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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

CryoTRANS: predicting high-resolution maps of rare conformations from self-supervised trajectories in cryo-EM

Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, enabling efficient determination of structures at near-atomic resolutions. However, a common challenge arises from the severe imbalance among various conformations of vitrified particles, leading to low-resolution reconstructions in rare conformations due to a lack of particle images in these quasi-stable states. We introduce CryoTRANS, a method that predicts high-resolution maps of rare conformations by constructing a self-supervised pseudo-trajectory between density maps of varying resolutions. This trajectory is represented by an ordinary differential equation parameterized by a deep neural network, ensuring retention of detailed structures from high-resolution density maps. By leveraging a single high-resolution density map, CryoTRANS significantly improves the reconstruction of rare conformations and has been validated on four real-world datasets: alpha-2-macroglobulin, actin-binding protein complexes, SARS-CoV-2 spike glycoprotein, and the 70S ribosome. CryoTRANS can also predict high-resolution structures in cryogenic electron tomography maps using a high-resolution cryo-EM map.Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, enabling efficient determination of structures at near-atomic resolutions. However, a common challenge arises from the severe imbalance among various conformations of vitrified particles, leading to low-resolution reconstructions in rare conformations due to a lack of particle images in these quasi-stable states. We introduce CryoTRANS, a method that predicts high-resolution maps of rare conformations by constructing a self-supervised pseudo-trajectory between density maps of varying resolutions. This trajectory is represented by an ordinary differential equation parameterized by a deep neural network, ensuring retention of detailed structures from high-resolution density maps. By leveraging a single high-resolution density map, CryoTRANS significantly improves the reconstruction of rare conformations and has been validated on four real-world datasets: alpha-2-macroglobulin, actin-binding protein complexes, SARS-CoV-2 spike glycoprotein, and the 70S ribosome. CryoTRANS can also predict high-resolution structures in cryogenic electron tomography maps using a high-resolution cryo-EM map.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Bending as a control knob for the electronic and optical properties of phosphorene nanoribbons

We have assessed mechanical bending as a powerful controlling tool for the electronic structure and optical properties of phosphorene nanoribbons. We use state-of-the-art density functional approximations in our work. The overall performance of the recently developed meta-generalized gradient approximation (meta-GGA) mTASK [Phys. Rev. Materials 5, 063803 (2021)] functional establishes the method as a useful alternative to the screened hybrid HSE06 for better band gaps of phosphorene nanoribbons. We present a detailed analysis to interpret the optical absorption of bent phosphorene nanoribbons using the GW-Bethe-Salpeter approximation. Finally, we demonstrate the important role of the unoccupied in-gap state and conclude that this in-gap state in armchair nanoribbons introduced by bending can significantly affect the properties of low-energy excitons and add some useful opportunities for applications in optoelectronic devices.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Characterizing crystalline defects in single nanoparticles from angular correlations of single-shot diffracted X-rays

Characterizing and controlling the uniformity of nanoparticles is crucial for their application in science and technology because crystalline defects in the nanoparticles strongly affect their unique properties. Recently, ultra-short and ultra-bright X-ray pulses provided by X-ray free-electron lasers (XFELs) opened up the possibility of structure determination of nanometre-scale matter with Å spatial resolution. However, it is often difficult to reconstruct the 3D structural information from single-shot X-ray diffraction patterns owing to the random orientation of the particles. This report proposes an analysis approach for characterizing defects in nanoparticles using wide-angle X-ray scattering (WAXS) data from free-flying single nanoparticles. The analysis method is based on the concept of correlated X-ray scattering, in which correlations of scattered X-ray are used to recover detailed structural information. WAXS experiments of xenon nanoparticles, or clusters, were conducted at an XFEL facility in Japan by using the SPring-8 Ångstrom compact free-electron laser (SACLA). Bragg spots in the recorded single-shot X-ray diffraction patterns showed clear angular correlations, which offered significant structural information on the nanoparticles. The experimental angular correlations were reproduced by numerical simulation in which kinematical theory of diffraction was combined with geometric calculations. We also explain the diffuse scattering intensity as being due to the stacking faults in the xenon clusters.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants

The serotonin transporter (SERT) is a member of the SLC6 neurotransmitter transporter family that mediates serotonin reuptake at presynaptic nerve terminals. SERT is the target of both therapeutic antidepressant drugs and psychostimulant substances such as cocaine and methamphetamines, which are small molecules that perturb normal serotonergic transmission by interfering with serotonin transport. Despite decades of studies, important functional aspects of SERT such as the oligomerization state of native SERT and its interactions with potential proteins remain unresolved. Here, we develop methods to isolate SERT from porcine brain (pSERT) using a mild, nonionic detergent, utilize fluorescence-detection size-exclusion chromatography to investigate its oligomerization state and interactions with other proteins, and employ single-particle cryo-electron microscopy to elucidate the structures of pSERT in complexes with methamphetamine or cocaine, providing structural insights into psychostimulant recognition and accompanying pSERT conformations. Methamphetamine and cocaine both bind to the central site, stabilizing the transporter in an outward open conformation. We also identify densities attributable to multiple cholesterol or cholesteryl hemisuccinate (CHS) molecules, as well as to a detergent molecule bound to the pSERT allosteric site. Under our conditions of isolation, we find that pSERT is best described as a monomeric entity, isolated without interacting proteins, and is ensconced by multiple cholesterol or CHS molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Nanometer-Thick Sr 2 IrO 4 Freestanding Films for Flexible Electronics

In this article, we report the structural and optical properties of nanoscale Sr 2 IrO 4 freestanding thin-films fabricated using a water-soluble Sr 3 Al 2 O 6 layer. The coherent lattice structure, phonon modes, two-magnon Raman scattering, and optical absorption spectra of the Sr 2 IrO 4 nanomembrane are analogous to those of the layered iridate epitaxial thin-films and single crystals. Remarkably, the formation of 3-unit-cell-thick SrIrO 3 and interfacial composite layers alleviates the antiphase boundaries at the Sr 2 IrO 4 /Sr 3 Al 2 O 6 interface, resulting in structurally-robust nanomembranes. Our experimental results show that this freestanding thin-film approach of layered oxides can provide techniques for tuning or realizing unprecedented states beyond conventional thin-film methods, suggesting a pathway in achieving flexible layered-oxide electronics.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Machine learning for deep elastic strain engineering of semiconductor electronic band structure and effective mass

Abstract The controlled introduction of elastic strains is an appealing strategy for modulating the physical properties of semiconductor materials. With the recent discovery of large elastic deformation in nanoscale specimens as diverse as silicon and diamond, employing this strategy to improve device performance necessitates first-principles computations of the fundamental electronic band structure and target figures-of-merit, through the design of an optimal straining pathway. Such simulations, however, call for approaches that combine deep learning algorithms and physics of deformation with band structure calculations to custom-design electronic and optical properties. Motivated by this challenge, we present here details of a machine learning framework involving convolutional neural networks to represent the topology and curvature of band structures in k -space. These calculations enable us to identify ways in which the physical properties can be altered through “deep” elastic strain engineering up to a large fraction of the ideal strain. Algorithms capable of active learning and informed by the underlying physics were presented here for predicting the bandgap and the band structure. By training a surrogate model with ab initio computational data, our method can identify the most efficient strain energy pathway to realize physical property changes. The power of this method is further demonstrated with results from the prediction of strain states that influence the effective electron mass. We illustrate the applications of the method with specific results for diamonds, although the general deep learning technique presented here is potentially useful for optimizing the physical properties of a wide variety of semiconductor materials.

Tsymbalov, Evgenii↗
DOE OSTI2020

Valence-to-core X-ray emission spectroscopy of vanadium oxide and lithiated vanadyl phosphate materials

In this work, we report valence-to-core (VTC) X-ray emission spectroscopy (XES) measurements and theoretical calculations of the electrochemical sequence ε-VOPO 4 , ε-LiVOPO 4 , ε-Li 2 VOPO 4 and the reference oxides V 2 O 3 , VO 2 , and V 2 O 5 . In our analysis of these results, we establish a framework for interrogating chemical bonding that is generally applicable to a wide range of systems, including complex, extended inorganic compounds. While this latter regime has garnered less focused application than, e.g. , metalloenzymes in many excellent catalysis studies, we show that the technique provides high utility in materials-focused energy storage research. Here, sensitivities to the local atomic structure and hybridization schemes are discussed in detail. Similarly, the effect of lithiation on oxidation, delocalization, and shifts in ligand valence energy levels are all readily apparent in the analyzed results. Finally, the TDDFT projections clearly reveal the directional dependencies of the valence band at each of the vanadium sites. Our results demonstrate laboratory-based X-ray spectroscopy instrumentation is a viable route for attaining well-resolved VTC-XES features for inorganic compounds of 3d transition metals, even for samples of limited quantity or suffering from sensitivity to the atmosphere. The experimental results are in good agreement with results produced by real-space Green's function and time-dependent density functional theory (TDDFT) methods, respectively. Hence, we propose that VTC-XES, when equipped with appropriate theoretical support, can be a valuable complement to X-ray absorption pre-edge features for more detailed characterization of a compound's electronic structure. We expect similar analyses will find application in a broad range of materials chemistry research and provide both fundamental and applied insights.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Hybridization effect on the x-ray absorption spectra for actinide materials: Application to PuB 4

Studying the local moment and 5 f -electron occupations sheds insight into the electronic behavior in actinide materials. X-ray absorption spectroscopy (XAS) has been a powerful tool to reveal the valence electronic structure when assisted with theoretical calculations. However, the analysis currently taken in the community on the branching ratio of the XAS spectra generally does not account for the hybridization effects between local f orbitals and conduction states. In this paper, we discuss an approach which employs the density functional theory plus Gutzwiller rotationally invariant slave boson method to obtain a local Hamiltonian for the single-impurity Anderson model, and calculates the XAS spectra by the exact diagonalization (ED) method. A customized numerical routine was implemented for the ED XAS part of the calculation. By applying this technique to the recently discovered 5 f -electron topological Kondo insulator Pu B 4 , we determined the signature of 5 f -electronic correlation effects in the theoretical x-ray spectra. Furthermore, we found that the Pu 5 f - 6 d hybridization effect provides an extra channel to mix the j = 5 / 2 and 7 / 2 orbitals in the 5 f valence. As a consequence, the resulting electron occupation number and spin-orbit coupling strength deviate from the intermediate-coupling regime.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Importance of Dispersion in the Molecular Geometries of Mn(III) Spin-Crossover Complexes

The computational investigation of the molecular geometries of a pair of manganese(III) spin-crossover complexes is reported. For the geometry of the quintet high-spin state, density functionals significantly overestimate Mn–Namine bond distances, although the geometry for the triplet intermediate-spin state is well described. Here, comparisons with several wave function-based methods demonstrate that this error is due to the limited ability of commonly used density functionals to recover dispersion beyond a certain extent. Among the methods employed for geometry optimization, restricted open-shell Møller–Plesset perturbation theory (MP2) appropriately describes the high-spin geometry but results in a slightly shorter Mn–O distance in both spin states. On the other hand, extended multistate complete active space second-order perturbation theory (XMS-CASPT2) provides a good description of the geometry for the intermediate-spin state but also sufficiently recovers dispersion, performing well for the high-spin state. Despite the fact that the electronic structure of both spin states is dominated by one-electron configuration, XMS-CASPT2 offers a balanced approach, leading to molecular geometries with much better agreement with experiment than MP2 and DFT. A scan along the Mn–N amine bond demonstrates that for these complexes coupled cluster methods (i.e., DLPNO-CCSD(T)) also yield bond distances in agreement with experiment while multiconfiguration pair density functional theory (MC-PDFT) is unable to recover dispersion well enough, analogous to single-reference DFT.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Prediction of Above-Room-Temperature Superconductivity in Lanthanide/Actinide Extreme Superhydrides

Achieving superconductivity at or above room temperature has been a century long held dream for physicists since the discovery of superconductivity in mercury in 1911. Following the recent predictions and ensuing synthesis of clathrate superhydride LaH 10 under pressure exhibiting extraordinary superconducting critical temperatures (T c ) of 250 260 K, we predict via advanced crystal structure search methods a new class of extremely hydrogen rich clathrate superhydrides. These MH 18 (M: rare earth/actinide metal atom) stoichiometric compounds consisting of H36 cage networks are predicted to host T c values above room temperature up to 330 K at pressures of 350 GPa. The bonding and electronic properties of these MH 18 clathrate superhydrides parallel those of atomic metallic hydrogen, giving rise to the highest superconducting temperatures predicted thus far for a thermodynamically stable hydride compound. In depth examination of these extreme superhydrides offers key insights for elucidating and further exploring phonon mediated superconductivity above room temperature in hydrogen rich and other low Z materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Bifurcation Analysis Reveals Solution Structures of Phase Field Models

The phase field method is playing an increasingly important role in understanding and predicting morphological evolution in materials and biological systems. Here, in this study, we develop a new analytical approach based on the bifurcation analysis to explore the mathematical solution structure of phase field models. Revealing such solution structures not only is of great mathematical interest but also may provide guidance to experimentally or computationally uncover new morphological evolution phenomena in materials undergoing electronic and structural phase transitions. To elucidate the idea, we apply this analytical approach to three representative phase field equations: the Allen-Cahn equation, the Cahn-Hilliard equation, and the Allen-Cahn-Ohta-Kawasaki system. The solution structures of these three phase field equations are also verified numerically by the homotopy continuation method.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Ionic Dopant-Induced Ordering Enhances the Thermoelectric Properties of a Polythiophene-Based Block Copolymer

Conjugated polymer-based block copolymers (CP-BCPs) are an unexplored class of materials for organic thermoelectrics. In this study, the authors report on the electronic conductivity (σ) and Seebeck coefficient (α) of a newly synthesized CP-BCP, poly(3-hexylthiophene)-block-poly (oligo-oxyethylene methacrylate) (P3HT-b-POEM), upon solution co-processing with lithium bis(trifluoromethanesulfonyl)imide (LiTFSI), and subsequently vapor-doping with a molecular dopant, 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ). It is found that the addition of the hydrophilic block POEM greatly enhances the processability of P3HT, enabling homogeneous solution-mixing with LiTFSI. Notably, interactions between P3HT-b-POEM with ionic species significantly improve molecular order and unexpectedly cause electrical oxidizing doping of P3HT block both in solution and solid-states, a phenomenon that has not been previously observed in Li-salt containing P3HT. Vapor doping of P3HT-b-POEM-LiTFSI thin films with F4TCNQ further enhances σ and yields a thermoelectric power factor PF = α 2 σ of 13.0 μW m -1 K -2 , which is more than 20 times higher than salt-free P3HT-b-POEM sample. Through modeling thermoelectric behaviors of P3HT-b-POEM with the Kang-Snyder transport model, the improvement in PF is attributed to higher electronic charge mobility originating from the enhanced molecular ordering of P3HT. The results demonstrate that solution co-processing CP-BCPs with a salt is a powerful method to control structure and performance of organic thermoelectric materials.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Epitaxial Design of Complex Nickelates as Electrocatalysts for the Oxygen Evolution Reaction

Abstract The oxygen evolution reaction (OER) is a crucial process in electrochemical water splitting, a promising technology to renewably yield hydrogen gas from water. Designing and developing earth‐abundant, efficient, and stable OER electrocatalysts to replace the most widely used but scarce RuO 2 and IrO 2 are thus of critical interest. Recently, ABO 3 ‐structured perovskite oxides, especially rare‐earth nickelates, are extensively studied for their potential use as OER electrocatalysts. In particular, the epitaxial synthesis of complex oxide thin films allows flexible and precise control over the materials so that their structure–stability–property relationships can be established. Using nickelate thin films as model systems, this review illustrates how epitaxial design allows researchers to test different hypotheses and proposed descriptors, as well as formulate new design principles. Following a brief introduction to the background of OER mechanisms, proposed activity descriptors, and synthesis methods, various epitaxial design strategies are surveyed including strain tuning, composition control, surface termination/orientation selection, defect engineering, and interface design. These have led to precise control over the atomic structures and electronic properties of nickelates which in turn determine their electrochemical performance. Finally, the remaining challenges and perspectives toward a deeper understanding and use of complex oxides as OER catalysts are discussed.

Choi, Min‐Ju↗
DOE OSTI2023

Synthesis, Hole Doping, and Electrical Properties of a Semiconducting Azatriangulene-Based Covalent Organic Framework

Two-dimensional covalent organic frameworks (2D COFs) containing heterotriangulenes have been theoretically identified as semiconductors with tunable, Dirac-cone-like band structures, which are expected to afford high charge-carrier mobilities ideal for next-generation flexible electronics. However, few bulk syntheses of these materials have been reported, and existing synthetic methods provide limited control of network purity and morphology. Here, we report transimination reactions between benzophenone-imine-protected azatriangulenes (OTPA) and benzodithiophene dialdehydes (BDT), which afforded a new semiconducting COF network, OTPA-BDT. The COFs were prepared as both polycrystalline powders and thin films with controlled crystallite orientation. Here, the azatriangulene nodes are readily oxidized to stable radical cations upon exposure to an appropriate p type dopant, tris(4-bromophenyl)ammoniumyl hexachloroantimonate, after which the network’s crystallinity and orientation are maintained. Oriented, hole-doped OTPA-BDT COF films exhibit electrical conductivities of up to 1.2 × 10 –1 S cm –1 , which are among the highest reported for imine-linked 2D COFs to date.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

3D Nanocrystallography and the Imperfect Molecular Lattice

Crystallographic analysis relies on the scattering of quanta from arrays of atoms that populate a repeating lattice. While large crystals built of lattices that appear ideal are sought after by crystallographers, imperfections are the norm for molecular crystals. Additionally, advanced X-ray and electron diffraction techniques, used for crystallography, have opened the possibility of interrogating micro- and nanoscale crystals, with edges only millions or even thousands of molecules long. These crystals exist in a size regime that approximates the lower bounds for traditional models of crystal nonuniformity and imperfection. Accordingly, data generated by diffraction from both X-rays and electrons show increased complexity and are more challenging to conventionally model. New approaches in serial crystallography and spatially resolved electron diffraction mapping are changing this paradigm by better accounting for variability within and between crystals. The intersection of these methods presents an opportunity for a more comprehensive understanding of the structure and properties of nanocrystalline materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Path Integral Monte Carlo Simulations of Iron Plasmas (Final Technical Report)

This documents is the final technical report for our grant entitled "Path Integral Monte Carlo Simulations of Iron Plasmas" that focused on developing path integral Monte Carlo (PIMC) computer simulations. This techniques will be developed to study plasmas composed of heavier elements including iron and other third row elements. Equations of state (EOS) and transport properties will be derived in the regime of warm dense matter (WDM) and dense plasmas where existing first-principles methods cannot be applied. While standard density functional theory (DFT) has been used to accurately predict the structure of many solids and liquids up to temperatures on the order of 100,000 K, this method is not applicable at much higher temperature because the number of partially occupied electronic orbitals reaches intractably large numbers or the use of finite-temperature free energy functionals in orbital-free DFT introduces an uncontrolled approximation. Here we focus on PIMC methods that become more and more efficient with increasing temperatures and still include all electronic correlation effects. In this approach, electronic excitations increase the efficiency rather than reduce it. While it had commonly been assumed this method could only be applied to elements without core electrons, we showed that PIMC with free-particle nodes works well for first-row elements (PRL 108 (2012) 115502). Most recently, we extended the applicability range of all-electron PIMC to second-row elements by adopting localized nodal surfaces (PRL 115 (2015) 176403). To simulate third-row elements efficiently under WDM conditions, we propose a new method to remove core electrons by introducing pseudo-nodes. We explain our approach step by step and present preliminary results. We focus our method development on getting PIMC simulations of iron to work because of its fundamental importance for WDM and astrophysics. Then we move on to krypton and copper-doped beryllium, a ICF ablator material. We plan to continue working on key second-row material such as Na, Mg, MgO, Al, silica, and silicon-doped plastic ablators. Our collaborators at LLNL, will use our PIMC EOS data both as comparisons to existing semi-empirical, EOS-generating schemes, and as input for continuum radiation hydrodynamics simulations. We will establish an efficient pipeline from PIMC to macroscopic continuum studies of materials response. An emphasis will be placed on benchmarking such methods for plasmas of heavy elements at the very high temperatures (~100 eV) and low densities that are generated when Hohlraum radiation heats the ablator material in indirect drive laser experiments. Results from changes to the EOS will be of immeasurable importance to the designers at the National Ignition Facility (NIF) and at other facilities. Starting with our EOS of Cu-doped Be, our second collaborator at LLE, will perform real-time simulations of laser fusion experiments at the Omega laser and at the NIF to determine how sensitive the compression path depends on the ablator EOS. Since our collaborator also has experience in performing orbital-free DFT calculations, we propose to compare predictions from this method with PIMC results. In joint publications, we plan to analyze the accuracy of different free-energy functionals in order to understand why existing orbital-free DFT calculations do not predict compression peaks along the shock Hugoniot curve that we see with PIMC. The peaks are caused by the ionization of various electron shells. Their accurate characterization is important to compare with experimental results. We will break new ground by developing PIMC techniques that can simulate iron and all other third row elements in the plasma and WDM regimes. We introduce the concept of pseudo-nodes for the efficient treatment of the core-electrons. The EOS and transport properties will be derived and published online in the form of a new WDM database. Our PIMC EOS calculations will benchmark and possibly replace semi-analytical EOS tables like QEOS or SESAME, which will impact the hydrocode simulation community and will affect the design of NIF targets. Our PIMC results will help to improve the accuracy of orbital-free DFT simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
NASA NTRS1976

Phase separation of metallic hydrogen-helium alloys

Calculations are presented for the thermodynamic functions and phase separation boundaries of solid metallic hydrogen helium alloys at temperatures between 0 K and 19,000 K and at pressures between 15 and 90 megabars. Expressions for the band structure energy of a randomly disordered alloy (including third order in the electron ion interaction) are derived and evaluated. Short and long range order are included by the quasi-chemical method, and lattice dynamics in the virtual crystal harmonic approximation. We conclude that at temperatures below 4,000 K there is complete phase separation of hydrogen helium alloys, and that a miscibility gap remains at the highest temperatures and pressures considered. The relevance of these results to models of the deep interior of Jupiter is briefly discussed.

Straus, D. M.↗
NASA NTRS1992

Piezoresistive stress sensors on (110) silicon wafers

Structural reliability of electronic packages has become an increasing concern for a variety of reasons including the advent of higher integrated circuit densities, power density levels, and operating temperatures. A powerful method for experimental evaluation of die stress distributions is the use of test chips incorporating integral piezoresistive sensors. In this paper, the basic equations needed for the design of stress sensors fabricated on the surface of (110) oriented silicon wafers have been presented. Several sensor rosette configurations have been explored, including the familiar three-element 0-45-90 rosette. Rosette designs have been found which minimize the necessary calibration procedures and permit more stress components to be measured. It has been established that stress sensors on the surface of (110) test chips are sensitive to four out of the six stress components at a point.

Kang, Y. L.↗