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At least 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including >660 000 educators, students and members of the curious public using PDB101.RCSB.org. PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators and students studying fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. During the past 2 years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with >40 external biodata resources. New features and resources are described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The Human Phenotype Ontology in 2021

The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for phenotype exchange. The HPO has grown steadily since its inception due to considerable contributions from clinical experts and researchers from a diverse range of disciplines. Here, we present recent major extensions of the HPO for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas. For example, the seizure subontology now reflects the International League Against Epilepsy (ILAE) guidelines and these enhancements have already shown clinical validity. We present new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease. These efforts will benefit software such as Exomiser by improving the accuracy and scope of cross-species phenotype matching. The computational modeling strategy used by the HPO to define disease entities and phenotypic features and distinguish between them is explained in detail. We also report on recent efforts to translate the HPO into indigenous languages. Finally, we summarize recent advances in the use of HPO in electronic health record systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Two-mode bosonic quoctit for high energy physics

In this work, we study a two-mode bosonic encoding of a quoctit inside a non-Abelian group-structured constellation of coherent states. This work is motivated by the importance of non-Abelian symmetry in particle physics and the desire to have transversal non-Abelian logical gates. We use the previously developed 2 T constellation of states used to encode a so-called 2 T qutrit. The fidelity of the 2 T quoctit is benchmarked against other bosonic qudits for different noise models and find it compare favorably when power constraints are considered. This paves the way for the construction of higher-dimensional qudits (e.g., a quicosotetrit with 2 T group structure) in bosonic systems with practical applications in quantum simulations of particle physics.

Kürkçüoglu, Doga Murat [Fermilab] (ORCID:000000031↗
DOE OSTI2026

Space-Charge-Limited van der Waals Spin Transistor

Integrating semiconducting and magnetic materials could combine transistorlike operation with nonvolatility and enable architectures such as logic in memory. Here, in this work, we employ correlated electrical transport and scanning nitrogen-vacancy center magnetic imaging to elucidate a spin transistor concept that amalgamates vertical and lateral hopping transport inside a 2D antiferromagnetic semiconductor, mechanistically distinct from vertical tunneling devices. Our device, based on a monolayer-bilayer junction in CrSBr, displays giant, gate-tunable magnetoresistance driven by the dual action of electrostatic doping on space-charge-limited lateral conduction and interlayer exchange coupling. Moreover, we visualize a field-trainable, layer-sharing effect that selects between coherent or domain-wall reversal at the spin-flip transition, enabling multilevel, memristive conductance states. Our layer-dependent space charge mechanism for convergent electrical and magnetic control opens opportunities to address limitations in contemporary computing.

2-dimensional systems↗
DOE OSTI2025

Stabilization of magnetic bubbles in [Ni/Co]n multilayers on an oxygen-reconstructed Nb(110) surface via an ultra-thin Cu interlayer

Magnetic thin films hosting topological spin textures, such as magnetic skyrmions, hold high potential for breakthroughs in the field of spintronics, due to good scalability and energy efficiency. Novel computational architectures such as memory-in-logic devices rely on material platforms able to host those topological spin textures. Furthermore, recently proposed designs of novel quantum information technologies are based on heterostructures where topological spin textures are in direct proximity to a superconducting layer. Here, we demonstrate the stabilization of out-of-plane magnetic bubbles in highly ordered [Ni/Co]n multilayers on a Nb(110) single crystal. This is achieved without the need for the removal of the well-known Nb(110)-oxide surface reconstruction, due to the introduction of an ultra-thin Cu interlayer in between the Nb substrate and the magnetic multilayer. The Cu interlayer generates a well-ordered hexagonal surface, which is key for the epitaxial growth of the [Ni/Co]n multilayers hosting the desired out-of-plane anisotropy. The magnetic ground state of the prepared material stacks is directly imaged via spin-polarized low-energy electron microscopy, revealing the presence of magnetic bubble domains with lateral sizes as small as 450 nm.

Dibajeh, Ahmad↗
DOE OSTI2026

Profusion of symmetry-protected qubits from stable ergodicity breaking

We show how combining a discrete symmetry with topological Hilbert space fragmentation can give rise to exponentially many topologically stable qubits protected by a single discrete symmetry. We illustrate this explicitly with the example of the CZ𝑝 model, where the encoded qubits are prethermally stable to arbitrary symmetry-respecting perturbations for parametrically long times, substantially enhancing the robustness of a recently proposed construction based on nontopological fragmentation. In this model, the encoded qubits naturally come in pairs for which a universal set of transversal logical gates can be performed, ruling out (by the Eastin-Knill theorem) the possibility of using them for quantum error correction. We also comment on the combination of symmetry enrichment and topological fragmentation more generally, and the implications for use of systems exhibiting Hilbert space fragmentation as quantum memories.

kinetically constrained models↗
DOE OSTI2026

Concatenated dual displacement code for continuous-variable quantum error correction

The continuous-variable (CV) Gaussian no-go theorem fundamentally limits the suppression of Gaussian displacement errors using only Gaussian gates and states. Prior studies have employed Gottesman-Kitaev-Preskill (GKP) states as ancillary qumodes to suppress small Gaussian displacement errors. However, when the displacement magnitude becomes large, inevitable lattice-crossing errors arise beyond the correctable range of the GKP state. To address this issue, we concatenate the Gaussian-noise-suppression circuit with an outer analog Steane code that corrects such occasional lattice-crossing events as well as other abrupt displacement errors. Contrary to conventional concatenation, which primarily aims to reduce logical error rates, the Steane-GKP duality in encoding provides complementary protection against displacement errors at different scales: The inner GKP layer employs non-Gaussian resources to suppress continuous Gaussian noise and reduce residual variance, while the outer analog Steane code corrects discrete lattice-crossing events that exceed the GKP correctable range. It is precisely this separation of error-mitigation roles that enables CV error correction. In contrast to prior work on concatenating GKP and repetition codes to establish error correction for discrete qubit/qudit encoding, we provide correction in the continuous encoding space. Analytical studies show that, under infinite squeezing, the concatenated code suppresses the variance of Gaussian displacement errors acting on all qumodes by up to 50%, while enabling unbiased correction of lattice-crossing errors with a success probability determined by the ratio between the residual Gaussian error standard deviation and the lattice-crossing magnitude. Even with finite squeezing, the proposed architecture still provides Gaussian-error suppression and lattice-crossing correction. Moreover, the presence of the outer analog Steane code relaxes the squeezing requirement of the inner GKP states, indicating near-term experimental feasibility. This work establishes a viable route toward fault-tolerant continuous-variable quantum computation and provides insight into the design of concatenated CV error-correcting architectures.

quantum error correction↗
DOE OSTI2026

Spectral Properties and Coding Transitions of Haar-Random Quantum Codes

A quantum error-correcting code with a nonzero error threshold undergoes a mixed-state phase transition when the error rate reaches that threshold. We explore this phase transition for Haar-random quantum codes, in which the logical information is encoded in a random subspace of the physical Hilbert space. We focus on the spectrum of the encoded system density matrix as a function of the rate of uncorrelated, single-qudit errors. For low error rates, this spectrum consists of well-separated bands, representing errors of different weights. As the error rate increases, the bands for high-weight errors merge. The evolution of these bands with increasing error rate is well described by a simple analytic ansatz. Using this ansatz, as well as an explicit calculation, we show that the threshold for Haar-random quantum codes saturates the hashing bound, and thus coincides with that for random stabilizer codes. For error rates that exceed the hashing bound, typical errors are uncorrectable, but postselected error correction remains possible until a much higher detection threshold. Postselection can in principle be implemented by projecting onto subspaces corresponding to low-weight errors, which remain correctable past the hashing bound.

decoherence↗
DOE OSTI2025

Nanoscale Quantum Imaging of Field-Free Deterministic Switching of a Chiral Antiferromagnet

Recently, unconventional spin-orbit torques (SOTs) with tunable spin generation have opened new pathways for designing novel magnetization control for cutting-edge spintronics innovations. A leading research thrust is to develop field-free deterministic magnetization switching for implementing scalable and energy favorable magnetic recording and storage, which have been demonstrated in conventional ferromagnetic and antiferromagnetic material systems. Here, in this work, we extend this advanced magnetization control strategy to chiral antiferromagnet Mn 3 ⁢Sn using spin currents with out-of-plane canted polarization generated from low-symmetry van der Waals (vdW) material WTe 2 . Numerical calculations suggest that dampinglike SOT of spins injected perpendicular to the kagome plane of Mn 3⁢ Sn serves as a driving force to rotate the chiral magnetic order, while the fieldlike SOT of spin currents with polarization parallel to the kagome plane provides the bipolar deterministicity to the magnetic switching in the absence of an external magnetic field. We further introduce scanning quantum microscopy to visualize nanoscale evolutions of Mn 3 ⁢Sn magnetic domains during the field-free switching process, corroborating the exceptionally large magnetic switching ratio up to 90%. Our results highlight the opportunities provided by hybrid SOT material platforms consisting of noncollinear antiferromagnets and low-symmetry vdW spin source materials for developing next-generation spintronic logic devices.

2-dimesional systems↗
DOE OSTI2025

Mechanisms enabling reconfigurability and long-term retention in vanadium oxide electrochemical memory

Phase coexistence in nanoscale electrochemical random-access memory (ECRAM) has recently been demonstrated to enable both information storage and extraordinary reconfigurability. These proof-of-principle demonstrations have left the mechanistic details of such a process unresolved. Particularly, the mechanisms that stabilize the multiple phases, and the underlying processes behind sustained memory retention, remain unclear, and are necessary to design such devices. Here we report microscale ECRAM devices composed of V⁢O𝑥, which enables us to directly probe the active region in an operando fashion using optical techniques. Using Raman mapping, we show the phase coexistence driven by the electrochemical injection of O vacancies to be spatially uniform (i.e., with no filaments). The stability was observed to be unusually long, with 1% loss over 14 years in ambient conditions. First-principles calculations of the oxygen vacancy formation energies in V⁢O 𝑥 further support the thermodynamic coexistence of multiple V⁢O 𝑥 phases and clarify the origin of the observed long-term retention in the ECRAM devices. Further, we demonstrate single devices that can be voltage programmed to exhibit synaptic, neuronal, and reconfigurable logic gate functionalities. Furthermore, we not only uncover the phase coexistence mechanism that may help device design, but also demonstrate the circuit-level applications of reconfigurability.

Electrical conductivity↗
DOE OSTI2020

Error detection on quantum computers improving the accuracy of chemical calculations

The ultimate goal of quantum error correction is to achieve the fault-tolerance threshold beyond which quantum computers can be made arbitrarily accurate. This requires extraordinary resources and engineering efforts. We show that even without achieving full fault-tolerance, quantum error detection is already useful on the current generation of quantum hardware. We demonstrate this by executing an end-to-end chemical calculation for the hydrogen molecule encoded in the [[4, 2, 2]] quantum error-detecting code. The encoded calculation with logical qubits significantly improves the accuracy of the molecular ground-state energy.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Universal quantum operation of spin-3/2 Blume-Capel chains

We propose a logical qubit based on the Blume-Capel model: A higher-spin generalization of the Ising chain which allows for an on-site anisotropy-preserving rotational invariance around the Ising axis. We show that such a spin-3/2 Blume-Capel model can also support localized Majorana zero modes at the ends of the chain. Inspired by known braiding protocols of these Majorana zero modes, upon appropriate manipulation of the system parameters, we demonstrate a set of universal gate operations which act on qubits encoded in the doubly degenerate ground states of the chain.

1-dimensional spin chains↗
DOE OSTI2025

Enhancing quantum memory lifetime with measurement-free local error correction and reinforcement learning

Reliable quantum computation requires systematic identification and correction of errors that occur and accumulate in quantum hardware. To diagnose and correct such errors, standard quantum error-correcting protocols utilize global error information across the system obtained by mid-circuit readout of ancillary qubits. We investigate circuit-level error-correcting protocols that are measurement-free and based on local error information. Such a local error correction (LEC) circuit consists of faulty multi-qubit gates to perform both syndrome extraction and ancilla-controlled error removal. We develop and implement a reinforcement learning framework that takes a fixed set of faulty gates as inputs and outputs an optimized LEC circuit. To evaluate this approach, we quantitatively characterize an extension of logical qubit lifetime by a noisy LEC circuit. For the two-dimensional (2D) classical Ising model and four-dimensional toric code, our optimized LEC circuit performs better at extending a memory lifetime compared with a conventional LEC circuit based on Toom's rule in a subthreshold gate error regime. We further show that such circuits can be used to reduce the rate of mid-circuit readouts to preserve a 2D toric code memory. Lastly, we discuss the application of the LEC protocol on dissipative preparation of quantum states with topological phases.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Cold ion beam in a storage ring as a platform for large-scale quantum computers and simulators: Challenges and directions for research and development

The purpose of this paper is to evaluate the possibility of constructing a large-scale storage-ring-type ion-trap system capable of storing, cooling, and controlling a large number of ions as a platform for scalable quantum computing (QC) and quantum simulations. In such a trap, the ions form a crystalline beam moving along a circular path with a constant velocity determined by the frequency and intensity of the cooling lasers. In this paper, we consider a large leap forward in terms of the number of ions that serve as qubits in QC, from fewer than 100 available in state of the art linear ion-trap devices today to an order of 10 5 crystallized ions in the storage-ring setup. This new trap design unifies two different concepts: the storage rings of charged particles and the linear ion traps used for QC and mass spectrometry. In this paper, we use the language of particle accelerators to discuss the ion state and dynamics. We outline the differences between the above concepts, analyze challenges of the large ring with a revolving chain of ions, and propose goals for the research and development required to enable future quantum computers with 1000 times more qubits than available today. The challenge of creating such a large-scale quantum system while maintaining the necessary coherence of the qubits and the high fidelity of quantum logic operations is significant. Performing analog quantum simulations may be an achievable initial goal for such a device. Quantum calculations and simulations of complex quantum systems will move forward both the fundamental science and the applied research. Nuclear and particle physics, many-body quantum systems, lattice gauge theories, and nuclear structure calculations are just a few examples in which a large-scale quantum simulation system will become a very powerful tool to move forward our understanding of nature.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Tailoring Spin-Wave Channels in a Reconfigurable Artificial Spin Ice

Artificial spin ices are ensembles of geometrically arranged interacting nanomagnets that have shown promising potential for the realization of reconfigurable magnonic crystals. Such systems allow for the manipulation of spin waves on the nanoscale and their potential use as information carriers. However, there are presently two general obstacles to the realization of artificial spin-ice-based magnonic crystals: the magnetic state of artificial spin ices is difficult to reconfigure and the magnetostatic interactions between the nanoislands are often weak, preventing mode coupling. We demonstrate, using micromagnetic modeling, that coupling a reconfigurable artificial spin-ice geometry made of weakly interacting nanomagnets to a soft magnetic underlayer creates a complex system exhibiting dynamically coupled modes. These give rise to spin-wave channels in the underlayer at well-defined frequencies, based on the artificial spin-ice magnetic state, which can be reconfigured. Finally, these findings open the door to the realization of reconfigurable magnonic crystals with potential applications for data transport and processing in magnonic-based logic architectures.

25 ENERGY STORAGE↗
DOE OSTI2021

Inverse Design of Plasma Metamaterial Devices for Optical Computing

We apply inverse-design methods to produce two-dimensional plasma metamaterial (PMM) devices. Backpropagated finite-difference frequency-domain (FDFD) simulations are used to design waveguides and demultiplexers operating under both TE and TM modes. Demultiplexing and waveguiding are demonstrated for devices composed of plasma elements with reasonable plasma densities of approximately 7 GHz, allowing for future in situ training and experimental realization of these designs. We also explore the possible applicability of PMMs to nonlinear boolean operations for use in optical computing. Functionally complete logical connectives (or and and) are achieved in the TM mode.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Topological spin texture in Janus monolayers of the chromium trihalides Cr(I, X ) 3

Topological magnetic states are promising for ultradense memory and logic devices. Recent progress in two-dimensional magnets encourages the idea to realize topological states, such as skyrmions and merons, in freestanding monolayers. However, monolayers such as CrI 3 lack Dzyaloshinskii-Moriya interactions (DMIs) and thus do not naturally exhibit skyrmions/merons but rather a ferromagnetic state. Here we propose the fabrication of Cr(I, $X)_3$ Janus monolayers, in which the Cr atoms are covalently bonded to the underlying I ions and top-layer Br or Cl atoms. By performing first-principles calculations and Monte Carlo simulations, we identify strong enough DMIs, which leads to not only helical cycloid phases, but also to topologically nontrivial states, such as the intrinsic domain wall skyrmions in Cr(I, Br) 3 and the magnetic-field-induced bimerons in Cr(I, Cl) 3 . Finally, microscopic origins of such spin textures are revealed as well.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Deep learning of accurate force field of ferroelectric HfO 2

The discovery of ferroelectricity in HfO 2 -based thin films opens up new opportunities for using this silicon-compatible ferroelectric to realize low-power logic circuits and high-density nonvolatile memories. The functional performances of ferroelectrics are intimately related to their dynamic responses to external stimuli such as electric fields at finite temperatures. Molecular dynamics is an ideal technique for investigating dynamical processes on large length and time scales, though its applications to new materials are often hindered by the limited availability and accuracy of classical force fields. Here we present a deep neural network–based interatomic force field of HfO 2 learned from ab initio data using a concurrent learning procedure. The model potential is able to predict structural properties such as elastic constants, equation of states, phonon dispersion relationships, and phase transition barriers of various hafnia polymorphs with accuracy comparable with density functional theory calculations. Here, the validity of this model potential is further confirmed by the reproduction of experimental sequences of temperature-driven ferroelectric-paraelectric phase transitions of HfO 2 with isobaric-isothermal ensemble molecular dynamics simulations. We suggest a general approach to extend the model potential of HfO 2 to related material systems including dopants and defects.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗