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Call for Large-Scale Research Proposals, FY2023



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EMSL's Call for FY2023 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.

Researchers from around the world can apply through this call to use EMSL resources and collaborate with EMSL scientists at no cost. Accepted proposals are valid for two years provided that sufficient progress toward the stated goals is accomplished in 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 competitive and approximately 30% of the proposals submitted will be accepted. Proposals will be evaluated according to the five review criteria listed below. Note that proposals that do not adhere to the guidance will not be considered. 

Focus topic areas

The focus topics for this call are aligned with EMSL’s mission to accelerate scientific discovery and pioneer new capabilities to understand biological and environmental processes across temporal and spatial scales. The topics are organized by EMSL’s three science areas — Environmental Transformations and Interactions; Functional and Systems Biology; and Computing, Analytics, and Modeling.

Environmental Transformations and Interactions (ETI) Science Area  

Learn more about the ETI Science Area on the EMSL website. Contact the ETI Science Area lead, John Bargar, if you have questions about these topics.  

  • ETI-1:  Development of mechanistic understanding of the surface chemistry of mineral-organic matter interactions and their ability to stabilize or destabilize soil carbon and nutrient pools (e.g., via microbial metabolism, nanoparticle or colloid formation) leading to elemental or nutrient cycling, fate, and transport in terrestrial and subsurface ecosystems or across 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 microbial and abiotic processes occurring at the molecular- to field site-scales and impacting hydro-biogeochemical controls that create, sustain, and/or limit hot spot and/or hot moment phenomena-associated fluxes (e.g., CO2, CH4, NH4, N2O, N2, other N, P, or S chemical species, and dissolved organic compounds) through lab- or field-based observation, or experimental manipulations. We also encourage proposals that employ in situ quantification of nutrient and chemical exchanges in the rhizosphere and/or spatially resolved metabolomics or elemental mapping of the root-rhizosphere-soil continuum.  
  • ETI-3:  Development of molecular-scale, mechanistic, and kinetic understanding of the unique hydro-biogeochemical processes driving elemental and nutrient cycling dynamics, their interactions, and feedbacks that define urban transition zones and/or coastal freshwater and saltwater terrestrial-aquatic interfaces. Proposals that test and/or develop data for hydrologic and/or biogeochemical models of these processes are of particular interest.  
  • ETI-4:  Understanding of the processes that result in the formation and evolution of biogenic and anthropogenic sources of aerosols and aging processes that modify their chemical, physical, and optical properties, or identification of specific aerosol characteristics (e.g., physical or chemical) that impact ice nucleation and/or warm cloud formation. Proposals that test and/or develop data for models of cloud-aerosol interactions or other models of atmospheric aerosol processes are of particular interest.  
  • ETI-5:  Understanding of molecular and physiological mechanisms that lead to resilience in natural ecosystems or vegetation, managed bioenergy cropping systems, urban and exurban systems, and/or other vulnerable ecosystems in response to perturbation (e.g., drought, flooding, nutrient limitation, temperature, elevated CO2). Proposals that investigate the role of plant-microbe interactions and/or develop and test metabolic or biogeochemical models of these processes are of particular interest.   
  • ETI-6:  Identification of different ideotypes of root system for better bioenergy crop adaptation to individual and combined abiotic stress conditions. Proposals that aim to study natural genetic variants, mutants, or transgenic plants for dissection of complex plant phenotypes and/or emergent plant phenotypes regulated by microbiomes into component genetic traits are encouraged. Proposals that develop or employ integrated multi-omics with root phenotyping approaches are also encouraged.  

Functional and Systems Biology (FSB) Science Area  

Learn more about the FSB Science Area on the EMSL website. Contact the FSB Science Area lead, Scott Baker, if you have questions about these topics.  

  • FSB-1:  Analysis of multi-cellular systems (e.g., microbial consortia, microbiomes, plants, plant-microbe associations, engineered microbial consortia) to enable predictive understanding of pathways/processes that underpin biogeochemical transformations, nutrient cycling (e.g., C, P, N, etc.), and degradation of recalcitrant compounds (e.g., plastic and lignin) in the environment.  
  • FSB-2:  Systems-level studies of cell-to-cell interactions, signaling, resource sharing, and communication within microbiomes and defined consortia that harbor the potential to produce biofuels, bioproducts, or biomaterials.  
  • FSB-3:  Analysis of 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-4: 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 other biological molecular processes.  
  • FSB-5:  Use of EMSL’s advanced structural biology and microscopy capabilities to characterize construction, composition, ultrastructure, or enzymatic deconstruction of cell structural components (e.g., microbial, plant, fungal, and algal cell walls) and synthetic polymers.  
  • FSB-6:  Systems biology studies of non-model organism systems to determine important metabolic pathways relevant to production of biofuels, bioproducts, materials, or degradation of lignin or plastic residues.   

Computation, Analytics, and Modeling (CAM) Science Area  

Learn more about the CAM Science Area on the EMSL website. Contact the FSB Science Area lead, Jay Bardhan, if you have questions about these topics.  

  • CAM-1:  Integration of multiple data types to predict the functionally-relevant structures, dynamics, and regulatory mechanisms of protein complexes.  Data types of particular interest include protein sequences, native MS, cross-linking MS, cryoEM/cryoET, HDX, bottom-up or top-down proteomics, SAXS/WAXS, and crystal or NMR structures of individual subunits.  
  • CAM-2:  Use of molecular and multi-scale simulations, as well as AI/ML, to understand biological and biogeochemical processes and their regulation.  Biological regulatory mechanisms of particular interest include metal-ion binding, post-translational modification, and transient complexation.  Biogeochemical processes of interest include mineral-organic matter interactions and their impacts on ecosystems.  
  • CAM-3:  Advancement of novel methods to analyze and integrate complex or heterogeneous data, such as high-dimensional/multivariate and multi-modal data.  Methods of particular interest include clustering, outlier detection, dimensionality reduction, topological or geometric approaches, methods that incorporate mechanistic (molecular, multi-scale, and PDE-based) models, interactive visualizations, and AI/ML techniques for limited training data (e.g. few shot learning). For mass spectrometry data, uncertainty propagation and predictive molecular search spaces are of additional interest.   
  • CAM-4:  Advancement of novel methods for analysis and integration of imaging data, including 3D data and dynamic imaging.  Areas of particular interest are segmentation, classification, object and anomaly detection, image clustering, correlating images of multiple types, recognition of dynamic or transient signals, and methods for limited training data or unlabeled data.  
  • CAM-5:  Development of software and models for hydro-biogeochemical processes, particularly elemental and nutrient cycling and transport. 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 studying the formation and evolution of secondary organic aerosol (SOA) molecules. The simulation of optical and physiochemical properties of SOAs is 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 perturbation; 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

All EMSL instruments and resources are available to users through this call. Applicants are also encouraged to consider emerging cutting-edge capabilities developed by EMSL scientists, including:  

  • Stable isotope probing and analysis platform that includes labeled CO2 plant-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)  
  • Cell-free expression pipeline to synthesize proteins of interest. Suitable for the synthesis of soluble proteins, membrane proteins, heterocomplexes, proteins of different origin, very large proteins. [More…]   
  • Krios cryoTEM for structural analysis of soluble or membrane protein complexes, isolated organelles, whole cells and small molecule crystals. [More…]  
  • Aquilos cryo-FIB/SEM for site-selective sample preparation for cryo-electron tomography or serial section slice-and-view 3D imaging of biofilms, tissues, or plant/microbe interactions. [More...]  
  • High-resolution micro-X-ray computed tomography system for characterization of plant root architecture and soil pore structure or soft X-ray nanotomography system for 3D nanoscale imaging of cells and biological materials.  [More...]  
  • 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. [More…]   
  • Tahoma, BER’s new heterogeneous (CPU/GPU) computing system for highly parallel modeling/simulation and data processing needs. [More…]  

Other capabilities that offer opportunities for novel and exciting experimental data include a variety of in-situ probes for NMR, advanced electron microscopy in a specialized “quiet facility", high-resolution mass spectrometry including a 21 Tesla FTICR MS, and Atom Probe Tomography. Learn more about these and other EMSL capabilities.   

How to Apply

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?