User Access

EMSL's Response

The recent upgrade to an 800 MHz cryoprobe will help the issue for the High Field biomolecular NMR community. The 900 MHz NMR has a standard HCN probe and the instrument is used for both solid-state and solution state experiments. With the addition of new 800 MHz and 900 MHz probes, we anticipate supporting a higher percentage of liquid experiments on the 800 MHz and more specialized solid state experiments on the 900 MHz.

EMSL's Response

The following capabilities were recently developed and are now available to users:

• Discrete Magic Angle Turning (DMAT) and continuous flow probe technologies for studying in situ catalysis
• Unique Sample Containment Rotor System for Magic Angle Spinning studies of Radionuclides
• Hyperpolarized Gas Facility for Magnetic Resonance Imaging (supports diverse projects including airway imaging and fuel cell imaging)
• Advanced probe designs for low temperature (10K) and high temperature solid-state NMR
• A new solid-state NMR probe purchased from Varian was installed on the 900-MHz magnet in December 2005. This 3.2-mm HXY magic-angle spinning probe allows the study of membrane-bound biomolecules that previously could not be studied using the 900-MHz system.

EMSL's Response

The HFMRF will be transitioning to a unified EMSL call facilitating requests for access to all resources in the entire EMSL. This will help those of you who wish to gain access to a broader range of capabilities, while at the same time allowing specific and larger requests for resources within the HFMRF.

EMSL's Response

EMSL's supercomputer, mpp2, has been specifically configured for running large scale computational jobs that cannot run on other clusters either because of available memory (RAM), local disk space, or I/O bandwidth. The queue tends to be very long because there are many researchers running calculations. Jobs with fewer processors requested (less than 256) go into the standard queue while jobs with 256 processors or more go to the top of the standard queue. Jobs requesting smaller numbers of processors are used to back-fill the queue to keep the machine busy. When a small job is to be run for 48 hours, it tends to wait longer in the queue for enough processors to be available for that long.

EMSL's Response

There is a short pool of 16 processors (8 nodes) available during working hours for development. The maximum run time for this pool is 30 minutes with a maximum of 8 processors.

EMSL's Response

EMSL is in the process of replacing the supercomputer (mpp2). We expect new hardware to start arriving next 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. Once everyone has been moved to the new computer, mpp2 will be taken out and additional hardware installed to build the final configuration. We anticipate the replacement computer to be at least 5 times the total capacity of mpp2.

EMSL's Response

Several software programs are available on the supercomputer (mpp2) with more being added. ACES II will be available later this year. Expensive software programs must be purchased by those who want to use them and have them installed.

EMSL's Response

The available SCALAPACK version works only with four byte integers. The MSCF has been working on getting SCALAPACK to run with eight byte integers. We hope to have the i8 version available soon.

EMSL's Response

The NWChem 5.0 release includes some of the capabilities that are mentioned, whereas some of the other capabilities are currently under development. The new version features much improved, both speed and memory usage, CCSD(T) modules for both open- and closed-shell systems. They have been shown to scale to thousands of processors and should have the capability to handle thousands of basis functions. Some other new features include vibrational SCF, renormalized and EOM CCSD methods, much improved QM/MM, hybrid functional and self-interaction correction for plane-wave methods, and an interface with the VENUS code for dynamics. The open-shell DFT second derivatives for frequencies is one of our priorities to get working in the next release, and work is under way that could lead to first derivatives for CCSD(T) methods. The new Ecce 4.0 release features an interface for the molecular dynamics code. An interface to the plane-wave code is one of the considerations for the future.

EMSL's Response

EMSL Chief Scientists, senior scientists at PNNL and users are currently working on a recapitalization plan for EMSL. The Department of Energy's Office of Biological and Environmental Research is planning to provide substantial capital funding to develop new capabilities and upgrade some of the old capabilities over the next five years. Recent upgrades/enhancements/new capabilities in the ES&B Facility include:

• Laser-Induced Breakdown Spectroscopy/Detection (LIBS/LIBD) capabilities for the investigation, detection, and quantitative analysis of environmentally important toxic metals such as Cr, Pb, As, S etc. as well as the detection of actinide-bearing aerosols and solid particles and nano-colloids in-situ were recently developed
• A gated intensified ultraviolet-visible CCD camera and spectrograph, and a InGaAs IR array detector were purchased in order to extend EMSL's time-resolved laser-induced fluorescence spectroscopy and imaging spectromicroscopy capabilities into both of the ultraviolet and infrared regions.
• In May 2006, the Spokane Cluster replaced the Seattle Cluster. The 32 node cluster is used to study emphasize environmental remediation, including electron transfer that involves metal oxides and metal complexes, reactions that involve halogenated organic molecules, and reactions at mineral surfaces.
• Raman confocal microscope that has modest high temperature and controlled atmosphere capabilities has recently been added to the ESB facility.
• A scanning probe microscope to be used for protein imaging and force measurements is now available. This new instrument will help researchers to meet the special requirements of life sciences microscopy (e.g., studies of delicate biological samples under physiological conditions) and provide detailed observations of molecular structures with unprecedented resolution and without the need for rigorous sample preparation and labeling.
• A single crystal x-ray diffractometer will be available Fall 2006.
• A micro-X-ray diffractometer will be purchased this FY and available to users summer 2007. The capillary cell for samples would prevent oxidation of air sensitive samples, and is ideal for smaller sample quantities.
• Applied-field (magnetic) Mössbauer spectroscopy capability is coming up to field. It will be available to users on a demonstration basis in late Fall 2006.

EMSL's Response

EMSL Chief Scientists, senior scientists at PNNL and users are currently working on a recapitalization plan for EMSL. The Department of Energy's Office of Biological and Environmental Research is planning to provide substantial capital funding to develop new capabilities and upgrade some of the old capabilities over the next five years. Recent upgrades/enhancements/new capabilities in the INS Facility include:

• Cryo TEM - this new capability adds major transmission electron microscopy (TEM) capabilities for life sciences: three- dimensional reconstruction by TEM tomography will literally bring a new dimension into all structural analyses. This state-of-the-art technology is based on acquirement of tilt series of a specimen and its software reconstruction and rendering. The TEM cryo stage will allow visualization of cells and macromolecules in their native hydrated state by physical fixation within ultra-thin, vitrified ice layer. This new instrument provides a vital tool for morphological and functional studies in the area of cell biology and proteomics.
• Ultrahigh Vacuum Scanning Probe Microscopy (SPM) Capability - EMSL recently developed an Ultra High Vacuum (UHV) system with Non-Contact (NC) Atomic Force Microscope (AFM)/Scanning Tunneling Microscope (STM) capability along with several surface science techniques to obtain single site chemical information.
• Dual FIB/SEM Capability - Focused ion beam/scanning electron microscope (FIB/SEM) systems are innovative instruments for nanoscience and engineering research that perform versatile tasks from prototyping novel architectures to materials analysis. The FIB has revolutionized micromachining for the semiconductor device industry and is becoming a powerful tool in precise, cost-effective sample preparation of materials for TEM characterization. We will utilize the full capability for nanomaterials synthesis and modification. This capability will include a cryo stage so that biological samples can be successfully handled. This capability is expected to be available for users by March 2007.
• TOF SIMS Capability - both biological systems and atmospheric chemistry will be enhanced by a new generation of Time of Flight Secondary Ion Mass Spectrometer capability that allows better depth resolution and extraction of information from environmentally unstable materials (biological and aerosol samples). Advances in the ion beam analysis capability will allow increased time resolution for atmospheric chemical analysis. This capability is expected to be available for users in summer 2007.
• Catalytic Reaction Chamber for Quantum XPS system - This system will add a new capability to Quantum and the planned capability will allow powder catalysis samples to be processed (heated in vacuum or in atmospheric pressure gas) before analysis by XPS. This allows catalysts to be processed and analyzed without destroying information and minimizing changes to oxidation state. The same system will also have a higher pressure reaction chamber where test catalytic reactions can be conducted and samples entered into the XPS system, again without air exposure. This capability is expected to be available for users in summer 2007.
• Energy Filtered Electron Capabilties: We have developed capabilities for electron energy-loss spectroscopy to enable identification of light elements, energy filtered imaging with energy specified electrons: elastic scattering, plasmon-loss, and core-loss electron and energy filtered electron diffraction in our high resolution TEM.
• Heavy Ion Elastic Recoil Detection Analysis (HIERDA): The scientific objective of this project is to develop high-resolution Time of Flight (ToF) Elastic Recoil Detection Analysis (ERDA) capability at the EMSL accelerator facility for simultaneous detection and absolute quantification of H, C, N, O, and other light elements as a function of depth in complex matrices containing heavy elements. Since this is a powerful method to investigate elemental concentrations in the surface regions, this capability can be effectively applied in many different areas including characterization of oxide thin films for optical, magnetic and catalysis applications and characterization of environmental and biological samples, which are the major focus areas at EMSL.

EMSL's Response

EMSL Chief Scientists, senior scientists at PNNL and users are currently working on a recapitalization plan for EMSL. The Department of Energy's Office of Biological and Environmental Research is planning to provide substantial capital funding to develop new capabilities and upgrade some of the old capabilities over the next five years. Recent upgrades/enhancements/new capabilities in the CPCS Facility include:

• Zeiss Incubator and QuadView System for cell growth control and protein imaging
• PEEM Cooling and Sample Transport Mechanism for studying catalytic and photocatalytic processes
• High Sensitivity Interface for PTR-MS to extend detection limits for VOCs and allow real time measurement of trace organic gases
• High Resolution TOF-MS and Light Scattering Module for rapid single particle measurements of complex organic species in particulates
• High-Resolution Mass Spectrometer LTQ-Orbitrap and support instrumentation for chemical characterization of organic aerosols
• SPLAT II - Second Generation of Single-Particle Laser Ablation Time-of-Flight Mass Spectrometer, which can measure the size and chemical composition of individual aerosol particles down to 50 nm with extremely high sensitivity and unprecedented precision.

EMSL's Response

The facility is in high demand and there is a need for more analyses/higher throughput in the HPMSF. The most straight forward way to address would be to increase the number of systems and space available 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. The rate at which these changes can be accomplished is constrained by the funding available.

EMSL's Response

EMSL Chief Scientists, senior scientists at PNNL and users are currently working on a recapitalization plan for EMSL. The Department of Energy's Office of Biological and Environmental Research is planning to provide substantial capital funding to develop new capabilities and upgrade some of the old capabilities over the next five years. Recent upgrades/enhancements/new capabilities in the HPMSF Facility include:

• Ion Mobility-MS at low pressures, planar FAIMS, ICR cell
• New Orbitrap and Finnagan TSQ Quantum delivered
• High pressure LC at 50 μm id capillary with 3 μm particles
• As it has since its inception, the Proteomics Research Information Storage and Management (PRISM) system has continued to increase in both size and capability to keep pace with both the EMSL proteomics facility and the proteomics field itself. Additional storage servers were added to bring the online capacity of PRISM itself up to 20 terabytes (there are approximately 70 terabytes currently in the EMSL NWFS archive). 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 over 200.
• The "OrbitrapTM" spectrometer that was acquired in September of 2005 has been fully integrated into the facility. This instrument adds to the growing capability to acquire both MS/MS data and accurate mass data more efficiently providing additional capability for working on new biological systems. A second "OrbitrapTM" mass spectrometer will be delivered to the facility in September.
• A 12-tesla system designed for intact protein work has been applied to three separate user projects making significant contributions to each. The development of electron capture dissociation (ETD) for the identification of post translational modifications (PTM) will continue this year.
• A new triple quadrupole mass spectrometer was delivered to the facility in September 2006. This instrument provides greater dynamic range than ion trap mass spectrometers and will be essential in the validation of candidate biomarkers that are discovered with our global proteomics analyses.
• 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. A demonstration of LC-MS analyses using these pumps has been demonstrated in the past by our group but these systems are the first which are configured to use them in a fully automated fashion on the proteomics production line. Both of these systems currently use Valco valves capable of 15,000 psi but can be reconfigured to utilize 20,000 psi valves when it can be demonstrated that those valves can operate robustly.

EMSL's Response

The EMSL website has been updated 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.

EMSL's Response

One of EMSL's goals is safety. EMSL strives to balance effective training while adhering to DOE and Lab training requirements.