Results for “Biophysical” — Page 23

DOE OSTI2021

LLNL Low dose-related research

LLNL has a long history of involvement in research into biological and biophysical methods for assessing ionizing radiation dose, and LLNL staff continue to participate in reviews of low dose related data as well as technology development for national security and population health purposes. A list of recent projects and funding agencies is provided in Table 1. LLNL has also maintained expertise in mammalian biology, radiobiology and cancer (computational and biological) over the last 5 years.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2023

2022 American Conference on Neutron Scattering (ACNS 2022)

The 11th American Conference on Neutron Scattering (ACNS 2022) will be held on June 5-9, 2022, in Boulder, CO. The Conference will provide essential information on the breadth and depth of current neutron-related research worldwide. Hosted by the Neutron Scattering Society of America, this year’s Conference will feature a combination of invited and contributed talks, poster sessions, and tutorials. Topics of the conference are: Advances in Neutron Facilities, Instrumentation and Software: Developments in sources, instrumentation, sample environments and control software. Hard Condensed Matter: Magnetism, correlated metals, quantum/topological materials, superconductors, ferroelectrics, multiferroics, glasses, and disorder phenomena. Submissions outlining examples of neutron scattering in industrial and engineering applications involving hard condensed matter systems are also encouraged. Soft Matter: Neutron studies of soft materials and related fields including in situ and in operando studies. Polymers, surfactants, emulsions, gels, nanoparticles, colloidal suspensions and more. Submissions of computational studies or applications of machine learning beneficial to neutron scattering experiments, as well as examples of neutron scattering in industrial and engineering applications are strongly encouraged. Biology, Biophysics and Biotechnology: Neutron studies of biological and biologically relevant systems. Proteins, bio membranes, biological assemblies, natural materials, nucleic acids, drug-delivery platforms and biomedical systems. Submissions of computational studies or applications of machine learning beneficial to biological neutron scattering experiments, as well as examples of neutron scattering in applied research involving biological systems, are strongly encouraged. Materials Chemistry and Energy: Neutron-based studies of functional materials and materials for energy applications. Examples include porous materials such as metal organic frameworks (MOFs), zeolites; phosphors; novel pigments; electrolytes; catalysts; ionic conductors/cathode materials; photovoltaic materials (hybrid perovskites); thermoelectrics; magnetocalorics/electrocalorics. Structural Materials and Engineering: Neutron scattering studies of materials and engineering processes including structural materials, concrete and metals, as well as engineering processes including combustion, corrosion, additive manufacturing, and others. Neutron Physics: Fundamental physical studies of the neutron and related areas. Emerging Applications in Neutron Scattering: Machine Learning and Data Science: Advances in computing power have contributed to rapidly evolving machine learning and data science fields that can be leveraged to the benefit of the neutron scattering community. The purpose of this session is to highlight recent advances in machine learning and data science and to serve as the foundation of a parallel data and computation track highlighting computation advances and applications in neutron scattering throughout the conference.

36 MATERIALS SCIENCE↗

DOE OSTI2023

In planta single-molecule imaging and holographic force spectroscopy to study real-time, multimodal turnover dynamics of polysaccharides and associated carbohydrate metabolites

Cellular production of polysaccharides from simple sugar molecules serves critical roles in a variety of metabolic processes essential to the survival of every living organism. In the context of photosynthetically fixed carbon, cell wall polysaccharides synthesis is particularly of interest for increased biomass accumulation for human food, animal feed, and bioenergy related applications. Despite a long history of research in plant cell biology, our understanding of in planta cell wall biosynthesis and its regulation is far from complete due to lack of a comprehensive microscopy toolkit that encompass the multiple spatial and temporal scales in which cell wall polysaccharides fibrils are synthesized and assembled into intricate cell wall networks. In this project, a multidisciplinary team of scientists from Rutgers University, Vanderbilt University, and Oak Ridge National Laboratory carried out innovative multimodal, multiscale microscopy studies of cell wall synthesis using single-molecule force-spectroscopy, super-resolution fluorescence microscopy, and in vivo live cell imaging. Our novel multimodal and holistic imaging approach revealed plant cell wall polysaccharides synthesis processes in unprecedented detail across multiple spatiotemporal scales, from a single-molecule to a single-cell. Besides, the team has made technical and scientific innovations across multiple research fields—microscopy, bioengineering, single-molecule biophysics, and plant biology, etc.—to accomplish the goals. The results from this project will greatly advance the mechanistic and holistic understanding of in planta cell wall synthesis, which will accelerate the development of better transgenic crops for bioenergy applications. Moreover, the new toolbox, combining powerful advanced microscopy assays with cell/protein engineering, will have broader impacts on molecular and cellular biology fields by paving the way for studying cellular processes occurring across multiple physical scales with multimodal microscopy methodologies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Machine Learning-driven Molecular Design for Therapeutic Discovery

The ongoing novel coronavirus pandemic (COVID-19) has highlighted the need for new therapeutics to counter the threat of emerging viral pathogens. The main proteases are a promising target for developing antiviral inhibitors. In this work, we utilized a novel combination of artificial intelligence-driven iterative design of covalent inhibitor candidates, physics-based computational modeling of protein-inhibitor interactions, and “All in One” Native MS biophysical assay screening and characterization of therapeutic candidates. With our existing expertise in hit generation using a particular scaffold as a starting point, we first generated tens of thousands of compounds that preserve the key scaffold. In order to optimize the candidates, we calculated about 136 descriptors consisting of 2D and 3D features for molecules targeting the SARS-CoV-2 Main protease (Mpro). These compounds were initially filtered according to properties and further sorted by predicted binding affinity using our automated docking modeling and machine learning methods. We tested a handful of candidates and identified two as inhibitors of Mpro with micromolar affinities.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

2023 SAGE-Camp Report

The 7 th Summer Physics Camp for Young Women was successfully held in person in 2023 from June 5 th to 16 th at the New Mexico School for the Arts in Santa Fe, NM at Hilo Intermediate School in Hawaii. This year’s camp was dedicated to the topic of Energy Security and was made possible thanks to the strong collaboration of Los Alamos, Sandia and Hawaii teams and the logistical and financial support of Los Alamos and Sandia National Laboratories, New Mexico Consortium, SAGE- Moore Foundation, LANL Foundation, ACS, IEE, APS four corners, N3B, Hawaii Museum of Science and Technology, New Mexico School for the Arts (NMSA) and Tech Source. The camp mobilized more than 120 volunteers who made the camp a success. The camp is free of charge to the students and included free lunch and snacks for the busy brains to have plenty of energy, also included all materials needed for the hands-on activities (like drone building, crystal structure, solar panels, wind turbine fabrication, soldering, coding etc) and also a stipend for students who attended for the full two weeks and for two educators and two student mentors in NM. The camp offered 32 high school students from New Mexico and 8 from Hawaii a unique opportunity to explore science topics and meet a broad range of role model professionals across STEM fields including astrophysics, cybersecurity, Energy fields, space science, engineering, biophysics, environmental science, robotics, computer science, nuclear engineering, radiological science, physics and chemistry. With nearly 120 volunteers who came mainly from Los Alamos National Laboratory (66%) and Sandia national laboratories (18%), two funded educators from NM, Dr. Weldon Beauchamp and Dr. Ellee Cook, and two educators from Hilo, Dr. Pascale Creek Pinner and LeAnn Ragasa, the camp was educationally sound and extremely varied. The collaboration with school educators is critical for the goal of this camp to not only impact students' lives but also improve STEM education in NM and Hawaii. The ultimate goal of the camp is to increase higher education aspirations of students, empower them to consider careers in STEM and learn more about the opportunities available to them in our local colleges and DOE National Laboratories. In addition, the camp also hired 2 past students as student mentors, Megan Odom and Elisea Jackson, who currently attend NMSA and were students at the camp in 2022 when it was virtual. The in-person camp which aims at empowering under-represented minorities in STEM in our community received more than 52 applications this year from all over NM and 8 applications from Hawaii. Our selection criteria are based on diversity, equity and inclusion, and students for whom the camp can be a life-changing opportunity are given a chance to attend the camp. During COVID, the camp was held virtually and gave the opportunity to students from remote areas in NM and Hawaii to attend from their homes. This year, fantastic families supported students everyday even when home was in remote areas in NM like Lea county, Sandoval county, Bernalillo or Mora county. The organizers hope next year they can offer a residential option for students from remote areas.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2023

Building a Computational and Experimental Rapid Response Pipeline to Counter the Coronavirus Disease 2019 Outbreak and Emerging Biothreats

The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs, especially where protective candidates can be rapidly identified or developed for emerging biothreats and escape variants. Current cutting-edge technologies for this purpose still rely on pathogen-exposed convalescent volunteers and a large screening effort to find a proverbial needle in a haystack. Computational design of protective antibodies based on pre-existing templates skips those requirements and allows for greater control over the breadth and target epitope, while also co-optimizing for potency and developability or other biophysical characteristics. We approached this problem by building and expanding an in vitro experimental rapid antibody production and characterization pipeline to support development of an autonomous, closed loop, active learning software system based on structural simulation and ground truth experimental data to design and evaluate antibody antigen interactions. Starting from early in the pandemic, we targeted SARS-CoV-2, the causative agent of COVID-19, by re-purposing neutralizing antibodies against SARS-CoV-1 that had been identified in the wake of that outbreak in the early 2000’s. We successfully re-targeted three different anti-SARS-CoV-1 antibodies to neutralize SARS-CoV-2 in vitro, where the antibodies were generated externally and tested through conventional binding and neutralization assays internally or with collaborators. As antibodies were identified from the blood of humans infected with SARS-CoV-2, we shifted to collaborate with academic partners to develop improved versions of their human-derived antibodies. This work reached its most important stage in rapid response to the emergence of the Omicron variant of concern (VOC) in late 2021. In a matter of weeks, enabled by on demand innovation to our screening pipeline, we computationally designed and experimentally characterized derivative antibodies of COV2-2130, one of two antibodies from Vanderbilt that form the basis of the AstraZeneca Evusheld prophylactic drug product. This drug product suffers a serious loss of efficacy against Omicron BA.1 and BA.1.1, the first Omicron strains. Due to tight integration of computational design and experimental evaluation, we were able to identify a pair of designs with potent neutralization of the main targets Omicron BA.1 and BA.1.1; but also the earlier Delta variant, and subsequent Omicron strains including BA.2, BA.4, BA.5, and BA.2.75, demonstrating that our multi-target design process can, by its nature, produce robust antibody designs that strictly improve over the parental antibody. These results, recognized by a 2022 Director’s Science and Technology award, have enabled the follow-on GUIDE program, to commence in FY23. While earlier design campaigns were substantially outsourced, we have engineered better and faster processes internally to better compliment, calibrate, and speed computational designs. As part of the follow-on GUIDE program, we will stand up a rapid and high-throughput antibody production and characterization facility staffed with the expertise and capabilities to foster our current collaboration across PLS and ENG as well as other partnerships toward computational design of biologics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

National User Resource for Biological Accelerator Mass Spectrometry

The National User Resource for Biological Accelerator Mass Spectrometry (User Resource) will provide isotopic analysis (primarily radiocarbon or 14C) by accelerator mass spectrometry (AMS) for NIH- funded researchers across the United States and will be the only User Resource of its type in the United States. The User Resource will provide measurement capability and expertise to a research community that requires highly sensitive, quantitative isotope analyses. Since commissioning a new accelerator mass spectrometer in June 2014, we have measured over 4000 samples a year for collaborators and service users. The User Resource will enable us to continue to meet these research needs, as well as provide for new users whose research programs would benefit from AMS as a measurement tool. The User Resource’s forte will be ultra-high sensitivity quantitation of radiocarbon and selected other radioisotopes for research studies where isotopes are required. Radioisotope labeling studies have been and will continue to be an important tool for addressing many complex biomedical science problems. AMS is a specialized and unique type of mass spectrometry that provides absolute quantitation of radiocarbon and other relevant radioisotopes with extreme sensitivity, having limits of detection in real samples on the order of a few attomol/mg of sample at measurement precisions of ~3%. It is the only instrumental method capable of quantifying radioisotope-labeled agents routinely in real-world samples with such precision and sensitivity. The sensitivity of AMS allows for the quantification of radiolabeled metabolites in extremely complex matrices of cells and organisms at very low concentrations and in small samples. AMS allows studies to be conducted without perturbing metabolism leading to more relevant quantification of metabolic rates and pathways. In addition, it enables quantification of pharmacokinetic and metabolic properties of toxicants at environmentally relevant concentrations in model systems as well as the ability to quantify pharmacokinetics and other molecular endpoints directly in humans. Such quantitative assessments can 1) improve risk assessment for toxicants, 2) address safety and efficacy considerations for therapeutic entities, 3) deepen understanding of xenobiotic and intermediary metabolism, 4) help understand the interactions between critical molecular pathways, and 5) improve efforts to model and predict various metabolic and biological states. These capabilities have been applied in a number of areas including research in carcinogenesis, toxicology, nutrition, pharmacology/drug development and basic biological science. As a NIGMS National Resource the National User Resource for Biological Accelerator Mass Spectrometry will help NIH funded scientists achieve a deeper understanding of the etiology of human health concerns by (1) enabling the quantification of pharmacokinetics and other molecular endpoints directly in humans; (2) offering the ability to conduct quantitative studies using biologics such as proteins or lipids, and thereby reducing the amount of radioisotope usage in biomedical labs; and (3) enabling more relevant studies of metabolic pathways in health and disease through the use of much lower, more biologically-relevant, concentrations of metabolic substrates in cells and intact organisms. Such studies support NIGMS’s basic biomedical research areas that contribute to the understanding of fundamental cellular and physiological principles and enable research supported by the Biophysics, Biomedical Technology, and Computational Biosciences (BBCB); Genetics and Molecular, Cellular, and Developmental Biology (GMCDB); Pharmacology, Physiology, Biological Chemistry (PPBC) and Training, Workforce Development, and Diversity (TWD) Divisions.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

Automated AI-driven Molecular Design for Therapeutic Discovery

In recent years, artificial intelligence and machine learning (AI/ML) approaches have revolutionized the process of designing new therapeutics, enabling scientists to rapidly respond to emerging threats from various pathogens. A prime example is the SARS-CoV-2 main protease, a key target for the development of antiviral inhibitors. In this study, we employed a novel, integrated approach that combines AI-driven iterative design of inhibitor candidates, screening based on physio-chemical properties and toxicity, physics-based computational modeling of protein-inhibitor interactions, and AI-assisted analysis of Native MS biophysical assay and characterization of designed candidates. Our deep learning 3D-scaffold model, which uses an input scaffold as a starting point, generated tens of thousands of compounds while preserving the key scaffold. To optimize these candidates, we calculated a comprehensive set of 136 descriptors, including both 2D and 3D molecular features, for compounds targeting the SARS-CoV-2 Main protease (Mpro) and a neurodegenerative disease-associated protein, cyclophilin (Cyp). The generated compounds were initially filtered based on their properties and then ranked according to their predicted binding affinity using our automated modeling and ML methods. Experimental validation of the Mpro candidates showing inhibitory activity demonstrates that our workflow can expedite the therapeutic discovery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Bringing Inorganic Carbon to Life: Developing Model Metalloenzymes for C1 Conversion Reactions

The global carbon cycle is carefully balanced through the use of specialized enzymes in plants, algae, bacteria, and archaea. A primordial metabolic pathway for the conversion of inorganic carbon into cellular biomass uses a large, nickel-containing enzyme called carbon monoxide dehydrogenase (CODH)/acetyl coenzyme A synthase (ACS). This system fixes carbon dioxide (CO 2 ) into carbon monoxide (CO) at the CODH site. The carbon monoxide is then used to generate acetyl coenzyme A, a biological building block, through a key carbon-carbon bond forming step at the nickel site in ACS. Despite the significance of these processes in the context of energy conversion, the fundamental chemistry underlying these transformations has remained elusive, in part due to the complexity of the natural enzyme. To better understand the principles governing these biological processes, which represent one-carbon (C 1 ) activation reactions, this project will develop functional models of CODH and ACS based on modifications to a small metalloprotein scaffold. Comprehensive characterization of these systems using advanced spectroscopic and biophysical techniques will reveal key elements responsible for conferring high levels of activity to the model systems, with implications for gaining insight into the mechanisms of the natural enzymes. Moreover, the principles learned from this research can be used to guide design of robust catalysts for efficient conversion of CO 2 and CO into liquid fuels.

10 SYNTHETIC FUELS↗

DOE OSTI2024

Oak Ridge National Laboratory Neutron Spin Echo Beamline on NB-2

Neutron Spin Echo (NSE) spectroscopy uniquely measures the Q-dependence of slow relaxation dynamics, and having such a machine at HFIR will advance polarized neutron spectroscopy and promote the study of biophysical and energy materials using neutrons. The 2018 Instrument Advisory Board (IAB) advises Neutron Sciences Directorate, ORNL to upgrade the cold neutron delivery system at HFIR, addressing geometrical challenges in neutron transfer from the bright cold source. This is being optimized now: the entrance to the guide system is moving closer to the source, and more guides are being added. However, there are still significant challenges to making the cold flux at the sample world-class. With the proposed guide system, NB-2 can deliver more than 10 6 polarized neutrons per cm 2 /sec below 8Å, and probably 10Å with further optimization. With no potential for running user experiments with neutrons longer than 15Å, the utility of such a machine for biological studies is limited. However, there is a large demand for this class of spectrometer in materials science, chemical engineering, and nanotechnology. Workshops held over the past decade and the three-source vision have highlighted the community's need for a low-angle, high-energy resolution spectrometer at HFIR. A detailed design study of this spectrometer is needed, focusing on optimizing the neutron delivery system for SANS-type studies. This neutron spectrometer would complement studies already performed on both SNSNSE and BASIS by overlapping and extend the dynamic range accessible, while acknowledging the proposed machine, EXPANSE, at the Second Target Station. Two technologies currently exist for such a spectrometer: traditional DC solenoids like those on BL-15 at SNS and IN15 at the ILL, and RF-flipper-based machines similar to RESEDA at FRMII. Either instrument would satisfy the scientific justification. However, there are strong business and scientific cases to utilize the thermal flux, the resonant expertise developed at ORNL, and the potential to utilize an entangled beam of neutrons to probe quantum matter by adopting the neutron resonant spin-echo configuration.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

National User Resource for Biological Accelerator Mass Spectrometry (Final Report)

The National User Resource for Biological Accelerator Mass Spectrometry (User Resource) will provide isotopic analysis (primarily radiocarbon or 14C) by accelerator mass spectrometry (AMS) for NIH- funded researchers across the United States and will be the only User Resource of its type in the United States. The User Resource will provide measurement capability and expertise to a research community that requires highly sensitive, quantitative isotope analyses. Since commissioning a new accelerator mass spectrometer in June 2014, we have measured over 4000 samples a year for collaborators and service users. The User Resource will enable us to continue to meet these research needs, as well as provide for new users whose research programs would benefit from AMS as a measurement tool. The User Resource’s forte will be ultra-high sensitivity quantitation of radiocarbon and selected other radioisotopes for research studies where isotopes are required. Radioisotope labeling studies have been and will continue to be an important tool for addressing many complex biomedical science problems. AMS is a specialized and unique type of mass spectrometry that provides absolute quantitation of radiocarbon and other relevant radioisotopes with extreme sensitivity, having limits of detection in real samples on the order of a few attomol/mg of sample at measurement precisions of ~3%. It is the only instrumental method capable of quantifying radioisotope-labeled agents routinely in real-world samples with such precision and sensitivity. The sensitivity of AMS allows for the quantification of radiolabeled metabolites in extremely complex matrices of cells and organisms at very low concentrations and in small samples. AMS allows studies to be conducted without perturbing metabolism leading to more relevant quantification of metabolic rates and pathways. In addition, it enables quantification of pharmacokinetic and metabolic properties of toxicants at environmentally relevant concentrations in model systems as well as the ability to quantify pharmacokinetics and other molecular endpoints directly in humans. Such quantitative assessments can 1) improve risk assessment for toxicants, 2) address safety and efficacy considerations for therapeutic entities, 3) deepen understanding of xenobiotic and intermediary metabolism, 4) help understand the interactions between critical molecular pathways, and 5) improve efforts to model and predict various metabolic and biological states. These capabilities have been applied in a number of areas including research in carcinogenesis, toxicology, nutrition, pharmacology/drug development and basic biological science. As a NIGMS National Resource the National User Resource for Biological Accelerator Mass Spectrometry will help NIH funded scientists achieve a deeper understanding of the etiology of human health concerns by (1) enabling the quantification of pharmacokinetics and other molecular endpoints directly in humans; (2) offering the ability to conduct quantitative studies using biologics such as proteins or lipids, and thereby reducing the amount of radioisotope usage in biomedical labs; and (3) enabling more relevant studies of metabolic pathways in health and disease through the use of much lower, more biologically-relevant, concentrations of metabolic substrates in cells and intact organisms. Such studies support NIGMS’s basic biomedical research areas that contribute to the understanding of fundamental cellular and physiological principles and enable research supported by the Biophysics, Biomedical Technology, and Computational Biosciences (BBCB); Genetics and Molecular, Cellular, and Developmental Biology (GMCDB); Pharmacology, Physiology, Biological Chemistry (PPBC) and Training, Workforce Development, and Diversity (TWD) Divisions. Over the next five years, our goals are to: 1. Improve the efficiency of operation for AMS measurements through installation of new interfaces to our AMS systems, technical modifications to improve gas accepting ion source efficiency and upgrading our data analysis software for improved ease of use and data reporting. 2. Increase the accessibility and visibility of ultra-sensitive 14C measurements for the biomedical research community by training of new investigators and expanding our national user base. 3. Provide high throughput, ultra-sensitive 14C analysis for the NIGMS and NIH user community.

47 OTHER INSTRUMENTATION↗

DOE OSTI2026

Assembly and Repair of the Photosystem II Reaction Center

This project investigated the biochemical and biophysical mechanisms governing assembly and repair of Photosystem II (PSII), the membrane protein complex responsible for solar-driven water oxidation in oxygenic photosynthesis. The work focused on three integrated areas: (1) protein–protein interactions that facilitate PSII assembly in cyanobacterial biogenesis centers, (2) the chemical mechanism of photo-assembly of the Mn 4 CaO 5 oxygen-evolving complex (OEC), and (3) mechanisms that target PSII reaction centers for degradation and repair in photosynthetic organisms. Using electron paramagnetic resonance spectroscopy, protein biochemistry, molecular genetics, quantitative mass spectrometry, and computational modeling, the project demonstrated that proton release events limit early steps of OEC assembly and that chloride and calcium ions facilitate Mn oxidation and intermediate stabilization. Complementary studies identified chaperone recruitment mechanisms in cyanobacterial PSII biogenesis centers and translation and protease factors involved in PSII turnover in Chlamydomonas. Together, these results establish proton management and coordinated protein quality control as central design principles in PSII assembly and repair and provide mechanistic insight relevant to biological and artificial photosynthetic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

A Data-driven Phytotechnology Framework for Identification and Remediation of Leached-Metals-Contaminated Soil Near Coal Ash Impoundments

This project developed and evaluated advanced remote sensing and machine learning approaches to identify, monitor, and address environmental contamination associated with coal combustion residual (CCR) impoundments and landfills at coal-fired power plants. In Phase I, historical and multi-temporal Sentinel-2 satellite imagery, groundwater monitoring data, and environmental variables were integrated to detect vegetation stress potentially caused by toxic metal leaching from coal ash disposal sites. Multiple vegetation and biophysical indices were analyzed to determine their effectiveness in identifying abnormal vegetation growth patterns linked to contamination. Results from case studies conducted at coal ash–impacted power plant sites in North Carolina and Virginia demonstrated that satellite-based vegetation monitoring can serve as an effective early indicator of environmental stress associated with metals such as arsenic, cadmium, cobalt, lead, lithium, radium, and thallium.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2026

Project 2.8: Biological Specimen Repository for the Mayak Project

Curation of the existing specimens, including Standard Operating Procedures: The Southern Urals Biophysics Institute (SUBI) will continue to manage the day-to-day operations of the biorepository, but will have to assume the financial costs of maintaining and purchasing equipment such as freezers; Standard Operating Procedures are already in place for all aspects of the operations, and the Georgetown University team will be available on a voluntary and ad hoc basis to answer any technical questions in the future. Acquisition and tracking of new specimens: SUBI will decide on the collection of new tissues and blood samples in the future, and on what scale, depending on available resources and research needs. The Georgetown University team is willing to provide advice on a voluntary and ad hoc basis. Procedures for receiving and approving specimen requests from users: SUBI can take over this function; Chris Loffredo and other qualified research scientists at Georgetown University would be willing to serve as Tissue Review Committee members on a voluntary and ad hoc basis. Biospecimens remaining at Georgetown University: pursuant to the original terms of the Biospecimen Transfer Agreement between SUBI and Georgetown University, all unused portions of specimens (FFPE blocks, slides, and frozen tissues) will be returned to SUBI at the conclusion of the approved scientific research for which they were transferred. It was anticipated that the return shipment of biospecimens would occur in the fall of 2023. However, at this time, due to international developments, there are no shipping companies who can provide such deliveries to Russia. For now, the biospecimens can remain at Georgetown University where they are stored at the Genomics and Epigenomics Shared Resource. There have not been any storage costs to date, but this could change in the future.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

A tale of two extremes: Temperature sensitivity of carbon loss from cool and hot soils

Soils represent the largest terrestrial carbon (C) pool, and the flux of carbon dioxide (CO 2 ) from soils to the atmosphere is ~ 6-10 times more than anthropogenic emissions. Understanding responses of soil CO 2 emissions to warming is crucial for evaluating feedback to ongoing environmental changes. The relationship between microbial respiration and temperature is typically modeled using a Q 10 function. Generally, observations of the apparent Q 10 of soil respiration are higher for cold vs. warm ecosystems, reflecting expected biophysical controls of Arrhenius kinetics. However, results from two field warming experiments in the tropics contradict this expectation, both observing extraordinarily high soil respiration responses to in situ warming. Our overall objective for the proposed work is to reduce uncertainty in temperature sensitivity of soil C loss by systematically synthesizing underlying mechanisms related to soil C turnover and stabilization. We are evaluating the temperature sensitivity of soil respiration in ecosystems across temperature extremes (e.g., arctic/boreal and tropical systems) by integrating data collected from field warming experiments with machine learning and biogeochemical models.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Residue Retention Requirement (Crop Residues)

County-level minimum residue (dry tons/acre/year) required to remain on fields to maintain soil carbon and limit erosion; defines the biophysical constraint on residue removal.

crop residue↗

DOE OSTI2020

Integrated Hydro-Terrestrial Modeling: Development of a National Capability

Water is one of our most important natural resources and is essential to our national economy and security. Multiple federal government agencies have mission elements that address national needs related to water. Each water-related agency champions a unique science and/or operational mission focused on advancing a portion of the nation’s ability to meet our water-related challenges. These diverse mission needs have engendered a rich and extensive base of water-related data and modeling capabilities. While useful for their intended purposes, these capabilities are not well integrated to address complex regional problems and overarching national problems. These major investments by a number of federal agencies, however, lay the foundation for an integrated hydro-terrestrial modeling and data infrastructure that will enhance knowledge, understanding, prediction, and management of the nation’s diverse water challenges. Creating a more seamless national hydro-terrestrial modeling and data capacity presents an enormous opportunity to advance operational as well as research capabilities leading to more effective water management. Advances are necessary not only in operational tools for forecasting but also in research to identify and resolve knowledge and data gaps that lead to unacceptable uncertainties in forecast outcomes. As such, close coordination across scientific, operational, and resource management communities is required. To this end, an interagency workshop on “Integrated Hydro-Terrestrial Modeling: Development of a National Capacity” was held at the National Science Foundation (NSF) headquarters in Alexandria, Virginia in September 2019, led jointly by the NSF, the U.S. Department of Energy (DOE) and the U.S. Geological Survey (USGS) and with broader interagency support provided through an interagency steering committee. This workshop provided a venue to bring together representatives of water-related agencies and their scientific partners (including university researchers) to initiate and refine a vision for a national Integrated Hydro-Terrestrial Modeling (IHTM) and data infrastructure and advance ideas towards its development. The workshop was designed to address three critical foci to advance the development of a national IHTM capacity: “Priority Water Challenges” around which to motivate and initiate development; Technical and methodological obstacles related to data and modeling; Organizational, structural, and cultural barriers that heretofore have impeded integration of capabilities across the federal and research landscapes. The following “Priority Water Challenge” domain areas represent targets for initiating development of the IHTM and were identified and selected in alignment with priorities of the administration’s Water Sub-Cabinet: (1) Nutrient loading, hypoxia, and harmful algal blooms; (2) Water availability in the western United States; and (3) Extreme weather-related water hazards. These water challenges span agency mission boundaries and encompass a broad range of geographies, complex system dynamics and feedbacks, and critical processes spanning hydrological, climatic, and biophysical systems as well as land-use/land-cover, agricultural, built infrastructure, societal, economic, and decisional environments. These three Priority Water Challenges cannot be fully addressed without leveraging complementary and synergistic capabilities across multiple agencies.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2020

Validation of the Community Land Model Version 5 over the Contiguous United States (CONUS) using in-situ and remote sensing datasets

The Community Land Model (CLM) is an effective tool to simulate the biophysical and biogeochemical processes and their interactions with the atmosphere. Although CLM Version 5 (CLM5) constitutes various updates in these processes, its performance in simulating energy, water and carbon cycles over the Contiguous United States (CONUS) at scales which land surface changes and hydrometeorological and hydroclimatological applications are more locally relevant is yet to be assessed. In this study, we conducted three simulations at 0.125? during 1979-2018 over the CONUS using different configurations of CLM, namely CLM5-biogeochemistry (CLM5BGC), CLM4.5BGC, and CLM5-satellite phenology (CLM5SP). We validated and compared their simulations against multiple remote-sensed and in-situ datasets. Overall, the parametric and structural updates (e.g., carbon cost for nitrogen uptake, variable soil thickness, dry surface layer) in CLM5 improve its ability in capturing terrestrial biogeochemical dynamics. The low evapotranspiration in CLM5BGC is associated with biases in simulating vegetation phenological characteristics rather than soil water limitations. The mismatch between CLM5BGC-simulated peak leaf area index and reference data can be attributed to CLM5BGC's inability in simulating phenology of trees and grasses. The differences between CLM-simulated irrigation and reference estimates can be attributed to differences between processes represented in models and in reality, and uncertainties in input and validation datasets. Evaluation against observations at small catchments suggest that hydrologic parameters needed to be calibrated to improve simulations of runoff, especially subsurface runoff. Additional efforts are needed to incorporate spatially-distributed plant phenology and physiology parameters and regional-specific agricultural management practices (e.g., planting, harvest).

54 ENVIRONMENTAL SCIENCES↗