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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Groundwater and Surface Water Flow (GSFLOW) model files for the East River, Colorado

The data package contains model input files and executables for the East River, Colorado (750 km2) located in the headwaters of the Upper Colorado River Basin. The code applied is the U.S. Geological Survey (USGS) Groundwater and Surface Water Flow (GSFLOW) model. The model contains a 100-m grid resolution to represent topographic complexity and a daily timestep accounts for energy and water partitioning between the snowpack, vegetation, soil zone and bedrock. The land surface model is dynamically linked to a three-dimensional groundwater flow model that allows for streamflow gaining and losing conditions. The groundwater model accounts for nine stratigraphic units and extends 400 m below land surface. Using this modeling framework we explore historical water budgets (water year 1987-2022) and the influence of seasonal warming and associated mechanisms driving groundwater declines and streamflow loss. A Readme_062424.txt file provides instructions on how to download all files. Input and output files are provided for the historical simulation representative of water years 1987 to 2022 (i.e. baseline) and the all-year +4C warming scenario. Instructions are provided to run the seasonal warming scenarios with warming applied only to the autumn, winter, spring or summer months. Modeled output used in figures for Carroll et al., 2024 are also provided with metadata describing where these data were obtained. This dataset additionally includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata; and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type.Updated on 06-24-2024: The dataset was updated to include model outputs (updated base.zip and 4C.zip files), figure source files (Figure_Source_Files.zip), an updated Readme file (Readme_062424.txt), climate input files (climate_input_files.zip), and the adoption of ESS-DIVE File Level Metadata and CSV reporting formats (inclusion of flmd.csv and dd.csv files).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Experimental and modeling investigation of binary liquid mixtures

Binary mixtures of liquids may be encountered in industrial or remote sensing scenarios and present challenges to positive identification compared to neat single-component liquids. Our investigation examines whether one can predict the optical properties of the mixture, i.e. its complex index of refraction, by assuming a linear superposition of the real and imaginary components of the index of refraction in proportion to the ratio of each constituent. To investigate this hypothesis various liquid mixtures were created using mass ratios. The mixtures were then characterized as to their complex index of refraction and used in numerical modeling calculations of thin liquid mixture films on surfaces and compared with composed mixtures using linear n and k synthetic mixtures where the n and k components of the complex index of refraction were combined in similar ratios. The comparison of modeling and experimental results is presented with recommendations for further investigation.

infrared (IR) spectroscopy, Liquid mixtures, compl↗
DOE OSTI2016

Light Makes a Surface Banana-Bond Split: Photodesorption of Molecular Hydrogen from RuO 2 (110)

The coordination of H2 to a metal center via polarization of its bond electron density, known as a Kubas complex, is the means by which H2 chemisorbs at Ru4+ sites on the rutile RuO2(110) surface. This distortion of electron density off an interatomic axis is often described as a ‘banana-bond.’ We show that the Ru-H2 banana-bond can be destabilized, and split, using visible light. Photodesorption of H2 (or D2) is evident by mass spectrometry and scanning tunneling microscopy. From time-dependent density functional theory, the key optical excitation splitting the Ru-H2 banana-bond involves an interband transition in RuO2 which effectively diminishes its Lewis acidity, and thereby weakening the Kubas complex. Such excitations are not expected to affect adsorbates on RuO2 given its metallic properties. Therefore, this common thermal co-catalyst employed in promoting water splitting is, itself, photo-active in the visible.

desorption↗
DOE OSTI2015

CONSTRAINTS ON THE SURFACE MAGNETIC FIELDS AND AGE OF A COOL HYPERGIANT: XMM-NEWTON X-RAY OBSERVATIONS OF VY CMa

The complex circumstellar ejecta of highly evolved, cool hypergiants are indicative of multiple, asymmetric mass-loss events. To explore whether such episodic, non-isotropic mass loss may be driven by surface magnetic activity, we have observed the archetypical cool hypergiant VY CMa with the XMM-Newton X-ray satellite observatory. The hypergiant itself is not detected in these observations. From the upper limit on the X-ray flux from VY CMa at the time of our observations (F {sub X,} {sub UL} ≈ 8 × 10{sup –14} erg cm{sup –2} s{sup –1}, corresponding to log L{sub X} /L {sub bol} ≤ –8), we estimate an average surface magnetic field strength fB ≤ 2 × 10{sup –3} G (where f is the filling factor of magnetically active surface regions). These X-ray results for VY CMa represent the most stringent constraints to date on the magnetic field strength near the surface of a hypergiant. VY CMa's mass loss is episodic, however, and the hypergiant may have been in a state of low surface magnetic activity during the XMM observations. The XMM observations also yield detections of more than 100 X-ray sources within ∼15' of VY CMa, roughly 50 of which have near-infrared counterparts. Analysis of X-ray hardness ratios and IR colors indicates that some of these field sources may be young, late-type stars associated with VY CMa, its adjacent molecular cloud complex, and the young cluster NGC 2362. Further study of the VY CMa field is warranted, given the potential to ascertain the evolutionary timescale of this enigmatic, massive star.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Constructing polyatomic potential energy surfaces by interpolating diabatic Hamiltonian matrices with demonstration on green fluorescent protein chromophore

Simulating molecular dynamics directly on quantum chemically obtained potential energy surfaces is generally time consuming. The cost becomes overwhelming especially when excited state dynamics is aimed with multiple electronic states. The interpolated potential has been suggested as a remedy for the cost issue in various simulation settings ranging from fast gas phase reactions of small molecules to relatively slow condensed phase dynamics with complex surrounding. Here, we present a scheme for interpolating multiple electronic surfaces of a relatively large molecule, with an intention of applying it to studying nonadiabatic behaviors. The scheme starts with adiabatic potential information and its diabatic transformation, both of which can be readily obtained, in principle, with quantum chemical calculations. The adiabatic energies and their derivatives on each interpolation center are combined with the derivative coupling vectors to generate the corresponding diabatic Hamiltonian and its derivatives, and they are subsequently adopted in producing a globally defined diabatic Hamiltonian function. As a demonstration, we employ the scheme to build an interpolated Hamiltonian of a relatively large chromophore, para-hydroxybenzylidene imidazolinone, in reference to its all-atom analytical surface model. We show that the interpolation is indeed reliable enough to reproduce important features of the reference surface model, such as its adiabatic energies and derivative couplings. In addition, nonadiabatic surface hopping simulations with interpolation yield population transfer dynamics that is well in accord with the result generated with the reference analytic surface. With these, we conclude by suggesting that the interpolation of diabatic Hamiltonians will be applicable for studying nonadiabatic behaviors of sizeable molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Recovery of Rare Earth Elements from Low-Grade Feedstock Leachates Using Engineered Bacteria

The use of biomass for sorption of rare earth elements (REEs) for bioremediation and biomining applications has been the subject of many recent investigations. However, REE adsorption by bioengineered systems has been scarcely documented, and rarely tested with complex natural feedstocks. In this study, we engineered E. coli cells for enhanced cell surface-mediated extraction of REEs. Using Lpp-OmpA as an anchor, up to 16 copies of a Lanthanide binding tag (LBT) per OmpA protein were displayed on the E. coli cell surface, resulting in a 2-fold increase in Tb adsorption capacity compared to control cells. To test the efficacy of engineered E. coli cells to extract REEs from complex source materials, biosorption was performed with leachates from two mine tailings and two rare earth deposits. Although control E. coli cells exhibited preferential adsorption of REEs over most metals, functionalization of the cell surface with LBT yielded several notable advantages. First, the efficiency of REE adsorption from all tested leachates was enhanced with distribution coefficients for individual REEs increased by 2-10 fold. Second, although, Cu, Al, Ga and Pb were found to be the best competitors for REE binding to the E. coli cell surface, LBT-display enhanced the cell surface affinity for REEs over all non-REEs except Cu. Third, LBT-display systematically enhanced the affinity of the cell surface for REEs as a function of decreasing atomic radii, providing a means to separate high value HREEs such as Dy and Tb from more common LREEs such as La. Altogether, our results demonstrate that REE biosorption of high efficiency and selectivity can be achieved by engineering the native bacterial surface.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Rotational Dynamics and Transition Mechanisms of Surface-Adsorbed Proteins

Assembly of biomolecules at solid-water interfaces requires molecules to traverse complex orientation-dependent energy landscapes through processes that are poorly understood, largely due to the dearth of in-situ single molecule measurements and statistical analyses of the rotational dynamics that define directional selection. Emerging capabilities in high-speed atomic force microscopy and machine learning have allowed us to directly determine the orientational energy landscape and observe and quantify the rotational dynamics for protein nanorods on the surface of muscovite mica under a variety of conditions. Comparisons with kinetic Monte Carlo simulations show that the transition rates between adjacent orientation-specific energetic minima can largely be understood through traditional models of in-plane Brownian rotation across a biased energy landscape, with resulting transition rates that are exponential in the energy-barriers between states. However, transitions between more distant angular states are decoupled from barrier height, with jump-size distributions showing a power-law decay that is characteristic of a non-classical Levy-flight random walk, indicating that large jumps are enabled by alternative modes of motion via activated states. The findings provide new insights into the dynamics of biomolecules at solid-liquid interfaces that lead to self-assembly, epitaxial matching and other orientationally anisotropic outcomes and define a general procedure for exploring such dynamics with implications for hybrid biomolecular-inorganic materials design.

Orientational energy landscapes, Rotational dynami↗
DOE OSTI2020

WHONDRS-GUI: a web application for global survey of surface water metabolites

Background The Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) is a consortium that aims to understand complex hydrologic, biogeochemical, and microbial connections within river corridors experiencing perturbations such as dam operations, floods, and droughts. For one ongoing WHONDRS sampling campaign, surface water metabolite and microbiome samples are collected through a global survey to generate knowledge across diverse river corridors. Metabolomics analysis and a suite of geochemical analyses have been performed for collected samples through the Environmental Molecular Sciences Laboratory (EMSL). The obtained knowledge and data package inform mechanistic and data-driven models to enhance predictions of outcomes of hydrologic perturbations and watershed function, one of the most critical components in model-data integration. To support efforts of the multi-domain integration and make the ever-growing data package more accessible for researchers across the world, a Shiny/R Graphical User Interface (GUI) called WHONDRS-GUI was created. Results The web application can be run on any modern web browser without any programming or operational system requirements, thus providing an open, well-structured, discoverable dataset for WHONDRS. Together with a context-aware dynamic user interface, the WHONDRS-GUI has functionality for searching, compiling, integrating, visualizing and exporting different data types that can easily be used by the community. The web application and data package are available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1484811 , which enables users to simultaneously obtain access to the data and code and to subsequently run the web app locally. The WHONDRS-GUI is also available for online use at Shiny Server ( https://xmlin.shinyapps.io/whondrs/ ).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The impact of mineral reactive surface area variation on simulated mineral reactions and reaction rates

Reactive transport modeling is an essential tool to simulate complex geochemical reactions in porous media that can impact formation properties including porosity and permeability. However, simulating these reactions is challenging due to uncertainties in model parameters, particularly mineral surface areas. Imaging has emerged as a powerful means of estimating model parameters including porosity and mineral abundance, accessibility and accessible surface area. However, these parameters, particularly mineral accessible surface area, vary with image resolution. This work aims to enhance understanding of the impact of image resolution and other means of estimating mineral reactive surface area on simulated mineral reactions and reaction rates. Mineral surface areas calculated from images with resolutions of 0.34 μm and 5.71 μm were used to simulate mineral reactions in the context of geologic CO 2 sequestration in the Paluxy formation at the continuum scale. Additional simulations were carried out using BET surface areas collected from the literature and geometric surface areas. Simulations were run for 7300 days and mineral volume fractions and effluent ion concentrations tracked and compared. Variations in mineral surface areas measured from images are within 1 order of magnitude and yield similar simulation results, indicating the impact of image resolution on simulated reactions and reaction rates is minimum for the resolutions and sample considered. In comparison, surface areas obtained from BET and geometric approaches are 1–4 orders of magnitude higher than image-obtained surface areas and result in greater simulated reaction rates and extents. Minerals with high reaction rates (calcite and siderite) are most impacted by surface area values at short times where simulated mineral volume fractions at longer times agree relatively well, even for simulations with several orders of magnitude variation in surface area. Phases with lower reaction rates, such as K-feldspar and muscovite, are predominantly impacted over longer times where variations in surface areas impact reaction extents and porosity evolution. Overall, variations in surface areas due to image resolution are small and result in little variation in simulated reactions and reaction rates while there are significant variations in simulation results when other surface area estimates are used. These variations, however, depend on the reactivity of the mineral phase where surface areas of fast-reacting phases largely impact simulations at short (hours to days) timescales and surface areas of slower-reactive phases impact longer term simulations (years).

58 GEOSCIENCES↗
DOE OSTI2015

Liquid-based gating mechanism with tunable multiphase selectivity and antifouling behaviour

Living organisms make extensive use of micro- and nanometre-sized pores as gatekeepers for controlling the movement of fluids, vapours and solids between complex environments. The ability of such pores to coordinate multiphase transport, in a highly selective and subtly triggered fashion and without clogging, has inspired interest in synthetic gated pores for applications ranging from fluid processing to 3D printing and lab-on-chip systems(1-10). But although specific gating and transport behaviours have been realized by precisely tailoring pore surface chemistries and pore geometries(6,11-17), a single system capable of controlling complex, selective multiphase transport has remained a distant prospect, and fouling is nearly inevitable(11,12). Here we introduce a gating mechanism that uses a capillary-stabilized liquid as a reversible, reconfigurable gate that fills and seals pores in the closed state, and creates a non-fouling, liquid-lined pore in the open state. Theoretical modelling and experiments demonstrate that for each transport substance, the gating threshold-the pressure needed to open the pores-can be rationally tuned over a wide pressure range. This enables us to realize in one system differential response profiles for a variety of liquids and gases, even letting liquids flow through the pore while preventing gas from escaping. These capabilities allow us to dynamically modulate gas-liquid sorting in a microfluidic flow and to separate a three-phase air-water-oil mixture, with the liquid lining ensuring sustained antifouling behaviour. Because the liquid gating strategy enables efficient long-term operation and can be applied to a variety of pore structures and membrane materials, and to micro- as well as macroscale fluid systems, we expect it to prove useful in a wide range of applications.

Hou, X↗
DOE OSTI2023

Freeform Hybrid Manufacturing: Binderjet, Structured Light Scanning, Confocal Microscopy, and CNC Machining

This paper describes a hybrid manufacturing approach for silicon carbide (SiC) freeform surfaces using binder jet additive manufacturing (BJAM) to print the preform and machining to obtain the design geometry. Although additive manufacturing (AM) techniques such as BJAM allow for the fabrication of complex geometries, additional machining or grinding is often required to achieve the desired surface finish and shape. Hybrid manufacturing has been shown to provide an effective solution. However, hybrid manufacturing also has its own challenges, depending on the combination of processes. For example, when the subtractive and additive manufacturing steps are performed sequentially on separate systems, it is necessary to define a common coordinate system for part transfer. This can be difficult because AM preforms do not inherently contain features that can serve as datums. Additionally, it is important to confirm that the intended final geometry is contained within the AM preform. The approach described here addresses these challenges by using structured light scanning to create a stock model for machining. Results show that a freeform surface was machined with approximately 70 µm of maximum deviation from that which was planned.

Dvorak, Jake (ORCID:0000000260989944)↗
DOE OSTI2014

A region-appearance-based adaptive variational model for 3D liver segmentation

Purpose: Liver segmentation from computed tomography images is a challenging task owing to pixel intensity overlapping, ambiguous edges, and complex backgrounds. The authors address this problem with a novel active surface scheme, which minimizes an energy functional combining both edge- and region-based information. Methods: In this semiautomatic method, the evolving surface is principally attracted to strong edges but is facilitated by the region-based information where edge information is missing. As avoiding oversegmentation is the primary challenge, the authors take into account multiple features and appearance context information. Discriminative cues, such as multilayer consecutiveness and local organ deformation are also implicitly incorporated. Case-specific intensity and appearance constraints are included to cope with the typically large appearance variations over multiple images. Spatially adaptive balancing weights are employed to handle the nonuniformity of image features. Results: Comparisons and validations on difficult cases showed that the authors’ model can effectively discriminate the liver from adhering background tissues. Boundaries weak in gradient or with no local evidence (e.g., small edge gaps or parts with similar intensity to the background) were delineated without additional user constraint. With an average surface distance of 0.9 mm and an average volume overlap of 93.9% on the MICCAI data set, the authors’ model outperformed most state-of-the-art methods. Validations on eight volumes with different initial conditions had segmentation score variances mostly less than unity. Conclusions: The proposed model can efficiently delineate ambiguous liver edges from complex tissue backgrounds with reproducibility. Quantitative validations and comparative results demonstrate the accuracy and efficacy of the model.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2020

Dynamic PRA-Based Estimation of PWR Coping Time Using a Surrogate Model for Accident Tolerant Fuel

In this study, we propose an interpolation-based response surface surrogate methodology to manage a large number of scenarios in dynamic probabilistic risk assessment. It adopts the shape Dynamic Time Warping algorithm to cluster the interpolation neighborhood from time series sample data. The interpolation method was adapted from Taylor Kriging to allow a reduced-order model of the Taylor series. In order to demonstrate its applicability to complex issues in risk assessment for nuclear engineering, an example risk response surface to estimate emergency core cooling system (ECCS) criteria for triplex silicon carbide (SiC) accident-tolerant fuel was constructed. The response surface was exploited to estimate the cumulative failure probability of the fuel cladding structure due to the uncertainties in operator actions and safety systems. The functional failures were assessed based on a combination of individual layer failures computed by coupling Risk Analysis Virtual Environment software with a pressurized water reactor 1000-MW(electric) RELAP5 model and the in-house fuel performance assessment module. Results showed that SiC cladding failure probability spiked less than 1 min after a large-break loss-of- coolant accident whenever the current ECCS criteria for Zircaloy-4 (Zr-4) cladding was used. However, it still provides an increased safety margin of three orders of magnitude compared to Zr-4. This positive margin could be utilized to relax active ECCS requirements by allowing deviations of up to 450 s in its actuation time. The proposed surrogate methodology generated a response surface of SiC cladding failure probability reasonably well, with a significant savings of computation time. This methodology is expected to be useful in the analysis of system response with complex uncertainty sources.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2016

Nanomineralogy as a new dimension in understanding elusive geochemical processes in soils: The case of low-solubility-index elements

Nanomineralogical studies of mineral surface coatings in soils reveal insights into biogeochemical processes that heretofore were not known to exist. This is a new dimension in understanding past and present biogeochemical processes in soils, and in this study it is a way to better understand the behavior of low-solubility-index elements such as Al, Ti, and Zr. Soils were sampled from selected sites in Sudbury (Ontario, Canada) that have been affected by acidification and particulate matter emissions from base-metal smelters with subsequent remediation within the past century. These anthropogenic processes have affected an entire landscape, but are now recorded in assemblages of nano-size phases that can be only studied using a combination of focused ion beam technology (for sample preparation) and high-resolution analytical transmission electron microscopy (for phase identification). A first generation of clay minerals (pre-acidification phase), their partial replacement by nano-size hematite and amorphous silica (anthropogenic acidification), and a second generation of clay minerals (post-acidification, including soil remediation) are products of changes in soil biogeochemical processes during these natural and anthropogenic-induced weathering stages. Furthermore, complex assemblages of nanophases formed prior to the second generation of clay minerals depict underlying mechanisms for the mobilization and sequestration of the low-solubility-index elements Zr and Ti under acidic conditions. The occurrence of baddeleyite (ZrO 2 ), anatase (TiO 2 ), and the Magneli phases Ti 4 O 7 and Ti 5 O 9 (all present at the nanoscale) suggest an influx of nanocolloidal Zr and Ti oxides during weathering of smelter-derived particulate matter. Kelyshite {NaZr[Si 2 O 6 (OH)]}, authigenic zircon (ZrSiO 4 ), and kleberite [Fe 3+ Ti 6 O 11 (OH) 5 ] are most likely products of the sequestration of the Zr- and Ti-bearing nanocolloids.

58 GEOSCIENCES↗
DOE OSTI2025

Crystallization of nanopore-confined imidazolium ionic liquids probed by temperature-resolved in situ grazing-incidence wide angle X-ray scattering (GIWAXS)

The crystallization behavior of ionic liquids (ILs) 1-butyl-3-methylimidazolium [BMIM] hexafluorophosphate [PF 6 ] and chloride [Cl] is investigated upon confinement in 2.3 or 8.2 nm diameter silica nanopore arrays, along with the effects of covalently modifying the pore walls with 1-(3-trimethoxysilylpropyl)3-methylimidazolium [TMS-MIM] + groups. In situ grazing-incidence wide angle x-ray scattering (GIWAXS) is performed during heating from as low as -110 °C to room temperature. Partially ordered “nanodomains” are observed in both ILs in the bulk molten state, but they are disrupted by nanoconfinement. Melting point depression consistent with capillary effects is observed for [BMIM][PF 6 ] in 2.3 nm pores. However, the melting point is elevated for [BMIM][PF 6 ] in 8.2 nm pores, which provide sufficient space to stabilize the crystalline phase. For [BMIM][Cl], crystallization is observed only in 8.2 nm bare silica pores, but the melting point is severely depressed. Tethering with IL-like [TMS-MIM + ] also promotes the crystallization of [BMIM][PF 6 ], resulting in elevated melting points. The combined effects of a larger pore size and pore surface tethering on [BMIM][PF 6 ] result in a single stable crystal phase that persists from -140 °C to 25 °C (vs. the bulk melting point of -11 °C). These results show that when ILs are used in confined systems, complex crystallization behavior can emerge depending on the counterion, pore size, and surface modification that require consideration of ion layering in the confined space in addition to surface free energy effects.

He, Yuxin [University of Kentucky, Lexington, KY (↗
DOE OSTI2017

Stellar surface as low-rank modification in iterative methods for binary neutron stars

We present a new multidomain spectral method for the treatment of non-spherical stellar surfaces in iterative methods for binary neutron stars. A stellar surface changes throughout the course of an iterative solution, potentially stalling the convergence. Our method affords low-complexity updates of the relevant subdomain preconditioners, thereby avoiding such stalling. Unlike current collocation (or nodal) approaches for treating surfaces (which rely on coordinate transformations to ensure that stellar surfaces arise at subdomain boundaries), our approach requires no regridding or nontrivial Jacobians. For polytropes with an equation of state specified by an integer polytropic index, our method delivers exponential accuracy with increased truncation, although for “stiff” equations of state (e.g. fractional) it suffers from the same accuracy loss as current methods. We have presented an outline of our approach before, but here present details with numerical tests.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗