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At least 505 records · Page 28

Dataset for manuscript "Equipartition and the temperature of maximum density of TIP4P/2005 water"

We simulate TIP4P/2005 water in the temperature range of 257 K to 318 K with time-steps 0.25, 0.50, 1.00, 2.00, and 4.00 fs. The density-temperature behavior obtained using 0.25 or 0.50 fs are in excellent agreement with each other but differ from those obtained using time-steps that have been shown earlier to lead to a breakdown of equipartition. The temperature of maximum density (TMD) is 277.15 K with time-step 0.25 or 0.50 fs, but is shifted to progressively lower values for longer time-steps, a trend that holds for different thermostat/barostat combinations. Enhancing the water-water dispersion interaction, as has been recommended for simulating disordered proteins in TIP4P/2005, degrades the description of the liquid-vapor phase envelope. We present a simple physically transparent reasoning to highlight the separation of the time-scales between translational and rotational motion. We also develop a metric, Chi, that we term the equipartition anomaly, to detect equipartition violations in simulations that include molecules that are treated as rigid objects. Calculating Chi is shown to be straightforward and sensitive to equipartition violations. A key takeaway from this study is that using sufficiently short time-steps (less than or equal to 0.5 fs) to preserve equipartition is essential for obtaining meaningful liquid water properties and for producing reliable simulation data, as correct-ensemble sampling is fundamental to ensure reproducibility across codes and simulation alogrithms. The included dataset provides the raw data used in the preparation of the graphs noted in the manuscript.

36 MATERIALS SCIENCE↗

Antibacterial Minerals: A geochemical approach to combating antibiotic resistance

The rapid rise of antibiotic resistant bacteria is seriously threatening our ability to treat lifethreatening infections. As a result, our approach to medicine and agriculture will require significant changes if we are to successfully maintain current levels of healthcare and food security. Certain naturally occurring clays have been shown to harbor antimicrobial properties and kill antibiotic resistant bacteria. These clays have been proposed as a new paradigm for fighting the potentially devastating effects of the post antibiotic era. However, natural samples, by their inherent properties, exhibit variable antibacterial effectiveness and the synthesis of minerals with reproducible antibacterial activity is needed. Our project focused on 3 specific aims; 1) develop synthetic versions of naturally occurring bactericidal minerals to control the chemical purity and antibacterial potency, 2) determine how effective these mineral formulations are at killing antibiotic resistant bacteria and 3) investigate the response of human skin cell cultures to these antibacterial minerals. Utilizing hydrothermal based methods our team was able to reproduce the antibacterial activity observed in natural antibacterial minerals, while eliminating unwanted elemental impurities. Importantly, we were able to create a mineral based bactericide that has reproducible reactivity that could provide a consistent dose response. These antibacterial mineral formulations are effective at killing common hospital acquired antibiotic resistant bacteria while providing minimal toxicity to human fibroblasts. Our research has optimized the antibacterial properties of antibacterial minerals to allow greater efficacy from a public health perspective.

59 BASIC BIOLOGICAL SCIENCES↗

Development of Coarse-Grained Models for Poly(4-vinylphenol) and Poly(2-vinylpyridine): Polymer Chemistries with Hydrogen Bonding

In this paper, we identify the modifications needed in a recently developed generic coarse-grained (CG) model that captured directional interactions in polymers to specifically represent two exemplary hydrogen bonding polymer chemistries—poly(4-vinylphenol) and poly(2-vinylpyridine). We use atomistically observed monomer-level structures (e.g., bond, angle and torsion distribution) and chain structures (e.g., end-to-end distance distribution and persistence length) of poly(4-vinylphenol) and poly(2-vinylpyridine) in an explicitly represented good solvent (tetrahydrofuran) to identify the appropriate modifications in the generic CG model in implicit solvent. For both chemistries, the modified CG model is developed based on atomistic simulations of a single 24-mer chain. This modified CG model is then used to simulate longer (36-mer) and shorter (18-mer and 12-mer) chain lengths and compared against the corresponding atomistic simulation results. We find that with one to two simple modifications (e.g., incorporating intra-chain attraction, torsional constraint) to the generic CG model, we are able to reproduce atomistically observed bond, angle and torsion distributions, persistence length, and end-to-end distance distribution for chain lengths ranging from 12 to 36 monomers. We also show that this modified CG model, meant to reproduce atomistic structure, does not reproduce atomistically observed chain relaxation and hydrogen bond dynamics, as expected. Simulations with the modified CG model have significantly faster chain relaxation than atomistic simulations and slower decorrelation of formed hydrogen bonds than in atomistic simulations, with no apparent dependence on chain length.

36 MATERIALS SCIENCE↗

Exploding Bridgewire (EBW) Detonators: An Example of Synergistic Multiphysics

Exploding bridgewire (EBW) detonators are highly temporally reproducible explosive devices that require the rapid discharge of a high‐voltage capacitance to operate and so are immune to most of the accidental hazards associated with traditional electric detonators. They have been demonstrated to be safe enough for use in high‐consequence explosive applications. Despite continued use for over 82 years, understanding the exact mechanism of operation has remained elusive. Various researchers have ascribed either deflagration‐to‐detonation (DDT) or shock‐to‐detonation (SDT) phenomena observed in other explosive events to explain the science behind the successful engineering; however, a rigorous justification has been absent. Previously, we have demonstrated a complex interaction in EBW detonators between large electrical currents, non‐equilibrium thermodynamic material states, plasma physics, powder compaction phenomena, shock physics, photochemistry, and rapid conventional explosive chemical reaction processes. Specifically, we have made progress in understanding the complex multiphysics that operates in these detonators and demonstrating that it is a serendipitous synergy between UV light emitted from the arc formed as the bridge is electrically exploded and the accompanying short‐duration shock transmitted into the explosive powder bed that allows these devices to function at practical capacitor sizes and charge voltages. This insight not only places the topic on a firmer scientific footing but potentially enables new approaches to safe detonator design.

36 MATERIALS SCIENCE↗

Exploring driving forces for length growth in graphene nanoribbons during chemical vapor deposition of hydrocarbons on Ge(0 0 1) via kinetic Monte Carlo simulations

Graphene grown slowly on Ge(0 0 1) using chemical vapor deposition of hydrocarbons leads to high-aspect ratio graphene nanoribbons with smooth edges and a technologically relevant band gap at room temperature; however, the driving forces leading to one-dimensional growth of such graphene crystals are not well understood. Here, we combine a lattice kinetic Monte Carlo approach based on steps in graphene growth and experimental measurements to study the growth of graphene nanoribbons via chemical vapor deposition on Ge(0 0 1). To identify potential reasons for growth of graphene as anisotropic ribbons, we study the impact of anisotropy in various growth parameters on the resulting graphene crystals. Comparing our model with experimental measurements indicates that anisotropy in the stabilization of a graphene precursor species bound to the graphene edge is the most likely reason why high aspect ratio graphene ribbons with smooth edges grow on Ge(0 0 1). Using the growth model developed here, we reproduce experimental trends in the synthesis of graphene nanoribbons on Ge(001) and arrive at an intuitive picture for their growth. These insights shed light on the driving forces governing this highly anisotropic regime of crystal growth.

36 MATERIALS SCIENCE↗

Implementation of dietary methionine restriction using casein after selective, oxidative deletion of methionine

Dietary methionine restriction (MR) is normally implemented using diets formulated from elemental amino acids (AA) that reduce methionine content to 0.17%. However, translational implementation of MR with elemental AA-based diets is intractable due to poor palatability. To solve this problem and restrict methionine using intact proteins, casein was subjected to mild oxidation to selectively reduce methionine. Diets were then formulated using oxidized casein, adding back methionine to produce a final concentration of 0.17%. The biological efficacy of dietary MR using the oxidized casein (Ox Cas) diet was compared with the standard elemental MR diet in terms of the behavioral, metabolic, endocrine, and transcriptional responses to the four diets. The Ox Cas MR diet faithfully reproduced the expected physiological, biochemical, and transcriptional responses in liver and inguinal white adipose tissue. Collectively, these findings demonstrate that dietary MR can be effectively implemented using casein after selective oxidative reduction of methionine.

59 BASIC BIOLOGICAL SCIENCES↗

Microscopic mechanism of unusual lattice thermal transport in TlInTe 2

We investigate the microscopic mechanism of ultralow lattice thermal conductivity (κ l ) of TlInTe 2 and its weak temperature dependence using a unified theory of lattice heat transport, that considers contributions arising from the particle-like propagation as well as wave-like tunneling of phonons. While we use the Peierls–Boltzmann transport equation (PBTE) to calculate the particle-like contributions (κ l (PBTE)), we explicitly calculate the off-diagonal (OD) components of the heat-flux operator within a first-principles density functional theory framework to determine the contributions (κ l (OD)) arising from the wave-like tunneling of phonons. At each temperature, T, we anharmonically renormalize the phonon frequencies using the self-consistent phonon theory including quartic anharmonicity, and utilize them to calculate κ l (PBTE) and κ l (OD). With the combined inclusion of κ l (PBTE), κ l (OD), and additional grain-boundary scatterings, our calculations successfully reproduce the experimental results. Our analysis shows that large quartic anharmonicity of TlInTe 2 (a) strongly hardens the low-energy phonon branches, (b) diminishes the three-phonon scattering processes at finite T, and (c) recovers the weaker than T –1 decay of the measured κ l .

36 MATERIALS SCIENCE↗

Coexistence of soft and hard magnetic phases in single layer amorphous Tb–Co thin films

Amorphous, ferrimagnetic Tb-Co thin films prepared with a thin Ta underlayer and either a Ta or a Pt overlayer show evidence of both soft and hard magnetic phases. At room temperature, the films exhibit conventional ferromagnetism, but low temperature magnetometry measurements reveal the decoupling of the two magnetic phases with decreasing temperature due to increased anisotropy energy of the hard layer at lower temperatures. Decreasing the film thickness to 2 nm, slightly above the superparamagnetic limit found at 1 nm, a soft, low-density phase was isolated and found to be present in all the films as confirmed with x-ray reflectivity and Rutherford backscattering spectrometry measurements. For greater thicknesses, the bottom layer retains its soft magnetic nature, while the remainder of the film is denser and has strong perpendicular magnetic anisotropy, leading to the exchange-spring behavior when the anisotropy becomes large, either at low temperatures or via a Pt overlayer that adds a strong interfacial anisotropy to the layer. Micromagnetic simulations of a soft/hard bilayer model with the experimentally determined anisotropy and magnetization parameters into a soft/hard bilayer model reproduced the experimental hysteretic behavior very well. These findings demonstrate how the magnetic state and the response of a-Tb-Co films to external fields can be controlled, providing a high degree of tunability that is promising for high-performance nanoscale devices.

36 MATERIALS SCIENCE↗

169 Tm ( n , γ ) cross section and statistical decay properties from measurements at the DANCE facility

Background: Radiative neutron capture on thulium, which is a monoisotopic element, plays a role in different applications such as nuclear astrophysics or nuclear burning environments. Considerable discrepancies—reaching 20%—exist between evaluations in the unresolved-resonance region. Furthermore, experimental data on statistical 𝛾 decay in odd-odd rare-earth nuclei is scarce. There are still open questions about the systematics of the so-called scissors mode in the 𝑀⁢1 photon strength function, especially in odd-odd nuclei. Purpose: This work is focused on two main topics—deriving experimental 169 Tm ⁢(𝑛,𝛾) cross section and studying statistical 𝛾 decay of 170 Tm, in particular properties of the scissors mode. Methods: The capture experiments to obtain experimental cross section were performed at the Los Alamos Neutron Science Center using the time-of-flight technique and employing the Detector for Advanced Neutron Capture Experiments. Measured coincident 𝛾-ray spectra were also compared with statistical simulations using the dicebox code to test different models of level density and photon strength functions. Results: The capture cross section was determined from 1.8 eV to 0.97 MeV, the broadest neutron-energy range ever measured for this isotope. Several new resonances have been observed. The statistical 𝛾 decay of 170 Tm cannot be reproduced without a scissors mode resonance centered at ≈ 3.3MeV. Conclusions: The measured cross section in the unresolved-resonance region is generally lower than the latest evaluations. The derived 169 Tm 𝑠-process abundance is expected to increase by a factor of 1.26, while the changes of the abundances of elements heavier than 169 Tm are in the order of 0.2%. The scissors mode properties in 170 Tm are similar to those deduced in previous analyses of neighboring nuclei 168 Er and 166 Ho .

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Low-energy magneto-optics of Tb 2 Ti 2 O 7 in a [111] magnetic field

The pyrochlore magnet Tb 2 Ti 2 O 7 shows a lack of magnetic order to low temperatures and is considered to be a quantum spin liquid candidate. Here we perform time-domain THz spectroscopy on high-quality Tb 2 Ti 2 O 7 crystals and study the low-energy excitations as a function of [111] magnetic field with high energy resolution. The low-energy crystal-field excitations change their energies anomalously under magnetic field. Despite several sharp field-dependent changes, we show that the material's spectrum can be described not by phase transitions but by field-dependent hybridization between the low-energy crystal-field levels. We highlight the strong coupling between spin and lattice degrees of freedom in Tb 2 Ti 2 O 7 as evidenced by the magnetic-field tunable crystal-field environment. Calculations based on single ion physics with field-induced symmetry reduction of the crystal-field environment can reproduce our data.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Using Direct Laboratory Measurements of Electron Temperature Anisotropy to Identify the Heating Mechanism in Electron-Only Guide Field Magnetic Reconnection

Anisotropic electron heating during electron-only magnetic reconnection with a large guide magnetic field is directly measured in a laboratory plasma through in situ measurements of electron velocity distribution functions. Electron heating preferentially parallel to the magnetic field is localized to one separatrix, and anisotropies of 1.5 are measured. The mechanism for electron energization is identified as the parallel reconnection electric field because of the anisotropic nature of the heating and spatial localization. These characteristics are reproduced in a 2D particle-in-cell simulation and are also consistent with numerous magnetosheath observations. A measured increase in the perpendicular temperature along both separatrices is not reproduced by our 2D simulations. Here, this work has implications for energy partition studies in magnetosheath and laboratory reconnection.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Imaging orbital ferromagnetism in a moiré Chern insulator

Capturing exotic magnetism Ferromagnetism is associated with the breaking of time-reversal symmetry, most frequently by the spin degree of freedom. Although the orbital motion of electrons can also contribute to ferromagnetism, in most materials, it is small relative to the spin contribution. Tschirhart et al. showed that the reverse is true in an unusual magnetic state hosted by twisted bilayer graphene. Their scanning magnetometry measurements were consistent with ferromagnetism of predominantly orbital origin. Science , abd3190, this issue p. 1323

Science & Technology - Other Topics↗

Evaluation of the Near-Surface Variables in the HRRR Weather Model Using Observations from the ARM SGP Site

Abstract The performance of version 4 of the NOAA High-Resolution Rapid Refresh (HRRR) numerical weather prediction model for near-surface variables, including wind, humidity, temperature, surface latent and sensible fluxes, and longwave and shortwave radiative fluxes, is examined over the Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) region. The study evaluated the model’s bias and bias-corrected mean absolute error relative to the observations on different time scales. Forecasts of near-surface geophysical variables at five SGP sites (HRRR at 3-km scale) were found to agree well with observations, but some consistent observation–forecast differences also occurred. Sensible and latent heat fluxes are the most challenging variables to be reproduced. The diurnal cycle is the main temporal scale affecting observation–forecast differences of the near-surface variables, and almost all of the variables showed different biases throughout the diurnal cycle. Results show that the overestimation of downward shortwave and the underestimation of downward longwave radiative flux are the two major biases found in this study. The timing and magnitude of downward longwave flux, wind speed, and sensible and latent heat fluxes are also different with contributions from model representations, data assimilation limitations, and differences in scales between HRRR and SGP sites. The positive bias in downward shortwave and negative bias in longwave radiation suggests that the model is underestimating cloud fraction in the study domain. The study concludes by showing a brief comparison with version 3 of the HRRR and shows that version 4 has better performance in almost all near-surface variables. Significance Statement A correct representation of the near-surface variables is important for numerical weather prediction models. This study investigates the capability of the latest NOAA High-Resolution Rapid Refresh (HRRRv4) model in simulating the near-surface variables by comparing against the Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) in situ observations. Among others, we find that the surface heat fluxes, such as sensible and latent heat fluxes, are the most difficult variables to be reproduced. This study also shows that the diurnal cycle has the dominant impact on the model’s performance, which means the majority of the outputted near-surface variables have the strong diurnal cycle in their bias errors.

54 ENVIRONMENTAL SCIENCES↗

Ocean physical‐biogeochemical interactions in the CMIP6 and E3SM Earth System Models

The primary objectives of this project are to quantify the spatio‐temporal linkages between physical climate and ocean biogeochemical variables in the U.S. Department of Energy (DOE) Energy Exascale Earth System Model (E3SM), in CMIP6 Earth System Models (ESMs), and in historical observations, to evaluate the E3SM’s ability to reproduce the observations, and to develop a solid diagnostic package to do so. It will revolve around four hypotheses and will focus on key physical and biogeochemical processes that regulate the upper ocean carbon and oxygen cycling: water mass distribution, ventilation, and biological production.

54 ENVIRONMENTAL SCIENCES↗

Southern Ocean polynyas and dense water formation in a high-resolution, coupled Earth system model

Antarctic coastal polynyas produce dense shelf water, a primary source of Antarctic Bottom Water that contributes to the global overturning circulation. This paper investigates Antarctic dense water formation in the high-resolution version of the Energy Exascale Earth System Model (E3SM-HR). The model is able to reproduce the main Antarctic coastal polynyas, although the polynyas are smaller in area compared to observations. E3SM-HR also simulates several occurrences of open-ocean polynyas (OOPs) in the Weddell Sea at a higher rate than what the last 50 years of the satellite sea ice observational record suggests, but similarly to other high-resolution Earth system model simulations. Furthermore, the densest water masses in the model are formed within the OOPs rather than on the continental shelf as is typically observed. Biases related to the lack of dense water formation on the continental shelf are associated with overly strong atmospheric polar easterlies, which lead to a strong Antarctic Slope Front and too little exchange between on- and off-continental shelf water masses. Strong polar easterlies also produce excessive southward Ekman transport, causing a build-up of sea ice over the continental shelf and enhanced ice melting in the summer season. This, in turn, produces water masses on the continental shelf that are overly fresh and less dense relative to observations. Our results indicate that high resolution alone is insufficient for models to properly reproduce Antarctic dense water; the large-scale polar atmospheric circulation around Antarctica must also be accurately simulated.

54 ENVIRONMENTAL SCIENCES↗

Reflectivities of uniform and broken stratiform clouds: An update

The reflectivities of uniform and broken stratiform clouds obtained from the NOAA-9 and NOAA-10 overpasses collected during the FIRE Marine Stratocumulus Intensive Field Observations (IFO) were compared, and these reflectivities were compared with those obtained through radiative transfer calculation performed for plane-parallel cloud models. The objective was to determine the extent to which plane-parallel radiative transfer calculations could reproduce the reflectivities observed for uniform clouds and to determine the extent to which finite cloud effects cause broken clouds to reflect differently than uniform clouds. The latter study is to provide guidance in the parameterization of finite cloud effects in general circulation climate models as well as to assess the ability of plane-parallel theory, which is used by ISCCP to retrieve cloud properties, to treat the reflectivities of broken clouds. Some results from this study were reported at the last FIRE Science Team meeting and some were reported elsewhere (Coakley and Briegleb, 1989). Improvements since the previous reports include: (1) the analysis of additional satellite passes, and (2) a modification to the analysis which helps to show the significance of the differences in reflectivities for uniform and broken clouds.

Coakley, James A., Jr.↗