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Call for Exploratory Research Proposals, FY 2027

Call opens June 1, 2026

Timeline

Proposal Call Opens

Proposals must employ one or more of the capabilities highlighted below to advance understanding in EMSL's three Science Areas (Functional and Systems Biology; Environmental Transformations and Interactions; and Computing, Analytics, and Modeling). As a guide, at least 30% of the research effort should focus on the highlighted capabilities listed below in terms of requested hours or samples analyzed. Other EMSL Instruments and Resources may be used to supplement your research plan. Interested users are encouraged to work closely with EMSL scientists when developing the letter of intent (LOI) and subsequent proposal.

We also encourage submissions that propose to use highlighted capabilities to investigate biogeochemical transformations, organisms, and cellular pathways central to the understanding of cycling, acquisition, concentration, and separation of critical minerals and materials (CMMs) in natural and artificial/anthropogenic environments as well as the cleanup and remediation of industrial waste streams. The latter include but are not limited to sediments, soils, and bioreactors, as well as process brines from geothermal, oil, and natural gas wells. Review a list of the Department of Energy (DOE) CMMs.

An LOI is required before submitting a proposal, and full proposals may only be submitted by invitation. The most recent versions of the EMSL templates for the LOI and full proposal must be downloaded and completed for proposals to be considered for review. EMSL will use dual anonymous peer review for this call. Full proposals must be anonymized to enable dual anonymous peer review. Successful proposals will include well-described research plans that can be completed within the 13-month project period.

Exploratory proposals are approximately a third of the duration and budget of a full Facilities Integrating Collaborations for User Science (FICUS) proposal. To help accomplish research goals during the 13-month time frame, we encourage applicants to focus the research narrative on one or possibly two objectives. For proposals that are awarded, we strongly encourage applicants to be ready to ship samples as close as possible to the project start date. All samples must be submitted to EMSL by June 1, 2027, unless an exception is made by the project manager and host Integrated Research Platform (IRP) leader.

Contacts 

For questions about the proposal submission process, please email EMSL User Program Services. 

For technical help with NEXUS, please email NEXUS Support. 

For scientific questions, contact the EMSL staff identified in the focus topics or highlighted capabilities of the proposal call. 

 

Highlighted capabilities
  • Single-cell proteomic and/or transcriptomic workflows (nanoPOTS/nanoSPLIT/splitSEQ) to quantitatively characterize phenotypic heterogeneity and spatial organization and to delineate cell-cell interactions underpinning the functioning of multicellular and/or multispecies microbial systems. (Contacts: Paul Piehowski and Alex Beliaev)   
     
  • High-fidelity, high-resolution imaging, chemical and spectroscopic analyses, and spatially resolved omics that deepen understanding of the mechanisms governing microbe-metals interactions central to the recovery of CMMs and products of economic value. Of particular interest are proposals that leverage EMSL's advanced analytical capabilities to explore biological pathways, which include but are not limited to catabolic, biosynthetic, and redox-mediated reactions, and the organisms and microbiomes participating in critical material transformations, transport, sequestration, and acquisition. (Contacts: James Evans, Paul Piehowski, and Alex Beliaev)   
     
  • High-throughput microbial phenotyping workflows integrating EMSL's capabilities for genomic library generation, including random mutagenesis (e.g., ARTP, RB-TnSeq) and targeted genome engineering (e.g., CRISPR-based libraries), with automated colony picking, arrayed library management, and phenotypic screening via plate-based assays, growth profiling, and biosensor readouts. Proposals may focus on optimizing library quality and diversity, developing automated phenotyping pipelines for specific organisms or readouts, and/or coupling library-scale phenotypic data with AI/ML-enabled approaches to accelerate genotype-phenotype mapping in environmentally relevant microorganisms. (Contacts: Erin Bredeweg, Scott Baker, Todd Edwards, and Alex Beliaev)   
     
  • EMSL's cell-free expression pipeline and high-throughput mass spectrometry (MS) for parallel same-sample metabolite and protein quantification in low complexity samples to support the development of workflows enabling enzyme/pathway kinetic studies. (Contacts: James Evans, Paul Piehowski, and Alex Beliaev)   
     
  • Experimental (e.g., cell-free expression, cryogenic electron microscopy [cryo-EM], native mass spectrometry, etc.) and/or computational (e.g., OpenFold, Boltz-1, molecular dynamics, etc.) workflows to accelerate the annotation of uncharacterized proteins, with particular emphasis on gene-to-structure and function workflows of fungal proteins, or proteins and protein complexes associated new biotechnologies and bioproducts, or with CMM binding or transport. (Contact: James Evans)   
     
  • MS-based discovery analysis for mapping post-translational modification (PTM) analyses in microbial systems with an emphasis on the impact of protein phosphorylation, acetylation, and ubiquitination on metabolic pathway regulation, growth rates, and bioproduct production. (Contacts: Paul Piehowski and Marina Gritsenko)   
     
  • Identification and relative quantification of secondary metabolites, especially siderophores and other metal coordinating species, in complex biological systems such as microbial consortia using liquid chromatography (LC) coupled with dual high-resolution MS (hybrid Fourier transform Orbitrap Exploris 480-21 Tesla ion cyclotron resonance mass spectrometry [FTICR-MS]). (Contact: Will Kew)   
     
  • Chemical imaging of pore-scale processes and features, including nano-minerals, host phases, and molecular/structure mechanisms of incorporation or association with host phases, with nanoscale to microscale compositional, morphological, and chemical characterization. Potential methods include the following:   
     
    • Scanning/transmission electron microscopy (S/TEM) with electron energy loss spectroscopy (EELS), nanometer scale. (Contact: Chongmin Wang)   
       
    • Atomic probe tomography (APT), nanometer scale. (Contact: Danny Perea)   
       
    • Scanning electron microscopy (SEM) with energy-dispersive X-ray spectroscopy (EDS), micrometer to millimeter scale. (Contact: Odeta Qafoku)   
       
    • AI-guided particle classification for SEM-EDS data, with emphasis on Fe-oxide particles co-associated with CMM. (Contact: Shuttha Shuttanandan)   
       
    • Time-of-flight secondary ion mass spectrometry (ToF-SIMS) micrometer to millimeter scale. (Contact: Zihua Zhu)   
       
    • Nano secondary ion mass spectrometry (nano-SIMS) nanometer to micrometer scale. (Contact: Jeremy Bougoure)   
       
    • X-ray photoelectron spectroscopic imaging (XPS) micrometer to millimeter scale. (Contact: Shuttha Shutthanandan)   
       
    • Matrix-Assisted Laser Desorption Ionization (MALDI) mass spectrometry imaging micrometer to millimeter scale. (Contact: Dušan Veličković)   
       
    • Nanospray Desorption Electrospray Ionization Mass Spectrometry (nano-DESI) micrometer to millimeter scale. (Contact: Greg Vandergrift)   
       
  • Isotopic imaging and isotopic-tracing workflows for coupled biogeochemical processes:   
     
    • NanoSIMS imaging of isotope ratios, isotopic labels, and trace elements, including Rare Earth Elements (REEs) and CMMs with high sensitivity (ppm) at high spatial resolution (50 nm). This is highly relevant for stable isotope probing (next bullet point) and is well suited for observing the fate of isotopically enriched compounds added in plant-microbe-soil systems. (Contact: Jeremy Bougoure)   
       
    • Stable isotope probing and analysis that includes plant and microbial labeling for studying root-microbial interactions in the rhizosphere, coupled with isotope ratio mass spectrometry (IRMS) and laser ablation isotope ratio mass spectrometry (LA-IRMS) for in situ analysis on the scale of 10s of µm. (Contacts: Vimal Balasubramanian and Amir Ahkami)   
       
    • Micromodels to resolve processes at pore scale for deployment in laboratory and field systems. Use or advance Terraform platforms to address fundamental processes under anoxic, anaerobic conditions and across diverse sample types, including rock fragments and other geomaterials not previously studied with Terraforms.   
       
      • RhizoChips to reproduce pore networks obtained from X-ray computed tomography analysis of soils, including Molecular Observation Network (MONet) soil cores. Submitters planning to propose mineral-printed RhizoChip projects are strongly encouraged to contact Jayde Aufrecht prior to LOI submission to determine whether they are in scope for an exploratory call project. (Contact: Jayde Aufrecht)   
         
      • Bioprinted native soil microbiomes for downstream omics phenotyping and soil aggregate micromodels. (Contact: Arunima Bhattacharjee)   
         
      • Rapid, high-throughput analysis of metabolites resulting from plant-microbe and microbe-microbe interactions in soils and sediments (SubTap platform). Micromodels are suitable for microbial incubation and growth. (Contact: Arunima Bhattacharjee)   
         
    • Multi-omics measurements to elucidate processes occurring in soils and sediments across scales, from pore to regional. Proposals should include at least 2 of the following methods or data types:   
       
      • Fourier Transform Ion Cyclotron resonance (FT-ICR) mass spectrometry. High-mass-resolution measurements of natural organic matter and metabolites in pore water. (Contact: Emily Graham)   
         
      • Liquid Chromatography Mass Spectrometry (LC-MS). (Contact: Emily Graham)   
         
      • Pyrolysis Gas Chromatography-Mass Spectrometry (Py-GC-MS), which can characterize a wide variety of polymers and composite materials that confound traditional gas chromatography–mass spectrometry (GC-MS) methods. (Contact: Greg Vandergrift)   
         
      • Metaproteomics. (Contact: Emily Graham)   
         
      • X-ray Computed Tomography (X-CT), Non-destructive measurement of 3-D pore structure in soils and rock down to a 40-micrometer spatial resolution. (Contact: Tamas Varga)   
         
    • Detection of volatile organic carbons (VOCs) emitted by soils and vegetation:   
       
      • Studies of root exudation and VOC generation in soils. (Contact: Amir Ahkami)   
         
      • Thermal desorption gas chromatography quadrupole time-of-flight mass spectrometry (TD-QTOF GC-MS). (Contact: Swarup China)   
         
      • Headspace solid-phase microextraction (HS-SPME) coupled with (TD-QTOF GC-MS) for profiling VOCs in soil and rhizosphere environments. (Contact: Swarup China)   
         
      • Soil VOC probe (new capability). The soil VOC probe is a custom-made belowground housing designed to collect VOCs from the upper ~30 cm of soil. During active sampling, an external pump draws soil air through laser-etched ports along the probe shaft and into a sorbent tube housed inside the probe, where VOCs are captured. (Contact: Swarup China)   
         
      • Time-Resolved Automated Volatile Organic Compound System (TRAVIS): Robust, accurate, lightweight field sampling system for VOCs and semi-VOCs. It may be deployed at ground level but is best leveraged in concert with uncrewed aerial systems such as balloons to sample volatile chemicals from various altitudes. (Contact: Swarup China)   
         
    • Ice Nucleation measurements of terrestrial-sourced particles:   
       
    • Assessment and application of novel computational strategies for incorporating molecular data into existing biogeochemical, watershed, and Earth system models. Submitters are encouraged to propose parameterizations of MONet data that could improve reaction networks or thermodynamic or kinetic pool representations within existing model frameworks. The use of AI models or other strategies for estimating, extrapolating, or scaling MONet parameters within the context of watershed and Earth system frameworks is also encouraged. Submitters should articulate how the proposed work will enable the utilization of MONet data in large-scale model frameworks (contacts: Arjun Chakrawal and Satish Karra). Proposals may utilize the numerical tools available in EMSL's PFLOTRAN Carbon Reaction Sandbox (contact: Glenn Hammond) or Pore2Chip/Chip2Flow workflows (contact: Maruti Mudunuru).   
       
    • Tests of innovative approaches for ontology refinement, alignment, and engineering, particularly if integrated with large language models. These tests should focus on the method's capacity to bridge or standardize ontologies or data models between the different research communities whose discoveries advance DOE Office of Science's Biological and Environmental Research (BER) program mission science, with the ultimate goal of enabling scientists to more easily develop an integrative understanding of biogeochemical and biological processes. (Contact: Montana Smith)   
       
    • Application, testing, and comparison of advanced methods for the multimodal integration of imaging data with other data streams. For instance, overlaying MS-based imaging data with abundance or concentration data can identify areas of interest for detailed sample collections. Accelerated, semiautomated methods (including but not limited to AI/ML-based ones) promise to accelerate discoveries from imaging capabilities such as confocal microscopy, fluorescence in situ hybridization, and MALDI. (Contact: Kelly Stratton)   
       
    • Identification and quantification of metabolites from Nuclear Magnetic Resonance (NMR) spectra. EMSL has developed a semiautomated capability to increase throughput as well as consistency, and datasets with novel or unusual BER-relevant metabolites are of particular interest. (Contact: Kelly Stratton)   
       
    • Assessment and application of novel computational strategies, particularly leveraging AI/ML, for converting raw molecular data from high-resolution MS into actionable scientific insights. Proposals should focus on improving our understanding of biogeochemical and biological processes, and studies focused on processing and annotating data from omics and complex mixtures are of particular interest. (Contacts: Aivett Bilbao and Yuri Corilo)   
       
    • Application of novel computational methods for the modeling and simulation of BER-relevant biological systems at molecular and cellular scales. Proposals should leverage newly developed approaches to simulate complex systems that were not previously tractable; accelerate the convergence of molecular simulations; improve accuracy through multiscale modeling, advanced sampling methods, or coupled atomistic-coarse-grained simulations; or gain new understanding of molecular behavior and regulation through post-simulation analysis. Studies that would advance model-experiment integration (ModEx) involving EMSL's experimental capabilities (e.g., cryo-electron tomography [CryoET]) are of particular interest. (Contacts: Margaret Cheung and Amity Andersen)   
       
    • Computational studies leveraging continuum reactive transport models derived from MONet soil data using EMSL's upscaling capabilities or studies applying novel statistical or AI/ML-based methods to MONet soil data. Proposals should focus on how the work advances capabilities to elucidate hydro biogeochemical processes or process parameters. (Contact: Satish Karra)   
       
    • Novel applications of new AI and statistical approaches to analyze and integrate EMSL data, especially in the context of BER-relevant public data resources such as other BER user facilities (e.g., using MAGI to integrate EMSL metabolomic data with genome data from the Joint Genome Institute). Studies aiming to integrate MONet data with public soil, flux, hydrology, and other geospatial data are highly encouraged. (Contact: Kelly Stratton)   
       
    • Identification, modeling, and/or optimization of proteins that bind critical materials or small molecules containing them. (Read DOE's critical minerals and materials definitions.) Investigations seeking to test new models' capabilities for predicting the behavior of such proteins are also of interest (e.g., protein language models or genome language models). Studies that would validate findings through experimental capabilities are encouraged but not required. (Contact: Satish Karra)   
       
    • Leveraging genome-scale metabolic models (GSMMs) to understand experimental results or develop novel experimental designs. Studies requiring model refinement using EMSL data and/or Joint Genome Institute (JGI) data are of special interest, as are studies using AI/ML to automate such refinement and studies leveraging novel methodologies. (Contacts: Satish Karra and Niaz Chowdhury)   
       
    • Interpretation and investigation of multi-omics data in the context of biological pathways, with particular emphasis on non-model organisms. EMSL has developed a new interactive visualization approach called PathwaySeeker that integrates traditional pathway databases with AI-based approaches. (Contacts: Lummy Monteiro and Kelly Stratton)   
       
    • Advancement of existing Pacific Northwest National Laboratory (PNNL) agentic AI infrastructure, including the ADEPT reference framework, or proposal of alternative approaches consistent with PNNL's agentic AI engineering practices. We welcome proposals that aim to test the decision-making capabilities of AI agents to accelerate BER research by enabling autonomous computational work; workflows of special interest include data transformations, ModEx and model-data integration, and simulations supporting hypothesis testing. (Contacts: Tim Boe and Abby Jerger)   
       
    • Use of EMSL's new Makerspace capability to build physical prototypes to help answer research questions in BER-relevant science areas. The capabilities will include 3-D printers (resin, high temperature, filament), laser engravers and cutters (CO2, ultraviolet [UV]), collaborative robotic equipment and liquid handlers, shared collaboration and storage spaces, dedicated design computers, and more. Example use cases include developing micrometer-resolution laser-etched 3-D models of soils to study processes using a reduced complexity experimental setup or developing custom field-deployable aerosol capture devices to study rhizosphere processes. Our 3-D printers could be used to print biologically compatible vessels to study perturbations of microbial growth or interfaces to capture the headspace of a 96-well plate. Users can access the capabilities remotely in collaboration with on-site staff, or they can opt to join us here at EMSL (travel and accommodations not provided). (Contacts: Hardeep Mehta or the Integrated Research Platform leader in your scientific domain)   
       
    • Use of EMSL's core automation lab capability (currently under development) to prototype and execute automated workflows. The space currently includes a Tecan Fluent liquid handler with integrated centrifugation, single-plate incubation with shaking, and multimode plate reading. It also includes collaborative robotic arms and will be expanding to include more instruments as we identify needs. (Contacts: Hardeep Mehta or the Integrated Research Platform leader in your scientific domain)

Review criteria

User proposals are peer-reviewed against the three criteria listed below. For each criterion, the reviewer rates the proposal as Outstanding, Excellent, Good, Fundamentally Sound, or Questionable Impact. In addition, the reviewer provides detailed comments on the quality of the proposal to support each rating, specifically noting the proposal's strengths and weaknesses. Finally, the reviewer provides overall comments and recommendations to support the ratings given. These scores and comments serve as the starting point for Proposal Review Panel (PRP) discussions. The PRP is responsible for the final score and recommendation to EMSL management. 

Criterion 1: Scientific merit and quality of the proposed research (50%) 

Potential Considerations: How important is the proposed activity to advancing knowledge and understanding within its own field or across different fields? To what extent does the proposed activity suggest and explore creative and original concepts? How well conceived and organized is the proposed activity? 

Criterion 2: Relevance of the proposed research to the missions of EMSL and the Biological and Environmental Research (BER) program (25%) 

EMSL's mission is to accelerate scientific discovery and pioneer new capabilities to understand biological and environmental processes across temporal and spatial scales. EMSL supports the mission of the Department of Energy Office of Science's Biological and Environmental Research (BER) program to achieve a predictive understanding of complex biological, Earth, and environmental systems for the nation's energy and infrastructure sustainability and security. The BER program seeks to understand the biological, biogeochemical, and physical processes that span from molecular and genomics-controlled scales to the regional and global scales that govern changes in watershed dynamics, climate, and the Earth system. 

Starting with the genetic information encoded in organisms' genomes, BER research seeks to discover the principles that guide the translation of genetic code into functional proteins and the metabolic and regulatory networks underlying the system biology of plants and microbes as they respond to and modify their environments. This predictive understanding will enable the design and reengineering of microbes and plants underpinning energy independence and a broad clean energy portfolio, including improved biofuels and bioproducts, improved carbon storage capabilities, and controlled biological transformation of materials such as nutrients and contaminants in the environment. 

BER research further advances the fundamental understanding of dynamic, physical, and biogeochemical processes required to systematically develop Earth system models that integrate across the atmosphere, land masses, oceans, sea ice, and the subsurface. These predictive tools and approaches are needed to inform policies and plans for ensuring the security and resilience of the nation's critical infrastructure and natural resources. 

Potential Considerations: What is the relationship of the proposed research to EMSL's and BER's missions? Does the research significantly advance mission goals and align with the focus topics for EMSL's science areas as outlined in the most recent Call for Proposals? How well does the project plan represent a unique or innovative application or development of EMSL capabilities? 

Criterion 3: Appropriateness and reasonableness of the request for EMSL resources for the proposed research (25%) 

Potential Considerations: Are EMSL capabilities and resources essential to performing this research? Are the proposed methods/approaches optimal for achieving the scientific objectives of the proposal? Are the requested resources reasonable and appropriate for the proposed research? Does the complexity and/or scope of effort justify the duration of the proposed project, including any modifications to EMSL equipment to carry out research? Is the specified work plan practical and achievable for the proposed research project? Is the amount of time requested for each piece of equipment clearly justified and appropriate? 

Submission Steps

Get Started

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Create an account for the EMSL User Portal and familiarize yourself with the requirements and policies for EMSL users.
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Develop a Research Plan

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Learn about EMSL's mission and available resources. Contact staff to discuss your needs.
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Submit a Letter of Intent

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Complete the standardized LOI form following the specified guidance. Upload this form to the EMSL User Portal and complete the electronic submission process.
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Submit a Full Proposal to the Dual Anonymous Call

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If invited, applicants are required to submit a 4-page project description using a standardized template and following detailed guidance. The Title, Abstract, Project Description, and References must be written in an anonymized format.
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