Pacific Northwest National Laboratory: User Guide

Pacific Northwest National Laboratory (PNNL) is a multi-program national laboratory operated for the United States Department of Energy (DOE) by Battelle Memorial Institute. For academic, national laboratory, and industrial researchers, PNNL serves as a gateway to national scientific user facilities, high-performance computing resources, and specialized instrumentation. External research teams access these advanced capabilities through competitive, merit-based proposal calls funded by the DOE Office of Science.

What it is

Pacific Northwest National Laboratory is one of seventeen DOE national laboratories, with primary stewardship under the DOE Office of Science. Founded in 1965 in Richland, Washington, PNNL conducts fundamental and applied research across environmental and biological sciences, clean energy, chemical transformations, and national security.

In research practice, PNNL is recognized for operating premier user facilities and collaborative infrastructure that no single university laboratory can maintain independently. Foremost among these is the Environmental Molecular Sciences Laboratory (EMSL), an Office of Science user facility funded through the Biological and Environmental Research (BER) program. PNNL also plays an operational leadership role in the multi-laboratory Atmospheric Radiation Measurement (ARM) user facility, maintaining observatories and aerial instrumentation deployed worldwide.

Who runs it and what it covers

PNNL is managed and operated by Battelle Memorial Institute under a management and operating (M&O) contract with the DOE. The laboratory is headquartered on its main campus in Richland, Washington, with specialized research centers in Seattle, Portland, the Marine and Coastal Research Laboratory in Sequim, Washington, and an office in Washington, D.C.

PNNL user facility programs cover fundamental scientific investigations in several core research domains:

Environmental Molecular Science: Molecular-level investigations of biogeochemical cycles, soil-microbe-plant interactions, mineral weathering, and contaminant fate and transport hosted at EMSL.
Biological Systems and Omics: High-throughput proteomics, metabolomics, lipidomics, transcriptomics, and structural biology examining microbial and plant communities.
Atmospheric and Earth Systems: Aerosol chemistry, cloud formation physics, and climate modeling supported by EMSL instrumentation and ARM field observatories.
Materials Characterization and Interfaces: In situ surface spectroscopy, high-resolution electron microscopy, atom probe tomography, and nuclear magnetic resonance (NMR) spectroscopy.
Computing and Advanced Analytics: High-performance computational modeling, multi-omics data integration, and molecular simulation workflows.

How to search or use it

External researchers access PNNL user facilities through structured proposal calls. For EMSL, all project proposals, peer reviews, and resource tracking are administered through the online NEXUS User Portal. The submission and access lifecycle consists of seven sequential steps:

Register in the NEXUS User Portal: The prospective principal investigator and all participating co-investigators must establish individual accounts in the EMSL User Portal (NEXUS). Each user must link an official ORCID iD to their user profile before they can be added to an active proposal form.
Consult EMSL Science Area Leads: Before drafting a narrative, applicants should contact the relevant Integrated Research Platform (IRP) lead or scientific staff. Facility staff evaluate whether the experimental design matches instrument capabilities and estimate instrument hours and sample throughput.
Review Open Calls and Submit a Letter of Intent: EMSL issues several distinct proposal calls annually, including Large-Scale Research calls, Exploratory Research calls, and joint calls such as the Facilities Integrating Collaborations for User Science (FICUS) program conducted with the Joint Genome Institute (JGI). For major calls, applicants must first submit a concise Letter of Intent (LOI) through NEXUS outlining project objectives.
Draft the Proposal Narrative: Once invited, investigators download the official Proposed Research template from the portal. The narrative must adhere to page limits and cover specific aims, scientific background, detailed work plan, potential impact on DOE missions, and biosketches for key investigators.
Specify Requested Resources in NEXUS: Within the portal interface, the applicant specifies the exact instruments requested, estimated machine runtime, sample preparation requirements, and computing allocations needed to achieve project milestones.
Execute an Institutional User Agreement: Before experimental work or sample delivery begins, the investigator’s home institution must execute a Non-Proprietary User Agreement (NPUA) with Battelle Memorial Institute. This five-year umbrella agreement governs intellectual property, liability, and open publication rights across all current and future projects from that institution.
Complete Onboarding and Safety Training: Upon proposal award, all named team members must complete facility safety registration, acknowledge terms of access, and agree to DOE open science and data management dissemination requirements.

Strengths and limits

Understanding the operational strengths and administrative boundaries of PNNL user facilities helps research groups design realistic experimental timelines:

No Facility User Fees for Open Science: Non-proprietary research accepted through peer-reviewed calls is fully funded by the DOE Office of Science, allowing researchers to use multi-million-dollar instrumentation at no cost to their home grants, provided findings are shared through open access publications.
Integrated Interdisciplinary Expertise: Facility access includes direct technical collaboration with resident instrument scientists and computational specialists who assist in data collection and advanced analysis.
Collaborative Joint Calls: Through the FICUS program, researchers submit a single unified proposal to access both EMSL molecular facilities and partner user facilities, eliminating duplicate administrative burdens.
Competitive Selection: Proposal acceptance is competitive and governed by rigorous scientific peer review based on scientific merit, feasibility, and alignment with DOE BER program priorities.
Institutional Agreement Dependencies: Project start dates depend on legal execution of the institutional NPUA; delays in institutional contract review can postpone experimental work.
Strict Publication Obligations: Non-proprietary access requires full disclosure of research methodologies and open dissemination of resulting data; projects requiring commercial confidentiality must pursue proprietary agreements under full cost-recovery fees.

Alternatives

While PNNL and EMSL specialize in molecular environmental science and biogeochemistry, external researchers requiring complementary physical characterization, beamline synchrotron radiation, or specialized materials synthesis can access other national scientific user facilities across the DOE complex:

Facility and Host Laboratory	Managing Contractor	Primary Scientific Focus	Core Specialized Capabilities	Access Model
Environmental Molecular Sciences Laboratory (EMSL) Pacific Northwest National Laboratory	Battelle Memorial Institute	Environmental molecular science, biogeochemistry, biological systems	High-field NMR, ultra-high-resolution mass spectrometry, cryo-EM, atom probe tomography	Competitive peer review via NEXUS portal; non-proprietary access at no cost
Advanced Photon Source (APS) Argonne National Laboratory	UChicago Argonne, LLC	High-energy synchrotron X-ray research, structural biology, materials science	High-brilliance hard X-ray beamlines, time-resolved scattering, macromolecular crystallography	General user proposals via Universal Proposal System; non-proprietary at no cost
Center for Nanophase Materials Sciences (CNMS) & SNS Oak Ridge National Laboratory	UT-Battelle, LLC	Nanoscale materials synthesis, functional properties, neutron scattering	Nanofabrication cleanrooms, scanning probe microscopy, pulsed spallation neutron beamlines	Semiannual call for proposals via IPTS portal; non-proprietary at no cost
The Molecular Foundry & NERSC Lawrence Berkeley National Laboratory	University of California	Nanoscale synthesis, theory, multi-disciplinary nanotechnology, supercomputing	Inorganic and organic nanofabrication, aberration-corrected TEM, high-performance computing	Semiannual peer-reviewed proposal submissions; non-proprietary at no cost

Frequently asked questions

Who is eligible to submit a user proposal to PNNL user facilities?

Researchers from academic institutions, non-profit research organizations, national laboratories, and commercial enterprises worldwide are eligible to submit proposals. Investigators do not need to be current DOE grant recipients to apply for user facility access.

What is the difference between non-proprietary and proprietary access at PNNL?

Non-proprietary access is awarded through competitive peer review at no charge to the investigator, provided all results and datasets are published openly in the peer-reviewed scientific literature. Proprietary access is available for commercial or confidential investigations where results remain private; proprietary users pay full-cost recovery rates for instrument runtime and staff assistance.

What is an EMSL Non-Proprietary User Agreement?

The Non-Proprietary User Agreement (NPUA) is a formal bilateral contract executed between Battelle Memorial Institute (operating PNNL) and the user’s home institution. It establishes standard terms regarding liability, intellectual property, and data publication rights, serving as a five-year umbrella agreement that covers all investigators from that institution.

How far in advance must researchers submit EMSL proposals?

EMSL proposal calls operate on structured annual or biannual cycles. Major calls, including Large-Scale and FICUS proposals, typically require submission three to six months prior to the planned start of the project year to allow time for technical feasibility screening, expert peer review, and institutional agreement verification.

Sources

Pacific Northwest National Laboratory, “About PNNL” and organizational profile, https://www.pnnl.gov/ (checked 2026-11-07).
Environmental Molecular Sciences Laboratory, “User Program Overview and Scientific Capabilities,” https://www.emsl.pnnl.gov/ (checked 2026-11-07).
Environmental Molecular Sciences Laboratory, “Proposals and NEXUS User Portal Guide,” https://www.emsl.pnnl.gov/proposals (checked 2026-11-07).
Atmospheric Radiation Measurement (ARM) User Facility, “Observatories and Capabilities Overview,” https://www.arm.gov/ (checked 2026-11-07).