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At least 937 records · Page 52
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Bioinformatics and 3D Structural Analysis of the Coronavirus Main Protease Active Site Diversity

Coronaviruses (Coronaviridae) such as SARS‐CoV‐2 (severe acute respiratory syndrome coronavirus) and MERS‐CoV (Middle East respiratory syndrome coronavirus) have been the source of recent outbreaks and global health concerns. While vaccines have been essential for controlling the SARS‐CoV‐2 (COVID‐19) pandemic, it is uncertain whether they will be effective against future coronavirus strains. Therefore, identification or design of a broad‐spectrum drug that targets highly conserved regions of the main protease of multiple coronavirus strains is essential in the long term. As part of a virtual summer research experience with the RCSB PDB, bioinformatics tools were employed to predict and construct 3D models of the coronavirus main protease (MPro) using SARS‐CoV‐2 as the template, with a focus on mutational trends and active sites. This study focused on the active sites of MPro, a cysteine protease essential for viral assembly and replication. Sequence alignments and structure modeling of MPro structures has identified conserved regions across multiple coronavirus strains. Inhibition of MPro halts coronavirus replication, making it an ideal drug target, and studies of MPro may foster and accelerate the discovery of high affinity broad‐spectrum drugs.

Wu Wu, Amy↗
DOE OSTI2023

Structure of the Ndc80 complex and its interactions at the yeast kinetochore–microtubule interface

The conserved Ndc80 kinetochore complex, Ndc80c, is the principal link between mitotic spindle microtubules and centromere-associated proteins. We used AlphaFold 2 (AF2) to obtain predictions of the Ndc80 ‘loop’ structure and of the Ndc80 : Nuf2 globular head domains that interact with the Dam1 subunit of the heterodecameric DASH/Dam1 complex (Dam1c). The predictions guided design of crystallizable constructs, with structures close to the predicted ones. The Ndc80 ‘loop’ is a stiff, α-helical ‘switchback’ structure; AF2 predictions and positions of preferential cleavage sites indicate that flexibility within the long Ndc80c rod occurs instead at a hinge closer to the globular head. Conserved stretches of the Dam1 C terminus bind Ndc80c such that phosphorylation of Dam1 serine residues 257, 265 and 292 by the mitotic kinase Ipl1/Aurora B can release this contact during error correction of mis-attached kinetochores. We integrate the structural results presented here into our current molecular model of the kinetochore–microtubule interface. The model illustrates how multiple interactions between Ndc80c, DASH/Dam1c and the microtubule lattice stabilize kinetochore attachments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Extending evolutionary forecasts across bacterial species

Improving evolutionary forecasting requires progressing from studying repeated evolution of a single genotype under identical conditions to formulating broad principles. These principles should enable predictions of how similar species will adapt to similar selective pressures. Evolve-and-resequence experiments with multiple species allow testing forecasts on different biological levels and elucidating the causes for failed predictions. Here, we show that forecasts for adaptation to static culture conditions can be extended to multiple species by testing previous predictions for Pseudomonas syringae and Pseudomonas savastanoi. In addition to sequence divergence, these species differ in their repertoire of biofilm regulatory genes and structural components. Consistent with predictions, both species repeatedly produced biofilm mutants with a wrinkly spreader phenotype. Predominantly, mutations occurred in the wsp operon, with less frequent promoter mutations near uncharacterized diguanylate cyclases. However, mutational patterns differed on the gene level, which was explained by a lack of conservation in relative fitness of mutants between more divergent species. The same mutation was the most frequent for both species suggesting that conserved mutation hotspots can increase parallel evolution. This study shows that evolutionary forecasts can be extended across species, but that differences in the genotype–phenotype–fitness map and mutational biases limit predictability on a detailed molecular level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control

Rootless plants in the genus Wolffia are some of the fastest growing known plants on Earth. Wolffia have a reduced body plan, primarily multiplying through a budding type of asexual reproduction. Here, we generated draft reference genomes for Wolffia australiana (Benth.) Hartog & Plas, which has the smallest genome size in the genus at 357 Mb and has a reduced set of predicted protein-coding genes at about 15,000. Comparison between multiple high-quality draft genome sequences from W. australiana clones confirmed loss of several hundred genes that are highly conserved among flowering plants, including genes involved in root developmental and light signaling pathways. Wolffia has also lost most of the conserved nucleotide-binding leucine-rich repeat (NLR) genes that are known to be involved in innate immunity, as well as those involved in terpene biosynthesis, while having a significant overrepresentation of genes in the sphingolipid pathways that may signify an alternative defense system. Diurnal expression analysis revealed that only 13% of Wolffia genes are expressed in a time-of-day (TOD) fashion, which is less than the typical ~40% found in several model plants under the same condition. In contrast to the model plants Arabidopsis and rice, many of the pathways associated with multicellular and developmental processes are not under TOD control in W. australiana, where genes that cycle the conditions tested predominantly have carbon processing and chloroplast-related functions. The Wolffia genome and TOD expression data set thus provide insight into the interplay between a streamlined plant body plan and optimized growth.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Quantum Mpemba effect without global symmetries

The Mpemba effect, where a system initially farther from equilibrium relaxes faster than one closer to equilibrium, has been extensively studied in classical systems and recently explored in quantum settings. While previous studies of the quantum Mpemba effect (QME) have largely focused on isolated systems with global symmetries, we argue that the QME is ubiquitous in generic, nonintegrable many-body systems lacking such symmetries, including U(1) charge conservation, spatial symmetries, and even energy conservation. Using paradigmatic models such as the quantum Ising model with transverse and longitudinal fields, we show that the QME can be understood through the energy density of initial states and their inverse participation ratio in the energy eigenbasis. Our findings provide a unified framework for the QME, linking it with classical thermal relaxation.

Bhore, Tanmay [University of Leeds (United Kingdom↗
DOE OSTI2025

Measurement of the parity-violating asymmetry in the 𝑁 → Δ transition at low 𝑄 2

Here, we report the measurement of the parity-violating asymmetry in the 𝑁 → Δ transition via the 𝑒 − + 𝑝 → 𝑒 − + Δ + reaction at two different kinematic points with low four-momentum transfer 𝑄 2 . Measurements were made with incident electron beam energies of 0.877 and 1.16 GeV, corresponding to 𝑄 2 values of 0.0111 and 0.0208 (GeV/c) 2 , respectively. These measurements put constraints on a low-energy constant in the weak Lagrangian, 𝑑 Δ , corresponding to a parity-violating electric-dipole transition matrix element. This matrix element has been shown to be large in the strangeness-changing channel, via weak hyperon decays such as Σ + → 𝑝⁢𝛾. The measurements reported here constrain 𝑑 Δ in the strangeness-conserving channel. The final asymmetries were −0.65±1.00⁢(stat.)±1.02⁢(syst.) ppm (parts per million) for 0.877 GeV and −3.59±0.82⁢(stat.)±1.33⁢(syst.) ppm for 1.16 GeV. With these results we deduce a small value for 𝑑 Δ , consistent with zero, in the strangeness-conserving channel, in contrast to the large value for 𝑑 Δ previously reported in the strangeness-changing channel.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Nonmagnetic fractional conductance in high mobility InAs quantum point contacts

In this paper, we report the magnetoelectronic properties of high mobility InAs quantum point contacts grown on InP substrates. The InAs quantum well is embedded between In 0.72 ⁢Ga 0.28 ⁢As cladding layers and In 0.81 ⁢Al 0.19 ⁢As barrier layers, and is populated via self-accumulation. The one-dimensional (1D) conductance reaches a maximum value of 17 plateaus, quantized in units of 2⁢𝑒 2 /ℎ, where 𝑒 is the fundamental unit of charge and ℎ is Planck's constant. The in-plane effective 𝑔 factor was estimated to be −10.9 ± 1.5 for subband 𝑁 = 1 and −10.8 ± 1.6 for subband 𝑁 = 2. Furthermore, a study of the nonmagnetic fractional conductance states at 0.2 (𝑒 2 /ℎ) and 0.1 (𝑒 2 /ℎ) is provided. While their origin remains under discussion, evidence suggests that they arise from strong electron-electron interactions and momentum-conserving backscattering between electrons in two distinct channels within the 1D region. This phenomenon may also be interpreted as an entanglement between the two channel directions facilitated by momentum-conserving backscattering.

Ballistic transport↗
DOE OSTI2025

51 V NMR evidence for interlayer-modulated charge order and a first-order low-temperature transition in CsV 3 ⁢Sb 5

Charge order in the kagome superconductor CsV 3 ⁢Sb 5 exhibits a complex three-dimensional organization and intermediate-temperature anomalies whose bulk character has remained unsettled. We use orientation-dependent 51 V NMR as a site-selective probe to determine the stacking of the charge density wave (CDW) state and its thermal evolution. Below 𝑇 CDW ≈ 94K, the field-linear splitting of the 51 V central transition together with the anisotropy of the Knight shift tensor identify an interlayer-modulated 3⁢𝑞 CDW whose local environments are consistent with a four-layer 2 × 2 × 4 stacking with mixed trihexagonal/Star-of-David distortions, in agreement with synchrotron x-ray determinations. For comparison, RbV 3 ⁢Sb 5 serves as a reference exhibiting a uniform trihexagonal 2 × 2 × 2 stacking, allowing us to isolate features unique to the 2 × 2 × 4 state in CsV 3 ⁢Sb 5 . With 𝐻 0 ∥ 𝑐, the 51 V quadrupolar satellites through the intermediate temperature scale near 𝑇 CO ≈ 65K reorganize into two well-resolved electric-field-gradient manifolds that coexist over a finite interval; their relative spectral weights interchange on cooling while the total integrated satellite intensity remains conserved and 𝜈 𝑄 within each manifold is nearly temperature independent. The coexistence without critical broadening, together with conserved intensity, provides bulk evidence consistent with a first-order charge-order transition near 𝑇 CO . Our measurements do not resolve whether this lower-temperature transition corresponds to a distinct in-plane order or a reorganization of the 3⁢𝑞 state; rather, they delimit this window and provide bulk, site-resolved constraints that connect prior reported anomalies to a thermodynamic first-order transition.

Wang, Xiaoling [California State Univ., East Bay, ↗
DOE OSTI2026

Majorana Edge Modes in Isolated Wires

Topological superconductors are believed to host exotic quasiparticle excitations known as Majorana zero modes (MZMs), with much of the evidence based on BCS mean-field theory. The direct application of mean-field arguments is tenuous in finite, isolated systems relevant in some experiments. Here, we develop a new correlation-based method for identifying MZMs in interacting, number-conserving systems. Using the density matrix renormalization group, we study fermion number-conserving models with long-range interactions, which under periodic boundary conditions exhibit robust topological and nontopological superconductivity, tuned by the strength of interaction [Ortiz et al., Phys. Rev. Lett. 113, 267002 (2014)]. We find evidence that, on the topological side, Majorana edge modes appear in open chains, manifesting as the vanishing of the energy splitting between odd- and even-parity ground states with increasing system size. Additionally, off-diagonal two-point correlation functions show nonlocal, parity-dependent edge effects. These correlations reveal the spatial structure of Majorana modes in the many-body wave function. We show that the correlation diagnostic applies broadly, including to short-range interacting models, where topological superconductivity is more fragile due to the absence of a bulk excitation gap.

Thomas-Markarian, Jaden↗
DOE OSTI2025

Symmetry-Energy Dependence of the Bulk Viscosity of Nuclear Matter

We clarify how the weak-interaction-driven bulk viscosity ζ and the bulk relaxation time τ Π of neutrino-transparent n p e matter depend on the nuclear symmetry energy. We show that, at saturation density, the equation-of-state dependence of these transport quantities is fully determined by the experimentally constrained nuclear symmetry energy S and its slope L . Variations of L can change the bulk viscosity by orders of magnitude, which can affect both the dissipative and the conservative tidal response of neutron stars. Furthermore, this suggests that both conservative and dissipative effects encoded in the gravitational-wave signatures of binary neutron star inspirals may help constrain nuclear symmetry-energy properties.

Neutron stars & pulsars↗
DOE OSTI2025

Modeling the differential rate for signal interactions in coincidence with noise fluctuations or large rate backgrounds

The characteristic energy of a relic dark matter interaction with a detector scales strongly with the putative dark matter mass. Consequently, experimental search sensitivity at the lightest masses will always come from interactions whose size is similar to noise fluctuations and low energy backgrounds in the detector. In this paper, we correctly calculate the net change in measured differential event rate due to low rate signal interactions that overlap in time with noise and backgrounds, accounting for both periods of time when the signal is coincident with noise/backgrounds and for the decreased amount of time in which only noise/backgrounds occur and we show that the introduction of random simulated signal events into the continuous raw data stream (a form of “salting”) provides a correct and practical implementation to estimate this net linear signal sensitivity. Unfortunately this does not apply to the situation with non negligible pileups as we show through explicit examples. Consequently, this exclusion technique should be complemented by less sensitive techniques that can separately exclude large rate, high pileup signal parameter space. An analysis threshold above the Gaussian-like noise component of the measured differential rate spectrum should also likely produce conservative limits. Though previous light mass dark matter searches did not correctly account for decreased background only live time effects in their signal sensitivity, conservative analysis choices likely protected their published limits from being nonconservative.

Li, Xinran↗
DOE OSTI2023

Quantum dynamics of non-Hermitian many-body Landau-Zener systems

Here, we develop a framework to solve a large class of linearly driven non-Hermitian quantum systems. Such a class of models in the Hermitian scenario is commonly known as multistate Landau-Zener models. The non-Hermiticity is due to the anti-Hermitian couplings between the diabatic levels. We find that there exists a conservation law, unique to this class of models, that describes the simultaneous growth of the unnormalized wave functions. These models have practical applications in Bose-Einstein condensates, and they can describe the dynamics of multispecies bosonic systems. The conservation law relates to a pair-production mechanism that explains the dissociation of diatomic molecules into atoms. We provide a general framework for both solvable and semiclassically solvable non-Hermitian Landau-Zener models. Our findings will open alternative avenues for a number of diverse emergent phenomena in explicitly time-dependent non-Hermitian quantum systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Topological orders of monopoles and hedgehogs: From electronic and magnetic spin-orbit coupling to quarks

Topological states of matter are, generally, quantum liquids of conserved topological defects. We establish this by constructing and analyzing topological field theories which introduce gauge fields to describe the dynamics of singularities in the original field configurations. In this work, homotopy groups are utilized to identify topologically protected singularities, and the conservation of their protected number is captured by a topological action term that unambiguously obtains from the given set of symmetries. Stable phases of these theories include quantum liquids with emergent massless Abelian and non-Abelian gauge fields, as well as topological orders with long-range quantum entanglement, fractional excitations, boundary modes, and unconventional responses to external perturbations. This paper focuses on the derivation of topological field theories and basic phenomenological characterization of topological orders associated with homotopy groups π n (S n ), n ≥ 1 . These homotopies govern monopole and hedgehog topological defects in d = n + 1 dimensions, and enable the generalization of both weakly interacting and fractional quantum Hall liquids of vortices to d > 2 . Hedgehogs have not been in the spotlight so far, but they are particularly important defects of magnetic moments because they can be stimulated in realistic systems with spin-orbit coupling, such as chiral magnets and d = 3 topological materials. We predict topological orders in systems with U(1) × Spin(d) symmetry in which fractional electric charge attaches to hedgehogs. Monopoles, the analogous defects of charge or generic U(1) currents, may bind to hedgehogs via Zeeman effect, or effectively emerge in purely magnetic systems. The latter can lead to spin liquids with different topological orders than that of the resonant valence bond spin liquid. Charge fractionalization of quarks in atomic nuclei is also seen as possibly arising from the charge-hedgehog attachment.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Sound in a System of Chiral One-Dimensional Fermions

In this paper, we consider a system of one-dimensional fermions moving in one direction, such as electrons at the edge of a quantum Hall system. At sufficiently long timescales the system is brought to equilibrium by weak interactions between the particles, which conserve their total number, energy, and momentum. The time evolution of the system near equilibrium is described by hydrodynamics based on the three conservation laws. We find that the system supports three sound modes. In the low-temperature limit one mode is a pure oscillation of particle density, analogous to the ordinary sound. The other two modes involve oscillations of both particle and entropy densities. In the presence of disorder, the first sound mode is strongly damped at frequencies below the momentum relaxation rate, whereas the other two modes remain weakly damped.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Fracton-elasticity duality in twisted moiré superlattices

We formulate a fracton-elasticity duality for twisted moiré superlattices, taking into account that they are incommensurate crystals with dissipative phason dynamics. From a dual tensor-gauge formulation, as compared to standard crystals, we identify twice the number of conserved charges that describe topological lattice defects, namely, disclinations and another type of defects that we dub discompressions. Furthermore, the key implication of these conservation laws is that both glide and climb motions of lattice dislocations are suppressed, indicating that dislocation networks may become exceptionally stable. We also generalize our results to other planar incommensurate crystals and quasicrystals.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Dipolar Bose-Hubbard model

We study a simple model of interacting bosons on a d-dimensional cubic lattice whose dynamics conserves both total boson number and total boson dipole moment. This model provides a simple framework in which several remarkable consequences of dipole conservation can be explored. As a function of chemical potential and hopping strength, the model can be tuned between gapped Mott insulating phases and various types of gapless condensates. The condensed phase realized at large hopping strengths, which we dub a Bose-Einstein insulator, is particularly interesting: despite having a Bose condensate, it is insulating, and despite being an insulator, it is compressible.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Unraveling higher-order contributions to spin excitations probed using resonant inelastic x-ray scattering

Resonant inelastic x-ray scattering (RIXS) is an evolving tool for investigating the spin dynamics of strongly correlated materials, which complements inelastic neutron scattering. In isotropic spin-$\frac{1}{2}$ Heisenberg antiferromagnetic (HAFM) spin chains, both techniques have observed non-spin-conserving (NSC) excitations confined to the two-spinon phase space. However, a recent O K-edge RIXS study of the one-dimensional HAFM Sr 2 CuO 3 observed spin-conserving (SC) four-spinon excitations outside the two-spinon phase space. Here, we demonstrate that analogous four-spinon excitations can also be accessed at the Cu L 3 edge in the related material SrCuO 2 . Through detailed modeling, we establish that these excitations appear in both the SC and NSC channels of the Cu L 3 edge, and are only captured by higher-order terms in the ultrashort core-hole lifetime expansion. Finally, since these terms encode information about spin-spin correlations extending beyond nearest neighbors, our results offer different possibilities for studying nonlocal spin correlations in quantum magnets.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Open-system spin transport and operator weight dissipation in spin chains

Here, we use nonequilibrium steady states to study the effect of dissipation-assisted operator evolution (DAOE) on the scaling behavior of transport in one-dimensional spin chains. We consider three models in the XXZ family: the XXZ model with staggered anisotropy, which is chaotic; XXZ model with no external field and tunable interaction, which is Bethe-ansatz integrable and (in the zero interaction limit) free-fermion integrable; and the disordered XY model, which is free-fermion integrable and Anderson localized. We find evidence that DAOE's effect on transport is controlled by its effect on the system's conserved quantities. To the extent that DAOE preserves those symmetries, it preserves the scaling of the system's transport properties; to the extent it breaks those conserved quantities, it pushes the system towards diffusive scaling of transport.

1-dimensional spin chains↗