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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The direct and indirect drivers shaping RNA viral communities in grassland soils

ABSTRACT Recent studies have revealed diverse RNA viral communities in soils. Yet, how environmental factors influence soil RNA viruses remains largely unknown. Here, we recovered RNA viral communities from bulk metatranscriptomes sequenced from grassland soils managed for 5 years under multiple environmental conditions including water content, plant presence, cultivar type, and soil depth. More than half of the unique RNA viral contigs (64.6%) were assigned with putative hosts. About 74.7% of these classified RNA viral contigs are known as eukaryotic RNA viruses suggesting eukaryotic RNA viruses may outnumber prokaryotic RNA viruses by nearly three times in this grassland. Of the identified eukaryotic RNA viruses and the associated eukaryotic species, the most dominant taxa were Mitoviridae with an average relative abundance of 72.4%, and their natural hosts, Fungi with an average relative abundance of 56.6%. Network analysis and structural equation modeling support that soil water content, plant presence, and type of cultivar individually demonstrate a significant positive impact on eukaryotic RNA viral richness directly as well as indirectly on eukaryotic RNA viral abundance via influencing the co-existing eukaryotic members. A significant negative influence of soil depth on soil eukaryotic richness and abundance indirectly impacts soil eukaryotic RNA viral communities. These results provide new insights into the collective influence of multiple environmental and community factors that shape soil RNA viral communities and offer a structured perspective of how RNA virus diversity and ecology respond to environmental changes. IMPORTANCE Climate change has been reshaping the soil environment as well as the residing microbiome. This study provides field-relevant information on how environmental and community factors collectively shape soil RNA communities and contribute to ecological understanding of RNA viral survival under various environmental conditions and virus-host interactions in soil. This knowledge is critical for predicting the viral responses to climate change and the potential emergence of biothreats.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Prokaryotic responses to a warm temperature anomaly in northeast subarctic Pacific waters

Recent studies on marine heat waves describe water temperature anomalies causing changes in food web structure, bloom dynamics, biodiversity loss, and increased plant and animal mortality. However, little information is available on how water temperature anomalies impact prokaryotes (bacteria and archaea) inhabiting ocean waters. This is a nontrivial omission given their integral roles in driving major biogeochemical fluxes that influence ocean productivity and the climate system. Here we present a time-resolved study on the impact of a large-scale warm water surface anomaly in the northeast subarctic Pacific Ocean, colloquially known as the Blob, on prokaryotic community compositions. Multivariate statistical analyses identified significant depth- and season-dependent trends that were accentuated during the Blob. Moreover, network and indicator analyses identified shifts in specific prokaryotic assemblages from typically particle-associated before the Blob to taxa considered free-living and chemoautotrophic during the Blob, with potential implications for primary production and organic carbon conversion and export.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Finite Element Analysis (FEA) for Water-Foam Fracturing of Granite Rock

In addition to the foam data that were obtained from literature and that were collected from the current study, simulation data was also generated from finite element analysis (FEA) conducted in this study using COMSOL Multiphysics software. The FEA models were built to simulate the experiments conducted at Oak Ridge National Laboratory (ORNL) on cement and granite samples. In these FEA models, temperature was kept at ambient while the pressure profile resembled the loading conditions during the ORNL experiments, where pressure was either monotonically increased or applied cyclically. The cement material was used as a model material and was used to study Von Mises stress and tensile stress distribution for different bore hole length geometry using a parametric sweep with water as fracturing fluid using solid-fluid interaction module. For the granite material, FEA models were developed for stress analysis of cylindrical samples with water or foam fluids. The solid mechanics module in COMSOL was implemented to solve for Von Mises stress and tensile stress. The fluid-structure interaction module was implemented to solve for water-foam interaction on granite cylinder with addition of fluid-loading on structure, i.e., large deformation in solid mechanics with no impact on fluid deformation. Foam was considered as a pseudo single-phase compressible fluid for which material properties were calculated from water and gas (nitrogen) phases. The density of foam is calculated as a function of the densities of water and nitrogen, while viscosity is a function of temperature. Four types of FEA analyses were modelled: 1. Monotonic injection with water 2. Monotonic injection with foam 3. Cyclic injection with water 4. Cyclic injection with foam All the COMSOL files are converted to a zip file which is save in .mph.

15 GEOTHERMAL ENERGY↗
DOE OSTI2020

Microsolvation in V + (H 2 O) n Clusters Studied with Selected-Ion Infrared Spectroscopy

Gas phase ion-molecule clusters of the form V + (H 2 O) n (n = 1-30) are produced by laser vaporization in a supersonic expansion. These ions are analyzed and mass-selected with a time-of-flight mass spectrometer and investigated with infrared laser photodissociation spectroscopy. The small clusters (n ≤ 7) are studied with argon tagging, while the larger clusters are studied via the elimination of water molecules. The vibrational spectra for the small clusters include only free O-H stretching vibrations, while larger clusters exhibit red-shifted hydrogen bonding vibrations. The spectral patterns reveal that the coordination around V + ions is completed with four water molecules. A symmetric square-planar structure forms for the n = 4 ion, and this becomes the core ion in larger structures. Clusters up to n = 8 have mostly two-dimensional structures, but hydrogen bonding networks evolve to three-dimensional structures in larger clusters. The free O-H vibration of AAD (acceptor-acceptor-donor) coordinated surface molecules converges to a frequency near that of bulk water by the cluster size of n = 30. However, the splitting of this vibration for AAD- versus AD-coordinated molecules is still different compared to other singly-charged or doubly-charged cation-water clusters. Finally, this indicates that cation identity and charge-site location in the cluster can produce discernible spectral differences for clusters in this size range.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Effects of Wind Shear and Aerosol Conditions on the Organization of Precipitating Marine Stratocumulus Clouds

Here this study examines how wind shear affects precipitating marine stratocumulus clouds under different cloud droplet number concentrations (N d ). We performed a series of large eddy simulations (LES) of nocturnal marine stratocumulus clouds using Cloud Model 1 (CM1). The simulations show that N d is the dominant factor for cloud cellular organization in this cloud regime rather than wind shear. Low N d characterizes the open cellular structure with a high in-cloud liquid water path (LWP). When wind shear is increased, the cloud fraction tends to decrease along with LWP, suggesting the cloud top region is significantly influenced by the entrainment and mixing of dry air from the free troposphere. We also examine cold pools in open and closed cellular clouds. Open-cell clouds produce larger and deeper cold pools compared to closed-cell clouds. Interestingly, cold pools can exist without surface precipitation and are produced by evaporation of light precipitation (drizzle) below the cloud base with weak downdrafts. The evaporation of raindrops and drizzle play an important role in initiating new convection, particularly where colliding outflows occur downstream of the cloud. This secondary convection contributes to the development and maintenance of the cloud cellular organization and formation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Potential energy profile for the Cl + (H 2 O) 3 → HCl + (H 2 O) 2 OH reaction. A CCSD(T) study

Four different reaction pathways are initially located for the reaction of Cl atom plus water trimer Cl + (H 2 O) 3 → HCl + (H 2 O) 2 OH using a standard DFT method. As found for the analogous fluorine reaction, the geometrical and energetic results for the four chlorine pathways are closely related. However, the energetics for the Cl reaction are very different from those for fluorine. Here in this paper, we investigate the lowest-energy chlorine pathway using the “gold standard” CCSD(T) method in conjunction with correlation-consistent basis sets up to cc-pVQZ. Structurally, the stationary points for the water trimer reaction Cl + (H 2 O) 3 may be compared to those for the water monomer reaction Cl + H 2 O and water dimer reaction Cl + (H 2 O) 2 . Based on the CCSD(T) energies, the title reaction is endothermic by 19.3 kcal mol -1 , with a classical barrier height of 16.7 kcal mol -1 between the reactants and the exit complex. There is no barrier for the reverse reaction. The Cl … (H 2 O) 3 entrance complex lies 5.3 kcal mol -1 below the separated reactants. The HCl … (H 2 O) 2 OH exit complex is bound by 8.6 kcal mol -1 relative to the separated products. The Cl + (H 2 O) 3 reaction is somewhat similar to the analogous Cl + (H 2 O) 2 reaction, but qualitatively different from the Cl + H 2 O reaction. It is reasonable to expect that the reactions between the chlorine atom and larger water clusters may be similar to the Cl + (H 2 O) 3 reaction. The potential energy profile for the Cl + (H 2 O) 3 reaction is radically different from that for the valence isoelectronic F + (H 2 O) 3 system, which may be related to the different bond energies between HCl and HF.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Conformational free energy landscape of a glutamate transporter and microscopic details of its transport mechanism

Removing glutamate from the synaptic cleft is vital for proper function of the brain. Excitatory amino acid transporters mediate this process by uptaking the neurotransmitter from the synaptic cleft back to the cell after its release. The archaeal homolog, Glt Ph , an aspartate transporter fromPyrococcus horikoshii, presents the best structurally characterized model for this family of transporters. In order to transport, Glt Ph undergoes elevator-like conformational changes between inward-facing (IF) and outward-facing (OF) states. Here, we characterize, at an atomic level, the OF⇌IF transition of Glt Ph in differentapo/bound states using a combination of ensemble-based enhanced sampling techniques, employing more than two thousand of coupled simulation replicas of membrane-embedded Glt Ph . The resulting free-energy profiles portray the transition ofapo/bound states as a complex four-stage process, while sodium binding alone locks the structure in one of its states. Along the transition, the transport domain (TD) disengages from the scaffold domain (SD), allowing it to move as a piston sliding vertically with respect to the membrane during the elevator-like motion of TD. Lipid interactions with residues comprising the SD–TD interface directly influence the large-scale conformational changes and, consequently, the energetics of transport. Structural intermediates formed during the transition leak water molecules and may correlate to the uncoupled Cl − ion conductance observed experimentally in both prokaryotic and mammalian glutamate transporters. Mechanistic insights obtained from our study provide a structural framework for better development of therapeutic for neurological disorders.

Science & Technology - Other Topics↗
DOE OSTI2026

A new capability for investigating the structure and dynamics of liquids at high pressures

Water and aqueous solutions are critical to many areas of science and technology. As a result, tremendous effort has been devoted to understanding them in detail. Despite over a century of research, fundamental questions about water and aqueous solutions remain unanswered. However, an intriguing possibility – that liquid water can exist in two thermodynamically distinct states – has emerged as the most likely explanation. The problem is that experimental confirmation of this hypothesis requires experiments on water at high pressures and low temperatures, conditions in which liquid water only exists briefly before turning into crystalline ice. This project investigated the feasibility of developing a new capability for study water and aqueous solutions under these challenging conditions. The physical constraints, such as the timescales for crystallization and thermal diffusion in supercooled water, were evaluated along with their impact on the design criteria for the instrument. Several basic design options were considered that could meet the technical requirements. The options were also evaluated with respect to their use of commercially available equipment versus the need for custom designs or in-house development. The project identified two viable options to pursue. The first option would use a high-pressure syringe pump in conjunction with fused silica (or sapphire) capillaries. The second option would use a diamond anvil cell. These options can both be used with optical spectroscopies, such as Raman or Infrared.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Ab Initio Study of Atomic and Electronic Structure of Promising Ba4XMn3O12 (X = Nb, Ce, Pr) Oxides for Solar Thermochemical Hydrogen Production

The two-step metal oxide water-splitting cycle is one of the most viable approach for Solar Thermochemical Hydrogen (STCH) production. Challenges exist in finding suitable oxides that can satisfy thermodynamics of the STCH redox cycle under viable range of temperatures and partial pressures. Recently, BXM family members, i.e., Ba4NbMn3O12 (BNM), Ba4CeMn3O12 (BCM), Ba4PrMn3O12 (BPM) are discovered to exhibit promising STCH performance. However, the magnetic degrees of freedom of their experimental crystal structures is not characterized, and only hypothetical models exist for their electronic structure. We performed Monte-Carlo sampling for the magnetic spin arrangement of Mn atoms to provide explicit atomic structure models for their ground state 12R polytype and determined the most stable spin configuration for each member after structure relaxation using density functional theory (DFT) calculations. We also elucidate the most stable charge configuration (Mn3+/Mn4+ arrangement) for BNM among the existing hypothesis in literature. We investigate these strongly correlated oxides using different levels of theory (DFT+U, Hybrid-DFT) to develop better understanding of their electronic structure. These calculations allowed us to develop a model based on molecular orbital interactions that help explain the observed changes in their experimental x-ray spectroscopy measurements. Thereby, help link differences in electronic structure of BXM family members to their varying water-splitting behavior. These structure models will further facilitate future in-depth defect studies to model STCH redox cycle of these oxides.

atomic and magnetic structure↗
DOE OSTI2024

Water-induced surface ordering facilitating the microcutting of ductile metals

Metal cutting is a crucial process in modern manufacturing. Enhancing the machinability of metals can significantly improve their production efficiency and surface integrity. Coating surface-active media (SAM) on the free surface of the metals before cutting is an easy method to improve machinability, which usually pertains to the category of the renowned Rehbinder effect. However, the existing SAM is usually hazardous and complex materials. Besides, the effect of SAM on the local structure of the metal surface remains unclear. In this study, water is employed as a simple yet often overlooked SAM in the microcutting of copper. Using water as SAM also allows the employment of X-ray absorption fine structure spectroscopy (XAFS) to study the local structure of copper with and without water coating. Results show that water coating on the free surface of copper can significantly reduce the cutting force and chip thickness, and improve the surface finish. Interestingly, removing the water coating enables the recovery of the cutting force, demonstrating a reversible effect. Based on the XAFS results and molecular dynamics simulation, a water-induced surface ordering mechanism is proposed to explain the findings from the microcutting experiments. This mechanism suggests that water molecules can induce surface ordering in copper, resulting in reduced surface energy and fracture toughness of copper, thus enhancing machinability. In conclusion, this work provides valuable insights into the comprehension of the Rehbinder effect and shows that picometer-scale modifications of the surface atom arrangement can considerably alter the deformation mode of metals, paving the way for the development of new manufacturing processes.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on H7NO6 by Materials Project

NH5O5H2O crystallizes in the orthorhombic P2_12_12_1 space group. The structure is zero-dimensional and consists of four nitric acid, dihydrate molecules and four water molecules.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Dual receptor-sites reveal the structural basis for hyperactivation of sodium channels by poison-dart toxin batrachotoxin

The poison dart toxin batrachotoxin is exceptional for its high potency and toxicity, and for its multifaceted modification of the function of voltage-gated sodium channels. By using cryogenic electron microscopy, we identify two homologous, but nonidentical receptor sites that simultaneously bind two molecules of toxin, one at the interface between Domains I and IV, and the other at the interface between Domains III and IV of the cardiac sodium channel. Together, these two bound toxin molecules stabilize α/π helical conformation in the S6 segments that gate the pore, and one of the bound BTX-B molecules interacts with the crucial Lys1421 residue that is essential for sodium conductance and selectivity via an apparent water-bridged hydrogen bond. Overall, our structure provides insight into batrachotoxin’s potency, efficacy, and multifaceted functional effects on voltage-gated sodium channels via a dual receptor site mechanism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Challenges in correlating oxygen stable isotope ratios of hydrates on uranium ore concentrates to process waters

Exchange of oxygen stable isotopes (δ 18 O values) between precipitation waters and uranium oxides is governed by thermodynamics or kinetics. It has been assumed that meteoric waters can be related to precipitation waters in uranium ore concentrates and their calcination and reduced uranium oxide products. With this assumption, the δ 18 O values of uranium materials could provide forensic signatures that identify the production history and geolocation of nuclear materials. To further exploit the potential of δ 18 O values in nuclear material analysis, this study examines the oxygen stable isotope exchange in two UOCs, magnesium diuranate (MDU) and sodium diuranate (SDU). MDU and SDU were synthesized from solutions of uranyl nitrate hexahydrate using precipitation waters with unique oxygen isotope compositions. The structures of the MDU and SDU were analyzed using powder X-ray diffraction (p-XRD) and thermal mass loss curves, while the δ 18 O values of waters generated during thermal decomposition were analyzed using a thermogravimetric analyzer coupled to an isotope ratio infrared spectrometer (TGA-IRIS). By p-XRD, the MDU was uniform and amorphous across all syntheses with residual crystalline material incorporated as a minor component. Combined with the TGA results, all of the MDU is likely amorphous MgU 2 O 7 ·3H 2 O with MgO impurities present throughout. In contrast, the SDU synthesis resulted in multiple phases with many samples exhibiting crystalline phases including a combination of Na(UO 2 ) 4 O 2 (OH) 5 ·5H 2 O and Na 2 (UO2) 6 O 4 (OH) 6 ·8H 2 O with a Na 2 U 2 O 7 minor phase. A small fraction of the SDU samples were amorphous with no crystalline XRD peaks observed. Mass loss curves of the SDU samples revealed that the amorphous samples contained inclusions of similar crystalline phases compared to the crystalline materials. The uniformity of the MDU samples enabled highly reproducible measurements of δ 18 O values of the water vapor yielded for two dehydration events at 170 °C and 500 °C. In contrast, the multiphase composition of the SDU samples resulted in poor reproducibility in δ 18 O values. In conclusion, neither system revealed any correlation between the δ 18 O values of precipitation water, and the waters released during dehydration of the UOCs.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2020

ReaxFF molecular dynamics simulations of electrolyte–water systems at supercritical temperature

We have performed ReaxFF molecular dynamics simulations of alkali metal–chlorine pairs in different water densities at supercritical temperature (700 K) to elucidate the structural and dynamical properties of the system. The radial distribution function and the angular distribution function explain the inter-ionic structural and orientational arrangements of atoms during the simulation. The coordination number of water molecules in the solvation shell of ions increases with an increase in the radius of ions. We find that the self-diffusion coefficient of metal ions increases with a decrease in density under supercritical conditions due to the formation of voids within the system. The hydrogen bond dynamics has been interpreted by the residence time distribution of various ions, which shows Li+ having the highest water retaining capability. The void distribution within the system has been analyzed by using the Voronoi polyhedra algorithm providing an estimation of void formation within the system at high temperatures. We observe the formation of salt clusters of Na+ and K+ at low densities due to the loss of dielectric constants of ions. The diffusion of ions gets altered dramatically due to the formation of voids and nucleation of ions in the system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Complete separation of benzene-cyclohexene-cyclohexane mixtures via temperature-dependent molecular sieving by a flexible chain-like coordination polymer

Abstract The separation and purification of C6 cyclic hydrocarbons (benzene, cyclohexene, cyclohexane) represent a critically important but energy intensive process. Developing adsorptive separation technique to replace thermally driven distillation processes holds great promise to significantly reduce energy consumption. Here we report a flexible one-dimensional coordination polymer as an efficient adsorbent to discriminate ternary C6 cyclic hydrocarbons via an ideal molecular sieving mechanism. The compound undergoes fully reversible structural transformation associated with removal/re-coordination of water molecules and between activated and hydrocarbon-loaded forms. It exhibits distinct temperature- and adsorbate-dependent adsorption behavior which facilitates the complete separation of benzene, cyclohexene and cyclohexane from their binary and ternary mixtures, with the record-high uptake ratios for C 6 H 6 /C 6 H 12 and C 6 H 10 /C 6 H 12 in vapor phase and highest binary and ternary selectivities in liquid phase. In situ infrared spectroscopic analysis and ab initio calculations provide insight into the host-guest interactions and their effect on the preferential adsorption and structural transformation.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Solvent Dynamics Are Critical to Understanding Carbon Dioxide Dissolution and Hydration in Water

Simulations of carbon dioxide (CO 2 ) in water may aid in understanding the impact of its accumulation in aquatic environments and help advance technologies for carbon capture and utilization (via, e.g., mineralization). Quantum mechanical (QM) simulations based on static molecular models with polarizable continuum solvation poorly reproduce the energetics of CO 2 hydration to form carbonic acid in water, independent of the level of QM theory employed. Only with density-functional-theory-based molecular dynamics and rare-event sampling, followed by energy corrections based on embedded correlated wavefunction theory (in conjunction with density functional embedding theory), can a close agreement between theory and experiment be achieved. Such multilevel simulations can serve as benchmarks for simpler, less costly models, giving insight into potential errors of the latter. The strong influence of sampling/averaging over dynamical solvent configurations on the energetics stems from the difference in polarity of both the transition state and product (both polar) versus the reactant (nonpolar). When a solute undergoes a change in polarity during reaction, affecting its interaction with the solvent, careful assessment of the energetic contribution of the solvent response to this change is critical. Here, we show that static models (without structural sampling) that incorporate three explicit water molecules can yield far superior results than models with more explicit water molecules because fewer water molecules yield less configurational artifacts. Static models intelligently incorporating both explicit (molecules directly participating in the reaction) and implicit solvation, along with a proper QM theory, e.g., CCSD(T) for closed-shell systems, can close the accuracy gap between static and dynamic models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Modeling the aqueous interface of amorphous TiO 2 using deep potential molecular dynamics

Amorphous titanium dioxide (a-TiO 2 ) is widely used as a coating material in applications such as electrochemistry and self-cleaning surfaces where its interface with water has a central role. However, little is known about the structures of the a-TiO 2 surface and aqueous interface, particularly at the microscopic level. In this work, we construct a model of the a-TiO 2 surface via a cut-melt-and-quench procedure based on molecular dynamics simulations with deep neural network potentials (DPs) trained on density functional theory data. After interfacing the a-TiO 2 surface with water, we investigate the structure and dynamics of the resulting system using a combination of DP-based molecular dynamics (DPMD) and ab initio molecular dynamics (AIMD) simulations. Both AIMD and DPMD simulations reveal that the distribution of water on the a-TiO 2 surface lacks distinct layers normally found at the aqueous interface of crystalline TiO 2 , leading to an ~10 times faster diffusion of water at the interface. Bridging hydroxyls (Ti 2 –O b H) resulting from water dissociation decay several times more slowly than terminal hydroxyls (Ti–O w H) due to fast Ti–O w H 2 → Ti–O w H proton exchange events. These results provide a basis for a detailed understanding of the properties of a-TiO 2 in electrochemical environments. Moreover, the procedure of generating the a-TiO 2 -interface employed here is generally applicable to studying the aqueous interfaces of amorphous metal oxides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗