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At least 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate

Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, cryoID , toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5′-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.

Methanosarcina acetivorans↗
DOE OSTI2025

Substituent effect on napthodithiophene-fused porphyrins: Understanding the unusual trend of fluorescence quantum yield quenching

A series of π-extended porphyrins containing thiophene units was prepared to investigate an unusual trend observed in the fluorescence quantum yield of naphtho[2,1-b:3,4-b']dithiophene-fused porphyrins. Monobenzoporphyrins carrying 2-thiophenyl (vinyl thiophene porphyrin) groups (2VTP, 2VTBr and Br2VTP) (numbering 2 and 3 refers to the position of sulfur on the thiophene ring) were synthesized through a Heck-based cascade reaction followed by a newly developed bromination method. These were converted to naphtho[2,1-b:3,4-b']dithiophene-fused porphyrin derivatives (FBr2VTP and F2VTBr) via ring closure with an intramolecular Scholl reaction. Increasingly larger Stokes shifts with a higher number of bromo groups were observed in the unfused π-extended molecular systems, reflecting the heavy atom effect. Fluorescence spectroscopy further confirmed the unusual trend seen in the previous work: structural rigidification in naphtho[2,1-b:3,4-b']dithiophene-fused porphyrins leads to longer fluorescence lifetimes but unexpectedly lowers the quantum yield. Adding one bromo group to the naphtho[2,1-b:3,4-b']dithiophene unit does not change this trend. Furthermore, the presence of two bromo groups prevents the quantum yield from dropping. DFT, TDDFT, and NICS analyses suggest a drastic change in aromaticity in the pyrrole ring where the naphtho[2,1-b:3,4-b']dithiophene is fused in FBr2VTP, which might contribute to the quantum yield reductions.

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

Develop On-Demand nanoplasmonic Device Concepts in a Semiconductor Compatible Hybrid System. Final Report

This report summarizes the research activities supported by the U.S. Department of Energy grant DE-SC-0010399. The goal of this project is to is to develop an on-demand nanoplasmonic platform that combines emerging oxide nanoelectronics with a low-loss semiconductor-friendly plasmonic materials. Toward this goal, several unique heterostructures formed between complex oxides and 2D layered materials have been developed. Based on these material systems, a set of atomic force microscope (AFM) based techniques have been developed that can allow long-living and reversible material phase transitions to be manipulated in nanoscale at room temperature. Using such technique and through interface coupling, we can effectively tune the plasmon propagations in unconventional plasmonic materials such as graphene and VO 2 . In addition, we also discovered a plethora of novel interface enabled electro-optic effects, including the spatial modulation of light using 2DEG, a giant programmable photothermoelectric effects at room temperature, a light induced superconducting transition, and a tunable giant third order optical nonlinearities. These major results are outlined in this report, along with lists of project participants and products.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Physi-sorption of H 2 on pure and boron-doped graphene monolayers: A dispersion-corrected DFT study

Carbon based materials are of interest as potential candidates for H 2 storage. Earlier work has been inconclusive on the effect of boron doping on the energy of H 2 binding. However, earlier work has been inconclusive on the definitive effect of boron doping on the energy of H 2 binding, i.e. isosteric heats of adsorption (Qst). In this work, we completed a systematic DFT study to evaluate this effect, and found that doping graphene with boron provides only minor enhancement in H 2 binding. More importantly, the presence of the electron deficient boron into a graphene ring introduces a defect, such as terminal hydrogen or distortion from planarity, which creates hydrogen adsorption sites with slightly increased Qst. The increase is from ~ 5 kJ/mol H 2 for the pure carbon matrix to ~6 - 7 kJ/mol for the boron doped system. The more strongly bond H 2 is located near the defect and shows little direct interaction with the boron. Most significant enhancement is found in systems where H 2 is confined between layers at a distance of about 7Å. In this case, the H 2 binding nearly doubles, to ~10 kJ/mol for both pure, undistorted graphene, and the 2% boron doped system, containing tetrahedral C atom distortion. Interestingly, at higher doping levels of boron, we found that the Qst decreases compared to the all carbon materials. These finding suggest that interplanar nanoconfinement may be more effective way to enhance H 2 binding than boron doping.

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

System-Independent X-Ray Characterization

We have developed a method for image reconstruction and analysis of dual-energy X-ray scans that has been demonstrated to yield a physically intuitive characterization of materials (by electron density and effective atomic number) in a system-independent way. Our methodology stands in contrast to common practice of reconstructing images to yield linear attenuation coefficients, which depend strongly on system spectral response. At the core of our method, a technique called dual-energy decomposition is used to generate spectral energy-independent characterizations of the attenuation properties of a material. Inputs to this decomposition include system spectral response estimates and dual-energy X-ray projection data. X-ray cross-section tables are used to convert decomposition results to physical feature estimates (electron density, effective atomic number). Our method currently works best for materials with atomic numbers below 22 (titanium). In prior work for DHS, we demonstrated in a controlled, no-clutter environment that the decomposition technique could be applied to scans of a well-characterized materials on multiple systems with different X-ray spectral responses. In cases where LAC values showed a standard deviation of as much as 20% of mean value, application of our method yielded results with standard deviations as low as 1–3% of mean value.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Exploring the Strong Interaction of Three-Body Systems at the LHC

Deuterons are atomic nuclei composed of a neutron and a proton held together by the strong interaction. Unbound ensembles composed of a deuteron and a third nucleon have been investigated in the past using scattering experiments, and they constitute a fundamental reference in nuclear physics to constrain nuclear interactions and the properties of nuclei. In this work, K + -d and p-d femtoscopic correlations measured by the ALICE Collaboration in proton-proton (pp) collisions at $\sqrt{s}$ = 13 TeV at the Large Hadron Collider (LHC) are presented. It is demonstrated that correlations in momentum space between deuterons and kaons or protons allow us to study three-hadron systems at distances comparable with the proton radius. The analysis of the K + -d correlation shows that the relative distances at which deuterons and protons or kaons are produced are around 2 fm. The analysis of the p-d correlation shows that only a full three-body calculation that accounts for the internal structure of the deuteron can explain the data. In particular, the sensitivity of the observable to the short-range part of the interaction is demonstrated. These results indicate that correlations involving light nuclei in pp collisions at the LHC will also provide access to any three-body system in the strange and charm sectors.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Charge transfer rate constants for the carotenoid-porphyrin-C 60 molecular triad dissolved in tetrahydrofuran: The spin-boson model vs the linearized semiclassical approximation

Charge transfer rate constants were calculated for the carotenoid-porphyrin-C 60 (CPC 60 ) molecular triad dissolved in explicit tetrahydrofuran. The calculation was based on mapping the all-atom anharmonic Hamiltonian of this system onto the spin-boson Hamiltonian. The mapping was based on discretizing the spectral density from the time correlation function of the donor–acceptor potential energy gap, as obtained from all-atom molecular dynamics simulations. Different spin-boson Hamiltonians were constructed for each of the possible transitions between the three excited electronic states in two different triad conformations. The rate constants of three possible transitions were calculated via the quantum-mechanically exact Fermi’s golden rule (FGR), as well as a progression of more approximate expressions that lead to the classical Marcus expression. The advantage of the spin-boson approach is that once the mapping is established, the quantum-mechanically exact FGR and the hierarchy of approximations are known in closed form. The classical Marcus charge transfer rate constants obtained with the spin-boson Hamiltonians were found to reproduce those obtained from all-atom simulations with the linearized semiclassical approximation, thereby confirming the equivalence of the two approaches for this system. Furthermore, within the spin-boson Hamiltonian, we also found that the quantum-mechanically exact FGR rate constants were significantly enhanced compared to the classical Marcus theory rate constants for two out of three transitions in one of the two conformations under consideration. The results confirm that mapping to the spin-boson model can yield accurate predictions for charge transfer rate constants in a system as complex as CPC 60 dissolved in tetrahydrofuran.

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

Phononic bus for coherent interfaces between a superconducting quantum processor, spin memory, and photonic quantum networks

A hybrid quantum system performs high-fidelity quantum state transduction between a superconducting (SC) microwave qubit and the ground state spin system of a solid-state artificial atom. This transduction is mediated via an acoustic bus connected by piezoelectric transducers to the SC microwave qubit. For SC circuit qubits and diamond silicon vacancy centers in an optimized phononic cavity, the system can achieve quantum state transduction with fidelity exceeding 99% at a MHz-scale bandwidth. By combining the complementary strengths of SC circuit quantum computing and artificial atoms, the hybrid quantum system provides high-fidelity qubit gates with long-lived quantum memory, high-fidelity measurement, large qubit number, reconfigurable qubit connectivity, and high-fidelity state and gate teleportation through optical quantum networks.

Englund, Dirk Robert↗
DOE OSTI2024

Circuit-Based Leakage-to-Erasure Conversion in a Neutral-Atom Quantum Processor

Atom-loss errors are a major limitation of current state-of-the-art neutral-atom quantum computers and pose a significant challenge for scalable systems. In a quantum processor with cesium atoms, we demonstrate proof-of-principle circuit-based conversion of this form of leakage error to erasure errors via leakage-detection units (LDUs), which nondestructively map information about the presence or absence of the qubit onto the state of an ancilla. We benchmark the performance of the LDU using a three-outcome low-loss state-detection method and find that the LDU detects atom-loss errors with approximately 93.4% accuracy, limited by technical imperfections of our apparatus. We further compile and execute a SWAP LDU, wherein the roles of the original data atom and ancilla atom are exchanged under the action of the LDU, providing “free refilling” of atoms in the case of atom loss. This circuit-based leakage-to-erasure error conversion is a critical component of a neutral-atom quantum processor where the quantum information may significantly outlive the lifetime of any individual atom in the quantum register. Finally, we demonstrate that LDUs may also be used to handle other forms of leakage errors where population moves to states outside of the computational subspace.

Chow, Matthew N. H. [Sandia National Laboratories ↗
DOE OSTI2021

Deterministic Fast Scrambling with Neutral Atom Arrays

Fast scramblers are dynamical quantum systems that produce many-body entanglement on a timescale that grows logarithmically with the system size N. Here, we propose and investigate a family of deterministic, fast scrambling quantum circuits realizable in near-term experiments with arrays of neutral atoms. We show that three experimental tools—nearest-neighbor Rydberg interactions, global single-qubit rotations, and shuffling operations facilitated by an auxiliary tweezer array—are sufficient to generate nonlocal interaction graphs capable of scrambling quantum information using only O(logN) parallel applications of nearest-neighbor gates. These tools enable direct experimental access to fast scrambling dynamics in a highly controlled and programmable way and can be harnessed to produce highly entangled states with varied applications.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Resolving atomic transport through iron oxide under irradiation using isotopic tracers

Structural materials in nuclear environments are exposed to complex and harsh conditions, including high temperatures, corrosive solutions, and irradiation. Material stability and likewise degradation are fundamentally controlled by atomic transport mechanisms. Here, we investigate the influence of radiation-induced, non-equilibrium point defect populations on mass transport within model oxide systems using isotopic tracers and atom probe tomography. An isotopically labelled hematite (a-Fe2O3) film was synthesized with 16O- and 18O-rich layers (>30nm and 10 nm, respectively) sequentially deposited via molecular beam epitaxy. One region of the film was proton irradiated to ~0.1 dpa at 450°C, and regions outside the beam spot provided a non-irradiated control of thermal annealing only. 3D APT was used to directly visualize the elemental and O-isotopic redistribution following both thermal and combined thermal and irradiation conditions. Complementary scanning transmission electron microscopy (STEM) was also employed to study the microstructural evolution. Error function fits of the 18O-concentration profiles enabled quantification of diffusion coefficients.

isotopic tracers, diffusion, proton irradiation, h↗
DOE OSTI2023

Optically pumped, radio-frequency atomic magnetometry with feedback stabilization

An optically pumped, atomic magnetometer incorporates a feedback system for stabilizing the magnetic bias field and suppressing unwanted background fields. The magnetic bias field is applied to a vapor cell containing host atoms of two different species, each of which resonates at a different Larmor frequency when both are subjected to the same magnetic bias field. One species provides the feedback for stabilizing the bias field, thereby creating a stabilizing magnetometer portion that nulls out the unwanted background fields. The other species provides magnetic field detection or signal reception on a radio communication frequency of interest, thereby creating a signal magnetometer portion that permits detection of the signal at the radio communication frequency.

Schwindt, Peter D. D.↗
DOE OSTI2020

Accelerated Modeling of Lithium Diffusion in Solid State Electrolytes using Artificial Neural Networks

Abstract Previous efforts to understand structure‐function relationships in high ionic conductivity materials for solid state batteries have predominantly relied on density functional theory (DFT‐) based ab initio molecular dynamics (MD). Such simulations, however, are computationally demanding and cannot be reasonably applied to large systems containing more than a hundred atoms. Here, an artificial neural network (ANN) is trained to accelerate the calculation of high accuracy atomic forces and energies used during such MD simulations. After carefully training a robust ANN for four and five element systems, nearly identical lithium ion diffusivities are obtained for Li 10 GeP 2 S 12 (LGPS) when benchmarking the ANN‐MD results with DFT‐MD. Applying the ANN‐MD approach, the effect of chlorine doping on the lithium diffusivity is calculated in an LGPS‐like structure and it is found that a dopant concentration of 1.3% maximizes ionic conductivity. The optimal concentration balances the competing consequences of effective atomic radii and dielectric constants on lithium diffusion and agrees with the experimental composition. Performing simulations at the resolution necessary to model experimentally relevant and optimal concentrations would be infeasible with traditional DFT‐MD. Systems that require a large number of simulated atoms can be studied more efficiently while maintaining high accuracy with the proposed ANN‐MD framework.

Rao, Karun K.↗
DOE OSTI2022

Towards Ab-Initio Simulations of Crystalline Defects at the Exascale Using Spectral Quadrature Density Functional Theory

Defects in crystalline solids play a crucial role in determining properties of materials at the nano, meso- and macroscales, such as the coalescence of vacancies at the nanoscale to form voids and prismatic dislocation loops or diffusion and segregation of solutes to nucleate precipitates, phase transitions in magnetic materials via disorder and doping. First principles Density Functional Theory (DFT) simulations can provide a detailed understanding of these phenomena. However, the number of atoms needed to correctly simulate these systems is often beyond the reach of many widely used DFT codes. The aim of this article is to discuss recent advances in first principles modeling of crystal defects using the spectral quadrature method. The spectral quadrature method is linear scaling with respect to the number of atoms, permits spatial coarse-graining, and is capable of simulating non-periodic systems embedded in a bulk environment, which allows the application of appropriate boundary conditions for simulations of crystalline defects. In this article, we discuss the state-of-the-art in ab-initio modeling of large metallic systems of the order of several thousand atoms that are suitable for utilizing exascale computing resourses.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Control of plasmons in doped topological insulators via basis atoms

Collective excitations in topologically nontrivial systems have attracted considerable attention in recent years. Here we study plasmons in the Su-Schrieffer-Heeger model whose low-energy electronic band is only partially filled, such that the system is metallic. Using the random phase approximation, we calculate the intra- and interband polarization functions and determine the bulk plasmonic dispersion from the dielectric function. In this work, we find that the sublattice basis states strongly affect the polarization functions and therefore control the system’s plasmonic excitations. By varying the real-space separation of these local orbitals, one can thus selectively enhance or suppress the plasmonic energies via a tunable trade-off between intraband and interband screening processes. Specifically, this mechanism can be used to stabilize undamped high energy plasmons that have already been reported in related models. We propose scenarios on how to control and observe these effects in experiments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Development of neural network force fields for corrosion studies

To fully understand the chemistry and physics of corrosion, novel methods of simulation must be developed. One approach is designing machine learning (ML) algorithms integrated with density functional theory to develop adaptive force fields to gain insight into corrosion behavior namely at the surface of metal oxides. Current methods of modeling corrosion are slow due to the computational cost of resolving both reaction mechanics and mass transport processes. Machine learning methods can be implemented to obtain structure-activity relationships at both the molecular and bulk scale while still retaining the accuracy of density functional theory (DFT) and significantly decreasing the time needed for simulations of complex chemical processes in the various environments of corrosion. Multiscale models are needed for corrosion studies to fully understand its processes not only at the atomic length scale (chemical bonding, energies, and forces), but also at the nano and meso length scales (solid-state physics and material science processes). Current methods of study include DFT, molecular dynamics, and Monte Carlo. The limitation of DFT is that only a small number of atoms or molecules can be simulated at that level of theory. Density functional theory is used to study the electronic structure of atoms and molecules, and calculate the force component of each atom. However, these calculations are limited to about 1000 atoms. Custom periodic boundary conditions (PBC) can be used to describe the various environments and defects that affect the atomic forces to produce a large data set from which a training set can be derived. Machine learning can be utilized to overcome the barrier of modeling macroscopic and multi-scale processes from ab initio calculations through the development of adaptive force fields. Local environments determine the atomic forces of a given system, therefore adaptive force fields must be created to produce reliable quantum mechanical calculations. This can be achieved by developing a learning algorithm that uses the mapped atomic forces or fingerprint as an input to produce energies and magnetic moments as output. A systematic approach was used to begin to build a data set in order to accurately describe the atomic forces in various environments. In Figure 4 below, a simple PBC cell of Fe{sub 2}O{sub 3} was first optimized. A surface optimization was performed next, followed by a hydroxylated surface optimization. Once this calculation has converged, the adsorption of halide species to the hydroxylated surface will be investigated. TensorFlow is an open source platform for machine learning developed by Google. Using a high level application program interface (API) such as Keras allows for building and training ML models easily in a number of different environments and languages. For this project, a neural network was developed within Anaconda in Python. Future Work: Further development of reference data set; Refining neural network and learning algorithm; Fingerprinting atomic environment to enable mapping of atomic force components; Choosing appropriate training set from reference data; Learning from training set and enabling non-linear mapping of training set fingerprints and the atomic forces; Estimation of uncertainty to identify ranges of outside applicability; Testing and analysis of molecular dynamic simulations.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Dust and Ions: Self Organization and Stability (Final Report)

This project explores the stability and structure of systems with non-reciprocal interactions, challenging the traditional understanding based on Newton's third law, which states that every action has an equal and opposite reaction. Reciprocal forces are fundamental to the stability of systems ranging in size from atomic nuclei to galactic clusters. Our research investigates what happens when the forces between two objects are not equal and opposite. We used dusty plasmas as a model system to study non-reciprocal interactions. In a plasma chamber, micron-sized dust particles acquire a negative charge and form 2D planar "dust crystals" when levitated by the electric field present in the plasma sheath at the interface between the plasma and the lower surface of the chamber. This electric field also drives a vertical ion flow, creating a positively charged "plasma wake" downstream of the dust grains. While horizontally aligned dust grains interact reciprocally, a slight vertical displacement causes non-reciprocal interactions due to the attraction of the lower dust grain to the upper dust grain’s ion wake. Our experiments investigated the range of plasma conditions (gas pressure and system power) where stable dusty plasma structures are able to self-organize, aided by the ion wake. We studied systems ranging from pairs of dust particles to large 2D crystals, providing insights into the conditions that lead to stable or unstable structures. We used numerical simulations to investigate how ion wakes changed in response to changes in the operating conditions as well as how the wakes of separate grains interact when dust grains are in close proximity.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Sensitivity of EDM experiments in paramagnetic atoms and molecules to hadronic CP violation

Experiments searching for the electric dipole moment (EDM) of the electron d e utilize atomic/molecular states with one or more uncompensated electron spins, and these paramagnetic systems have recently achieved remarkable sensitivity to d e . If the source of CP violation resides entirely in the hadronic sector, the two-photon exchange processes between electrons and the nucleus induce CP-odd semileptonic interactions, parametrised by the Wilson coefficient C SP , and provide the dominant source of EDMs in paramagnetic systems instead of d e . We evaluate the C SP coefficients induced by the leading hadronic sources of CP violation, namely nucleon EDMs and CP-odd pion-nucleon couplings, by calculating the nucleon-number-enhanced CP-odd nuclear scalar polarisability, employing chiral perturbation theory at the nucleon level and the Fermi-gas model for the nucleus. This allows us to translate the ACME EDM limits from paramagnetic ThO into novel independent constraints on the QCD theta term |$\bar θ$| < 3 × 10 –8 , proton EDM |d p | < 2 × 10 –23 e cm, isoscalar CP-odd pion-nucleon coupling |$\bar g$$^{(1)}_{πNN}$| < 4 × 10 –10 , and color EDMs of quarks |$\tilde d$ u -$\tilde $d d | < 2 × 10 –24 cm. We note that further experimental progress with EDM experiments in paramagnetic systems may allow them to rival the sensitivity of EDM experiments with neutrons and diamagnetic atoms to these quantities.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗