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At least 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Mapping causal patterns in crystalline solids

The evolution of the atomic structures of the combinatorial library of Sm-substituted thin film BiFeO 3 along the phase transition boundary from the ferroelectric rhombohedral phase to the non-ferroelectric orthorhombic phase is explored using scanning transmission electron microscopy. Localized properties, including polarization, lattice parameter, and chemical composition, are parameterized from atomic-scale imaging, and their causal relationships are reconstructed using a linear non-Gaussian acyclic model. This approach is further extended to explore the spatial variability of the causal coupling using the sliding window transform method, which revealed that new causal relationships emerged at both the expected locations, such as domain walls and interfaces, and at additional regions forming clusters in the vicinity of the walls or spatially distributed features. While the exact physical origins of these relationships are unclear, they likely represent nanophase-separated regions in the morphotropic phase boundaries. Overall, we posit that an in-depth understanding of complex disordered materials away from thermodynamic equilibrium necessitates understanding not only the generative processes that can lead to observed microscopic states but also the causal links between multiple interacting subsystems.

Causal inference↗
DOE OSTI2025

Driving Electron Transfer in Photosystem I Using Far-Red Light: Overall Perspectives

Photosystem I (PSI) is a photosynthetic protein–pigment complex that, upon photoexcitation, transfers electrons to ferredoxin, facilitating the production of NADPH. Isolated PSI reaction centers (RCs) have also been used in hybrid systems to reduce protons and produce ‘biohydrogen’. This review article examines how various cyanobacteria with similar photosynthetic machinery utilize different wavelengths of light to execute photosynthetic electron transport through PSI. Key factors, such as, the structure of the electron transfer cofactors, the protein environment surrounding the primary donor pigments and hydrogen-bonding interactions with the surrounding protein matrix are analyzed to understand their roles in maintaining efficient electron transfer when it is driven using photons of different energies. We compare PSI complexes with known atomic structures from four species of cyanobacteria, Thermosynechococcus elongatus, Acaryochloris marina, Halomicronema hongdechloris, and Fischerella thermalis. T. elongatus is typical of most oxygenic photosynthetic organisms in that it requires visible light and uses only chlorophyll a (Chl a ) in PSI. In contrast, H. hongdechloris and F. thermalis are photoacclimating species capable of producing Chl f and Chl d that use red light when little visible light is available. A. marina , on the other hand, is adapted to red light conditions and consistently utilizes Chl d as its primary photosynthetic pigment, maintaining a stable pigment composition. Here, we explore the structural and functional differences between the PSI RCs of these organisms and the impact of these differences on electron transport. The structural differences in the cofactors influence both the absorption wavelengths of the cofactors and the energy levels of the intermediate states of electron transfer. An analysis of the surrounding protein shows how it has been adapted and underscores the interplay between the pigment structure, protein environment, and hydrogen bonding networks in tuning the efficiency and adaptability of photosynthetic mechanisms across different species of cyanobacteria.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Bayesian Learning of Adatom Interactions from Atomically Resolved Imaging Data

Atomic structures and adatom geometries of surfaces encode information about the thermodynamics and kinetics of the processes that lead to their formation, and which can be captured by a generative physical model. In this work, we develop a workflow based on a machine-learning-based analysis of scanning tunneling microscopy images to reconstruct the atomic and adatom positions, and a Bayesian optimization procedure to minimize statistical distance between the chosen physical models and experimental observations. We optimize the parameters of a 2- and 3-parameter Ising model describing surface ordering and use the derived generative model to make predictions across the parameter space. For concentration dependence, we compare the predicted morphologies at different adatom concentrations with the dissimilar regions on the sample surfaces that serendipitously had different adatom concentrations. The proposed workflow can be used to reconstruct the thermodynamic models and associated uncertainties from the experimental observations of materials microstructures. The code used in the manuscript is available at https://github.com/saimani5/Adatom_interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Thermally stable perpendicular magnetic anisotropy features of [Co/Pd]{sub m} multilayer matrix integrated with [CoO/Pd]{sub n} bottom layer

We evaluated the perpendicular magnetic anisotropy (PMA) features of a hybrid [CoO/Pd]{sub 2}/[Co/Pd]{sub 7} multilayer (ML) matrix under annealing in which the [CoO/Pd]{sub 2} bottom layer was inserted. Annealing allowed for the diffusion of oxygen atoms existing in the inserted [CoO/Pd]{sub 2} layer, leading to an atomic structural reconfiguration event. The hybrid matrix was crucial to result in a higher effective anisotropy energy (3.40 Merg/cc) than an ordinary [Co/Pd]{sub 7} ML matrix (1.25 Merg/cc) under annealing at 450 °C. X-ray photoelectron spectroscopy confirmed the presence of Co-O bonding states and annealing dependent oxygen atom diffusion. The possible nature of the enhanced PMA features is discussed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Investigation of the structure of Cs{sub 3}(HSO{sub 4}){sub 2}(H{sub 2}PO{sub 4}) single crystals

Cs{sub 3}(HSO{sub 4}){sub 2}(H{sub 2}PO{sub 4}) single crystals, obtained for the first time based on a systematic study of the phase diagram of the CsH{sub 2}PO{sub 4}–CsHSO{sub 4}–H{sub 2}O ternary system, have been studied by X-ray diffraction. The atomic structure of the crystals at room temperature is determined, and their structural features are analyzed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Structural basis of cohesin cleavage by separase

Accurate chromosome segregation requires timely dissolution of chromosome cohesion after chromosomes are properly attached to the mitotic spindle. Separase is absolutely essential for cohesion dissolution in organisms from yeast to man. It cleaves the kleisin subunit of cohesin and opens the cohesin ring to allow chromosome segregation. Cohesin cleavage is spatiotemporally controlled by separase-associated regulatory proteins, including the inhibitory chaperone securin, and by phosphorylation of both the enzyme and substrates. Dysregulation of this process causes chromosome missegregation and aneuploidy, contributing to cancer and birth defects. Despite its essential functions, atomic structures of separase have not been determined. Here we report crystal structures of the separase protease domain from the thermophilic fungus Chaetomium thermophilum, alone or covalently bound to unphosphorylated and phosphorylated inhibitory peptides derived from a cohesin cleavage site. These structures reveal how separase recognizes cohesin and how cohesin phosphorylation by polo-like kinase 1 (Plk1) enhances cleavage. Consistent with a previous cellular study, mutating two securin residues in a conserved motif that partly matches the separase cleavage consensus converts securin from a separase inhibitor to a substrate. Furthermore, our study establishes atomic mechanisms of substrate cleavage by separase and suggests competitive inhibition by securin.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Atom vacancies and electronic transmission Stark effects in boron nanoflake junctions

Finite-sized boron nanomaterials have received little attention in comparison to their graphene-like 2D boron analogues. It is with systems of precise atomic structures where the electrical conductance can be most fruitfully analyzed at the fundamental level. To understand how conductance varies with respect to the electronic structure, and particularly with vacancies, we study finite-sized boron nanoflakes (BNFs) and closely examine their remarkable changes in physical properties. Unlike carbon-based materials, we find from non-equilibrium Green's functions density functional theory (NEGF-DFT) calculations that the charge transport of BNFs with 35–37 atoms is modulated by site-specific atomic vacancies. Here, the BNF with no vacancy (B 37 ) shows significantly lower conductivity (9.23 μS), than B 36 with one vacancy (46.1 μS), and lower still than with two vacancies (B 35 , 54.2 μS). From the thermopower function, these nanomaterials change from strong hole conductors to electron and back to hole conductors with the addition of each vacancy, from a doublet (B 37 ) to singlet (B 36 ) to doublet (B 35 ) ground state, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Pressure Effects on the 4 f Electronic Structure of Light Lanthanides

Adopting the satellite structure of the $\mathcal{Lγ_1}$ line in nonresonant x-ray emission spectra, we probe the high-pressure evolution of the bare 4f signature of the early light lanthanides at ambient temperature. For Ce and Pr the satellite peak experiences a sudden reduction concurrent with their respective volume collapse (VC) transitions. These new experimental results are supported by calculations using state-of-the-art extended atomic structure codes for Ce and Pr, and also for Nd, which does not exhibit a VC. Here, our work suggests that changes to the 4f occupation are more consistently associated with evolution of the satellite than is the reduction of the 4f moment. Indeed, we show that in the case of Ce, mixing of a higher atomic angular momentum state, driven by the increased hybridization, acts to obscure the expected satellite reduction. These measurements emphasize the importance of a unified study of a full set of microscopic observables to obtain the most discerning test of the underlying, fundamental f-electron phenomena at high pressures.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Tuning the Electronic Structure of Anatase Through Fluorination

A highly fluorinated anatase lattice has been recently reported, providing a new class of materials whose general chemical formula is T i1-x $\square$ x X 4x O 2-4x (X - = F - or OH - ). To characterise the complex structural features of the material and the different F environments, we here apply a computational screening procedure. After deriving a polarisable force—field from DFT simulations, we screen in a step-wise fashion a large number of possible configurations differing in the positioning of the titanium vacancies ($\square$) and of the fluorine atoms. At each step only 10% of the configurations are retained. At the end of the screening procedure, a configuration is selected and simulated using DFT-based molecular dynamics. This allows us to analyse the atomic structure of the material, which is strongly disordered, leading to a strong decrease (by 0.8 eV) of the band gap compared to conventional anatase.

Science & Technology - Other Topics↗
DOE OSTI2014

Mn L{sub 2,3}-edge X-ray absorption spectroscopic studies on charge-discharge mechanism of Li{sub 2}MnO{sub 3}

The redox reaction of Mn in Li{sub 2}MnO{sub 3} was studied by X-ray absorption spectroscopy and ab initio multiplet calculation. Associated with the de-intercalation of Li-ion, small but clear spectral changes were observed in Mn-L{sub 2,3} X-ray absorption near edge structure (XANES). The systematic ab initio multiplet calculations of Mn-L{sub 2,3} XANES revealed that the spectral changes in the experiment could not simply be ascribed to the change of the valency from Mn{sup 4+} to Mn{sup 5+} but can be explained well by the changes of local atomic structures around Mn{sup 4+} due to the Li de-intercalation. Our results suggest that the electronic state of oxygen should change during charging in Li{sub 2}MnO{sub 3}.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Path integral Monte Carlo simulations of dense carbon-hydrogen plasmas

Carbon-hydrogen plasmas and hydrocarbon materials are of broad interest to laser shock experimentalists, high energy density physicists, and astrophysicists. Accurate equations of state (EOSs) of hydrocarbons are valuable for various studies from inertial confinement fusion to planetary science. By combining path integral Monte Carlo (PIMC) results at high temperatures and density functional theory molecular dynamics results at lower temperatures, we compute the EOSs for hydrocarbons from simulations performed at 1473 separate (ρ, T)-points distributed over a range of compositions. These methods accurately treat electronic excitation effects with neither adjustable parameter nor experimental input. PIMC is also an accurate simulation method that is capable of treating many-body interaction and nuclear quantum effects at finite temperatures. These methods therefore provide a benchmark-quality EOS that surpasses that of semi-empirical and Thomas-Fermi-based methods in the warm dense matter regime. By comparing our first-principles EOS to the LEOS 5112 model for CH, we validate the specific heat assumptions in this model but suggest that the Grüneisen parameter is too large at low temperatures. Based on our first-principles EOSs, we predict the principal Hugoniot curve of polystyrene to be 2%-5% softer at maximum shock compression than that predicted by orbital-free density functional theory and SESAME 7593. By investigating the atomic structure and chemical bonding of hydrocarbons, we show a drastic decrease in the lifetime of chemical bonds in the pressure interval from 0.4 to 4 megabar. We find the assumption of linear mixing to be valid for describing the EOS and the shock Hugoniot curve of hydrocarbons in the regime of partially ionized atomic liquids. We make predictions of the shock compression of glow-discharge polymers and investigate the effects of oxygen content and C:H ratio on its Hugoniot curve. In conclusion, our full suite of first-principles simulation results may be used to benchmark future theoretical investigations pertaining to hydrocarbon EOSs and should be helpful in guiding the design of future experiments on hydrocarbons in the gigabar regime.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Selective Antisite Defect Formation in WS 2 Monolayers via Reactive Growth on Dilute W-Au Alloy Substrates

Defects are ubiquitous in 2D materials and can affect the structure and properties of the materials and also introduce new functionalities. Methods to adjust the structure and density of defects during bottom-up synthesis are required to control the growth of 2D materials with tailored optical and electronic properties. In this study, the authors present an Au-assisted chemical vapor deposition approach to selectively form S W and S2 W antisite defects, whereby one or two sulfur atoms substitute for a tungsten atom in WS 2 monolayers. Guided by first-principles calculations, they describe a new method that can maintain tungsten-poor growth conditions relative to sulfur via the low solubility of W atoms in a gold/W alloy, thereby significantly reducing the formation energy of the antisite defects during the growth of WS 2 . The atomic structure and composition of the antisite defects are unambiguously identified by Z-contrast scanning transmission electron microscopy and electron energy-loss spectroscopy, and their total concentration is statistically determined, with levels up to ≈5.0%. Furthermore, scanning tunneling microscopy/spectroscopy measurements and first-principles calculations also verified these antisite defects and revealed the localized defect states in the bandgap of WS 2 monolayers. This bottom-up synthesis method to form antisite defects should apply in the synthesis of other 2D materials.

2D materials↗
DOE OSTI2016

Mitochondrial Hsp90 is a ligand-activated molecular chaperone coupling ATP binding to dimer closure through a coiled-coil intermediate

Heat-shock protein of 90 kDa (Hsp90) is an essential molecular chaperone that adopts different 3D structures associated with distinct nucleotide states: a wide-open, V-shaped dimer in the apo state and a twisted, N-terminally closed dimer with ATP. Although the N domain is known to mediate ATP binding, how Hsp90 senses the bound nucleotide and facilitates dimer closure remains unclear. In this paper we present atomic structures of human mitochondrial Hsp90 N (TRAP1 N ) and a composite model of intact TRAP1 revealing a previously unobserved coiled-coil dimer conformation that may precede dimer closure and is conserved in intact TRAP1 in solution. Our structure suggests that TRAP1 normally exists in an autoinhibited state with the ATP lid bound to the nucleotide-binding pocket. ATP binding displaces the ATP lid that signals the cis-bound ATP status to the neighboring subunit in a highly cooperative manner compatible with the coiled-coil intermediate state. We propose that TRAP1 is a ligand-activated molecular chaperone, which couples ATP binding to dramatic changes in local structure required for protein folding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

First principles-based multiscale atomistic methods for input into first principles nonequilibrium transport across interfaces

This issue of PNAS features “nonequilibrium transport and mixing across interfaces,” with several papers describing the nonequilibrium coupling of transport at interfaces, including mesoscopic and macroscopic dynamics in fluids, plasma, and other materials over scales from microscale to celestial. Most such descriptions describe the materials in terms of the density and equations of state rather than specific atomic structures and chemical processes. It is at interfacial boundaries where such atomistic information is most relevant. However, there is not yet a practical way to couple these phenomena with the atomistic description of chemistry. The starting point for including such information is the quantum mechanics (QM). However, practical QM calculations are limited to a hundred atoms for dozens of picoseconds, far from the scales required to inform the continuum level with the proper atomistic description. To bridge this enormous gap, we need to develop practical methods to extend the scale of the atomistic simulation by several orders of magnitude while retaining the level of QM accuracy in describing the chemical process. Here, these developments would enable continuum modeling of turbulent transport at interfaces to incorporate the relevant chemistry. In this perspective, we will focus on recent progress in accomplishing these extensions in first principles-based atomistic simulations and the strategies being pursued to increase the accuracy of very large scales while dramatically decreasing the computational effort.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Electronic Structure-Based Discovery of Hybrid Photovoltaic Materials on Next-Generation HPC Platforms

Organic and hybrid organic-inorganic materials other significant opportunities for applications in photovoltaics (PV) and other semiconductor applications. The versatility of organic synthesis affords broad flexibility in terms of fine-tuning the properties of the molecular components. For purely organic materials, the interfaces to inorganic electrodes are a key component that determines the efficiency of eventual devices. In organic-inorganic hybrid materials, atomic-scale inorganic components are integrated with the organic functionality to form tightly integrated, crystalline semiconductor materials with potentially entirely new electronic and carrier transport characteristics. In either organic-inorganic interfaces or hybrid materials, the key properties are governed by the details of the atomic structure, which is virtually impossible to foresee based on empirical criteria. Predictive simulations of the structure and electronic properties of such materials or interfaces would thus greatly enhance our ability to identify the most promising organic-inorganic combinations faster, reducing the need for time consuming experimental synthesis attempts while navigating a complex materials space.

14 SOLAR ENERGY↗
DOE OSTI2024

Monitoring Redox Processes in Lithium-Ion Batteries by Laboratory-Scale Operando X-ray Emission Spectroscopy

Tracking changes in the chemical state of transition metals in alkali-ion batteries is crucial to understanding the redox chemistry during operation. X-ray absorption spectroscopy (XAS) is often used to follow the chemistry through observed changes in the chemical state and local atomic structure as a function of the state-of-charge (SoC) in batteries. In this study, we utilize an operando X-ray emission spectroscopy (XES) method to observe changes in the chemical state of active elements in batteries during operation. Operando XES and XAS were compared by using a laboratory-scale setup for four different battery systems: LiCoO 2 (LCO), Li[Ni 1/3 Co 1/3 Mn 1/3 ]O 2 (NMC111), Li[Ni 0.8 Co 0.1 Mn 0.1 ]O 2 (NMC811), and LiFePO 4 (LFP) under a constant current charging the battery in 10 h (C/10 charge rate). We show that XES, despite narrower chemical shifts in comparison to XAS, allows us to fingerprint the battery SOC in real time. We further demonstrate that XES can be used to track the change in net spin of the probed atoms by analyzing changes in the emission peak shape. As a test case, the connection between net spin and the local chemical and structural environment was investigated by using XES and XAS in the case of electrochemically delithiated LCO in the range of 2–10% lithium removal.

25 ENERGY STORAGE↗
DOE OSTI2018

Accelerated Evolution of Surface Chemistry Determined by Temperature and Cycling History in Nickel-Rich Layered Cathode Materials

Nickel-rich layered cathode materials have the potential to enable cheaper and higher energy lithium ion batteries. However, these materials face major challenges (e.g., surface reconstruction, microcracking, potential oxygen evolution) that can hinder the safety and cycle life of lithium ion batteries. Many studies of nickel-rich materials have focused on ways to improve performance. Understanding the effects of temperature and cycling on the chemical and structural transformations is essential to assess the performance and suitability of these materials for practical battery applications. This study is focused on the spectroscopic analysis of surface changes within a strong performing LiNi 0.8 Mn 0.1 Co 0.1 O 2 (NMC811) cathode material. We found that surface chemical and structural transformations (e.g., gradient metal reduction, oxygen loss, reconstruction, dissolution) occurred quicker and deeper than expected at higher temperatures. Even at lower temperatures, the degradation occurred rapidly and eventually matched the degradation at high temperatures. Despite these transformations, our performance results showed that a better performing nickel-rich NMC is possible. Establishing relationships between the atomic, structural, chemical, and physical properties of cathode materials and their behavior during cycling, as we have done here for NMC811, opens the possibility of developing lithium ion batteries with higher performance and longer life. Finally, our study also suggests that a separate, systematic, and elaborate study of surface chemistry is necessary for each NMC composition and electrolyte environment.

25 ENERGY STORAGE↗