorporated to allow phase identifications based on crystallographic data obtained from EBSD and compositional data based on EDXS. In addition, the instrument allows specimens prepared by FIB micromachining to be manipulated for scanning transmission electron microscopy (STEM) imaging or fabrication purposes such as welding to a TEM sample grid without breaking the vacuum within the instrument. The samples prepared using FIB are planned to be analyzed by several surface and bulk sensitive electron, ion and x-ray based capabilities including Auger Electron Spectroscopy (AES), x-ray photoelectron spectroscopy (XPS), secondary ion mass spectrometry (SIMS), and TEM. This instrumentation will be installed in June 2007 and, we expect this to be available for users in August/September 2007.

Scanning Multi-probe Surface Analysis System (SMSAS): This instrument is a multi-technique surface analysis instrument based on elemental mapping using either scanning small spot x-rays or the electronics in the analyzer. This scanning technology provides high performance micro-area spectroscopy, chemical imaging, and secondary electron imaging with high spatial resolution. This system will include a monochromatic high resolution Al x-ray source, a non-monochromatic dual anode x-ray source, and a high resolution hemispherical analyzer for x-ray photoelectron spectroscopy (XPS); an intense He lamp for ultraviolet photoelectron spectroscopy (UPS); an argon ion gun for sputter depth profiling; and a C₆₀ ion gun for high resolution sputter depth profiling in organic and bio systems. This system will have an excellent dual beam charge neutralization method provides effortless analysis of insulating samples using a combination of low energy ions and electrons. The system is equipped with an introduction chamber and a glove box for sample transfer under controlled environment. In addition, we have plans to build a side chamber with limited processing capabilities and the existing transfer technology so that the portable transfer systems including vacuum suitcases can be attached to the main system through the side chamber. This system will be installed in August 2007 and it is expected to be available for users in October 2007.

EMSL's Response

Recent upgrades and new capabilities in the CPCS Facility include:

• FTICR data acquisition system. This new system was procured to replace an older system no longer serviced by its vendor. This instrument will support structural and thermodynamic studies of molecules. Full operation of this instrument is expected in early Fiscal Year 2007.
• Zeiss Incubator and QuadView System. This new system will be used for cell growth control and protein imaging. It is expected to be operational in early Fiscal Year 2007.
• High-sensitivity interface for proton transfer reaction mass spectrometer. This system will extend detection limits for volatile organic compounds and allow real-time measurement of trace organic gases collected from atmospheric samples. It is expected to be operational in Fiscal Year 2007.
• High-resolution time-of-flight mass spectrometer and light-scattering module. This system will be used for rapid single-particle measurements of complex organic species in particulates. It is expected to be delivered in mid-Fiscal Year 2007 and be operational soon after.
• High-resolution mass spectrometer LTQ-Orbitrap and support instrumentation. This system will be used for chemical characterization of organic aerosols. This system is expected to be fully operational in Fiscal Year 2007.
• Environmental scanning electron microscope. Two systems were procured, with one received so far.

EMSL's Response

The facility is in high demand and thus the a need for more analyses/higher throughput. The most straight forward way to address would be to increase the number of systems, processors and staff available for maintenance for the facility. To date there has only been a limited ability to expand the space for the facility and until that is possible there will be fundamental limits on the throughput of the facility and longer waits for analyses to be done. Within these constraints we actively working to upgrade the instruments within the facility and to improve the robustness of the liquid chromatography (LC) platforms which are the limiting step that controls throughput. We have recently improved the lifetime of our electrospray ionization (ESI) emitters, are incorporating improved valves and are modifying the LC platforms for 4 column operation to improve their throughput.

Recent upgrades/enhancements/new capabilities in the HPMSF Facility include:

• A 12-tesla system designed for intact protein work has been applied to three separate user projects making significant contributions to each. The recapitalization effort will provide a nano-fraction collector for the system that will allow us to identify some of the isoforms and modified proteins that we have detected at low copy number.
• The second "Orbitrap™" mass spectrometer was delivered to the facility and has been fully integrated into proteomics production line.
• The new triple quadrupole mass spectrometer has been installed in the facility in September 2006 and is now being used to validate the potential biomarkers that have been identified in global proteomics studies.
• Two completely brand new LC systems were built during FY06. Both of these are configured as dual-mixer systems and both of them use 20,000 psi Teledyne/ISCO syringe pumps. They are now in routine operation and one of them has been configured with 75µm id capillary columns and has been very robust in use.

EMSL's Response

Plans are in progress to reallocate space within the EMSL that may allow us to address these needs. It will however take some time as new laboratory space needs to be constructed that will house some of the current occupants of the EMSL.

EMSL's Response

As it has since its inception, the Proteomics Research Information Storage and Management (PRISM) system has continued to develop and integrate within its data management and analysis schemes state of the art software. Providing quantitative data is a continuing challenge for all mass spectrometers that use electrospray ionization and interpreting the peptide data to provide protein quantities is a challenge that we continue to address. Progress has been made for biologically simpler systems, such as prokaryote cell lines, but the challenge for more complex biological systems will always be present. Plans are also progressing for a more direct link between the PRISM system and the EMSL data archive to essentially provide unlimited storage. Storage servers were added to bring the online capacity of PRISM up to 20 terabytes. Several new analysis processing machines were added as well as a new SEQUEST cluster. This has brought the total number of computational processing units to more than 200.

EMSL's Response

Safety is one of EMSL's goals. EMSL strives to balance effective training while adhering to DOE and Lab training requirements. We do encourage users to do as much of their training as possible online before they arrive.

EMSL's Response

The EMSL website was updated again in attempt to make the user proposal process clearer. The new webpage and policy describing the basic requirements for a proposal and the review criteria and process should make the procedure more explanatory.

November 1, 2006, EMSL implemented a new Call for Proposals structure. A user policy update memo describing these changes was sent to participants on open proposals. We understand your frustration during this time of process change. Proposals may be submitted in response to specific calls for proposals at specific times of the year, or in response to the Open Call at any time during the year. Resource allocation is dependent on the nature of the proposal and length of access time. In order to ensure fairness, and track usage of resources in the EMSL, all work in the EMSL requires an active proposal, following policy in the EMSL Operations Manual.