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DOE OSTI2021

Cognitive analysis of metabolomics data for systems biology

Cognitive computing is revolutionizing the way big data are processed and integrated, with artificial intelligence (AI) natural language processing (NLP) platforms helping researchers to efficiently search and digest the vast scientific literature. Most available platforms have been developed for biomedical researchers, but new NLP tools are emerging for biologists in other fields and an important example is metabolomics. NLP provides literature-based contextualization of metabolic features that decreases the time and expert-level subject knowledge required during the prioritization, identification and interpretation steps in the metabolomics data analysis pipeline. Here, we describe and demonstrate four workflows that combine metabolomics data with NLP-based literature searches of scientific databases to aid in the analysis of metabolomics data and their biological interpretation. Additionally, the four procedures can be used in isolation or consecutively, depending on the research questions. The first, used for initial metabolite annotation and prioritization, creates a list of metabolites that would be interesting for follow-up. The second workflow finds literature evidence of the activity of metabolites and metabolic pathways in governing the biological condition on a systems biology level. The third is used to identify candidate biomarkers, and the fourth looks for metabolic conditions or drug-repurposing targets that the two diseases have in common. The protocol can take 1–4 h or more to complete, depending on the processing time of the various software used.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Numerical assessment of fault impact on caprock seals during CO 2 sequestration

Coupled fluid-flow and geomechanical analysis of caprock integrity has gained a lot of attention among scientists and researchers investigating the long-term performance of geologic carbon storage systems. Reactivation of pre-existing fractures within the caprock or re-opening of faults can create permeable pathways which can influence the seal integrity. Stability of the caprock during and after injection of super-critical CO 2 , and the impact of pre-existing fractures in the presence or absence of one or multiple faults have been investigated in this study. The impact of the wellbore orientation and the injection rate are among other key factors in understanding the structural trapping mechanisms within such geological formations. In this study, we numerically investigated the impact of each of these factors. This study revealed the interplay between joints and faults and how different leakage pathways are formed and under which scenario they play a dominant role in terms of CO 2 leakage. Finally, this study also highlights the role of one versus multiple faults in the domain and the importance of the fault hydrological property in forming leakage pathway.

58 GEOSCIENCES↗

DOE OSTI2022

Metallic Technetium Sequestration in Nickel Core/Shell Microstructure during Fe(OH)2 Transformation with Ni doping

This study investigates the impacts of Ni doping on technetium-99 (Tc) sequestration in aqueous solutions through transformation of Fe(OH)2(s) to iron spinel (magnetite) under alkaline conditions. Extensive solid characterization was performed for the mineral phases produced, as well as the Tc/Ni speciation and distribution within these phases. X-ray diffraction results show that iron spinel was the dominant mineral product without detectable Ni incorporation. The doped Ni ions mainly precipitated as fine Fe/Ni oxide/hydroxide particles, including strongly reduced nanometer?sized spheroidal Ni-rich and metallic Ni phases. High-resolution analytical scanning transmission electron microscopy using energy dispersive X-ray spectroscopy and electron energy loss spectroscopy on the produced solid samples (focused ion beam-prepared specimens) revealed three Tc distribution domains dominated by nanocrystals and, especially, a Tc-rich metallic phase. Instances of metallic Tc were specifically found in spheroidal, Ni-rich and metallic nanoparticles exhibiting a core/shell microstructure that suggests strong reduction and sequential precipitation of Ni-Tc-Ni. Mass balance analysis showed nearly 100% Tc removal from the 4.8 × 10-4 M Tc solutions. The finding of the metallic Tc encapsulation indicates that Tc sequestration through Ni-doped Fe(OH)2(s)?to?iron spinel transformation process likely provides an alternative treatment pathway for Tc removal and could be combined into further waste treatment approaches.

Wang, Guohui↗

DOE OSTI2025

Models and Measurements Quantify Photon Recycling, Charge-Carrier Diffusion and Photon Scattering Contributions to Photoluminescence in InP Nanowire Arrays

Nanowire arrays present many unique advantages for solar-to-chemical energy conversion. One possible advantage is that photon recycling between neighboring nanowires has the potential to increase solar energy conversion efficiencies. Here, in this work, we explore three underlying mechanisms of optical and electronic coupling between neighboring nanowires─incident photon scattering, photon recycling, and charge-carrier transport from the photoexcited nanowire to the neighboring nanowire via the underlying substrate─using single nanowire-level microscopy and spectroscopy measurements. We present a comprehensive analysis of light absorption and emission of a single nanowire at open circuit, and subsequent re-absorption and re-emission by a neighboring nanowire. We developed a novel correlated single nanowire microspectroscopy and widefield imaging methodology to spatially resolve photon communication pathways between neighboring nanowires and selectively image re-emitted and reflected photons. We developed unique multiphysics models to couple wave optics and semiconductor photophysics to especially isolate contributions from photon recycling and electronic transport to photon emission from neighboring nanowires. By systematically varying the morphologies of the nanowires modeled, we identified pathways to maximize photon recycling between neighboring nanowires. We concluded that the measured photoluminescence is more strongly influenced by the diffusion of charge carriers as compared to photon recycling in materials with moderate-to-large charge-carrier mobilities (>10 cm 2 V –1 s –1 ), and that photon recycling dictates photoluminescence intensity only when the charge-carrier mobility is low (<1 cm 2 V –1 s –1 ). The experimental and simulation platforms developed herein for photon management strategies can be leveraged by the semiconductor photocatalysis community to enhance solar-to-chemical conversion efficiencies in semiconductor nanowire arrays.

25 ENERGY STORAGE↗

DOE OSTI2021

Bayesian Inference for Integrating Yarrowia lipolytica Multiomics Datasets with Metabolic Modeling

Optimizing the metabolism of microbial cell factories for yields and titers is a critical step for economically viable production of bioproducts and biofuels. In this process, tuning the expression of individual enzymes to obtain the desired pathway flux is a challenging step, in which data from separate multiomics techniques must be integrated with existing biological knowledge to determine where changes should be made. Following a design-build-test-learn strategy, building on recent advances in Bayesian metabolic control analysis, we identify in this work key enzymes in the oleaginous yeast Yarrowia lipolytica that correlate with the production of itaconate by integrating a metabolic model with multiomics measurements. To this extent, we quantify the uncertainty for a variety of key parameters, known as flux control coefficients (FCCs), needed to improve the bioproduction of target metabolites and statistically obtain key correlations between the measured enzymes and boundary flux. Based on the top five significant FCCs and five correlated enzymes, our results show phosphoglycerate mutase, acetyl-CoA synthetase (ACSm), carbonic anhydrase (HCO3E), pyrophosphatase (PPAm), and homoserine dehydrogenase (HSDxi) enzymes in rate-limiting reactions that can lead to increased itaconic acid production.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Critical role of solvent-modulated hydrogen-binding strength in the catalytic hydrogenation of benzaldehyde on palladium

Protic and non-protic solvents influence the rate of benzaldehyde hydrogenation on Pd by one order of magnitude in the following sequence of increasing reactivity, dioxane < tetrahydrofuran < water < methanol. Despite these differences, the reaction pathway does not change; the majority of turnovers occurs via a Langmuir-Hinshelwood mechanism by stepwise addition of sorbed H to sorbed benzaldehyde, first to the carbonyl O and then to the C atom of the formyl group, forming benzyl alcohol. An analysis of the solvation energies shows that both ground and transition states are destabilized by the solvents compared to the same reaction at the gas-solid interface. The destabilization extent of the reacting organic substrates in both states are similar and, therefore, compensate each other, making the net kinetic effects inconsequential. In consequence, the marked reactivity differences arise solely from the differences in the surface stabilization of adsorbed hydrogen adatoms moderated by the four solvents-more weakly bound hydrogen adatoms, because of their solvation by solvent, exhibit higher rates of their hydrogenation reaction in kinetically relevant attack on the C atom.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

A pyroxene-based quantum magnet with multiple magnetization plateaus

Pyroxenes (AMX 2 O 6 ) consisting of infinite one-dimensional edge-sharing MO 6 chains and bridging XO 4 tetrahedra are fertile ground for finding quantum materials. Thus, here, we have studied calcium cobalt germanate (CaCoGe 2 O 6 ) and calcium cobalt silicate (CaCoSi 2 O 6 ) crystals in depth. Heat capacity data show that the spins in both compounds are dominantly Ising-like, even after being manipulated by high magnetic fields. On cooling below the Néel temperatures, a sharp field–induced transition in magnetization is observed for CaCoGe 2 O 6 , while multiple magnetization plateaus beneath the full saturation moment are spotted for CaCoSi 2 O 6 . Our analysis shows that these contrasting behaviors potentially arise from the different electron configurations of germanium and silicon, in which the 3d orbitals are filled in the former but empty in the latter, enabling electron hopping. Thus, silicate tetrahedra can aid the interchain superexchange pathway between cobalt(II) ion centers, while germanate ones tend to block it during magnetization.

Science & Technology - Other Topics↗

DOE OSTI2025

Yeast Transformation on Hamilton Vantage (YT Vantage) v1

Our software program is designed for the Hamilton Vantage liquid handling robot, automating the Build step in the Design-Build-Test-Learn (DBTL) cycle for Saccharomyces cerevisiae. This program minimizes human intervention, enabling rapid identification of pathway bottlenecks and genes that enhance verazine production. The program takes competent yeast and plasmid DNA as input and generates an output library of engineered strains compatible with automated colony picking, high-throughput culturing, and chemical extraction for downstream LC-MS analysis. A user-friendly interface, developed using the Hamilton Method Editor software, allows for on-demand parameter customization. By automating this process, our program streamlines the construction of Saccharomyces cerevisiae, reducing manual labor and increasing efficiency. While the manual process is well-documented, integration with robotic automation is less common, making our program a valuable tool for researchers. With this software, we achieved 2-5 fold increases in verazine production, demonstrating its potential to accelerate research in this field.

Louie, Randy [Lawrence Berkeley National Laborator↗

DOE OSTI2026

Design Status and Experimental Strategy for Initial Molten Salt Irradiation Experiments in HFIR

The development and deployment of molten salt reactor (MSR) technologies require experimental capabilities that can evaluate molten fuel salt behavior and structural material performance under representative irradiation conditions. Although modeling and separate effects testing provide important insight, there remains a critical lack of in-pile data that capture the coupled effects of neutron irradiation, temperature, salt chemistry, and time. Informed by lessons learned from historical MSR programs and recent international irradiation efforts, this report presents a structured approach to addressing existing gaps in molten salt irradiation testing using the High Flux Isotope Reactor (HFIR). A phased irradiation strategy is presented that incrementally increases experimental complexity while managing cost, risk, and facility constraints. The framework progresses from passive, nonfueled static capsule experiments to fueled, instrumented, and ultimately circulating molten salt systems, providing a pathway for materials screening, mechanistic understanding, and qualification-relevant testing. The report defines a near-term Phase 1 passive capsule concept, associated irradiation conditions, and a conceptual post-irradiation examination strategy. Ongoing modeling, out-of-pile testing, and safety analysis activities are described to support continued capability maturation and to enable future phases of molten salt irradiation testing in support of MSR technology deployment.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2021

Integration of Open-Source URBANopt and Dragonfly Energy Modeling Capabilities into Practitioner Workflows for District-Scale Planning and Design

High-performance districts and communities offer opportunities for reducing energy use, emissions, and costs, and can be instrumental in helping cities achieve their climate goals. The design of such communities requires identification of opportunities early on and their re-evaluation throughout the planning process. There is a need for energy modeling tools that connect 3D Computer-Aided Design (CAD) platforms to simulation engines, enabling detailed energy analysis of districts within the workflows and tools used by practitioners. This paper introduces the Dragonfly and URBANoptTM combined toolset that supports the creation of urban models from a range of geometry formats typically used by designers and planners, and provides an integrated pathway to simulate district-scale energy systems. The toolset is piloted by a global architecture and master planning firm to evaluate several key urban-scale technical questions for the design of a district in Chicago. The findings indicate that, while energy savings can be achieved through traditional architectural studies and enhancements to individual building efficiency, the modeling toolset helps identify additional savings and insights that can be achieved when considering district-scale energy systems. Finally, this study demonstrates how the Dragonfly/URBANopt toolset can integrate with master planning workflows, thereby enabling an iterative performance-based design process.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2023

Xanthos Output Dataset Under ISIMIP3b Selected CMIP6 Scenarios: 1850 - 2100

Overview Xanthos is an open-source hydrologic model, written in Python, designed to quantify and analyze global water availability. Xanthos simulates historical and future global water availability on a monthly time step at a spatial resolution of 0.5 geographic degrees. Xanthos was designed to be extensible and used by scientists that study global water supply and work with the Global Change Analysis Model (GCAM). Details This dataset includes Xanthos outputs forced by the ISIMIP3b bias-adjusted CMIP6 climate forcing (1850 - 2100). There are 30 scenarios consists of 10 Coupled Model Intercomparison Project phase 6 (CMIP6) General Circulation Models (GCM) and 3 Shared Socioeconomic Pathways (SSP). Each folder is named as cmip6_{gcm}_{ensemble-member}_{ssp}. 10 CMIP6 GCMs: GFDL-ESM4, IPSL-CM6A-LR, MPI-ESM1-2-HR, MRI-ESM2-0, UKESM1-0-LL, CanESM5, CNRM-CM6-1, CNRM-ESM2-1, EC-Earth3, and MIROC6 3 SSP-RCP Scenarios: SSP1-2.6, SSP3-7.0, and SSP5-8.5 The table below summarizes the details of output variables within each scenario folder. | Output Variable | File Short Name | Spatial Resolution | Unit | | ----------------------------------------------- | -------------------------------------- | -------------------------------- | --------------------- | | Runoff | q | 0.5x0.5 degree | km3/month | | Runoff | Basin_runoff | GCAM basin | km3/month | | Runoff | Country_runoff | Country | km3/month | | Runoff | GCAMRegion_runoff | GCAM region | km3/month | | Streamflow | avgchflow | 0.5x0.5 degree | m3/second | | Potential Evapotranspiration | pet | 0.5x0.5 degree | km3/month | | Actual Evapotranspiration | aet | 0.5x0.5 degree | km3/month | | Accessible Water | accessible_water | GCAM basin | km3/year | | Hydropower Generation | actual_hydro | GCAM region | EJ/year |

Climate Change↗

DOE OSTI2023

Xanthos Output Dataset Under ISIMIP3b Selected CMIP6 Scenarios: 1850 - 2100

Climate Change↗

NASA NTRS2012

The Spatial Distribution of Organic Matter and Mineralogical Relationships in Carbonaceous Chondrites

Organic matter present within primitive carbonaceous meteorites represents the complex conglomeration of species formed in a variety of physically and temporally distinct environments including circumstellar space, the interstellar medium, the Solar Nebula & Jovian sub-nebulae and asteroids. In each case, multiple chemical pathways would have been available for the synthesis of organic molecules. Consequently these meteorites constitute a unique record of organic chemical evolution in the Universe and one of the biggest challenges in organic cosmochemistry has been in deciphering this record. While bulk chemical analysis has provided a detailed description of the range and diversity of organic species present in carbonaceous chondrites, there is virtually no hard experimental data as to how these species are spatially distributed and their relationship to the host mineral matrix, (with one exception). The distribution of organic phases is nevertheless critical to understanding parent body processes. The CM and CI chondrites all display evidence of low temperature (< 350K) interaction with aqueous fluids, which based on O isotope data, flowed along thermal gradients within the respective parent bodies. This pervasive aqueous alteration may have led to aqueous geochromatographic separation of organics and synthesis of new organics coupled to aqueous mineral alteration. To address such issues we have applied the technique of microprobe two-step laser desorption / photoionization mass spectrometry (L2MS) to map in situ the spatial distribution of a broad range of organic species at the micron scale in the freshly exposed matrices of the Bells, Tagish Lake and Murchison (CM2) carbonaceous chondrites.

Clemett, S. J.↗

DOE OSTI2020

Comprehensive Baseline Environmental Monitoring of an Interim Legacy Waste Store in Arid Zone Australia - 20062

Radionuclide containing soil and rubble from the clean-up of a former uranium, thorium and rare earth minerals processing research facility carried out in the early 50's and 60's is currently stored at the Woomera Test Range in South Australia awaiting final disposal. Prior to developing a final disposal pathway commensurate with waste acceptance criteria, a comprehensive baseline environmental monitoring has been carried out to establish the background radiation levels. The survey included in situ gamma scanning of the surface soil ({sup 238}U, {sup 232}Th, {sup 40}K), a laboratory analysis of 86 soil samples (from 0-20 cm depth), which involved XRF measurements (U, Th, and rare earth metals) and spectroscopic analysis ({sup 238}U, {sup 232}Th, {sup 226}Ra and daughter nuclides). A time series of radon concentration measurements in air was established, while soil radon ({sup 222}Rn) and thoron ({sup 220}Rn) flux measurements were undertaken at 18 different locations. The 2018 comprehensive baseline survey demonstrated radiation levels in the immediate vicinity of the Woomera interim waste store are typical background values of soil and rock. No contamination was detected. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2026

Techno Economic Analysis for Production of Renewable Natural Gas and Value-Added Chemicals from Forest Biomass Residues (CRADA Final Report)

West Biofuels - in collaboration with the University of California San Diego, the University of California Davis, the National Laboratory of the Rockies (NLR), the Colorado School of Mines’ Center for Hydrate Research, Placer County Air Pollution Control District, the Sierra Business Council, and the Southern California Gas Company (SoCalGas)-will demonstrate an innovative pathway to convert forest biomass to renewable gas (RG). The project, Production of Pipeline Grade Renewable Natural Gas and Value-Added Chemicals from Forest Biomass Residues, will utilize an existing pilot-scale gasification system and data and lessons learned from a lab-scale catalytic reactor design, develop, and demonstrate an integrated pilot-scale RG process with a scaled-up catalytic reactor and hydrate-based gas separation process. This robust and simple process uses a commercial proven gasifier, a commercially available catalyst that can tolerate gas contaminants, and a gas separation process that simplifies the downstream processing. Current testing has shown that the process can yield a large amount of methane rich renewable gas in addition to a mixture of propanol, ethanol and other higher alcohols and the relative amounts can be controlled by shifting the process conditions. This process is novel and groundbreaking because the product mixture of RG and valuable alcohols byproducts makes RG production economically feasible at $\$$12 per million British thermal units (MMBtu) or less using forest biomass from high hazard zones.

09 BIOMASS FUELS↗

DOE OSTI2020

Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species

Background: Research around the weedkiller Roundup is among the most contentious of the twenty-first century. Scientists have provided inconclusive evidence that the weedkiller causes cancer and other life-threatening diseases, while industry-paid research reports that the weedkiller has no adverse effect on humans or animals. Much of the controversial evidence on Roundup is rooted in the approach used to determine safe use of chemicals, defined by outdated toxicity tests. We apply a system biology approach to the biomedical and ecological model species Daphnia to quantify the impact of glyphosate and of its commercial formula, Roundup, on fitness, genome-wide transcription and gut microbiota, taking full advantage of clonal reproduction in Daphnia. We then apply machine learning-based statistical analysis to identify and prioritize correlations between genome-wide transcriptional and microbiota changes. Results: We demonstrate that chronic exposure to ecologically relevant concentrations of glyphosate and Roundup at the approved regulatory threshold for drinking water in the US induce embryonic developmental failure, induce significant DNA damage (genotoxicity), and interfere with signaling. Furthermore, chronic exposure to the weedkiller alters the gut microbiota functionality and composition interfering with carbon and fat metabolism, as well as homeostasis. Using the “Reactome,” we identify conserved pathways across the Tree of Life, which are potential targets for Roundup in other species, including liver metabolism, inflammation pathways, and collagen degradation, responsible for the repair of wounds and tissue remodeling. Conclusions: Our results show that chronic exposure to concentrations of Roundup and glyphosate at the approved regulatory threshold for drinking water causes embryonic development failure and alteration of key metabolic functions via direct effect on the host molecular processes and indirect effect on the gut microbiota. The ecological model species Daphnia occupies a central position in the food web of aquatic ecosystems, being the preferred food of small vertebrates and invertebrates as well as a grazer of algae and bacteria. The impact of the weedkiller on this keystone species has cascading effects on aquatic food webs, affecting their ability to deliver critical ecosystem services.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Analysis of degradation products in thermally treated TATB

Delineating the chemical composition of TATB (1,3,5-triamino-2,4,6-trinitrobenzene) residues produced from the exposure to abnormal thermal environments should lead to a better understanding of the decomposition paths. Identifying and quantifying each compound in thermally produced residues, monitors which compounds are degrading or forming along the decomposition route, as well as providing input for the kinetic models of those pathways. Here, in this paper, we report the methodology of isolating, identifying, and where possible, quantifying soluble compounds present in solid residues of thermally treated TATB (330 °C for tens of minutes). Samples were extracted with DMSO, separated using chromatography, and quantified using their absorption at 354 nm. Identification of unknown compounds was accomplished using high resolution mass spectrometry. TATB, F1 (diamino-dinitro-benzofurazan), HO-TATB (2,4,6-triamino-1-hydroxyl-3,5-dinitrobenzene), and T4A (1-chloro-3,5-dinitro-2,4,6-triaminobenzene) were trace compounds detected in the unreacted TATB. Ten more compounds that formed in the residues were structurally identified including F2 (amino-nitro-difurazan). Several more compounds were observed but not completely identified. We propose possible structures for the unknowns. Of the compounds formed, F1 was the most abundant compound reaching 4.5 % by weight of the degraded solid sample. Other degradation compounds were estimated to sum to trace levels, well below 1 %. Most compounds were new, having not been detected and identified in previous studies of production grade and thermally aged TATB. Many compounds only reached detectable concentrations after several min of thermal exposure.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Large Polarization and Susceptibilities in Artificial Morphotropic Phase Boundary PbZr 1– x Ti x O 3 Superlattices

The ability to produce atomically precise, artificial oxide heterostructures allows for the possibility of producing exotic phases and enhanced susceptibilities not found in parent materials. Typical ferroelectric materials either exhibit large saturation polarization away from a phase boundary or large dielectric susceptibility near a phase boundary. Both large ferroelectric polarization and dielectric permittivity are attained wherein fully epitaxial (PbZr 0.8 Ti 0.2 O 3 ) n /(PbZr 0.4 Ti 0.6 O 3 ) 2 n ( n = 2, 4, 6, 8, 16 unit cells) superlattices are produced such that the overall film chemistry is at the morphotropic phase boundary, but constitutive layers are not. Here, long- ( n ≥ 6) and short-period ( n = 2) superlattices reveal large ferroelectric saturation polarization ( P s = 64 µC cm –2 ) and small dielectric permittivity (ε r ≈ 400 at 10 kHz). Intermediate-period ( n = 4) superlattices, however, exhibit both large ferroelectric saturation polarization ( P s = 64 µC cm –2 ) and dielectric permittivity (ε r = 776 at 10 kHz). First-order reversal curve analysis reveals the presence of switching distributions for each parent layer and a third, interfacial layer wherein superlattice periodicity modulates the volume fraction of each switching distribution and thus the overall material response. This reveals that deterministic creation of artificial superlattices is an effective pathway for designing materials with enhanced responses to applied bias.

36 MATERIALS SCIENCE↗