William R. Wiley Environmental Molecular Sciences Laboratory (EMSL)

William R. Wiley Environmental Molecular Sciences Laboratory (EMSL)

The Environmental Molecular Sciences Laboratory (EMSL), at Pacific Northwest National Laboratory, began operations in 1997, and currently provides the scientific user community with a broad range of premier instruments for molecular to mesoscale research, as well as production high performance computing (HPC) and optimized computational codes for molecular to continuum-scale modeling and simulation. With more than 50 premier instruments, individual non-proprietary and proprietary users and user teams from academia, national laboratories, other federal agencies, and industry can use multiple capabilities and iterate between experiment and simulation to obtain a mechanistic understanding of physical, chemical and biological processes and interactions that underpin larger-scale biological, environmental, climate, and energy challenges. To maintain capabilities at state-of-the-art, EMSL not only obtains new capabilities, but some EMSL scientists design and build new instruments and enhance existing instruments. EMSL scientists also create, make use of, and enhance open-source computational codes to meet the evolving research needs of the scientific community.

DOE Mission Relevance

EMSL is strategically aligned with the overall mission of the U.S. Department of Energy to ensure America’s security and prosperity by addressing its energy, environmental and nuclear challenges through transformative science and technology solutions. Within DOE, EMSL also addresses the missions and strategic directions of the DOE Office of the Undersecretary for Science and Energy, the DOE Office of Science and the DOE Office of Biological and Environmental Research.

 For BER, EMSL seeks to enable users to obtain a systems-level understanding of how genomic information is translated into functional capabilities of living systems to enable prediction or redesign of metabolic processes for sustainable bioenergy and environmental purposes, and to understand fundamental molecular-scale properties of natural and anthropogenic inputs to improve predictions of key environmental and atmospheric processes.

These scientific directions are organized under EMSL’s four science themes: Atmospheric Aerosol Systems (AAS), Biological Dynamics and Design (BDD), Energy Materials and Processes (EMP), and Terrestrial and Subsurface Ecosystems (TSE). The EMSL science themes build on EMSL’s scientific expertise and guide planning for future capabilities. Each science theme has a specific leadership area of focus and is led by an EMSL scientist.


EMSL has three categories of proposal types: 1) General, 2) Scientific Partner, and 3) Annual. All proposals are peer reviewed, and proposals are submitted through the EMSL user portal.

Potential users may submit a General proposal for any of the EMSL User Program capabilities at any time. Time awards are made throughout the year.

EMSL accepts Letters of Intent for Scientific Partner proposals at any time. Scientific partner proposals can be submitted by a single user or groups of users who are interested in partnering with staff at EMSL to improve an existing capability or develop and build new or unique capabilities that enhance EMSL’s user program. Awards are made throughout the year.

EMSL’s Annual proposal call is usually issued in mid-December and may include options to:  a) Focus on Science Theme topics, b) Team on large Research Campaigns, or c) Use multiple facilities (e.g., the FICUS – Facilities Integrating Collaborations for User Science) call.

Proposals are encouraged that couple experiments with theory, modeling or simulation, and access is typically granted beginning October 1 following award decisions. Science Theme proposals are responsive to one or more of the four EMSL science themes. Research Campaigns are solicited in specific areas and not only combine experimental and computational research efforts but also multiple methods and approaches. These proposals are most often larger in size than most Science Theme user projects and involve partnerships between external users and EMSL staff to combine measurements, computation and/or data in ways not previously possible. FICUS proposals enable applicants to combine the power of genomics and molecular characterization under one effort. For FICUS proposals, Letters of Intent are required. These are reviewed by staff from both EMSL and JGI for DOE mission relevance, and invited proposals are peer reviewed by a joint panel of reviewers identified by EMSL and JGI.

Capabilities and Applications

EMSL’s capabilities are organized into eight groups: 1) Cell Isolation and Systems Analysis, 2) Deposition and Microfabrication, 3) Mass Spectrometry, 4) Microscopy, and 5) Molecular Science Computing. 6) NMR and EPR, 7) Spectroscopy and Diffraction, and 8) Subsurface Flow and Transport.

Some capabilities can be remotely operated/used from another institution or location (e.g, the HPC system and the mass spectrometers) and run 24/7, but most of the instruments require staff support and are only available 10h/day, five days/week.  Some capabilities are used to synthesize or analyze unique materials or surfaces.  A few capabilities can be deployed outside the building in “field campaigns.” Some external users collaborate with EMSL staff to develop modules or upgrade the open-source NWChem code or other software products.

In late 2011, EMSL opened the Quiet Wing, a unique research environment that houses an integrated suite of ultrasensitive microscopy instruments. The Quiet Wing protects against acoustic noise, floor vibrations, air flow, temperature fluctuation and electromagnetic interference, and enables users to apply these instruments for studying fundamental, atomic-level reactions relevant to catalysis, energy storage, subsurface science and microbial and plant biology.

In early 2013, EMSL opened the Radiochemistry Annex. The Annex includes laboratory space that is designed for studying contaminated environmental materials and examining radionuclides and chemical signatures, and it features NMR capabilities as well as several types of surface science analysis capabilities.

Data Sharing Policy

Allocations of time on EMSL’s capabilities are contingent on adherence to EMSL’s terms and conditions as well as EMSL’s data management and release policy.


BER is committed to managing the operations of EMSL to the highest standards of overall performance using merit evaluation with independent peer review. The expectation is that EMSL will achieve an average operation time of greater than or equal to 98% of the total scheduled annual operating time. The EMSL Operating Hoursare tracked quarterly.

More Information about the Program and Its Accomplishments

The EMSL User Program seeks to attract new, highly qualified users and honor their major contributions through a variety of Fellowships and Awards, including extended user visits and the ability to play a role in shaping EMSL’s future directions.

User science highlights and publications as well as EMSL activities and news are made available through a variety of communications mechanisms on the EMSL web site: EMSL Newsletter (The Molecular Bond), Workshop Reports, Journal Covers and Research Publications and Science Highlights, General News and Feature Stories. The EMSL Virtual Tour provides additional insight into some of the premier instruments and laboratories in EMSL.

To showcase the science, people and capabilities that constitute a problem-solving environment, EMSL uses a variety of multimedia tools, including an RSS feed, videos and animations, images, print products and social networking capabilities including Facebook, Twitter, YouTube, Flickr, and LinkedIn.

Program Manager

Mr. Paul E. Bayer
Climate and Environmental Sciences Division, SC-23.1
U.S. Department of Energy, GTN Bldg.
1000 Independence Avenue, SW
Washington, DC 20585-1290
Phone: (301) 903-5324
Fax: (301) 903-8519
E-mail: paul.bayer@science.doe.gov