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A National User Facility for the Scientific Community

Workshop: Background and Objectives

The Development of New User Research Capabilities in Environmental Molecular Science

  • August 1-2, 2006
  • W.R. Wiley Environmental Molecular Sciences Laboratory
  • Richland, WA

The Environmental Molecular Sciences Laboratory (EMSL) was conceived by PNNL Director William R. Wiley and his leadership team some twenty years ago. An extensive set of workshops were organized involving experts in experimental and theoretical molecular sciences to define the rationale and scope of what is now the W. R. Wiley Environmental Molecular Sciences Laboratory. However, much has changed in the science and technology universe since EMSL was dedicated in 1997, and these changes in science and technology require that we re-examine our priorities in the context of 21st Century challenges. It is therefore timely to organize a workshop that takes both a snapshot of the environmental molecular sciences in 2006 and establishes a plan for user capabilities for research in environmental molecular sciences for the next decade.

Scope of the Workshop

The objective of the workshop will be to define important science challenges for the next decade, describe limitations in present approaches, and identify major tools and advances in the measurement sciences needed to pursue advanced research in the environmental molecular sciences. Although participants are invited to articulate additional themes or areas, it is assumed that the current strategic plan that articulates EMSL's science themes will serve as the framework for the workshop. The four current science themes are 1) Biological Interactions and Interfaces, 2) Geochemistry/Biogeochemistry and Surface Science, 3) Atmospheric Aerosol Chemistry, and 4) Science of Interfacial Phenomena.

During the workshop the insights of workshop participants will be collected in written form and by taking notes during the discussions. This information will be collected to assemble participants' collective views on:

  1. Key scientific challenges in the area of environmental molecular sciences that should be addressed over the next ten years. Talks during the meeting will project into the future, but workshop attendees are also encouraged to think about these challenges before the workshop. (What science challenges should EMSL capabilities be updated to address.)
  2. Important technical challenges and opportunities that if adequately addressed will provide the research tools to enable progress on the scientific challenges. (What research techniques will fuel cutting edge science.)
  3. Recommendations on any specific capabilities where investments should be made to meet or address the technical challenges.

Below are one or more examples of key science challenges and related technology challenges have been created for each science theme. These are to serve as examples to stimulate your thinking and provide a general view of the types of information we are seeking to assemble. Participants are encouraged to think about and even prepare (and submit) their thoughts on these topics before the meeting.

Biological Interactions and Interfaces

Understanding and optimizing the response of biological systems to the interaction with their environment can have a significant impact on achieving viable solutions to several problems of national concern. For example, anaerobic microbial metabolism is of direct relevance to the Department of Energy (DOE) missions in environmental stewardship (contaminant bioremediation, microbial impacts on global warming through production and sequestration of methane and carbon dioxide), clean and secure energy (methane and H2 from wastes as alternative energy sources), and basic science (cycling of carbon, nitrogen, metals, and radionuclides). Thus, molecular scale measurements, and the corresponding insight into biochemical processes, can lead us to new predictive computational models that will provide a solid basis for using microbes effectively and safely to mitigate the impacts of energy-production-related activities on the environment and human health.

Recent advances in whole genome sequencing for a variety of organisms and structure/function relationships of proteins have contributed to a rapid transition of the biological research paradigm towards understanding biology from a global perspective. As a result, biology is evolving to a quantitative, ultimately predictive science where the ability to collect and productively use large amounts of biological data is crucial. This requires unraveling a variety of molecular level biochemical process; as well as, interfacial processes that can occur between the organism and external substrates (e.g. mineral, plant, or microbial surfaces). Examples of overarching scientific challenges include:

  • Relating the fundamental changes in biochemistry and protein production to changes in the genome and the subsequent response to environmental stress.
  • Unraveling the composition, 3-D structure, and dynamics of the outer microbial membrane and the molecular level interactions of microbe-plant or microbe-mineral interactions.

Examples of key technical challenges and what investments are needed to address these issues and develop a robust user program are outlined below.

Characterization of the global cellular proteome including 3-D protein structures, dynamics, and post-translational modifications

This will require the development of methods for intact protein identification, multi-protein complexes, and metallo-proteins. These capabilities must also be able to identify proteins that are present at relatively low concentration but which are important in metabolic processes and the wide range of proteins from mixed cultures of organisms. In addition these analyses need to be conducted in high throughput mode to handle the large number of samples necessary.

Examples of possible investment opportunities include: Development of NMR-centric chemo-stats and bioreactors that enable the study of cellular systems in-situ in real time, new proteomics approaches that combine ion mobility with MS, capabilities for sub-cellular fractionation that can be used along with proteomics to provide information on protein localization (links to imaging), pulsed and CW EPR capabilities at up to 10 Tesla, and a possible 21T FTICR.

Identification of the fundamental mechanisms of interfacial microbial reactivity including membrane modifications and interactions with both biotic and abiotic interfaces

This includes evaluating the localization of proteins, lipids and other components on the microbial surface, determining the exchange of metabolites and other biomolecules, evaluating electron exchange processes between microbes and surfaces, and determining the mechanisms of microbial attachment to surfaces.

Examples of possible investment opportunities include: HRTEM to examine microbial and plant surfaces in situ, AFM capabilities to determine microbial-surface attachment forces, and methods to determine the composition, 3-D structure, and location of surface bound proteins and LPS molecules.

Atmospheric Aerosol Chemistry

Atmospheric aerosols, microscopic particles suspended in air, play an important role in global climate change. Variations of aerosols are recognized as a significant climate forcing factor, a factor that alters the planetary radiation balance onto and away from the earth and thus tends to cause global temperature change. In addition, recent observations have linked aerosols to changes in haze and cloud formation which lead to regional climate changes. We are concerned with the climate forcing due to changing aerosol concentration and composition, both the direct radiative forcing by the aerosols and the indirect radiative forcing caused by effects of aerosols on cloud properties. These climate forcings effects due to changes of aerosols are not well determined, especially in the case of anthropogenic aerosols. Indeed, aerosols are one of the greatest sources of uncertainty in interpretation of climate change of the past century and in projection of future climate change.

This science theme is focused on advancing the state of knowledge of aerosol physics and chemistry from molecular to regional and global scales and their impact on climate change. Key molecular level scientific challenges include:

  • Unraveling the chemical composition and morphology of aerosol particles and how these factors change with time (aging process) in the atmosphere.
  • Defining the molecular level mechanisms of nucleation and growth of aerosols and how these processes determine final aerosol composition and their ability to serve as cloud condensation nuclei.

Examples of key technical challenges and what investments are needed to address these issues and develop a robust user program are outlined below.

Development of novel analytical techniques for comprehensive chemical and physical characterization of aerosols

These capabilities can include characterizing size, composition, morphology, chemical reactivity and cloud interactions of particles in both field and laboratory environments.

Examples of possible investment opportunities include: HRTEM to determine 3-D structure of organic aerosol particles, XPS, MS, and other techniques to determine elemental and chemical composition, and portable instrumentations to determine aerosol composition in field studies.

Development of capabilities to unravel mechanisms of aerosol nucleation and growth.

As the possible composition of atmospheric aerosols change in the future in response to burning different fuels (biomass) or other anthropogenic emissions it becomes necessary to predict how these changes in emission can impact aerosol formation and the subsequent effects on climate forcing.

Examples of possible investment opportunities include: development of time-resolved single particle aerosol characterization capabilities and development of molecular level models of aerosol nucleation and growth.

Biogeochemistry and Subsurface Science

One of the most challenging and pressing issues confronting DOE and the nation is the safe and cost-effective management of environmental pollutants and the remediation of hazardous waste sites. The DOE is responsible for managing some 40 million cubic meters of contaminated soils and 1.7 trillion gallons of contaminated ground water. At Hanford alone, millions of gallons of highly radioactive and hazardous wastes in hundreds of underground tanks have leaked causing extensive contamination of the soil and groundwater. These issues are National problems. For example, across the US, thousands of Superfund sites exist with various levels and types of contamination ranging from organics (PCBs, carbon tetrachloride, TCE), heavy metals (Hg, Cr, Pb, As), inorganics (phosphates, nitrates) to radionuclides (U, Tc, tritium, Pu, Sr, Cs, Am).

Molecular level processes, such as aqueous complexation or adsorption to different mineral phases, often controls the transport and fate of contaminants in the environment. Unraveling these molecular level phenomena at the mineral/water interface is a key objective of this science theme area. Correspondingly, microorganisms native to DOE contaminated site have a profound affect on the biogeochemical cycling of contaminants and thus greatly influences their transport and fate. Unraveling the molecular processes at the microbe/mineral interface is, therefore, also of fundamental importance. As a result molecular level studies of interfacial geochemistry and biogeochemical reactions has been an active area of research for more than a decade.

Research efforts have progressed from studies of ideal mineral surfaces to more complex heterogeneous interfaces and from studies of batch systems involving whole cells to studies of individual microbe surface proteins or cytochromes. Future molecular level scientific challenges include:

  • Unraveling the importance of coupled processes in mineral surface chemistry. These processes include the impact of surface proton adsorption with electron transport in the solid, the local impact of initial ion adsorption on subsequent adsorption of ions of similar or different type, and the overall coupling of surface transport processes with reactivity.
  • Unraveling the fundamental mechanisms of microbe-mineral attachment. These processes impact the movement of microbes in the subsurface and their impact on in situ bioremediation (also related to the theme area of biological interactions and interfaces).
  • Unraveling the mechanisms of electron transfer between microbes and mineral surfaces. Electron transfer reactions are critical to microbial growth, reduction and immobilization of important DOE contaminants (Tc, U), and subsurface biogeochemistry.

Examples of key technical challenges and what investments are needed to address these issues and develop a robust user program are outlined below.

Development of enhanced in situ probes of mineral surface reactivity.

Examining molecular level processes at the mineral-water interface in real-time under in situ conditions remains a key challenge in interfacial science (see also science of interfacial phenomena below).

Examples of possible investment opportunities include: A high resolution TEM equipped with an environmental cell, development of enhanced spatial resolution in existing mineral surface probes such as XPS, TOF-SIMS, and Auger spectroscopy, a micro-XRD unit to map out mineral assemblages in 3-D, and interfacially sensitive optial methods (SHG, FFG).

Enhanced methods to probe the interactions at the microbe-mineral interface

The microbe-mineral interface presents a special challenge owing to the complexity of both the mineral and microbe surfaces coupled with the relatively confined interfacial region.

Examples of possible investment opportunities include: enhanced capabilities to examine microbial surface structure under hydrated conditions, confocal microscopy to examine microbe surface, and AFM and other probes of microbe/mineral interfaces.

Enhanced capabilities to handle radioactive materials

Many subsurface contamination issues of concern to the DOE result from past releases of radioactive materials. Developing or better utilizing current capabilities in molecular level surface science is a key to understanding the environmental fate and transport of these radionuclides.

Examples of possible investment opportunities include: a "second use" of current EMSL instrumentation in a radiochemical annex or other facility and development of instrumentation that can be miniaturized for use in glove boxes or other smaller atmospheric controlled environments.

Methods and techniques for examining microscale flow and reactivity in confined environments

Many important geochemical reactions take place in relatively confined environments such as rock fractures or between mineral grains where both the local chemical environment and the transport processes are quite different from the bulk solution.

Investment opportunities would relate to upgrading the current EMSL Subsurface Flow and Transport Experimental Laboratory (SFTEL) to examine microscale flow and reactivity in heterogeneous microenvironments. Possible upgrades could include: microfocused X-Ray tomography to obtain 3-D pore structures and NMR methods to measure pore structure and ion diffusion.

Science of Interfacial Phenomena: Tailored Interfacial Structures for Dynamics, Reactivity, and Transport

Material systems with interfaces designed and optimized (tailored) to have specific properties are essential to many technologies needed to maintain a secure environment and obtain a stable energy future for the nation. Hydrogen production and storage, solid-oxide fuel cell research and development, materials for next-generation nuclear reactors, radiation detectors and chemical sensors, the creation of a new generation of selective efficient and stable catalysts, and the development of solid-state lighting are all examples of technical areas that rely on improved understanding and control of molecular-level structural, dynamic, and transport properties of interfaces. This science theme focuses on developing an understanding and gaining control of structure-function relationships at the atomic level that will allow, for example, the design of catalytic activity and selectivity.

In 1990 EMSL identified as a key science challenge the extension of the level of experimental and theoretical understanding available for metal and semiconductor surfaces to metal oxide, hydroxide, layered silicate and other insulating systems. This challenge links into several of the current science theme areas and provided a focus to identification of instrumentation that was included in EMSL. Although major progress has been made in addressing this topic, it remains an important key science challenge. However, the progress in understanding and controlling properties of oxide surfaces and interfaces also leads to (or enables) some possible additional key science challenges including:

  • Expanding our understanding and ability to control the properties of increasingly complex oxide surfaces, interfaces, and films. These materials and the related interfaces are relevant to geochemical and biogeochemical processes and to the creation of films/materials with designed chemical, electronic, magnetic and optical properties related to sensor, detector, catalysis, and energy needs.
  • Developing sufficient understanding of interface mediated chemical and photochemical processes to design catalyst, photocatalyst and other structures with enhanced reactivity and optimized selectivity. Such processes are critical for many different environmentally related applications including contaminant reduction and hydrogen production.
  • Obtaining an understanding of the relationships between electronic excitation processes and atomic mobility. This interaction impacts to the stability (and properties) of inorganic (especially insulating) and organic electronic/optical systems and interfaces, radiation detectors, nuclear materials, and information obtained from experimental probes such as electron microscopy and x-ray measurements.

Examples of key technical challenges and investments needed to address these issues and develop a robust user program:

Develop the ability to grow and characterize complex materials (including oxides and oxide films) with well defined structures, surfaces and interfaces

The ability to create model and novel materials with well defined surfaces and interfaces provides an essential starting point for many studies.

Design of an updated Oxygen Plasma Assisted Molecular Beam Epitaxy system with refined flux control is an example of a possible investment in this area. High resolution characterization tools are also critical possibly including magnetic force probed based NMR, HRTEM, and HRXPS.

Technologies that enable site specific chemistry measurements, real time data collection, and analysis and in situ (or operando) capabilities would significantly facilitate the scientific advances in these areas

The ability to handle specimens without inadvertent exposure to ambient atmosphere is also important for many studies.

Possible investment opportunities include: Advanced TEM capabilities designed to examine chemical reactions, anaerobic specimen transfer capabilities, optical systems designed for real time analysis of interfaces (including second harmonic generation, vibrational spectroscopy, and 3d confocal microscopy), variable temperature scanning probe microscopy, and environmentally controlled micro and real time x-ray spectroscopy.

Technologies that enable the rapid synthesis and characterization of materials along with and other types of enhanced sample throughput methodologies can enhance understanding of many areas where large numbers of variable are important and where statistical data is critical

Investment opportunities include micro-XRD with automated analysis of multiple samples, new generation XPS and other capabilities with more rapid data collection, Focused Ion Beam and other methods that speed preparation of special (TEM, HRAES) samples.

Finally, it is recognized that capabilities at different levels are needed in EMSL to address the science issues. These include routine laboratory equipment, sophisticated versions capabilities that are applicable in a variety of areas and unique "marquee" capabilities that enable science to move into new areas. Although input in all areas is welcome, the primary focus of this workshop is on the unique advanced capabilities that are needed. It may be appropriate, however, for participants to conclude that in some area of science that "new" application of instruments frequently used in a different area can move the field forward.