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DOE OSTI2021

New high-throughput endstation to accelerate the experimental optimization pipeline for synchrotron X-ray footprinting

Synchrotron X-ray footprinting (XF) is a growing structural biology technique that leverages radiation-induced chemical modifications via X-ray radiolysis of water to produce hydroxyl radicals that probe changes in macromolecular structure and dynamics in solution states of interest. The X-ray Footprinting of Biological Materials (XFP) beamline at the National Synchrotron Light Source II provides the structural biology community with access to instrumentation and expert support in the XF method, and is also a platform for development of new technological capabilities in this field. Hee, the design and implementation of a new high-throughput endstation device based around use of a 96-well PCR plate form factor and supporting diagnostic instrumentation for synchrotron XF is described. This development enables a pipeline for rapid comprehensive screening of the influence of sample chemistry on hydroxyl radical dose using a convenient fluorescent assay, illustrated here with a study of 26 organic compounds. The new high-throughput endstation device and sample evaluation pipeline now available at the XFP beamline provide the worldwide structural biology community with a robust resource for carrying out well optimized synchrotron XF studies of challenging biological systems with complex sample compositions.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

NASA NTRSDate not supplied

Enabling Open and Interoperable Science: Multi-Omics Data Processing Platform with NASA GeneLab Standardized Bioinformatics Workflows for Space and Earth Research

Multi-omics biological data continues to be generated at an astounding pace. Genomics, transcriptomics, metabolomics, and proteomics, or collectively known as multi-omics data, are used to assess biological functions, and provide invaluable insights into human, animal, plant, and environmental health both on Earth and in Space. Despite the abundance of these valuable data, the need for bioinformatics expertise, particularly as it relates to the niche filed of space biology, and a lack of accessible resources for processing these data limit their usefulness in deriving biological insights. The NASA Open Science Data Repository (OSDR) provides access to omics data from various spaceflight and analog studies. To enhance the accessibility and reusability of these data, GeneLab (part of OSDR) designs and implements standardized, community-driven, open-source bioinformatics workflows to transform raw omics data into standardized processed data. Currently, GeneLab-processed data from hundreds of space studies have been reused for meta-analyses. This has led to new insights and scientific publications that extend beyond the initial research, thereby enriching our understanding of molecular-scale biological responses to the space environment. To make these bioinformatics workflows open and accessible, GeneLab teamed up with DOE-funded initiatives, including the National Microbiome Data Collaborative (NMDC), to create the NASA EDGE [Empowering the Development of Genomics Expertise] Bioinformatics web-based platform. NASA EDGE utilizes shared compute resources to run the GeneLab standardized bioinformatics workflows, which eliminates the need for researchers to have their own high performance computing cluster. The web-based platform makes complicated biological analyses incredibly easy to perform, thus expanding the reach of these analyses to bioinformatics novices, students, and even citizen scientists enabling them to contribute to scientific discoveries and progress. The authors will demonstrate how the NASA EDGE platform can be used to process microbial omics data hosted on OSDR as well as user-generated omics datasets using GeneLab’s standard workflows.

Amanda M. Saravia-Butler↗

DOE OSTI2023

Emergence of Unstable Focused Flow Induced by Variable‐Density Flows in Vertical Fractures

Abstract Fluids with different densities often coexist in subsurface fractures and lead to variable‐density flows that control subsurface processes such as seawater intrusion, contaminant transport, and geologic carbon sequestration. In nature, fractures have dip angles relative to gravity, and density effects are maximized in vertical fractures. However, most studies on flow and transport through fractures are often limited to horizontal fractures. Here, we study the mixing and transport of variable‐density fluids in vertical fractures by combining three‐dimensional (3D) pore‐scale numerical simulations and visual laboratory experiments. Two miscible fluids with different densities are injected through two inlets at the bottom of a fracture and exit from an outlet at the top of the fracture. Laboratory experiments show the emergence of an unstable focused flow path, which we term a “runlet.” We successfully reproduce the unstable runlet using 3D numerical simulations and elucidate the underlying mechanisms triggering the runlet. Dimensionless number analysis shows that the runlet instability arises due to the Rayleigh‐Taylor instability (RTI), and flow topology analysis is applied to identify 3D vortices that are caused by the RTI. Even under laminar flow regimes, fluid inertia is shown to control the runlet instability by affecting the size and movement of vortices. Finally, we confirm the emergence of a runlet in rough‐walled fractures. Since a runlet dramatically affects fluid distribution, residence time, and mixing, the findings in this study have direct implications for the management of groundwater resources and subsurface applications.

Environmental Sciences & Ecology↗

DOE OSTI2025

Structural biology at the National Synchrotron Light Source II

The structural biology program at the National Synchrotron Light Source II presents a coordinated set of instruments, software and research opportunities for the interested user. We describe in some detail the research capabilities enabled by the Center for BioMolecular Structure. The evolution of the resources is described in detail, considering three major themes: automation, micro-focusing and computation prediction.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Distributed Acoustic Sensing as a Distributed Hydraulic Sensor in Fractured Bedrock

Distributed acoustic sensing (DAS) was originally intended to measure oscillatory strain at frequencies of 1 Hz or more on a fiber optic cable. Recently, measurements at much lower frequencies have opened the possibility of using DAS as a dynamic strain sensor in boreholes. A fiber optic cable mechanically coupled to a geologic formation will strain in response to hydraulic stresses in pores and fractures. A DAS interrogator can measure dynamic strain in the borehole, which can be related to fluid pressure through the mechanical compliance properties of the formation. Because DAS makes distributed measurements, it is capable of both locating hydraulically active features and quantifying the fluid pressure in the formation. We present field experiments in which a fiber optic cable was mechanically coupled to two crystalline rock boreholes. The formation was stressed hydraulically at another well using alternating injection and pumping. The DAS instrument measured oscillating strain at the location of a fracture zone known to be hydraulically active. Rock displacements of less than 1 nm were measured. Laboratory experiments confirm that displacement is measured correctly. These results suggest that fiber optic cable embedded in geologic formations may be used to map hydraulic connections in three-dimensional fracture networks. A great advantage of this approach is that strain, an indirect measure of hydraulic stress, can be measured without beforehand knowledge of flowing fractures that intersect boreholes. The technology has obvious applications in water resources, geothermal energy, CO 2 sequestration, and remediation of groundwater in fractured bedrock.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Genomes to Structure and Function Workshop Report 2022

The goal of the U.S. Department of Energy (DOE) Biological and Environmental Research (BER) Program is to achieve a predictive understanding of complex biological, earth, and environmental systems with the aim of advancing the nation’s energy and infrastructure security. (https://www.energy.gov/science/ ber/biological-and-environmental-research). To pursue this goal, collaborations among experts in diverse research areas that lead to multidisciplinary projects are indispensable. The roles of DOE’s User Facilities, which offer unique and powerful resources for such research projects, are evolving, and expectations for the facilities are increasing. To respond to Users’ needs, the Joint Genome Institute (JGI) and Environmental Molecular Sciences Laboratory (EMSL) initiated the Facilities Integrating Collaborations for User Science (FICUS) program in 2014. This collaboration has grown into a popular and successful program, advancing more than 100 multidisciplinary projects to date. Similarly, the new interFacility collaborations among the JGI, EMSL, and User resources for BER structural biology and imaging at the Basic Energy Science (BES) Program’s synchrotron and neutron facilities are becoming essential for cutting-edge transdisciplinary science. To further explore the need for the BER research community to combine genomic, functional, and structural approaches to advance their research, an organizing committee was formed to develop and jointly host a 3-part workshop. The committee’s members represented seven DOE National Laboratory User Facilities (Appendix 1 lists the members). The “Genomes to Structure and Function” virtual workshop (see Appendices 2–5) was composed of three sessions. The first session, titled “Molecular Structures” (October 27– 28, 2021), highlighted diverse integrative experimental and computational approaches correlating structural data with sequencing and functional information, as well as predicting protein structures to model complex biological systems. The second session, “Intracellular Organization, and Material Synthesis and Decomposition” (December 15–16, 2021), covered imaging methods for observing, quantifying, and manipulating biosystems. The third session, “Imaging the Rhizosphere and Cellular Organization” (January 26–27, 2022) emphasized advanced and non-invasive imaging techniques applied to plant root-microbe-soil interactions.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRSDate not supplied

NASA Institutional Scientific Collection and Biospecimen Sharing Program at Ames Research Center

For decades, NASA and their international partners have flown and conducted non-human biological experiments in space to understand the effects of spaceflight and address potential biological hazards. It is imperative to understand the basic science and health risks associated with spaceflight, along with developing countermeasures, as humanity ventures back to the Moon, and then to Mars and beyond. Sending organisms into space is a costly endeavor which makes space-flown biological specimens a valuable resource. To enable maximum scientific return, samples not required by the Principal Investigators are harvested, preserved and archived in NASA’s Institutional Scientific Collection (ISC) at Ames Research Center (ARC). These specimens are collected according to well-established SOPs that maintain their quality and integrity. To enable new discoveries, the samples are then made available to the international scientific community through NASA’s Biospecimen Sharing Program (BSP). The NASA ISC currently stores over 32,000 specimens from Shuttle, International Space Station and ground-based investigations. Tissues are predominantly from mice and rats, though samples are also available from bacteria and quail. The specimens include tissues from all biological systems including musculoskeletal, neurosensory, reproductive, respiratory, circulatory, and digestive and are stored at -80°C, -20°C, +4°C, or ambient. Descriptive metadata is available for all samples. Historically, these tissues have been used for a wide range of analyses, including histology, genomics, and transcriptomics. Also available through the ISC are tissue from NASA’s Space Radiation Laboratory. To study the effects of space radiation, researchers irradiate biological specimens and unused samples are made available through the LSDA. These biospecimens and data are made available through the public Life Sciences Data Archive (LSDA) website to promote basic discovery, pre-clinical and clinical science. Visit the NASA ISC-BSP website for more information. Websites: https://lsda.jsc.nasa.gov/ ; https://www.nasa.gov/ames/research/space-biosciences/isc-bsp

Space Flown Biospecimens↗

NASA NTRSDate not supplied

NASA Institutional Scientific Collection and Biospecimen Sharing Program at Ames Research Center

Space Flown Biospecimens↗

DOE OSTI2024

Wastewater reuse benefits for municipal complete retention lagoons: Life cycle assessment and dynamic modeling

Complete retention lagoons with wastewater reuse for agricultural purposes may offer sustainability advantages over alternative systems for small communities in semiarid regions. This study quantifies the environmental life cycle impact of adopting agriculture water reuse systems using case study data to estimate operating and building infrastructure impacts and spatial–temporal modeling to quantify resource trade-offs. Water reuse system benefits are highly dependent on supply–storage–demand dynamics. The relative size of irrigated agricultural land to the lagoon size was the most significant factor influencing site water application rates. The benefits are sensitive to changes in air emissions occurring from the agricultural land and further emphasize the importance of proper fertilizer management when adopting water reuse systems. Wastewater reuse from complete retention lagoons reduce life cycle GHG emissions, primarily through excavation reductions, offset fertilizer use, and especially from increased crop yields from wastewater reuse at previously rainfed sites.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in Panicum hallii

The morphological diversity of the inflorescence determines flower and seed production, which is critical for plant adaptation. Hall's panicgrass (Panicum hallii, P. hallii) is a wild perennial grass that has been developed as a model to study perennial grass biology and adaptive evolution. Highly divergent inflorescences have evolved between the 2 major ecotypes in P. hallii, the upland ecotype (P. hallii var hallii, HAL2 genotype) with compact inflorescence and large seed and the lowland ecotype (P. hallii var filipes, FIL2 genotype) with an open inflorescence and small seed. Here we conducted a comparative analysis of the transcriptome and DNA methylome, an epigenetic mark that influences gene expression regulation, across different stages of inflorescence development using genomic references for each ecotype. Global transcriptome analysis of differentially expressed genes (DEGs) and co-expression modules underlying the inflorescence divergence revealed the potential role of cytokinin signaling in heterochronic changes. Comparing DNA methylome profiles revealed a remarkable level of differential DNA methylation associated with the evolution of P. hallii inflorescence. We found that a large proportion of differentially methylated regions (DMRs) were located in the flanking regulatory regions of genes. Intriguingly, we observed a substantial bias of CHH hypermethylation in the promoters of FIL2 genes. The integration of DEGs, DMRs, and $K_a$/$K_s$ ratio results characterized the evolutionary features of DMR-associated DEGs that contribute to the divergence of the P. hallii inflorescence. This study provides insights into the transcriptome and epigenetic landscape of inflorescence divergence in P. hallii and a genomic resource for perennial grass biology.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1992

A hybrid regenerative water recovery system for lunar/Mars life support applications

Long-duration manned space missions will require integrated biological and physicochemical processes for recovery of resources from wastes. This paper discusses a hybrid regenerative biological and physicochemical water recovery system designed and built at NASA's Crew and Thermal Systems Division at Johnson Space Center. The system is sized for a four-person crew and consists of a two-stage, aerobic, trickling filter bioreactor; a reverse osmosis system; and a photocatalytic oxidation system. The system was designed to accommodate high organic and inorganic loadings and a low hydraulic loading. The bioreactor was designed to oxidize organics to carbon dioxide and water; the reverse osmosis system reduces inorganic content to potable quality; and the photocatalytic oxidation unit removes residual organic impurities (part per million range) and provides in situ disinfection. The design and performance of the hybrid system for producing potable/hygiene water is described. Aspects of the system such as closure, automation and integration are discussed and preliminary results presented.

Verostko, Charles E.↗

DOE OSTI2021

Using Complex Probability Amplitudes to Simulate Solute Transport in Composite Porous Media

Probability amplitudes are fundamental to quantum mechanics and offer robust descriptions of complicated systems, which have allowed physicists to explain behaviors inaccessible to classical physics. This article ponders how some of the same conceptual underpinnings of the mathematics used for modeling quantum systems might be applied to subsurface water resources problems and speculates how these tools could facilitate applications on quantum computers. A probability amplitude-based model for describing advective-dispersive transport in porous media using linear operators is investigated. The proposed complex valued model decomposes spreading into two “sub-continuum partial dispersion” coefficients, and this recovers classical spreading when the sum of these coefficients is the Fickian dispersion coefficient. However, the probability amplitudes have a manyto-one relationship to a probability distribution, so it embeds a level of heterogeneity into seemingly equivalent functions. Two propagators with different sub-continuum coefficients may have the same macroscopic behavior when either is considered in isolation, but when they act on the other the system’s behavior changes. Additionally, differences in the amplitudes cause a reduction in spreading as velocity correlations are disrupted, despite both propagators having identical dispersion coefficients, and this cannot be achieved using classical methods without changing the dispersion coefficient. The main point is that these amplitude-based models offer a way to embed information about the system into the propagators, instead of just “averaging it out” when making an upscaled model.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Bayesian Poroelastic Aquifer Characterization From InSAR Surface Deformation Data. Part I: Maximum A Posteriori Estimate

Characterizing the properties of groundwater aquifers is essential for predicting aquifer response and managing groundwater resources. In this work, we develop a high-dimensional scalable Bayesian inversion framework governed by a three-dimensional quasi-static linear poroelastic model to characterize lateral permeability variations in groundwater aquifers. In this work, we determine the maximum a posteriori (MAP) point of the posterior permeability distribution from centimeter-level surface deformation measurements obtained from Interferometric Synthetic Aperture Radar (InSAR). The scalability of our method to high parameter dimension is achieved through the use of adjoint-based derivatives, inexact Newton methods to determine the MAP point, and a Mat´ern class sparse prior precision operator. Together, these guarantee that the MAP point is found at a cost, measured in number of forward/adjoint poroelasticity solves, that is independent of the parameter dimension. We apply our methodology to a test case for a municipal well in Mesquite, Nevada, in which InSAR and GPS surface deformation data are available. We solve problems with up to 320,824 state variable degrees of freedom (DOFs) and 16,896 parameter DOFs. A consistent treatment of noise level is employed so that the aquifer characterization result does not depend on the pixel spacing of surface deformation data. Our results show that the use of InSAR data significantly improves characterization of lateral aquifer heterogeneity, and the InSAR-based aquifer characterization recovers complex lateral displacement trends observed by independent daily GPS measurements.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Differentiable, Learnable, Regionalized Process-Based Models With Multiphysical Outputs can Approach State-Of-The-Art Hydrologic Prediction Accuracy

Predictions of hydrologic variables across the entire water cycle have significant value for water resources management as well as downstream applications such as ecosystem and water quality modeling. Recently, purely data-driven deep learning models like long short-term memory (LSTM) showed seemingly insurmountable performance in modeling rainfall runoff and other geoscientific variables, yet they cannot predict untrained physical variables and remain challenging to interpret. Here, we show that differentiable, learnable, process-based models (called δ models here) can approach the performance level of LSTM for the intensively observed variable (streamflow) with regionalized parameterization. We use a simple hydrologic model HBV as the backbone and use embedded neural networks, which can only be trained in a differentiable programming framework, to parameterize, enhance, or replace the process-based model's modules. Without using an ensemble or post-processor, δ models can obtain a median Nash-Sutcliffe efficiency of 0.732 for 671 basins across the USA for the Daymet forcing data set, compared to 0.748 from a state-of-the-art LSTM model with the same setup. For another forcing data set, the difference is even smaller: 0.715 versus 0.722. Meanwhile, the resulting learnable process-based models can output a full set of untrained variables, for example, soil and groundwater storage, snowpack, evapotranspiration, and baseflow, and can later be constrained by their observations. Both simulated evapotranspiration and fraction of discharge from baseflow agreed decently with alternative estimates. The general framework can work with models with various process complexity and opens up the path for learning physics from big data.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Hydroxyl radical‐driven transformations of bisphenol A and 2,4‐dinitroanisole: Experimental and computational analysis

Abstract This study used experimental and computational analysis to investigate the advanced oxidation of bisphenol A (BPA) and 2,4‐dinitroanisole (DNAN). The pseudo first‐order reaction rate constants depended on the molar peroxide ratio and were between 0.13 and 0.28 min −1 for BPA and between 0.018 and 0.032 min −1 for DNAN. The kinetic differences appear to be due in part to the energy requirements for oxidation, which depended on the reaction mechanism but were typically lower for BPA than they were for DNAN. Density functional theory (DFT) was used to develop transformation pathways that included experimentally‐detected byproducts. The most energetically favored pathway for BPA oxidation begins with the formation of hydroxylated derivatives, while for DNAN, the most energetically favorable degradation pathway begins with the substitution of the methoxy group. Overall, these findings demonstrate the power of combining experimental and computational tools to reveal transformation mechanisms during water treatment. Practitioner Points Advanced oxidation transformations for two emerging water pollutants, bisphenol A and dinitroanisole, was investigated. The observed reaction kinetics depended on molar peroxide ratio in a manner that is in keeping with previous findings. Density functional theory‐based analysis revealed reaction energy requirements and degradation pathways.

Engineering↗

DOE OSTI2022

Exploring drought-responsive crucial genes in Sorghum

Drought severely affects global food production. Sorghum is a typical drought-resistant model crop. Based on RNA-seq data for Sorghum with multiple time points and the gray correlation coefficient, this paper firstly selects candidate genes via mean variance test and constructs weighted gene differential co-expression networks (WGDCNs); then, based on guilt-by-rewiring principle, the WGDCNs and the hidden Markov random field model, drought-responsive crucial genes are identified for five developmental stages respectively. Enrichment and sequence alignment analysis reveal that the screened genes may play critical functional roles in drought responsiveness. A multilayer differential co-expression network for the screened genes reveals that Sorghum is very sensitive to pre-flowering drought. Furthermore, a crucial gene regulatory module is established, which regulates drought responsiveness via plant hormone signal transduction, MAPK cascades, and transcriptional regulations. The proposed method can well excavate crucial genes through RNA-seq data, which have implications in breeding of new varieties with improved drought tolerance.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

High-Resolution Measurement of Soil Thermal Properties and Moisture Content Using a Novel Heated Fiber Optics Approach

Hydrological parameters are scale dependent. Efficient monitoring techniques capable of measuring hydrological parameters, such as soil moisture content (θ), over a wide range of spatial scales are essential for understanding the complexity of water and energy movement across the landscape. Techniques to measure θ over spatial scales in the range from centimeters to thousands of meters, however, are sorely lacking. Recent improvements in the distributed temperature sensing (DTS) technology supported the development of novel techniques to fill that gap. However, improvements in the accuracy and applicability of DTS techniques are still needed. This study investigates the possibility of improving the accuracy of the fiber optics dual-probe heat-pulse (FO-DPHP) DTS technique by using a new design to maintain the spacing between the FO-DPHP probes and by introducing a novel data interpretation approach. The accuracy of the novel FO-DPHP design was tested at different θ in a sand column experiment. The FO-DPHP measurements obtained using traditional and novel data interpretation approaches were compared against independent measurements from several calibrated soil water content (EC5) sensors. Monte-Carlo analyses were also performed to assess the impact of DTS measurement errors on the accuracy achieved using the data interpretation approaches. The novel design and data interpretation approach allowed for accurate measurements of soil thermal properties and θ without the need to perform a hard-to-achieve soil-specific calibration. Measured θ had mean errors and standard deviations <0.03 and <0.01 m 3 m -3 , respectively, for moisture conditions ranging from dry to near saturation. The standard deviation in the measured heat capacity was <0.01 MJ m -3 K -1 .

42 ENGINEERING↗

DOE OSTI2021

Hyporheic Exchange Driven by Submerged Rigid Vegetation: A Modeling Study

Flow-vegetation interaction affects fluid flow hydraulics and associated material transport in river corridors. Concomitant changes in pressure within the flow field due to the presence of vegetation may act as a driver for the formation of hyporheic flow across the sediment-water interface. This potentially important process, however, has yet to be studied. In order to investigate vegetation-induced hyporheic exchange, a series of numerical models of interlinked surface-subsurface flow modified by plant stems was conducted. Periodically staggered plant stem arrays on a flat sediment bed were considered within a coupled multiphysics computational fluid dynamics approach. Plants were idealized as rigid cylinders and arranged in different streamwise and spanwise spacing distances. Each vegetation array was then subjected to a broad range of flow Reynolds Numbers (Re). The results showed that hyporheic flow occurs in all conditions with the presence of vegetation. The vegetation-induced hyporheic flux is found to be a function of Re via a power law. The flux increases with interstem space until the space reaches the distance that rigid stems no longer affect the flow structures in the vicinity of each other. Larger intervegetation distances lead to a larger hyporheic zone. A direct comparison with bedforminduced hyporheic flow showed that vegetation can induce higher hyporheic flux through relatively shallower exchange zones. The results of all the simulations were synthesized into predictive models for hyporheic flux, bulk residence time and exchange depth based on drag coefficient, vegetation density, and Reynolds Number.

54 ENVIRONMENTAL SCIENCES↗