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Results for “Potential Structures”

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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Methanobactin from methanotrophs: genetics, structure, function and potential applications

ABSTRACT Aerobic methane-oxidizing bacteria of the Alphaproteobacteria have been found to express a novel ribosomally synthesized post-translationally modified polypeptide (RiPP) termed methanobactin (MB). The primary function of MB in these microbes appears to be for copper uptake, but MB has been shown to have multiple capabilities, including oxidase, superoxide dismutase and hydrogen peroxide reductase activities, the ability to detoxify mercury species, as well as acting as an antimicrobial agent. Herein, we describe the diversity of known MBs as well as the genetics underlying MB biosynthesis. We further propose based on bioinformatics analyses that some methanotrophs may produce novel forms of MB that have yet to be characterized. We also discuss recent findings documenting that MBs play an important role in controlling copper availability to the broader microbial community, and as a result can strongly affect the activity of microbes that require copper for important enzymatic transformations, e.g. conversion of nitrous oxide to dinitrogen. Finally, we describe procedures for the detection/purification of MB, as well as potential medical and industrial applications of this intriguing RiPP.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

The structural information filtered features (SIFF) potential: Maximizing information stored in machine-learning descriptors for materials prediction

Machine learning inspired potentials continue to improve the ability for predicting structures of materials. However, many challenges still exist, particularly when calculating structures of disordered systems. These challenges are primarily due to the rapidly increasing dimensionality of the feature-vector space which in most machine-learning algorithms is dependent on the size of the structure. In this article, we present a feature-engineered approach that establishes a set of principles for representing potentials of physical structures (crystals, molecules, and clusters) in a feature space rather than a physically motivated space. Our goal in this work is to define guiding principles that optimize information storage of the physical parameters within the feature representations. In this manner, we focus on keeping the dimensionality of the feature space independent of the number of atoms in the structure. Our Structural Information Filtered Features (SIFF) potential represents structures by utilizing a feature vector of low-correlated descriptors, which correspondingly maximizes information within the descriptor. We present results of our SIFF potential on datasets composed of disordered (carbon and carbon–oxygen) clusters, molecules with C 7 O 2 H 2 stoichiometry in the GDB9-14B dataset, and crystal structures of the form (Al x Ga y In z ) 2 O 3 as proposed in the NOMAD Kaggle competition. Our potential's performance is at least comparable, sometimes significantly more accurate, and often more efficient than other well-known machine-learning potentials for structure prediction. However, primarily, we offer a different perspective on how researchers should consider opportunities in maximizing information storage for features.

36 MATERIALS SCIENCE↗
DOE OSTI2025

New Dimension in Ab Initio Electronic Structure Theory: Temperature, Pressure, and Chemical Potential

Ab initio electronic structure theory has transformed gas-phase molecular science with its predictive ability. In the attempt to bring such predictive ability to macroscopic systems and condensed matter, the theory must integrate quantum mechanics with statistical thermodynamics, so that thermodynamic functions such as free energy, internal energy, entropy, and chemical potentials are computed as functions of temperature in a systematically converging series of approximations. Here, a general, versatile strategy of elevating ab initio electronic structure theory to nonzero temperatures is introduced and discussed.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Towards next-generation optical potentials for nuclear reactions and structure calculations

Optical-model potentials (OMPs) are critical ingredients for basic and applied nuclear physics. Present-day computational capabilities allow us to generate data-driven nucleon-nucleus OMPs that are non-local and exactly dispersive (as theoretically required to be), include statistically-sound uncertainty quantification, and are trained on both scattering and bound-state data from a wide area of the nuclear chart. Combined together, these features allow for significant improvement in fidelity and extrapolative power of the model. Here, we present preliminary work toward the development and training of such an OMP. The capability of the model to describe data at this first stage is encouraging.

Perrotta, Salvatore Simone [Lawrence Livermore Nat↗
DOE OSTI2024

Towards next-generation optical potentials for nuclear reactions and structure calculations

Optical-model potentials (OMPs) are critical ingredients for basic and applied nuclear physics. Present-day computational capabilities allow us to generate data-driven nucleon-nucleus OMPs that are non-local and exactly dispersive (as theoretically required to be), include statisticallysound uncertainty quantification, and are trained on both scattering and bound-state data from a wide area of the nuclear chart. Combined together, these features allow for significant improvement in fidelity and extrapolative power of the model. Here, we present preliminary work toward the development and training of such an OMP. The capability of the model to describe data at this first stage is encouraging.

Perrotta, S.↗
DOE OSTI2024

Insights into the structure and dynamics of K + ions at the muscovite–water interface from machine learning potential simulations

The surfaces of many minerals are covered by naturally occurring cations that become partially hydrated and can be replaced by hydronium or other cations when the surface is exposed to water or an aqueous solution. These ion exchange processes are relevant to various chemical and transport phenomena, yet elucidating their microscopic details is challenging for both experiments and simulations. Here, in this work, we make a first step in this direction by investigating the behavior of the native K + ions at the interface between neat water and the muscovite mica (001) surface with ab-initio -based machine learning molecular dynamics and enhanced sampling simulations. Our results show that the desorption of the surface K + ions in pure ion-free water has a significant free energy barrier irrespective of their local surface arrangement. In contrast, facile K + diffusion between mica’s ditrigonal cavities characterized by different Al/Si orderings is observed. This behavior suggests that the K + ions may favor a dynamic disordered surface arrangement rather than complete desorption when exposed to deionized water.

Ab-initio molecular dynamics↗
DOE OSTI2021

Naegleria fowleri: Protein structures to facilitate drug discovery for the deadly, pathogenic free-living amoeba

Naegleria fowleri is a pathogenic, thermophilic, free-living amoeba which causes primary amebic meningoencephalitis (PAM). Penetrating the olfactory mucosa, the brain-eating amoeba travels along the olfactory nerves, burrowing through the cribriform plate to its destination: the brain’s frontal lobes. The amoeba thrives in warm, freshwater environments, with peak infection rates in the summer months and has a mortality rate of approximately 97%. A major contributor to the pathogen’s high mortality is the lack of sensitivity of N . fowleri to current drug therapies, even in the face of combination-drug therapy. To enable rational drug discovery and design efforts we have pursued protein production and crystallography-based structure determination efforts for likely drug targets from N . fowleri . The genes were selected if they had homology to drug targets listed in Drug Bank or were nominated by primary investigators engaged in N . fowleri research. In 2017, 178 N . fowleri protein targets were queued to the Seattle Structural Genomics Center of Infectious Disease (SSGCID) pipeline, and to date 89 soluble recombinant proteins and 19 unique target structures have been produced. Many of the new protein structures are potential drug targets and contain structural differences compared to their human homologs, which could allow for the development of pathogen-specific inhibitors. Five of the structures were analyzed in more detail, and four of five show promise that selective inhibitors of the active site could be found. The 19 solved crystal structures build a foundation for future work in combating this devastating disease by encouraging further investigation to stimulate drug discovery for this neglected pathogen.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Tackling Disorder in γ‐Ga 2 O 3

Abstract Ga 2 O 3 and its polymorphs are attracting increasing attention. The rich structural space of polymorphic oxide systems such as Ga 2 O 3 offers potential for electronic structure engineering, which is of particular interest for a range of applications, such as power electronics. γ‐Ga 2 O 3 presents a particular challenge across synthesis, characterization, and theory due to its inherent disorder and resulting complex structure–electronic‐structure relationship. Here, density functional theory is used in combination with a machine‐learning approach to screen nearly one million potential structures, thereby developing a robust atomistic model of the γ‐phase. Theoretical results are compared with surface and bulk sensitive soft and hard X‐ray photoelectron spectroscopy, X‐ray absorption spectroscopy, spectroscopic ellipsometry, and photoluminescence excitation spectroscopy experiments representative of the occupied and unoccupied states of γ‐Ga 2 O 3 . The first onset of strong absorption at room temperature is found at 5.1 eV from spectroscopic ellipsometry, which agrees well with the excitation maximum at 5.17 eV obtained by photoluminescence excitation spectroscopy, where the latter shifts to 5.33 eV at 5 K. This work presents a leap forward in the treatment of complex, disordered oxides and is a crucial step toward exploring how their electronic structure can be understood in terms of local coordination and overall structure.

36 MATERIALS SCIENCE↗
DOE OSTI2024

The Atacama Cosmology Telescope: A Measurement of the DR6 CMB Lensing Power Spectrum and Its Implications for Structure Growth

We present new measurements of cosmic microwave background (CMB) lensing over 9400 deg of the sky. These lensing measurements are derived from the Atacama Cosmology Telescope (ACT) Data Release 6 (DR6) CMB data set, which consists of five seasons of ACT CMB temperature and polarization observations. We determine the amplitude of the CMB lensing power spectrum at 2.3% precision (43σ significance) using a novel pipeline that minimizes sensitivity to foregrounds and to noise properties. To ensure that our results are robust, we analyze an extensive set of null tests, consistency tests, and systematic error estimates and employ a blinded analysis framework. Our CMB lensing power spectrum measurement provides constraints on the amplitude of cosmic structure that do not depend on Planck or galaxy survey data, thus giving independent information about large-scale structure growth and potential tensions in structure measurements. The baseline spectrum is well fit by a lensing amplitude of A lens = 1.013 ± 0.023 relative to the Planck 2018 CMB power spectra best-fit ΛCDM model and A lens = 1.005 ± 0.023 relative to the ACT DR4 + WMAP best-fit model. From our lensing power spectrum measurement, we derive constraints on the parameter combination $S^{CMBL}_{8}$ ≡ σ 8 (Ω m /0.3) 0.25 of $S^{CMBL}_{8}$ = 0.818 ± 0.022 from ACT DR6 CMB lensing alone and $S^{CMBL}_{8}$ = 0.813 ± 0.018 when combining ACT DR6 and Planck NPIPE CMB lensing power spectra. These results are in excellent agreement with ΛCDM model constraints from Planck or ACT DR4 + WMAP CMB power spectrum measurements. Our lensing measurements from redshifts z ~ 0.5–5 are thus fully consistent with ΛCDM structure growth predictions based on CMB anisotropies probing primarily z ~ 1100. We find no evidence for a suppression of the amplitude of cosmic structure at low redshifts.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

A deep learning interatomic potential developed for atomistic simulation of carbon materials

Interatomic potentials based on neural-network machine learning method have attracted considerable attention in recent years owing to their outstanding ability to balance the accuracy and efficiency in atomistic simulations. In this work, a neural-network potential (NNP) for carbon is generated to simulate the structural properties of various carbon structures. The potential is trained using a database consisting of crystalline and liquid structures obtained by the first-principles density functional theory (DFT) calculations. The developed potential accurately predicts the energies and forces in crystalline and liquid carbon structures, the energetic stability of defected graphene, and the structures of amorphous carbon as the function of density. As a result, the excellent accuracy and transferability of the NNP provide a promising tool for accurate atomistic simulations of various carbon materials with faster speed and much lower cost.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Development of coal-derived carbon-based structural unit as a potential new building material

Coal combustion for energy has not only wasted the hydrogen-rich volatile matters but also results in CO 2 emission causing serious environmental issues. An integrated coal pyrolysis and solvent extraction process under elevated temperatures in an inert atmosphere is implemented to convert as-mined coal from Wyoming Powder River Basin to functional carbon elements such as pyrolysis char (PC). This paper presents the development and fabrication of new carbon-based structural unit (CSU) using pulverized PC and two coal-derived pitches (mesophase pitch and tar pitch) to attain high compressive strength greater than 30 MPa, low thermal conductivity less than 0.30 W/m.K, and low density less than 1.25 g/cm 3 . CSUs have the potential to overcome the current challenges with cement and concrete through pressurized fabrication followed by carbonization. This study aims to develop CSU with nearly 100% coal-derived carbon material for structural application in buildings. The effects of pressing pressures, carbonization temperatures, and binder contents on the density and mechanical and thermal properties of CSU samples are investigated. The study concludes that mesophase pitch produces a better performance of CSU samples, a combination of 100 MPa pressing pressure and carbonization temperature of 900 ⁰C yields the highest compressive strength, and a 25% MP content is recommended for low-cost CSU fabrication. Furthermoer, CSU has a much lower density, lower thermal conductivity, higher compressive strength, and higher strength-to-density ratio than normal concrete.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Properties and Acceleration Mechanisms of Electrons Up To 200 keV Associated With a Flux Rope Pair and Reconnection X-Lines Around It in Earth's Plasma Sheet

The properties and acceleration mechanisms of electrons (<200 keV) associated with a pair of tailward traveling flux ropes and accompanied reconnection X-lines in Earth's plasma sheet are investigated with MMS measurements. Energetic electrons are enhanced on both boundaries and core of the flux ropes. The power-law spectra of energetic electrons near the X-lines and in flux ropes are harder than those on flux rope boundaries. Theoretical calculations show that the highest energy of adiabatic electrons is a few keV around the X-lines, tens of keV immediately downstream of the X-lines, hundreds of keV on the flux rope boundaries, and a few MeV in the flux rope cores. The X-lines cause strong energy dissipation, which may generate the energetic electron beams around them. The enhanced electron parallel temperature can be caused by the curvature-driven Fermi acceleration and the parallel electric potential. Betatron acceleration due to the magnetic field compression is strong on flux rope boundaries, which enhances energetic electrons in the perpendicular direction. Electrons can be trapped between the flux rope pair due to mirror force and parallel electric potential. Electrostatic structures in the flux rope cores correspond to potential drops up to half of the electron temperature. The energetic electrons and the electron distribution functions in the flux rope cores are suggested to be transported from other dawn-dusk directions, which is a 3-dimensional effect. The acceleration and deceleration of the Betatron and Fermi processes appear alternately indicating that the magnetic field and plasma are turbulent around the flux ropes.

58 GEOSCIENCES↗
DOE OSTI2024

Numerical Simulation of Infrasound Resonance in Underground Tunnel Structures

Remote observation of infrasound resonant signals emanating from underground tunnel structures could potentially allow the remote quantification of the geometry of the underground structures in which the signals were generated. However, the sensitivity of these observations to tunnel geometry and changes in that geometry are unknown. In this report we outline a numerical simulation study with the following three objectives: 1. Can we model infrasound resonance using numerical simulations? 2. What is the sensitivity of the modeled observations to changes in tunnel geometry or boundary conditions? And 3. Can we accurately model resonant observations of explosions occurring in Redmond Salt Mine in Central Utah. In this report we outline affirmative answers to the first two objectives, but we were unable to accurately model the Redmond Explosions due to numerical instability in the model of the complex structure of the mine. Recommendations for future work emphasize the need to acquire additional datasets and to explore a more data-based approach in which changes in data signatures are detected as a first step towards developing a method which inverts resonant infrasound signals for tunnel geometry.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Structure of the (110) Ln ScO 3 ( Ln =Gd,Tb,Dy) surfaces

The surface reconstruction on the (110) surface of LnScO 3 (Ln=Gd,Tb,Dy) has been investigated using x-ray photoelectron spectroscopy, atomic force microscopy, and transmission electron diffraction coupled with higher-level density-functional theory methods. The experimental techniques generate constraints on the surface chemistry and structure that are used to inform the theoretical comparison of a number of potential surface structures. The resulting structure is then compared to experimental aberration-corrected transmission electron microscopy results using multislice simulation. The surfaces of both single-crystalline substrates and hydrosauna synthesized nanoparticles exhibit a Sc-rich double layer with a Sc 3 O 4 termination.

36 MATERIALS SCIENCE↗