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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 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Interplays of electron and nuclear motions along CO dissociation trajectory in myoglobin revealed by ultrafast X-rays and quantum dynamics calculations

Significance In this multidisciplinary study, we investigated local and global structural responses upon carbon monoxide (CO) dissociation from the heme iron(II) in myoglobin in solution using ultrafast X-ray absorption and scattering. CO dissociation was optically triggered and pulsed X-rays probed structural and electronic changes as a function of time, revealing an iron(II) spin state transition and nuclear motions propagating from the active site throughout the entire protein. Quantum mechanical computational results were used to assign the iron K-edge absorption features, and to map out electronic and nuclear trajectories during Fe–CO bond elongation and heme macrocycle doming. The study has important implications for heme–protein function and the interaction of small molecule substrates with the metal active centers in enzymes.

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

Stress-dependent activation entropy in thermally activated cross-slip of dislocations

Cross-slip of screw dislocations in crystalline solids is a stress-driven thermally activated process essential to many phenomena during plastic deformation, including dislocation pattern formation, strain hardening, and dynamic recovery. Molecular dynamics (MD) simulation has played an important role in determining the microscopic mechanisms of cross-slip. However, due to its limited timescale, MD can only predict cross-slip rates in high-stress or high-temperature conditions. The transition state theory can predict the cross-slip rate over a broad range of stress and temperature conditions, but its predictions have been found to be several orders of magnitude too low in comparison to MD results. This discrepancy can be expressed as an anomalously large activation entropy whose physical origin remains unclear. Here, we resolve this discrepancy by showing that the large activation entropy results from anharmonic effects, including thermal softening, thermal expansion, and soft vibrational modes of the dislocation. We expect these anharmonic effects to be significant in a wide range of stress-driven thermally activated processes in solids.

Science & Technology - Other Topics↗
DOE OSTI2024

Perturbative diffraction methods resolve a conformational switch that facilitates a two-step enzymatic mechanism

Enzymes catalyze biochemical reactions through precise positioning of substrates, cofactors, and amino acids to modulate the transition-state free energy. However, the role of conformational dynamics remains poorly understood due to poor experimental access. This shortcoming is evident with Escherichia coli dihydrofolate reductase (DHFR), a model system for the role of protein dynamics in catalysis, for which it is unknown how the enzyme regulates the different active site environments required to facilitate proton and hydride transfer. Here, we describe ligand-, temperature-, and electric-field-based perturbations during X-ray diffraction experiments to map the conformational dynamics of the Michaelis complex of DHFR. We resolve coupled global and local motions and find that these motions are engaged by the protonated substrate to promote efficient catalysis. This result suggests a fundamental design principle for multistep enzymes in which pre-existing dynamics enable intermediates to drive rapid electrostatic reorganization to facilitate subsequent chemical steps.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A theory of phonon-induced friction on molecular adsorbates

In this manuscript, we provide a general theory for how surface phonons couple to molecular adsorbates. Our theory maps the extended dynamics of a surface’s atomic vibrational motions to a generalized Langevin equation, and by doing so captures these dynamics in a single quantity: the non-Markovian friction. The different frequency components of this friction are the phonon modes of the surface slab weighted by their coupling to the adsorbate degrees of freedom. Using this formalism, we demonstrate that physisorbed species couple primarily to acoustic phonons while chemisorbed species couple to dispersionless local vibrations. We subsequently derive equations for phonon-adjusted reaction rates using transition state theory and demonstrate that these corrections improve agreement with experimental results for CO desorption rates from Pt(111).

Science & Technology - Other Topics↗
DOE OSTI2021

New reactions of diazene and related species for modelling combustion of amine fuels

Potential energy surfaces for reactions involving N 2 H 2 isomers of diazene (diimide) have been explored using density functional theory, with energies based on coupled-cluster theory. A focus is on processes that create or consume these species, and isomerisation between the E (trans) and Z (cis) forms of HNNH. Furthermore, these include isomerisation and dissociation pathways for HNNH, addition of H atoms to form N 2 H 3 , abstraction by H atoms yielding short-lived NNH, and abstraction reactions of H with N 2 H 3 . Transition state and capture theories are applied for high-pressure-limiting behaviour, while low-pressure and falloff regions are characterised via the methods of Troe and coworkers. Rate constants and thermochemistry are provided to improve models of diamine chemistry, relevant to the combustion of NH 3 especially at high concentrations, high pressures or under reducing conditions. Results indicate that amine radical recombination mainly yields the E HNNH isomer, while H-abstraction from N 2 H 3 results in E HNNH and H 2 NN. However, at elevated temperature E → Z isomerisation becomes competitive, and Z HNNH, being more reactive, acts to enhance the diazene consumption rate.

10 SYNTHETIC FUELS↗
DOE OSTI2024

Modeling bicarbonate formation in an alkaline solution with multi-level quantum mechanics/molecular dynamics simulations

Understanding carbonate speciation and how it may be modulated is essential for the advancement of carbon dioxide (CO 2 ) capture and storage technologies, which often rely on the transformation of CO 2 into carbonate, e.g. via the formation of carbonate minerals. To date, few atomic-level, quantum-mechanics-based simulations have been carried out to characterize how carbonic acid (H 2 CO 3 ) and bicarbonate ($HCO^{-}_{3}$) form in aqueous solution, and how pH affects this process. Recently, Martirez and Carter utilized rare-event sampling density functional theory molecular dynamics simulations in combination with multi-level embedded correlated wavefunction theory, thus accounting for both solvent dynamics and electron correlation accurately, to elucidate the mechanism of H 2 CO 3 formation in neutral solution (J. Am. Chem. Soc., 145, 12561, 2023). Here, we perform a complementary simulation using the same method to map out the energetics of $HCO^{-}_{3}$ formation from dissolved CO 2 in basic solution. We find that, as in H 2 CO 3 formation, including water dynamics is important to obtain an accurate prediction of the energetics for the aforementioned reaction. Furthermore, only with MD did we identify the correct pathway for the reaction, in which water – not hydroxide – acts as the initial nucleophile and only at the transition state does it lose a proton.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Quasi-equilibrium predictions of water desorption kinetics from rapidly-heated metal oxide surfaces

Controlling sub-microsecond desorption of water and other impurities from electrode surfaces at high heating rates is crucial for pulsed power applications. Despite the short time scales involved, quasi-equilibrium ideas based on transition state theory (TST) and Arrhenius temperature dependence have been widely applied to fit desorption activation free energies. Here, we apply molecular dynamics (MD) simulations in conjunction with equilibrium potential-of-mean-force (PMF) techniques to directly compute the activation free energies (ΔG*) associated with desorption of intact water molecules from Fe 2 O 3 and Cr 2 O 3 (0001) surfaces. The desorption free energy profiles are diffuse, without maxima, and have substantial dependences on temperature and surface water coverage. Incorporating the predicted ΔG* into an analytical form gives rate equations that are in reasonable agreement with non-equilibrium molecular dynamics desorption simulations. We also show that different ΔG* analytical functional forms which give similar predictions at a particular heating rate can yield desorption times that differ by up to a factor of four or more when the ramp rate is extrapolated by 8 orders of magnitude. This highlights the importance of constructing a physically-motivated ΔG* functional form to predict fast desorption kinetics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Potential for large-scale deployment of offshore wind-to-hydrogen systems in the United States

This study explores the role of producing low-carbon hydrogen using water electrolysis powered by offshore wind in facilitating the United States’ transition to a net-zero emissions economy by 2050. This research introduces an open-source scenario analysis tool for offshore wind-to-hydrogen systems, aiming to assess the impact of technology, regional considerations, and policy incentives on the cost of producing low-carbon hydrogen through offshore wind. Conducting a regional techno-economic analysis at four U.S. coastal sites, the study evaluates two energy transmission configurations and examines associated costs for the years 2025, 2030, and 2035. The results highlight that locations using fixed-bottom technology may achieve cost-competitive water electrolysis hydrogen production by 2030 through leveraging geologic hydrogen storage and federal policy incentives. Furthermore, floating technology locations are expected to see an average 38% reduction in the levelized cost of hydrogen from 2025 to 2035.

17 WIND ENERGY↗
DOE OSTI2020

Enabling robust offline active learning for machine learning potentials using simple physics-based priors

Abstract Machine learning surrogate models for quantum mechanical simulations have enabled the field to efficiently and accurately study material and molecular systems. Developed models typically rely on a substantial amount of data to make reliable predictions of the potential energy landscape or careful active learning (AL) and uncertainty estimates. When starting with small datasets, convergence of AL approaches is a major outstanding challenge which has limited most demonstrations to online AL. In this work we demonstrate a Δ-machine learning (ML) approach that enables stable convergence in offline AL strategies by avoiding unphysical configurations with initial datasets as little as a single data point. We demonstrate our framework’s capabilities on a structural relaxation, transition state calculation, and molecular dynamics simulation, with the number of first principle calculations being cut down anywhere from 70%–90%. The approach is incorporated and developed alongside AMP torch , an open-source ML potential package, along with interactive Google Colab notebook examples.

Shuaibi, Muhammed↗
DOE OSTI2021

Deep reinforcement learning for predicting kinetic pathways to surface reconstruction in a ternary alloy

Abstract The majority of computational catalyst design focuses on the screening of material components and alloy composition to optimize selectivity and activity for a given reaction. However, predicting the metastability of the alloy catalyst surface at realistic operating conditions requires an extensive sampling of possible surface reconstructions and their associated kinetic pathways. We present CatGym, a deep reinforcement learning (DRL) environment for predicting the thermal surface reconstruction pathways and their associated kinetic barriers in crystalline solids under reaction conditions. The DRL agent iteratively changes the positions of atoms in the near-surface region to generate kinetic pathways to accessible local minima involving changes in the surface compositions. We showcase our agent by predicting the surface reconstruction pathways of a ternary Ni 3 Pd 3 Au 2 (111) alloy catalyst. Our results show that the DRL agent can not only explore more diverse surface compositions than the conventional minima hopping method, but also generate the kinetic surface reconstruction pathways. We further demonstrate that the kinetic pathway to a global minimum energy surface composition and its associated transition state predicted by our agent is in good agreement with the minimum energy path predicted by nudged elastic band calculations.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Gamma-ray observations of MAXI J1820+070 during the 2018 outburst

ABSTRACT MAXI J1820+070 is a low-mass X-ray binary with a black hole (BH) as a compact object. This binary underwent an exceptionally bright X-ray outburst from 2018 March to October, showing evidence of a non-thermal particle population through its radio emission during this whole period. The combined results of 59.5 h of observations of the MAXI J1820+070 outburst with the H.E.S.S., MAGIC and VERITAS experiments at energies above 200 GeV are presented, together with Fermi-LAT data between 0.1 and 500 GeV, and multiwavelength observations from radio to X-rays. Gamma-ray emission is not detected from MAXI J1820+070, but the obtained upper limits and the multiwavelength data allow us to put meaningful constraints on the source properties under reasonable assumptions regarding the non-thermal particle population and the jet synchrotron spectrum. In particular, it is possible to show that, if a high-energy (HE) gamma-ray emitting region is present during the hard state of the source, its predicted flux should be at most a factor of 20 below the obtained Fermi-LAT upper limits, and closer to them for magnetic fields significantly below equipartition. During the state transitions, under the plausible assumption that electrons are accelerated up to ∼500 GeV, the multiwavelength data and the gamma-ray upper limits lead consistently to the conclusion that a potential HE and very-HE gamma-ray emitting region should be located at a distance from the BH ranging between 1011 and 1013 cm. Similar outbursts from low-mass X-ray binaries might be detectable in the near future with upcoming instruments such as CTA.

Astronomy & Astrophysics↗
DOE OSTI2021

Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease

Abstract Long interspersed nuclear element-1 (L1) is an autonomous non-LTR retrotransposon comprising ∼20% of the human genome. L1 self-propagation causes genomic instability and is strongly associated with aging, cancer and other diseases. The endonuclease domain of L1’s ORFp2 protein (L1-EN) initiates de novo L1 integration by nicking the consensus sequence 5′-TTTTT/AA-3′. In contrast, related nucleases including structurally conserved apurinic/apyrimidinic endonuclease 1 (APE1) are non-sequence specific. To investigate mechanisms underlying sequence recognition and catalysis by L1-EN, we solved crystal structures of L1-EN complexed with DNA substrates. This showed that conformational properties of the preferred sequence drive L1-EN’s sequence-specificity and catalysis. Unlike APE1, L1-EN does not bend the DNA helix, but rather causes ‘compression’ near the cleavage site. This provides multiple advantages for L1-EN’s role in retrotransposition including facilitating use of the nicked poly-T DNA strand as a primer for reverse transcription. We also observed two alternative conformations of the scissile bond phosphate, which allowed us to model distinct conformations for a nucleophilic attack and a transition state that are likely applicable to the entire family of nucleases. This work adds to our mechanistic understanding of L1-EN and related nucleases and should facilitate development of L1-EN inhibitors as potential anticancer and antiaging therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism

Abstract DNA glycosylase MutY plays a critical role in suppression of mutations resulted from oxidative damage, as highlighted by cancer-association of the human enzyme. MutY requires a highly conserved catalytic Asp residue for excision of adenines misinserted opposite 8-oxo-7,8-dihydroguanine (OG). A nearby Asn residue hydrogen bonds to the catalytic Asp in structures of MutY and its mutation to Ser is an inherited variant in human MUTYH associated with colorectal cancer. We captured structural snapshots of N146S Geobacillus stearothermophilus MutY bound to DNA containing a substrate, a transition state analog and enzyme-catalyzed abasic site products to provide insight into the base excision mechanism of MutY and the role of Asn. Surprisingly, despite the ability of N146S to excise adenine and purine (P) in vitro, albeit at slow rates, N146S-OG:P complex showed a calcium coordinated to the purine base altering its conformation to inhibit hydrolysis. We obtained crystal structures of N146S Gs MutY bound to its abasic site product by removing the calcium from crystals of N146S-OG:P complex to initiate catalysis in crystallo or by crystallization in the absence of calcium. The product structures of N146S feature enzyme-generated β-anomer abasic sites that support a retaining mechanism for MutY-catalyzed base excision.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

High-Resolution Laser Spectroscopy on the Hyperfine Structure of 255Fm (𝑍=100)

We report on high-resolution laser spectroscopy of 255Fm (𝑇1/2=20 h), one of the heaviest nuclides available from reactor breeding. The hyperfine structures in two different atomic ground-state transitions at 398.4 nm and 398.2 nm were probed by in-source laser spectroscopy at the RISIKO mass separator in Mainz, using the perpendicularly illuminated laser ion source and trap (PI-LIST) high-resolution ion source. Experimental results were combined with hyperfine fields from various atomic ab initio calculations, in particular using multiconfiguration Dirac-Hartree-Fock theory, as implemented in grasp18. In this manner, the nuclear magnetic dipole and electric quadrupole moments were derived to be 𝜇=−0.75⁢(5) 𝜇N and 𝑄s=+5.84⁢(13) eb, respectively. The magnetic moment indicates occupation of the 𝜈⁢7/2⁢[613] Nilsson orbital, while the large quadrupole moment confirms strong, stable prolate deformation consistent with systematics in the heavy actinides. Comparisons with available expectation values from nuclear theory show good agreement, providing a stringent benchmark for the used theoretical models. These results revise earlier data and establish 255Fm as a reference isotope for future high-resolution studies.

Ezold, Julie [ORNL] (ORCID:0000000250550022)↗
DOE OSTI2020

Correlations Between Fission Fragment and Neutron Anisotropies in Neutron-Induced Fission

Several sources of angular anisotropy for fission fragments and prompt neutrons have been studied in neutron-induced fission reactions. These include kinematic recoils of the target from the incident neutron beam and the fragments from the emission of the prompt neutrons, preferential directions of the emission of the fission fragments with respect to the beam axis due to the population of particular transition states at the fission barrier, and forward-peaked angular distributions of pre-equilibrium neutrons which are emitted before the formation of a compound nucleus. In addition, there are several potential sources of angular anisotropies that are more difficult to disentangle: the angular distributions of prompt neutrons from fully accelerated fragments or from scission neutrons, and the emission of neutrons from fission fragments that are not fully accelerated. Here, we study the effects of the first group of anisotropy sources, particularly exploring the correlations between the fission-fragment anisotropy and the resulting neutron anisotropy. While kinematic effects were already accounted for in our Hauser-Feshbach Monte Carlo code cgmf, anisotropic angular distributions for the fission fragments and pre-equilibrium neutrons resulting from neutron-induced fission on 233,234,235,238 U, 239,241 Pu, and 237 Np have been introduced for the first time. The effects of these sources of anisotropy are examined over a range of incident neutron energies, from thermal to 20 MeV, and compared with experimental data from the Chi-Nu liquid scintillator array. The anisotropy of the fission fragments is reflected in the anisotropy of the prompt neutrons, especially as the outgoing energy of the prompt neutrons increases, allowing for an extraction of the fission-fragment anisotropy to be made from a measurement of the neutrons.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Ultrawide Temperature Range Super-Invar Behavior of R 2 (Fe,Co) 17 Materials ( R = Rare Earth)

Super Invar (SIV), i.e., zero thermal expansion of metallic materials underpinned by magnetic ordering, is of great practical merit for a wide range of high precision engineering. However, the relatively narrow temperature window of SIV in most materials restricts its potential applications in many critical fields. Here, we demonstrate the controlled design of thermal expansion in a family of R 2 (Fe,Co) 17 materials (R=rare Earth). We find that adjusting the Fe-Co content tunes the thermal expansion behavior and its optimization leads to a record-wide SIV with good cyclic stability from 3–461 K, almost twice the range of currently known SIV. In situ neutron diffraction, Mössbauer spectra and first-principles calculations reveal the 3d bonding state transition of the Fe-sublattice favors extra lattice stress upon magnetic ordering. On the other hand, Co content induces a dramatic enhancement of the internal molecular field, which can be manipulated to achieve “ultrawide” SIV over broad temperature, composition and magnetic field windows. Furthermore, these findings pave the way for exploiting thermal-expansion-control engineering and related functional materials.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Iodine Vacancies do not Cause Nonradiative Recombination in Halide Perovskites

The iodine vacancy (V I ) has frequently been discussed as a strong nonradiative recombination center in halide perovskites. This proposition was mainly based on the presence of charge-state transition levels in the band gap, as found in early first-principles calculations. In this work, we perform accurate hybrid-density-functional calculations for V I in CsPbI 3 , CsSnI 3 , and CsGeI 3 and find that V I does not have any transition levels in the band gap in CsPbI 3 , in contrast to the results from calculations based on semilocal functionals. The iodine vacancy V I does introduce levels in the band gap in CsSnI 3 and CsGeI 3 , but our explicitly computed nonradiative capture coefficients demonstrate that V I has a negligible impact on nonradiative recombination. Our study corrects a misunderstanding of the role of V I in the iodide-based perovskites, and shifts the focus toward identifying and mitigating actual recombination centers in order to further improve the optoelectronic performance.

14 SOLAR ENERGY↗
DOE OSTI2025

Robust error calibration for serial crystallography

Serial crystallography is an important technique with unique abilities to resolve enzymatic transition states, minimize radiation damage to sensitive metalloenzymes and perform de novo structure determination from micrometre-sized crystals. This technique requires the merging of data from thousands of crystals, making manual identification of errant crystals unfeasible. cctbx.xfel.merge uses filtering to remove problematic data. However, this process is imperfect, and data reduction must be robust to outliers. We add robustness to cctbx.xfel.merge at the step of uncertainty determination for reflection intensities. This step is a critical point for robustness because it is the first step where the data sets are considered as a whole, as opposed to individual lattices. Robustness is conferred by reformulating the error-calibration procedure to have fewer and less stringent statistical assumptions and incorporating the ability to down-weight low-quality lattices. We then apply this method to five macromolecular XFEL data sets and observe the improvements to each. The appropriateness of the intensity uncertainties is demonstrated through internal consistency. This is performed through theoretical CC 1/2 and I /σ relationships and by weighted second moments, which use Wilson's prior to connect intensity uncertainties with their expected distribution. This work presents new mathematical tools to analyze intensity statistics and demonstrates their effectiveness through the often underappreciated process of uncertainty analysis.

Mittan-Moreau, David W.↗