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Results for “molecular evolution”

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 1,261 records · Page 70
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Transforming an Ionic Conductor into an Electronic Conductor via Crystallization: In Situ Evolution of Transference Numbers and Structure in (La,Sr)(Ga,Fe)O 3–x Perovskite Thin Films

Mixed-conducting perovskites are workhorse electrochemically active materials, but typical high-temperature processing compromises their catalytic activity and chemo-mechanical integrity. Low-temperature pulsed laser deposition of amorphous films plus mild thermal annealing is an emerging route to form homogeneous mixed conductors with exceptional catalytic activity, but little is known about the evolution of the oxide-ion transport and transference numbers during crystallization. Here the coupled evolution of ionic and electronic transport behavior and structure in room-temperature-grown amorphous (La,Sr)(Ga,Fe)O 3-x films as they crystallize is explored. In situ ac-impedance spectroscopy with and without blocking electrodes, simultaneous capturing-synchrotron-grazing-incidence X-ray diffraction, dc polarization, transmission electron microscopy, and molecular dynamics simulations to evaluate isothermal and non-isothermal crystallization effects and the role of grain boundaries on transference numbers is combined. Ionic conductivity increases by ≈2 orders of magnitude during crystallization, with even larger increases in electronic conductivity. Consequently, as crystallinity increases, LSGF transitions from a predominantly ionic conductor to a predominantly electronic conductor. The roles of evolving lattice structural order, microstructure, and defect chemistry are examined. Grain boundaries appear relatively nonblocking electronically but significantly blocking ionically. The results demonstrate that ionic transference numbers can be tailored over a wide range by tuning crystallinity and microstructure without having to change the cation composition.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Recent Advances in X-ray Absorption Near Edge Structure (XANES) Simulation for Catalysis: Theories and Applications

X-ray absorption spectroscopy (XAS) is a powerful spectroscopic technique for characterizing catalytic active sites. In particular, X-ray Absorption Near Edge Structure (XANES) provides insights into the oxidation state and local coordination environment of the absorbing atom, shedding light on the catalytic structure. Computational XANES simulations provide one-on-one correspondence between the molecular structure and their corresponding spectra, making them an effective approach for interpreting experimental XANES features. This work outlines various theories used to simulate XANES spectra and highlights recent advancements in computational XANES applications for homogeneous, heterogeneous, and single-atom catalysts focusing on identifying the active site structures, the site heterogeneity, and the dynamic evolution of catalysts.

Xu, Jiayi↗
DOE OSTI2023

Atomistic simulations and machine learning of solute grain boundary segregation in Mg alloys at finite temperatures

Understanding solute segregation thermodynamics is the first step in investigating grain boundary (GB) properties, such as strong yttrium (Y) effects on grain growth and texture evolution in micro-scale polycrystalline magnesium (Mg) alloys. To estimate the average GB segregation behavior in low-solute-concentration Mg alloys (e.g., 2 at.% Y), a state-of-the-art spectral approach is applied based on a per-site segregation energy spectrum for Y solute atoms at zero K obtained from molecular statistics (MS) simulations of ~10 4 GB sites in Mg symmetric tilt GBs (STGBs). Although selected MS simulation results are consistent with verification by density functional theory (DFT) calculations, estimates of average segregation tendency based on the zero-K energy spectrum deviate from experimental observations. To resolve this problem, thermodynamic integration (TI) methods based on molecular dynamics (MD) simulations are used to determine the per-site segregation free energies of Y at representative GB sites, which show contributions beyond harmonic approximations can be important for certain GB sites at high temperatures. A surrogate model of per-site segregation free energy is constructed from a small set of TI data points using stacking cross-validation regressors and physics-informed descriptors. This model is applied to predict the Y segregation free energy spectra for thousands of GB sites in Mg STGBs with uncertainty quantification. Finally, the average segregation tendency predicted by the spectral approach based on the free energy spectra agrees well (within the uncertainty range) with experimental observations for micro-scale polycrystalline Mg alloys at typical thermomechanical processing temperatures (500 ~ 800 K), where thermodynamic equilibrium states are likely to be achieved due to fast diffusion.

Atomistic simulations↗
NASA NTRS1978

Ames interactive molecular model building system - A 3-D computer modelling system applied to the study of the origin of life

The investigation of specific interactions among biological molecules must take into consideration the stereochemistry of the structures. Thus, models of the molecules are essential for describing the spatial organization of potentially interacting groups, and estimations of conformation are required for a description of spatial organization. Both the function of visualizing molecules, and that of estimating conformation through calculations of energy, are part of the molecular modeling system described in the present paper. The potential uses of the system in investigating some aspects of the origin of life rest on the assumption that translation of conformation from genetic elements to catalytic elements would have been required for the development of the first replicating systems subject to the process of biological evolution.

Coeckelenbergh, Y.↗
NASA NTRS1979

Star and planetary system formation in collapsing, viscous, rotating clouds

The results of a preliminary investigation of several processes that are of interest both for the formation of stars and for the evolution of planetary systems are presented. It is shown that turbulent viscosity is capable of playing an important role in conveying angular momentum over time scales that are short enough to be significant. Meridional circulation can also act in this fashion during some phases of the evolution. This transport may reduce the probability of formation of the rings that have been found by most earlier investigators. Transport and mixing on a faster than cooling time scale should also inhibit usual modes of fragmentation and the present work casts some doubt on the multiple successive fragmentation scenarios that lead from a massive molecular cloud to a collection of roughly solar mass protostars. The conditions that are probable in the disks that would exist at varying phases of collapse are examined and it is concluded that turbulent viscosity would be very important in a pre-solar nebula.

Wiita, P. J.↗
NASA NTRS1990

Perception of interstellar structure - Facing complexity

Some orthodox notions concerning the structure and evolution of star-forming regions are challenged; it is proposed that they arise largely by a dual process in which conceptual models are fashioned after categories which are in great part reflections of observational limitations, and the models are projected onto interpretations of data. Several examples are discussed. The need for internal support of molecular clouds is questioned. It is suggested that the inverse density-size relation often claimed for clouds and accounted for by several theoretical models is an artifact caused by limited dynamic range column density detectability, selection bias, distance uncertainties, and internal density gradients, and is contradicted by several unbiased surveys. Column density structures mapped with a large spatial and column density dynamic range are found to be dominated by irregular, connected, and nested forms on all sides. These features and a technique for the quantification of the complex structure are illustrated with a densely-sampled column density image of the Taurus region constructed from IRAS data.

Scalo, John↗
NASA NTRS2006

Use of Laboratory Data to Model Interstellar Chemistry

Our laboratory research program is about the formation of molecules on dust grains analogues in conditions mimicking interstellar medium environments. Using surface science techniques, in the last ten years we have investigated the formation of molecular hydrogen and other molecules on different types of dust grain analogues. We analyzed the results to extract quantitative information on the processes of molecule formation on and ejection from dust grain analogues. The usefulness of these data lies in the fact that these results have been employed by theoreticians in models of the chemical evolution of ISM environments.

Vidali, Gianfranco↗
NASA NTRS1994

Continuous in vitro evolution of bacteriophage RNA polymerase promoters

Rapid in vitro evolution of bacteriophage T7, T3, and SP6 RNA polymerase promoters was achieved by a method that allows continuous enrichment of DNAs that contain functional promoter elements. This method exploits the ability of a special class of nucleic acid molecules to replicate continuously in the presence of both a reverse transcriptase and a DNA-dependent RNA polymerase. Replication involves the synthesis of both RNA and cDNA intermediates. The cDNA strand contains an embedded promoter sequence, which becomes converted to a functional double-stranded promoter element, leading to the production of RNA transcripts. Synthetic cDNAs, including those that contain randomized promoter sequences, can be used to initiate the amplification cycle. However, only those cDNAs that contain functional promoter sequences are able to produce RNA transcripts. Furthermore, each RNA transcript encodes the RNA polymerase promoter sequence that was responsible for initiation of its own transcription. Thus, the population of amplifying molecules quickly becomes enriched for those templates that encode functional promoters. Optimal promoter sequences for phage T7, T3, and SP6 RNA polymerase were identified after a 2-h amplification reaction, initiated in each case with a pool of synthetic cDNAs encoding greater than 10(10) promoter sequence variants.

Non-NASA Center↗
DOE OSTI2025

Review of radiation-induced defects in GaAs

Radiation-resilient optoelectronic materials are highly desired in space and nuclear applications, and understanding the relevant defects and electronic processes in those materials is crucial for both current and next-generation applications. GaAs is a prototypical semiconductor that serves as a foundational system for describing and understanding optoelectronic devices. In this review, both experimental studies and molecular dynamics (MD) simulations of irradiated GaAs are reviewed, with particular emphasis on the deep-level transient spectroscopy, irradiation-induced amorphization zones, and MD predictions of damage structures. The MD results are also compared to predictions of the non-ionized energy-loss model. Recent theoretical studies, in particular, density functional theory based calculations on the simple intrinsic defects and defect clusters in GaAs, are also reviewed. These defects have an important role in dictating the evolution of GaAs in radiation damage environments, as they impact the coupled dynamics of charge carriers. Finally, possible gaps and challenges toward the general understanding of defect evolution in GaAs are discussed.

36 MATERIALS SCIENCE↗
NASA NTRS2017

Chemical Complexity Induced by Efficient Ice Evaporation in the Barnard 5 Molecular Cloud

Cold gas-phase water has recently been detected in a cold dark cloud, Barnard 5 located in the Perseus complex, by targeting methanol peaks as signposts for ice mantle evaporation. Observed morphology and abundances of methanol and water are consistent with a transient non-thermal evaporation process only affecting the outermost ice mantle layers, possibly triggering a more complex chemistry. Here we present the detection of the complex organic molecules (COMs) acetaldehyde (CH3CHO) and methyl formate (CH3OCHO), as well as formic acid (HCOOH) and ketene (CH2CO), and the tentative detection of di-methyl ether (CH3OCH3) towards the ''methanol hotspot'' of Barnard 5 located between two dense cores using the single dish OSO 20 m, IRAM 30 m, and NRO 45 m telescopes. The high energy cis-conformer of formic acid is detected, suggesting that formic acid is mostly formed at the surface of interstellar grains and then evaporated. The detection of multiple transitions for each species allows us to constrain their abundances through LTE and non-LTE methods. All the considered COMs show similar abundances between approx. 1 and approx. 10% relative to methanol depending on the assumed excitation temperature. The non-detection of glycolaldehyde, an isomer of methyl formate, with a [glycolaldehyde]/[methyl formate] abundance ratio lower than 6%, favours gas phase formation pathways triggered by methanol evaporation. According to their excitation temperatures derived in massive hot cores, formic acid, ketene, and acetaldehyde have been designated as ''lukewarm'' COMs whereas methyl formate and di-methyl ether were defined as ''warm'' species. Comparison with previous observations of other types of sources confirms that lukewarm and warm COMs show similar abundances in low-density cold gas whereas the warm COMs tend to be more abundant than the lukewarm species in warm protostellar cores. This abundance evolution suggests either that warm COMs are indeed mostly formed in protostellar environments and/or that lukewarm COMs are efficiently depleted by increased hydrogenation efficiency around protostars.

ISM: molecules↗
DOE OSTI2022

Design and characterization of surface molecular assemblies for the preparation of solar fuels

A key issue in solar energy conversion is the utilization of solar energy for the preparation of solar fuels. In this area, artificial photosynthesis offers promising approaches for the conversion of H 2 O and CO 2 into usable solar fuels. This review highlights both the design and characterization of surface molecular assemblies for the preparation of solar fuels. It includes mechanistic summaries of the details of the underlying surface chemical reactions including water oxidation and proton/water reduction. The surface mechanisms are shown to integrate molecular reactivity with surface electron transfer in integrated assemblies that lead to impressive efficiencies for water oxidation and proton or CO 2 reduction.

catalysts and catalysis↗
DOE OSTI2020

Sonic horizons and causality in phase transition dynamics

A system gradually driven through a symmetry-breaking phase transition is subject to the Kibble-Zurek mechanism (KZM). As a consequence of the critical slowing down, its state cannot follow local equilibrium, and its evolution becomes nonadiabatic near the critical point. In the simplest approximation, that stage can be regarded as an “impulse” where the state of the system remains unchanged. It leads to the correct KZM scaling laws. However, such a “freeze-out” might suggest that the coherence length of the nascent order parameter remains unchanged as the critical region is traversed. By contrast, the original causality-based discussion emphasized the role of the sonic horizon: Domains of the broken symmetry phase can expand with a velocity limited by the speed of the relevant sound. This effect was demonstrated in the quantum Ising chain where the dynamical exponent z = 1 and quasiparticles excited by the transition have a fixed speed of sound. To elucidate the role of the sonic horizon, in this paper we study two systems with z > 1 where the speed of sound is no longer fixed, and the fastest excited quasiparticles set the size of the sonic horizon. Their effective speed decays with increasing transition time. In the extreme case, the dynamical exponent z can diverge such as in the Griffiths region of the random Ising chain where the localization of excited quasiparticles freezes the growth of the correlation range when the critical region is traversed. Of particular interest is an example with z < 1 , the long-range extended Ising chain, where there is no upper limit to the velocity of excited quasiparticles with small momenta. Initially, the power-law tail of the correlation function grows adiabatically, but in the nonadiabatic stage it lags behind the adiabatic evolution.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Nonparallel transcriptional divergence during parallel adaptation

Abstract How underlying mechanisms bias evolution toward predictable outcomes remains an area of active debate. In this study, we leveraged phenotypic plasticity and parallel adaptation across independent lineages of Trinidadian guppies ( Poecilia reticulata ) to assess the predictability of gene expression evolution during parallel adaptation. Trinidadian guppies have repeatedly and independently adapted to high‐ and low‐predation environments in the wild. We combined this natural experiment with a laboratory breeding design to attribute transcriptional variation to the genetic influences of population of origin and developmental plasticity in response to rearing with or without predators. We observed substantial gene expression plasticity, as well as the evolution of expression plasticity itself, across populations. Genes exhibiting expression plasticity within populations were more likely to also differ in expression between populations, with the direction of population differences more likely to be opposite those of plasticity. While we found more overlap than expected by chance in genes differentially expressed between high‐ and low‐predation populations from distinct evolutionary lineages, the majority of differentially expressed genes were not shared between lineages. Our data suggest alternative transcriptional configurations associated with shared phenotypes, highlighting a role for transcriptional flexibility in the parallel phenotypic evolution of a species known for rapid adaptation.

Fischer, Eva K.↗
DOE OSTI2021

Activation of dislocations in Mg with solute Y

Mg-Y cast alloy shows excellent ductility (elongation to failure > 15%) compared with pure Mg and commercial Mg cast alloys. By monitoring the microstructure evolution during an in situ tensile test of a Mg-2.5 wt%Y alloy, we identify the activation of prismatic slip, which is rare in Mg. Synchrotron X-ray micro-beam Laue diffraction (μ-Laue) and transmission electron microscopy revealed the morphology of prismatic slip bands and individual dislocations. Density functional theory and molecular dynamics calculations indicate that solute Y can significantly reduce the stacking fault energy (SFE) along direction on prismatic plane in Mg lattice and thus facilitate the nucleation of dislocations during deformation. The presence of free dislocations in the Mg lattice can also lead to nucleation of {10–12} twins even under unfavorable geometric conditions.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Topological response of the anomalous Hall effect in MnBi 2 Te 4 due to magnetic canting

Three-dimensional (3D) compensated MnBi 2 Te 4 is antiferromagnetic, but undergoes a spin-flop transition at intermediate fields, resulting in a canted phase before saturation. In this work, we experimentally show that the anomalous Hall effect (AHE) in MnBi 2 Te 4 originates from a topological response that is sensitive to the perpendicular magnetic moment and to its canting angle. Synthesis by molecular beam epitaxy allows us to obtain a large-area quasi-3D 24-layer MnBi 2 Te 4 with near-perfect compensation that hosts the phase diagram observed in bulk which we utilize to probe the AHE. This AHE is seen to exhibit an antiferromagnetic response at low magnetic fields, and a clear evolution at intermediate fields through surface and bulk spin-flop transitions into saturation. Throughout this evolution, the AHE is super-linear versus magnetization rather than the expected linear relationship. We reveal that this discrepancy is related to the canting angle, consistent with the symmetry of the crystal. Our findings bring to light a topological anomalous Hall response that can be found in non-collinear ferromagnetic, and antiferromagnetic phases.

36 MATERIALS SCIENCE↗
DOE OSTI2022

In situ ion irradiation of amorphous TiO 2 nanotubes

Understanding of structural and morphological evolution in nanomaterials is critical in tailoring their functionality for applications such as energy conversion and storage. Here, we examine irradiation effects on the morphology and structure of amorphous TiO 2 nanotubes in comparison with their crystalline counterpart, anatase TiO 2 nanotubes, using high-resolution transmission electron microscopy (TEM), in situ ion irradiation TEM, and molecular dynamics (MD) simulations. Anatase TiO 2 nanotubes exhibit morphological and structural stability under irradiation due to their high concentration of grain boundaries and surfaces as defect sinks. On the other hand, amorphous TiO 2 nanotubes undergo irradiation-induced crystallization, with some tubes remaining only partially crystallized. The partially crystalline tubes bend due to internal stresses associated with densification during crystallization as suggested by MD calculations. Furthermore, these results present a novel irradiation-based pathway for potentially tuning structure and morphology of energy storage materials.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Stress Intensity Thresholds for Development of Reliable Brittle Materials

Brittle material failure in high consequence systems can appear random and unpredictable at subcritical stresses. Gaps in our understanding of how structural flaws and environmental factors (humidity, temperature) impact fracture propagation need to be addressed to circumvent this issue. A combined experimental and computational approach composed of molecular dynamics (MD) simulations, numerical modeling, and atomic force microscopy (AFM) has been undertaken to identify mechanisms of slow crack growth in silicate glasses. AFM characterization of crack growth as slow as 10 -13 m/s was observed, with some stepwise crack growth. MD simulations have identified the critical role of inelastic relaxation in crack propagation, including evolution of the structure during relaxation. A numerical model for the existence of a stress intensity threshold, a stress intensity below which a fracture will not propagate, was developed. This transferrable model for predicting slow crack growth is being incorporated into mission-based programs.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Plasma Surface Interactions: Predicting the Performance and Impact of Dynamic PFC Surfaces

The objective of this project is to develop, and integrate, high-performance simulation tools capable of predicting plasma-facing component (PFC) operating lifetime and the impact of the evolving surface morphology of tungsten-based PFCs on plasma contamination, including the dynamic recycling of fuel species and tritium retention, in future magnetic fusion devices. Establishing a fundamental physical understanding and developing predictive capabilities of plasma-surface interactions (PSI) requires simultaneously addressing complex and diverse physics occurring over a wide range of length (Angstroms to meters) and time (femtoseconds to years) scales, as well as integrating extensive physical processes across the plasma–surface interface. This requires development of not only detailed physics models and computational strategies at each scale, but also algorithms and methods to couple them effectively in a way that can be robustly validated. Deploying these tools requires the continued development and coupling of leadership-scale computational codes to describe the boundary plasma and the evolving PFC surface, as well as a host of simulations that bridge disparate scales to address complex physical and computational issues at the plasma–surface interface in multi-component materials systems for magnetic fusion energy development beyond ITER.

36 MATERIALS SCIENCE↗