William R. Wiley Environmental Molecular Sciences Laboratory

1
William R. WileyEnvironmental MolecularSciences
Laboratory

• Theresa L. Windus
• Technical lead for Molecular Sciences Software
  Group and the Visualization and User Services
  Group
• December 2, 2004

2
National User Facility
William R. Wileys Vision An innovative
multipurpose user facility providing synergism
between the physical, mathematical, and life
sciences.
Dr. William R. Wiley PNNL Director 1984-1994

• EMSLs Mission
• To provide advanced experimental and
  computational resources to scientists engaged in
  fundamental research on the physical, chemical,
  and biological processes that underpin
  environmental and other critical scientific issues

• Signature Characteristics
• Integration of theory, modeling, and simulation
  with experiment
• Multidisciplinary teams and collaborative mode of
  operation to solve major scientific problems of
  interest to DOE and the nation
• Teams who develop extraordinary tools and
  methodologies

3
EMSL User Demographics
Scientists around the world can access the
resources at EMSL through a peer-reviewed-proposal
system.
1348 Users in FY04
U.S. non-DOE Govt. Agencies
Other
Foreign
U.S. Universities Industry

• United States Use FY98-03

U.S. DOE
Proposal Funding Agencies
4
Extraordinary Tools Staff

• EMSL Facilities
• Chemistry Physics of Complex Systems
• Environmental Spectroscopy Biogeochemistry
• High Field Magnetic Resonance
• High Performance Mass Spectrometry
• Interfacial Nanoscale Science
• Molecular Science Computing

• Support
• Computer and Network Services
• Instrument Development Laboratory
• User Services and Outreach

5
Chemistry Physics of Complex Systems Facility
fosters fundamental research in the natural
sciences to provide the basis for new and
improved energy technologies and for
understanding and mitigating the environmental
impacts of energy use and contaminant releases.

• Instrumentation
• High-intensity and high-sensitivity surface
  chemistry systems
• Systems for thermal and nonthermal interfacial
  chemistry research
• Single-molecule and non-linear imaging microscopy
  systems
• Systems for molecular-scale synthesis and
  characterization of model materials
• Electron microbeam for live-cell radiation
  biology research
• Environmental scanning electron microscope

CONTACT Roy Gephardt (roy.gephardt_at_pnl.gov)
6
Environmental Spectroscopy Biogeochemistry
is involved in experimental and modeling studies
of chemical phenomena and mechanisms on mineral
and microbe surfaces and on complex heterogeneous
environmental materials from soils, sediments,
and groundwater zones.

• Instrumentation
• Laser-induced fluorescence, nonlinear,
  photoacoustic, Raman, and ultraviolet-visible
  spectrometers
• Near-mid-far Fourier transform infrared
  spectrometer/ microscope
• Mossbauer and electron paramagnetic resonance
  spectrometers
• Scanning tunneling and atomic force microscopes
• Multi-fluid flow/transport cells
• Geochemistry molecular modeling software
• General Analytical Equipment

CONTACT Nancy Foster-Mills (nancy.foster_at_pnl.gov)
7
High Field Magnetic Resonance Facility
provides state-of-the-art nuclear magnetic
resonance (NMR) and electron paramagnetic
resonance (EPR) instrumentation for determining
molecular structures that impact environmental
remediation and biological health effects.

• Instrumentation
• Twelve NMR spectrometers (ranging from 300 to 900
  MHz) and one pulsed EPR spectrometer, with
  capabilities in high-field liquid-state,
  solid-state and micro-imaging techniques
• Combined optical and magnetic resonance
  microscope
• Low-temperature probes for metallo-protein
  chemistry and structure
• Virtual NMR capability to enable use and
  collaboration with EMSL scientists by remote users

CONTACT David Hoyt (david.hoyt_at_pnl.gov)
8
Virtual NMR Access at HFMRF
400 500 Tuesday NMR Tutorial Remote Access

• Secure, remote operation of spectrometers via
  internet
• Live consultations using collaboration tools
• Reduced travel costs and more flexible scheduling
• 20 of facility users elect to use remote access
  tools.

Publications Hoyt, D.W., et al. (2004)
Expanding your Laboratory by Accessing
Collaboratory Resources. Analytical and
Bioanalytical Chemistry 378 (1) 1408-1410.
Chin, G., et al. (2002) Social Networks in the
Virtual Science Laboratory. Communication of the
Association for Computing Machinery 45 (8)
87-92. Keating KA, et al. (2000) Development
and Use of a Virtual NMR Facility, J. Mag. Res.,
143 p. 172-183.
9
Prediciting and understanding NMR properties
Bert de Jong
Uranyl compounds
Solvated
NH4TcO4 crystal
Temperature effects in pertechnetates
Record anisotropy predicted and measured
Collaboration with experimentalists Herman Cho
(NMR) John Abrefah a.o. (Synthesis)
10
High Performance Mass Spectrometry Facility
provides cutting-edge mass spectrometry
capabilities that focus on global proteomics
research and allow visualization and analyses of
proteins of a cell in greater detail.

• Instrumentation
• Fourier transform ion cyclotron resonance mass
  spectrometers, ranging from 7, 9.4, to 11.5
  tesla, with electrospray ionization sources
• Sciex QSTARR quadrupole time-of-flight mass
  spectrometer
• Five Finnigan LCQ ion trap spectrometers
• Finnigan TSQ 7000 triple quadrupole spectrometer
• Ultra-high pressure liquid chromatographs

CONTACT Harold Udseth (harold.udseth_at_pnl.gov)
11
High Throughput Proteomics
1 Experiment per hour 5000 spectra per
experiment 4 MByte per spectrum Per
instrument 20 Gbytes per hour 480 Gbytes per
day These are estimates based on today's
technologies.
9.4 Tesla High Throughput Mass Spectrometer
Time to analyze offsite 1 week Time to
analyze onsite 48 hours Time to analyze
onsite with smart storage 2 hours
12
Peptide Identification from Spectral Data

• Strand of amino acids peptide
• Peptides are small pieces of proteins
• Proteins perform virtually all functions of cells

• THE EXPERIMENTAL PROCESS
• Collections of proteins are sent to PNNL
• Proteins are separated and broken into peptides
  and then into peptide fragments by energy beam
• Mass of all the fragments (spectrum) is measured

• IDENTIFYING THE FRAGMENTS WITH POLYGRAPH
• Scan database of known proteins for candidates
• Generate hypothetical spectrum of each candidate
  
• Compare each candidate spectrum to experimental
  spectrum and determine the best match
• POLYGRAPH can now identify thousands of proteins
  by analyzing their spectra from among hundreds
  of thousands of candidates in a matter of minutes!

13
Create information about the proteins in
biological samples using mass spectrometer data
36 Organisms 129 Research
Campaigns 10,950 Prepared Samples 22,341 MS
Instrument Runs 76,543 Automated Analyses 30
TB Data / results files 210 Databases 350
GB Data in databases
14
Interfacial Nanoscale Science Facility
is involved in researching a variety of oxide
mineral films and interfaces, nanoscale
materials, electronic and catalysis materials,
microfabrication and microanalytical separations,
and sensing.

• Instrumentation
• Molecular beam epitaxy, chemical vapor and
  sputter deposition
• State-of-the-art surface science tools
• High-resolution electron microscopes and x-ray
  diffraction instrumentation
• Ultra-high vacuum, liquid, and ambient
  environment scanning probes
• Gas chromatography, NOx analyzer, and RX100
  testing and characterizing system
• Clean-room capabilities and research tools for
  microfabrication

CONTACT Theva Thevuthasan (theva_at_pnl.gov)
15
Molecular Science Computing Facility
provides a high-performance computer with Intel
Itanium2 processors, Quadrics interconnect, and
HP RX2600 nodes, which supports a wide range of
environmental molecular science.

• Instrumentation
• Allocated to users accomplishing peer-reviewed
  Grand Challenge science in support of DOE
  missions
• 1,976-processor system in 978 nodes, with 11.8
  Teraflop peak, 6.8 Terabytes of memory and 500
  Terabytes of disk
• 250 TB of archival storage
• Silicon Graphics 3400 graphics and visualization
  server with integrated video and audio editing
  system
• Molecular Science Software Suite, including
  NWChem, Extensible Computational Chemistry
  Environment, and ParSoft

CONTACT Theresa Windus (theresa.windus_at_pnl.gov)
Kevin Regimbal
(kevin.regimbal_at_pnl.gov)
16
Extensible Computational Chemistry Environment -
Ecce

• a comprehensive problem solving environment (PSE)
  for molecular modeling and simulation. Key
  components include
• common graphical user interfaces
• scientific modeling management
• seamless transfer of information between
  applications
• persistent data storage
• integrated scientific data management
• tools for ensuring efficient use of computing
  resources across a distributed network
• visualization of multi-dimensional data structures

Linux port is now available!
17
Collaboratory for Multi-scale Chemical Science

• Impact of chemical science relies upon flow of
  information across physical scales
• Data from smaller scales supports models at
  larger scales
• Critical science lies at scale interfaces
• Molecular properties, transport
• Mechanism validation, reduction
• Chemistry fluid interactions
• The pedigree of information matters
• The propagation of data pedigree across scales is
  difficult
• Validation and data reliability is often a
  post-publication process
• Multi-scale science faces barriers
• Normal publication route is slow
• Numerous sub-disciplines employ different
  applications, formats, models
• Centers of excellence are geographically
  distributed

18
Collaboration Network
DOE Science Grid
19
EMSL Grand Challenges

• Biogeochemistry
• Jim Fredrickson and John Zachara, PNNL
• Electron transfer processes in microbial-mineral
  environments
• Crosses at least 4 of the facilities additional
  external instrumentation

Three year timeframe for success.

• Biology
• Himadri B. Pakrasi, Department of Biology,
  Washington University
• Systems Analysis of the Dynamics of Membrane
  Architecture, Composition and Function in
  Cyanobacteria
• In the Roadmapping phase, but anticipated to use
  at least 4 of the facilities additional
  external instrumentation

20
Issues

• Complexity
• In a facility
• Across facilities (experiment and computation for
  example)
• Proprietary formats
• MANY formats
• Must be able to trust data
• Errors must be quantified
• All provenance must be exposed
• Data Publication Policy (Social issues)
• Chicken and egg problem
• Need next level
• Visualization that allows exploration of
  information ex. comparisons, merging and
  linkages
• Knowledge is really what we are after - A set of
  transparent and scalable tools, middleware, and
  services for the creation, analysis,
  dissemination, evaluation, and use of data,
  information, and knowledge by individuals,
  groups, and communities A digital place for
  performing all aspects of science
• Advisor capabilities ranging from novice to
  expert
• Additional remote steering of instrumentation
• Facilitate publication