# Presentation: 221810

## William R. WileyEnvironmental MolecularSciences Laboratory

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

## National User Facility

- 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

**National User Facility**

**William R. Wiley’s Vision:**
- An innovative multipurpose user facility providing *“synergism between the physical, mathematical, and life sciences.”*

**Dr. William R. Wiley**
- PNNL Director
- 1984-1994

## EMSL User Demographics

**EMSL User Demographics**

**United States Use **FY98-03

*Scientists around the world can access the resources at EMSL through a peer-reviewed-proposal system. *

**Proposal Funding Agencies**

**U.S. DOE**

**U.S. non-DOE Govt. Agencies**

**Other**

**U.S. Universities**
**& Industry**

**Foreign**

*1348 Users in FY04*

## 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

**Extraordinary Tools & Staff**

## 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@pnl.gov](mailto:roy.gephardt@pnl.gov)__)_

**Chemistry & Physics of Complex Systems Facility**

## 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@pnl.gov](mailto:nancy.foster@pnl.gov)__)_

**Environmental Spectroscopy & Biogeochemistry**

## 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@pnl.gov](mailto:david.hoyt@pnl.gov)__)_

**High Field Magnetic Resonance Facility**

## Virtual NMR Access at HFMRF

- 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.

**4:00 – 5:00 Tuesday   NMR Tutorial: Remote Access**

_**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.

## Prediciting and understanding NMR

**properties**

- Collaboration with experimentalists
- Herman Cho (NMR)
- John Abrefah a.o. (Synthesis)

_**Uranyl compounds**_

***Record anisotropy predicted and measured***

**Bert de Jong**

_**Temperature effects **_
_**in pertechnetates**_

***NH******4******TcO******4****** crystal***

***Solvated***

## 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@pnl.gov](mailto:harold.udseth@pnl.gov)_)

**High Performance Mass Spectrometry Facility**

## 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.

- Time to analyze offsite:  			1 week
- Time to analyze onsite: 			48 hours
- Time to analyze onsite with smart storage:  	2 hours

**High Throughput Proteomics **

## 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*!

## Create information about the proteins in biological samples using mass spectrometer data

**     ****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**

**Create information about the proteins in biological samples using mass spectrometer data**

## 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@pnl.gov](mailto:theva@pnl.gov)_)

**Interfacial & Nanoscale Science Facility**

## 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@pnl.gov](mailto:theresa.windus@pnl.gov)_)
-                     Kevin Regimbal (_[kevin.regimbal@pnl.gov](mailto:kevin.regimbal@pnl.gov)_)

**Molecular Science Computing Facility**

## 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!**

## 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 **

## Collaboration Network

*DOE Science Grid*

## 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

**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

*Three year timeframe for success.*

## 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