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Call for Large-Scale Research Proposals, FY2022

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EMSL's Call for FY2022 Large-Scale EMSL Research Proposals is seeking leading-edge research activities to advance scientific understanding in each of EMSL’s science areas, as well as novel applications of EMSL capabilities. The focus topics announced below aim to advance scientific understanding in areas of interest to, or aligned with, those of the Department of Energy (DOE), Office of Science, Biological and Environmental Research (BER) Program and EMSL. Accepted proposals are valid for two years provided that a summary and extension request demonstrate sufficient progress toward the stated goals for the first year. A select number of lead investigators may be invited to submit project plans to extend the work for a third year.

Access to EMSL capabilities is highly competitive, and approximately 30% of the proposals submitted will be accepted. Requirements change, so be sure to follow all guidance closely. Proposals will be evaluated according to the five review criteria listed below. Note that proposals that do not adhere to guidance will not be considered.

New this year: A letter of intent must be submitted prior to submitting a full proposal. See the Letter of Intent Guidance for more details.

How To Submit a Proposal

  • Submit a Letter of Intent by February 8
  • Submit a full proposal by March 26, if invited following Letter of Intent review
  • Letters of Intent and Full Proposals must be submitted through the User Portal
  • For help, contact User Services at 509-371-6003 or emsl@pnnl.gov

Focus Topic Areas

Environmental Transformations and Interactions (ETI) Science Area

The ETI science area focuses on the mechanistic and predictive understanding of environmental (physiochemical, hydrological, biogeochemical), microbial, plant and ecological processes in above- and below-ground ecosystems, the atmosphere, and their interfaces. EMSL provides the experimental, computational, and simulation expertise to investigate and model cycling, transformation, and transport of critical nutrients, elements, contaminants, and atmospheric aerosols. Experiment and modeling approaches will accelerate mechanistic understanding of coupled soil-microbe-plant-atmosphere molecular processes and their interdependencies, ultimately informing models of ecosystem processes and land-atmosphere interactions at larger scales. Contact Nancy Hess, ETI Science Area lead, if you have questions about the call topics or to discuss your project idea.

ETI Call Topics

  • ETI-1: Develop mechanistic understanding of the surface chemistry of mineral-organic matter interactions and their ability to stabilize or destabilize soil carbon pools, nutrients, and contaminants (e.g. via microbial respiration, nanoparticle, or colloid formation) leading to elemental or contaminant cycling, fate and transport in terrestrial and subsurface ecosystems and at their interfaces. Proposals that test and/or develop data for biogeochemical models of these processes are of particular interest.
  • ETI 2: Development of new mechanistic insights on the molecular- to fine-scale hydro-biogeochemical controls that create, sustain, and/or limit hot spot and/or hot moment phenomena associated fluxes (e.g. CO2, CH4, NH4, N2, P, S) through lab- or field-based observation, or experimental manipulations.
  • ETI 3: Develop molecular-scale, mechanistic, and kinetic understanding of the unique hydro-biogeochemical processes driving elemental and nutrient cycling dynamics, their interactions, and feedbacks that define freshwater and saltwater terrestrial-aquatic interfaces. Proposals that test and/or develop data for biogeochemical models of these processes are of particular interest.
  • ETI 4: Understand molecular and physiological mechanisms that lead to resilience of plants and their associated microbial communities in natural ecosystems and managed bioenergy cropping systems in response to perturbation by environmental stressors (e.g., drought, nutrient limitation, temperature, elevated CO2). Proposals that test and/or develop data for metabolic models of these processes or biogeochemical models are of particular interest.
  • ETI 5: Determine the physical and chemical properties that make some aerosols more efficient ice-nucleating particles than others; investigate the role of primary biological particles as ice nucleating particles. Proposals that test and/or develop data for models of cloud-aerosol interactions or other models of atmospheric processes are of particular interest.
  • ETI 6: Understand the processes that result in the formation and growth of organic and biogenic aerosols and aging processes that result in changes in their chemical, physical, and optical properties. Proposals that test and/or develop data for models of cloud-aerosol interactions or other models of atmospheric processes are of particular interest.

Functional and Systems Biology (FSB) Science Area

The FSB science area focuses on elucidating and harnessing the biochemical pathways that connect gene functions to complex phenotypic responses through a deep understanding of interactions within cells, among cells in communities, and between cellular membrane surfaces and their environment for microbes and plants. This understanding encompasses experimental observations, metabolic reconstruction, and modeling, leading to improved strategies for designing plants, fungi, and microbes for biofuels and bio-based products, as well as unraveling the complexities of carbon, nutrient, and elemental cycles within cells and their immediate environments. Contact Scott Baker, FSB Science Area lead, if you have questions about the call topics or to discuss your project idea.

FSB Call Topics

  • FSB-1: Analyze multicellular systems (e.g., microbial consortia, microbiomes, plants, plant-microbe associations) to enable predictive understanding of the regulation and interactions of various nutrient cycles (C, N, P, and S) in biological systems in the environment.
  • FSB-2: Analyze metabolic pathways to support synthetic biology approaches for the production of biofuels, bioproducts, and biomaterials, coupled with data-driven validation and product/material characterization.
  • FSB-3: Structural and computational biology studies to characterize proteins encoded by “genes of unknown function” and/or improve understanding of enzyme active-site chemistry, macromolecular assemblies, protein-protein interactions, bio-organic mineral interactions, biosynthesis of materials, enzymatic degradation, and modification of plastic waste and other biological molecular processes.
  • FSB-4: Use EMSL’s advanced multi-omic, microscopy, and structural biological analyses to characterize construction, composition, or enzymatic deconstruction of cell structural components (e.g. microbe, plant, fungal, and algal cell walls).
  • FSB-5: Systems biology studies of non-model organism systems relevant to production of biofuels, bioproducts, materials, or degradation of plastic residues.
  • FSB-6: Analysis of biological systems manipulated by use of novel genetic tools (i.e., artificial/synthetic chromosomes, CRISPR-Cas, and other high throughput genome genetic engineering methods) that advance or create improved strategies for efficient design or redesign of biological systems.

Computation, Analytics, and Modeling (CAM) Science Area

The CAM science area focuses on combining advanced data analytics and visualization and computational modeling and simulation with state-of-the-art experimental data generation to develop a predictive understanding of biological and environmental systems. Our cohesive approach to integrating experimental and computational methods advances predictive approaches to biodesign for biofuel/bioproduct production and accelerates research to understand the molecular mechanisms underlying biological and hydro-biogeochemical processes controlling the flux of materials (e.g., carbon, nutrients, and contaminants) in the environment. Contact Lee Ann McCue, CAM Science Area Lead, if you have questions about the call topics or to discuss your project idea.

CAM Call Topics

  • CAM-1: Development of metabolic modeling approaches that support predictive simulation of biofuel, bioproduct, or biomaterial production. Development of metabolic modeling approaches that integrate mechanistic models with data-driven approaches and modeling approaches that integrate novel combinations of experimental data sources and support a MODEX approach are of particular interest.
  • CAM-2: Development of machine learning/deep learning approaches to associate genes/genotypes or proteins/metabolites with phenotype at the organism-scale. Methods that relate model predictions to experimental imaging data, especially time-series imaging data are of particular interest.
  • CAM-3: Development of computational models of protein structure and function for BER mission-relevant enzyme-substrate interaction, protein-protein interaction, or protein-mineral interaction, that support predictive approaches to biodesign. Approaches that encompass development of visualization and interactive visualizations, including virtual reality are of particular interest.
  • CAM-4: Development of multi-scale models of the rhizosphere, from the molecular- to system-scale, that support predictions of resilience of the plant/microbiome system to environmental perturbation, and use methods that leverage recent advances in machine learning to identify causal interactions across scales.
  • CAM-5: Development of software and models for hydro-biogeochemical processes, particularly elemental and nutrient cycling. Methods that integrate novel combinations of experimental and field data sources to support a MODEX approach are of particular interest.
  • CAM-6: Development of predictive modeling approaches for organic aerosol-cloud interactions. Modeling how the optical and physiochemical properties of organic aerosols impact cloud formation are of particular interest.

Other: Novel Applications

  • OTH-1: Projects should be aimed at stretching the boundaries of scientific integration of EMSL capabilities. Outcomes should have long-term benefits to DOE/BER missions involving biofuels, biomaterials, and bioproducts production; plant-microbe interactions and nutrient exchange; ecosystem resilience or plasticity in response to environmental stress; and land-atmosphere exchanges and feedbacks. For high-risk exploratory studies aimed at assessing the general feasibility or establishing proof of principle for a proposed approach or study design, the scope should be limited to a scale required to demonstrate novel results, with the possibility of expanded support after successful completion.

 

Highlighted Capabilities

EMSL’s mission is to accelerate scientific discovery and pioneer new capabilities to understand biological and environmental processes across temporal and spatial scales. EMSL leads the scientific community toward a predictive understanding of complex biological and environmental systems to enable sustainable solutions to the nation’s energy and environmental challenges. While applications will be accepted that address any aspect of the DOE mission areas, special consideration will be given to projects that address the specific areas within each Science Area, especially those in which research: (i) leads to disruptive scientific advances; (ii) couples experiments with modeling/simulation; or (iii) develops and applies new or enhanced computational capabilities to support EMSL's research objectives.

Prospective users are strongly advised to contact the staff contacts listed below, to discuss proposal ideas and possible research collaborations with EMSL staff.

Emerging capabilities. Applicants should consider emerging cutting-edge capabilities that are available to users who coordinate their proposals with the EMSL scientists leading their development. The capabilities include but are not limited to the following:

  • Stable isotope probing and analysis platform that includes labeled CO2plant growth facilities, NMR, IRMS, and NanoSIMS (Contact: Jim Moran, Mary Lipton, or Pubudu Handakumbura)
  • Transcriptomics and proteomics from single or a small number of cells detected and isolated by flow cytometry, fluorescence microscopy and/or laser capture micro-dissection and enabled by microfluidics and nanoPOTS (Contact: Galya Orr or Ying Zhu)
  • New structural biology approaches combining cell-free expression and native mass spectrometry capabilities for characterization of protein complexes (Contact: Irina Novikova or Mowei Zhou)
  • New Krios cryoTEM for atomic resolution structural analysis of protein complexes, organelles, whole cells and small molecule crystals. (Contact: Trevor MoserAmar Parvate, or James Evans)
  • New Aquilos cryo-FIB/SEM for site-selective sample preparation for cryo-EM/tomography or serial section slice-and-view 3D imaging of large tissue or plant/microbe interactions. (Contact: Trevor Moser or James Evans)
  • Soft X-ray nanotomography system for 3D nanoscale imaging of cells and biological materials (Contact: James Evans or Scott Lea)
  • High-resolution micro-X-ray computed tomography system for characterization of plant root architecture and soil pore structure (Contact: Tamas Varga or Mark Bowden)
  • Noninvasive root imaging platform for monitoring and characterizing plant root systems in transparent growth medium (Contact: Amir Ahkami or Thomas Wietsma)
  • Interactive data visualization tools that support exploration of complex natural organic matter or proteomics data and comparison of data across treatment groups (Contact: Jay Bardhan)
  • Tahoma, BER’s new heterogeneous computing system for highly parallel modeling/simulation and data processing needs. Tahoma is a combination of 160 CPU nodes and 24 GPU nodes, with an estimated peak performance of 0.57 PetaFLOPs. This system will support computational research requiring significant memory (384 or 1536 GByte per node RAM) as well as processing speed to enable data mining, image processing, and multiscale modeling. (Contact: Jay Bardhan).

Other capabilities that offer opportunities for novel and exciting experimental data include a variety of in-situ probes for NMRadvanced electron microscopy in a specialized “quiet facility", high-resolution mass spectrometry including a 21 Tesla FTICR, and Atom Probe Tomography

Review criteria

User proposals are peer reviewed against five criteria listed below. For each criterion, the reviewer rates the proposal Outstanding, Excellent, Good, Fundamentally Sound, or Questionable Impact as well as providing detailed comments on the quality of the proposal to support each rating, noting specifically the proposal's strengths and weaknesses. The reviewer also 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: Qualifications of the proposed research team to achieve proposal goals and contribute to high-impact science (10%)

Potential Considerations: Does the proposal team, combined with relevant EMSL staff expertise, possess the breadth of skill/knowledge to successfully perform the proposed research and drive progress in this science area? If successful, would the proposed research deliver high-impact products (for example, be publishable in high-impact journals)?

Note: Impact factors are a measure of the average number of citations per published articles. Journals with higher impact factors reflect a higher average of citations per article and are considered more influential within their scientific field.

Criterion 3: Relevance of the proposed research to EMSL's mission (10%)

EMSL’s mission is to accelerate scientific discovery and pioneer new capabilities to understand biological and environmental processes across temporal and spatial scales. EMSL leads the scientific community toward a predictive understanding of complex biological and environmental systems to enable sustainable solutions to the nation’s energy and environmental challenges.

EMSL supports the mission of the Biological and Environmental Research (BER) program in the Department of Energy to achieve a predictive understanding of complex biological, earth, and environmental systems for energy and infrastructure security, independence, and prosperity. BER 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 the genetic code into the functional proteins and the metabolic and regulatory networks underlying the systems biology of plants and microbes as they respond to and modify their environments. This predictive understanding will enable 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 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.

Note: Projects with direct relevance in these areas will have the best chance for selection. Other projects of scientific significance also are welcomed, but the applicant should clearly outline how the project will further a DOE mission or other areas with economic or societal impact.

Potential Considerations: What is the relationship of the proposed research to EMSL's mission? Does the research project significantly advance the mission goals? How well does the project plan represent a unique or innovative application or development of EMSL capabilities?

Criterion 4: Impact of the proposed research on one or more EMSL Science Areas (20%)

Potential Considerations: Will the proposed research advance scientific and/or technological understanding of issues pertaining to one or more EMSL science areas? To what extent does the proposed research suggest and explore creative and original concepts related to one or more EMSL science areas? How strongly does it relate to the science area's focused topics as outlined in the most recent Call for Proposals? How well will it advance EMSL along the directions specifically outlined in the focused topics?

Criterion 5: Appropriateness and reasonableness of the request for EMSL resources for the proposed research (10%)

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?