Science Area Research

Environmental Molecular Sciences Laboratory

Grant amount: Unspecified amount in in-kind support

Deadline: Mar 5, 2018

Applicant type: Research Scientist Postdoctoral Researcher Faculty

Funding uses: Research

Location of project: Anywhere in the world

Location of residency: Anywhere in the world

Must travel to: Benton County, Washington

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EMSL's Call for FY2019 Proposals is seeking leading-edge research activities to advance scientific understanding in each of EMSL’s science areas. The Science Areas announced below aim to advance scientific understanding in areas of interest to, or aligned with, those of the Department of Energy (DOE) Office of Biological and Environmental Research (BER) 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. Requirements change, so be sure to check the Proposal Guidance for Use in Fiscal Year 2018 and fully understand what needs to be included in your submission. Proposals will be evaluated according to five review criteria, as part of the Proposal Review process. Note that proposals that do not adhere to the proposal package guidance cannot be considered.


EMSL’s mission is to lead molecular-level discoveries for the DOE and its Office of Biological and Environmental Research that translate to predictive understanding and accelerated solutions for national 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 areas of emphasis within each Science Area, especially those in which molecular-scale research:

  • transforms understanding of key phenomena; 
  • couples experiments on natural or engineered systems with modeling, simulation or theory;
  • exploits the diversity of EMSL capabilities; or
  • develops and applies new or enhanced computational capabilities to support EMSL's research objectives

Prospective users are strongly advised to contact the relevant Science Lead(s) or Capability Lead(s) to discuss proposal ideas and possible research collaborations with EMSL staff. Prospective users interested in coupling experimental and computational approaches, or developing novel computational modeling and informatics methods that support research within the focus topics should contact the Lead Scientist for Multiscale Modeling or the Lead Scientist for Computational Sciences.

Applicants should note that there are also newer capabilities that offer opportunities to obtain novel and exciting experimental data to advance scientific objectives. Details about these are available on the EMSL capabilities web page. They include a variety of in-situ probes for NMR, advanced electron and dynamic transmission electron microscopy in a specialized “quiet” facility, super resolution fluorescence microscopy for live cell imaging, high-resolution mass spectrometry including a 21 Tesla FTICR, advanced ‘omics and microfluidic capabilities, a 3.4 petaflop supercomputer, interactive data visualization tools, NanoSIMS, and Atom Probe Tomography. Users also have access to the EMSL phytotron for plant growth and imaging.

If you are unsure what instruments would be best for your project, you can search instruments by research area to see a list of commonly requested instruments.

Focus Topics by Science Area

Biological Sciences Area

The Biological Sciences Area focuses on biological “machines,” processes, and interactions within cells, among cells in communities, and between cellular membrane surfaces and their immediate environment for microbes (archaea, bacteria, algae), fungi, and plants. Research supported by this area focuses on improving mechanistic understanding of how molecular and genetic information are translated into processes that cross spatial and organizational scales: biological machines, cellular components/compartments, whole cells/organisms, consortia, multispecies communities, and ecosystems. This understanding will advance accurate metabolic reconstructions and enable creation of predictive models/simulations to improve strategies for designing plants, fungi, and microbes for biofuels and bio-based products, and unravel the complexities of carbon, nutrient, and elemental cycles within cells and their immediate environment.

Proposals addressing important questions in the following specific areas are encouraged, particularly as they relate to plants, fungi, and microbes in biofuel and bioproduct production and biologically-driven carbon, nutrient, and elemental cycling:

  • Experimental and modeling approaches focused on molecules and pathways involved in intra- and inter-cellular signaling and/or metabolic pathways whose intermediates provide building blocks for biosynthesis of biofuels and bioproducts;
  • Cellular and molecular characterization of energy metabolism and storage processes, including their underlying molecular pathways, subcellular localization, and transport mechanisms;
  • Integrated modeling and structural biology studies to understand enzyme active site chemistry, protein-protein interactions, and other molecular processes of the enzymatic systems involved in biomass deconstruction or metabolic pathways involved in biofuel and bioproduct production;
  • Experimental approaches to enable genotype to phenotype advances in single organisms and communities, and predictive models of individual and single species plant growth, performance, and composition, as a function of genotype and environment;
  • Elucidation of post-transcriptional and post-translational processes and modifications influencing and regulating metabolic pathways, energy storage, biomass accumulation, and abiotic stress tolerance and/or an understanding of the dynamics of assembly, spatial organization and functioning of membrane structures, eukaryotic organelles, bacterial communities, and multi-cellular systems that impact the production, fate, and transport of biomolecules;
  • Modeling and simulation of molecular processes and metabolic pathways to support synthetic biology, coupled with data driven validation;
  • Experimental and modeling approaches with biological systems (e.g., bacteria, fungi, microbial consortia, plants, plant-microbe associations) to enable predictive understanding of nutrient (C, N, P, and S) flux.

Environmental Sciences Area

The Environmental Sciences Area focuses on mechanistic and predictive understanding of fundamental ecological, hydrological, biogeochemical, and microbial processes in the terrestrial and subsurface ecosystems, their interfaces, and their interactions from molecular- to ecosystem-scale. Of particular interest is understanding the cycling, transformation, and transport of critical biogeochemical elements (e.g., C, N, S, P, Mn, Fe, and Ca) and contaminants within the terrestrial and subsurface ecosystems. A key goal is mechanistic understanding of biogeochemical, hydrologic, and microbial processes in heterogeneous soils and sediments and their interactions that give rise to complex and emergent phenomena at larger scales. Incorporating this knowledge into hierarchal multiscale models will improve prediction of elemental, nutrient, and water cycling that impacts Earth system functions as well as promote cost-effective, sustainable solutions to contaminant management.

Proposals to advance fundamental and predictive understanding in the following areas are especially encouraged:

  • Develop molecular-scale mechanistic understanding of the geochemical, biological, and hydrologic processes driving elemental (C, N, P, etc.) cycling in soils (especially rhizosphere root-microbe-fungi-soil interactions), terrestrial/aquatic interfaces, and subsurface environments;
  • Investigate the role of hydrologic processes that create biogeochemical gradients and microbial niches at pore- to core-scale in terrestrial and subsurface ecosystems;
  • Characterize molecular chemistry and dynamics of natural organic matter and investigate the mechanisms and processes that influence microbial and plant access to carbon substrates;
  • Understand mineral surface complexation/associations, redox reactions, nanoparticle and colloid formation, and their impact on the reactivity, fate, and transport of anthropogenic contaminants and complexes in terrestrial, aquatic and subsurface ecosystems;
  • Identify molecular profiles, functional traits, and signatures indicative of ecosystem function and response to perturbation (e.g., nutrient limitation, hydrologic stress).

Science Area Alignment with BER

The DOE Biological and Environmental Research (BER) program supports several user facilities, including EMSL, as well as a number of process and modeling research activities. Research within the BER program seeks to achieve fundamental understanding and prediction of complex biological, Earth, and environmental systems for energy and infrastructure security. Research efforts span a wide range of temporal and spatial scales from sub-micron to global, individual molecules to ecosystems, and nanoseconds to multi-decadal. BER advances and integrates process-level understanding of complex systems across these scales by coupling observations, experiments, and theory with modeling and simulation to address DOE missions.

BER’s biological systems research provides fundamental understanding to predict, manipulate, and design biological processes that underpin innovations for bioenergy and bioproduct production, and to enhance the understanding of carbon, nutrient, and inorganic element transformations in support of DOE’s environmental missions. The research seeks to characterize and predictively understand intra- and inter-cellular microbial (archaeal, bacterial, fungal) and plant systems, and their functioning within the immediate surrounding environment using molecular, genomic and other –omic approaches, structural imaging and analyses, other experimental approaches, and computational analyses and modeling. Foundational knowledge of the structure and function of these biological systems and their surrounding environment underpins the ability to leverage natural processes.

BER’s research on earth and environmental systems seeks to characterize and predictively understand feedbacks between Earth and energy systems and includes studies on atmospheric physics and chemistry, ecosystem ecology, hydrology and biogeochemistry, and development and validation of Earth system and climate prediction models extending from regional to global scales. BER’s land surface/subsurface research is focused on capturing the structure, functions, and interactions among the land, coastal areas, freshwater systems, soils/sediments, groundwater, and geologic components in a variety of models, and their interfaces with the microbes, plants, and higher organisms of the living Earth system. How the range of physical, chemical and biological processes interact and function, and how they change over temporal and spatial scales are also major areas of focus.

You can learn more about this opportunity by visiting the funder's website.


  • Researchers are invited to apply for the opportunity to collaborate with nationally recognized experts and use unparalleled state-of-the-art instruments and facilities at 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.


  • Preference is given to proposals within the selected focus topics, especially those in which molecular-scale research:
    • transforms understanding of key phenomena;
    • couples experiments on natural or engineered materials/systems with modeling, simulation or theory;
    • integrates techniques to address a relevant science question; or
    • develops and applies new or enhanced computational capabilities to support science theme objectives.