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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM

The atomic coordinates derived from cryo-electron microscopy (cryo-EM) maps can be inaccurate when the voxel scaling factors are not properly calibrated. Here, we describe a method for correcting relative voxel scaling factors between pairs of cryo-EM maps for the same or similar structures that are expanded or contracted relative to each other. We find that the correction of scaling factors reduces the amplitude differences of Fourier-inverted structure factors from voxel-rescaled maps by up to 20–30%, as shown by two cryo-EM maps of the SARS-CoV-2 spike protein measured at pH 4.0 and pH 8.0. This allows for the calculation of the difference map after properly scaling, revealing differences between the two structures for individual amino acid residues. Unexpectedly, the analysis uncovers two previously overlooked differences of amino acid residues in structures and their local structural changes. Furthermore, we demonstrate the method as applied to two cryo-EM maps of monomeric apo-photosystem II from the cyanobacteria Synechocystis sp. PCC 6803 and Thermosynechococcus elongatus. The resulting difference maps reveal many changes in the peripheral transmembrane PsbX subunit between the two species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Multimodal Analysis of Reaction Pathways of Cathode Materials for Lithium Ion Batteries

Conversion mechanism in lithium ion batteries provides higher capacity than intercalation mechanism since multiple numbers of electrons and lithium ions are associated. However, poor cycling stability, large voltage hysteresis, and low energy efficiency have been great challenges of conversion reaction. To address those issues, conversion-type electrode materials have been reformed via doping or substituting other elements. For example, iron fluorides (FeF 2 , FeF 3 ) have modified as iron oxyfluorides (FeF 1-x O x ), showing enhanced long-term stability. Furthermore, co-substituted (both anion and cation substituted) Fe 0.9 Co 0.1 OF (FeCoOF) was demonstrated excellent cycling stability. (capacity of 350 mAh g -1 at a current of 500 mA g -1 for 1000 cycles). Substituting anion and cation in iron fluoride has been suggested as an effective method to achieve better reversibility but understanding of lithiation reactions in co-substituted FeCoOF is not clear. This work takes advantage of ex-situ/ in-situ synchrotron X-ray based techniques and transmission electron microscopy to elucidate structural changes with lithium ion, which may provide fundamental insights into modifying conversion-type materials. Figure 1 presents discharge-charge curves and pair distribution function patterns acquired at each potential. As lithium ions were inserted, structural changes were noticed both at short-range and long-range. However, long-range ordering was nearly maintained even at 1 V, indicating absence of conversion reaction. Figure 2 shows lithiation induced structural evolution of a single FeCoOF nanorod observed in real time. As lithiation proceeds, the width of nanorods shows a stepwise increase, particularly A in figure 2d, which may indicate multiple steps of lithiation occur. Considering that conversion reaction takes place around 2 V in FeF 3 , co-substitution Co and O into iron fluoride may change thermodynamic features of lithiation reactions by lowering the initiation potential for conversion reaction. Instead, phase transformations occur at long-range order, which may help maintaining structural integrity during operation, eventually, achieving cycling stability.

25 ENERGY STORAGE↗
DOE OSTI2020

Synthesis, Redox, and Spectroscopic Properties of Pd(II) 10,10-Dimethylisocorrole Complexes Prepared via Bromination of Dimethylbiladiene Oligotetrapyrroles

Two brominated 10,10-dimethylisocorrole (10-DMIC) derivatives containing Pd(II) centers have been prepared and characterized. These compounds were prepared via bromination of 10,10-dimethylbiladiene-based oligotetrapyrroles. Bromination of free base 10,10-dimethylbiladiene (DMBil1) followed by metalation with Pd(OAc) 2 , as well as bromination of the corresponding Pd(II) dimethylbiladiene complex (Pd[DMBil1]) provide routes to Pd(II) hexabromo-10,10-dimethyl-5,15-bis(pentafluorophenyl)-isocorrole (Pd[10-DMIC-Br 6 ]) and Pd(II) octabromo-10,10-dimethyl-5,15-bis(pentafluorophenyl)-isocorrole (Pd[10-DMIC-Br 8 ]). The solid-state structures of the two brominated isocorrole complexes are presented, as is that for a new decabrominated dimethylbiladiene derivative (DMBil-Br 10 ). The electronic and spectroscopic properties of the brominated biladiene and isocorrole derivatives were probed using a combination of voltammetric methods and steady-state UV–vis absorption and emission experiments. Data obtained from these experiments allow the properties of the brominated biladiene and isocorrole derivatives to be compared to previously studied biladiene derivatives (i.e., DMBil1 and Pd[DMBil1]). CV and DPV experiments demonstrate that Pd[10-DMIC-Br 6 ] and Pd[10-DMIC-Br 8 ] support well-behaved multielectron redox chemistry, similar to that which has been observed for other nonaromatic tetrapyrroles containing sp 3 -hybridized meso-carbons. Here, spectroscopic experiments reveal that bromination of the dimethylbiladiene core shifts this system’s UV–vis absorption profile to lower energy and that the dimethylisocorrole complexes support panchromatic absorption profiles that extend across the UV–vis and into the near-IR region. Photosensitization experiments demonstrate that unlike previously studied Pd(II) biladiene constructs, DMBil-Br 10 , Pd[10-DMIC-Br 6 ], and Pd[10-DMIC-Br 8 ] support limited triplet excited state chemistry with O 2 , indicating that the novel nonaromatic tetrapyrrole derivatives described in this work may be best suited for applications other than singlet oxygen sensitization.

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

Curing the Divergence in Time-Dependent Density Functional Quadratic Response Theory

While time-dependent density functional theory has emerged as a method of choice for computing electronic spectra and response of molecules and materials, its reliability is hindered by the adiabatic approximation that is commonly made. In this work, we address one problematic aspect that arises from this approximation: an incorrect pole structure in the quadratic response function, leading to unphysical divergences in excited state-to-state transition probabilities and hyperpolarizabilties. We find the form of the exact quadratic response kernel and derive a practical and accurate approximation that cures the divergence. Here, we demonstrate our results on excited state-to-state transition probabilities of a model system and of the LiH molecule.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Structural studies of the IFNλ4 receptor complex using cryoEM enabled by protein engineering

Abstract IFNλ4 has posed a conundrum in human immunology since its discovery in 2013, with its expression linked to complications with viral clearance. While genetic and cellular studies revealed the detrimental effects of IFNλ4 expression, extensive structural and functional characterization has been limited by the inability to express and purify the protein, complicating explanations of its paradoxical behavior. In this work, we report a method for robust production of IFNλ4. We then use yeast surface display to affinity-mature IL10Rβ and solve the 72 kilodalton structures of IFNλ4 (3.26 Å) and IFNλ3 (3.00 Å) in complex with their receptors IFNλR1 and IL10Rβ using cryogenic electron microscopy. Comparison of the structures highlights differences in receptor engagement and reveals a distinct 12-degree rotation in overall receptor geometry, providing a potential mechanistic explanation for differences in cell signaling, downstream gene induction, and antiviral activities. Further, we perform a structural analysis using molecular modeling and simulation to identify a unique region of IFNλ4 that, when replaced, enables secretion of the protein from cells. These findings provide a structural and functional understanding of the IFNλ4 protein and enable future comprehensive studies towards correcting IFNλ4 dysfunction in large populations of affected patients.

Science & Technology - Other Topics↗
DOE OSTI2022

Relaxation time approximations in PAOFLOW 2.0

Abstract Regardless of its success, the constant relaxation time approximation has limited validity. Temperature and energy dependent effects are important to match experimental trends even in simple situations. We present the implementation of relaxation time approximation models in the calculation of Boltzmann transport in 2.0 and apply those to model band-structures. In addition, using a self-consistent fitting of the model parameters to experimental conductivity data, we provide a flexible tool to extract scattering rates with high accuracy. We illustrate the approximations using simple models and then apply the method to GaAs, Si, $$\hbox {Mg}_3\hbox {Sb}_2$$ Mg 3 Sb 2 , and $$\hbox {CoSb}_3$$ CoSb 3 .

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

A fresh perspective on the role of band bending, and related contributors, in light-driven production of electricity and chemicals

It is widely known that semiconductor-based solar energy conversion could power our planet. This is in part because high-quality semiconductor structures are unrivalled in their ability to separate photogenerated electrons and holes. One effective approach to achieving this photoinduced charge separation relies on a phenomenon known as “band bending”. But details to justify why band bending results in photoinduced charge separation are more complex than often appreciated. This underappreciation is an impediment to the rational, hypothesis-driven design of next-generation approaches to solar energy conversion. Herein we show, by means of derivations rooted in physical chemistry, that several phenomena – not just band bending – can facilitate photoinduced charge separation, and that each is influenced by nonequilibrium species concentration and a parameter, such as diffusion coefficient or rate coefficient, that introduces dynamics. To help visualize the impact of each phenomenon, we introduce plots that depict their contributions as free energy, force, flux, force constant, and rate. We reveal that spatial dopant distributions that define band bending are predictors of initial photogenerated species transport rates. But charge separation alone does not guarantee high-efficiency operation. A photogenerated change in energy that is freely available to do useful work is also essential, and is strongly dependent on semiconductor optical properties and reaction kinetics. Notably, this information reveals that specificity of interfacial chemical reactions – even when they are not preceded by charge separation elsewhere – can result in efficient solar energy conversion. We expect that this tutorial will guide researchers in their pursuit to uncover new mechanisms for light to perform useful work.

14 SOLAR ENERGY↗
DOE OSTI2022

CO 2 laser heating system for in situ radial x-ray absorption at 16-BM-D at the Advanced Photon Source

Here we present a portable CO 2 laser heating system for in situ x-ray absorption spectroscopy (XAS) studies at 16-BM-D (High Pressure Collaborative Access Team, Advanced Photon Source, Argonne National Laboratory). Back scattering optical measurements are made possible by the implementation of a Ge beamsplitter. Optical pyrometry is conducted in the near-infrared, and our temperature measurements are free of chromatic aberration due to the implementation of the peak-scaling method and mode scrambling of the input signal. Laser power stabilization is established using electronic feedback, providing a steady power over second timescales - crucial for longer XAS collections. Examples of in situ high pressure–temperature extended x-ray absorption fine structure measurements of ZrO 2 are presented to demonstrate this new capability.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Charge density wave and superconductivity in the disordered Holstein model

The interplay between electron-electron correlations and disorder has been a central theme of condensed matter physics over the past several decades, with particular interest in the possibility that interactions might cause delocalization of an Anderson insulator into a metallic state, and the disrupting effects of randomness on magnetic order and the Mott phase. In this work, we extend this physics to explore electron-phonon interactions and show, via exact quantum Monte Carlo simulations, that the suppression of the charge density wave correlations in the half-filled Holstein model by disorder can stabilize a superconducting phase. Our simulations thus capture qualitatively the suppression of charge ordered phases and emergent superconductivity recently seen experimentally.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

End-to-end orientation estimation from 2D cryo-EM1images

Cryo-electron microscopy (cryo-EM) is a Nobel Prize-winning technique for deter-mining high-resolution 3D structures of biological macromolecules. A 3D structure is reconstructed from hundreds of thousands of noisy 2D projection images. However, existing 3D reconstruction methods are still time-consuming, and one of the major computational bottlenecks is to recover the unknown orientation of the particle in16each 2D image. The dominant methods typically exploit expensive global search on each image to estimate the missing orientations. Here, a novel end-to-end supervised learning method is introduced to directly recover the missing orientations from 2D cryo-EM images. A neural network is used to approximate the mapping from images to orientations. Furthermore, a robust loss function is proposed for optimizing the parameters of the network, which can handle both asymmetric and symmetric 3D structures. Experiments on synthetic datasets with various symmetry types confirm that the neural network is capable of recovering orientations from 2D cryo-EM images, and the results on one real cryo-EM dataset further demonstrate its potential in more challenging imaging conditions.

3D reconstruction↗
DOE OSTI2025

Non-Abelian quasiparticles and topological superconductivity for the quantum information science

The research performed on this proposal lead to significant progress in understanding spectra of charge carrier holes in spin 3/2 valence bands in two-dimensional systems and topological phenomena in these systems; resulted in enhanced knowledge of topological excitations, such as Majorana fermions and parafermions in electron and hole systems; lead to new breakthroughs in understanding quantum Hall systems, which is an important breeding ground for topological excitations; contributed to understanding of several aspects of theory of spin-orbit interactions; and understanding of hybrid superconductor/semiconductor structures. Methods and techniques used or developed in the research were effective in achieving its results. Some of the developed methods have been used by the research community. The achieved results are beneficial for both theorists and experimentalists in condensed matter and related areas of research, developed knowledge is important for progress in quantum science and technology, and therefore is of benefit to the public.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Benchmarking Adaptive Variational Quantum Eigensolvers

By design, the variational quantum eigensolver (VQE) strives to recover the lowest-energy eigenvalue of a given Hamiltonian by preparing quantum states guided by the variational principle. In practice, the prepared quantum state is indirectly assessed by the value of the associated energy. Novel adaptive derivative-assembled pseudo-trotter (ADAPT) ansatz approaches and recent formal advances now establish a clear connection between the theory of quantum chemistry and the quantum state ansatz used to solve the electronic structure problem. Here we benchmark the accuracy of VQE and ADAPT-VQE to calculate the electronic ground states and potential energy curves for a few selected diatomic molecules, namely H 2 , NaH, and KH. Using numerical simulation, we find both methods provide good estimates of the energy and ground state, but only ADAPT-VQE proves to be robust to particularities in optimization methods. Another relevant finding is that gradient-based optimization is overall more economical and delivers superior performance than analogous simulations carried out with gradient-free optimizers. The results also identify small errors in the prepared state fidelity which show an increasing trend with molecular size.

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

Editorial: Quantum Information and Quantum Computing for Chemical Systems

Quantum computing has emerged as an exciting inter-disciplinary research topic that cuts across the traditional fields of physics, computer science, and engineering. It is a revolutionary model of computation that has offered new insights into methods for modeling and simulation of chemical systems. Applications of quantum computing to chemistry have demonstrated rapid progress on both theoretical and experimental fronts. Past theoretical efforts have shown how to adapt quantum computation to a variety of problems including electronic structure and molecular dynamics. In addition, the development of quantum algorithms for quantum chemistry has been stimulated by the greater availability of more capable quantum computing devices. Advances in the number and quality of qubits continues to enable remarkable proof-of-concept demonstrations working towards a milestone of quantum computational advantage.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

Revealing the Full Potential of Glycolated Mixed Ionic-Electronic Semiconductors – Symmetric Monomer Polymerization to Boost Electrochemical Transistor Performance

Organic electrochemical transistors (OECTs) enable the transduction of ionic signals into electronic outputs, positioning them as ideal candidates for next-generation sensing and (bio)signal processing applications. Recent years have witnessed the development of various OECT channel materials, affording insights into structural fine-tuning to achieve optimal performance and/or stability. However, homocouplings, commonly present in alternating conjugated polymers, have largely been overlooked. This study investigates the effect of homocoupling on OECT materials by employing two synthesis methods – standard Stille polymerization and an alternative symmetric approach – to create the p-type enhancement-mode benchmark polymer pgBTTT. The impact of homocoupling, and its absence, is studied by comparing the bulk properties of the two polymers and evaluating their respective OECT metrics. The new, homocoupling-free polymer exhibits a notably improved OECT performance ( μC *), mainly due to an average 3-fold increase in electronic mobility (μ).

defects↗
DOE OSTI2024

Resolving electron and hole transport properties in semiconductor materials by constant light-induced magneto transport

The knowledge of minority and majority charge carrier properties enables controlling the performance of solar cells, transistors, detectors, sensors, and LEDs. Here, we developed the constant light induced magneto transport method which resolves electron and hole mobility, lifetime, diffusion coefficient and length, and quasi-Fermi level splitting. We demonstrate the implication of the constant light induced magneto transport for silicon and metal halide perovskite films. We resolve the transport properties of electrons and holes predicting the material’s effectiveness for solar cell application without making the full device. The accessibility of fourteen material parameters paves the way for in-depth exploration of causal mechanisms limiting the efficiency and functionality of material structures. To demonstrate broad applicability, we further characterized twelve materials with drift mobilities spanning from 10 –3 to 10 3 cm 2 V –1 s –1 and lifetimes varying between 10 –9 and 10 –3 seconds. The universality of our method its potential to advance optoelectronic devices in various technological fields.

14 SOLAR ENERGY↗
DOE OSTI2020

Domain Separated Density Functional Theory for Reaction Energy Barriers and Optical Excitations

We recently proposed Domain Separated Density Functional Theory (DS-DFT), a framework that allows for the combination of different levels of theory for the computation of the electronic structure of molecules. Here, this work discusses the application of DS-DFT to the computation of transition-state energy barriers and optical absorption spectra. We considered several hydrogen abstraction reactions and optical spectra of molecule/metal cluster systems, including the absorption of individual species such as carbon monoxide, methane, and molecular hydrogen to a Li6 cluster. We present and discuss two domain-separated methods: i), the screened-density approximation (SDA), and, ii), linearly weighted exchange (LWE). We find that SDA, which is applied as a hybridization based on atomic domains, could be useful to computing energy barriers, whereas LWE is suited for the analysis of electronic properties such as ground-state gaps, excitation energies, and oscillator strengths.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Electronic transport, thermal transport, thermal expansion, and magnetization in the strongly correlated metal LaNi⁢O 3

Perovskite structured LaNiO 3 is a strongly correlated metal with intriguing thermal and magnetic properties. The volume dependence of calculated and measured physical properties can add additional critical information to develop a more in-depth understanding of this strongly correlated phenomenon. Taking advantage of recent single crystal LaNiO 3 growth using the floating-zone method, we have measured the thermal expansion, the magnetostriction, and the pressure dependence of the magnetic susceptibility, which then allows derivation of the Grüneisen parameters γ e = $\frac{dlnN(E_F)}{d lnV}$, γ χ = $\frac{dlnχ}{d lnV}$, as well as of electric and thermal transport properties. We simulate the volume dependence of structural and magnetic properties using Density Functional Theory calculations at the Generalized Gradient Approximation level. A large discrepancy between experimental values and calculated ones suggests that strong correlations are likely to be dynamic in nature. This study also provides a side-by-side comparison of measurements in single crystal and polycrystalline samples of LaNiO 3 to elucidate intrinsic materials properties. A broad hump at high temperatures in the temperature dependence of magnetization found in the single crystal sample of LaNiO 3 has been rationalized by a model that includes the influence of electron correlations on the Landau diamagnetism.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Microfracture-pore structure characterization and water-rock interaction in three lithofacies of the Lower Eagle Ford Formation

The microfracture-pore structures and water-rock interactions of eight samples of three typical lithofacies (three limestone, three wackestone, and two mudstone) from the Lower Eagle Ford Formation have been investigated using an integrated methodology. The methods used were X-ray diffraction (XRD), total organic carbon (TOC) content, pyrolysis, thin-section petrography, scanning electron microscopy (SEM), mercury intrusion porosimetry (MIP), spontaneous water imbibition, and water vapor & nitrogen physisorption. Petrophysical properties such as organic richness, maturity, mineral composition, types and patterns of microfractures and pores, porosity, pore-throat size distribution, pore size distribution, pore connectivity, water adsorption and desorption behavior were determined from these methods, and the results compared among the three lithofacies. For example, the three limestone EAS samples and three wackestone DM samples show a low porosity range from 2.02–3.35%, whereas the two mudstone VRU samples exhibit a much large average porosity of 11.7% by MIP results. Nitrogen physisorption results show that pore size distributions have a good similarity in N2 adsorption volume for the samples with similar lithology. Microfractures are morphologically divided into seven types, with their definitions & pictorial examples presented and possible formation mechanisms proposed. In addition, the water vapor physisorption behavior and their controlling factors are discussed. Here, the water adsorption capacity shows a positive relationship (R 2 = 0.90) with clay content and a negative relationship (R 2 = 0.99) with carbonate content. In general, this integrated study of microfracture-pore structure characterization and water-rock interaction provides some insights of water vapor adsorption behavior in different lithofacies and whether microfractures could be an important pathway for fluid flow.

58 GEOSCIENCES↗