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At least 667 records · Page 37

Single-molecule investigations of single-chain cellulose biosynthesis

Cellulose biosynthesis in sessile bacterial colonies originates in the membrane-integrated bacterial cellulose synthase (Bcs) AB complex. We utilize optical tweezers to measure single-strand cellulose biosynthesis by BcsAB from Rhodobacter sphaeroides . Synthesis depends on uridine diphosphate glucose, Mg 2+ , and cyclic diguanosine monophosphate, with the last displaying a retention time of ∼80 min. Below a stall force of 12.7 pN, biosynthesis is relatively insensitive to force and proceeds at a rate of one glucose addition every 2.5 s at room temperature, increasing to two additions per second at 37°. At low forces, conformational hopping is observed. Single-strand cellulose stretching unveiled a persistence length of 6.2 nm, an axial stiffness of 40.7 pN, and an ability for complexes to maintain a tight grip, with forces nearing 100 pN. Stretching experiments exhibited hysteresis, suggesting that cellulose microstructure underpinning robust biofilms begins to form during synthesis. Cellohexaose spontaneously binds to nascent single cellulose strands, impacting polymer mechanical properties and increasing BcsAB activity.

59 BASIC BIOLOGICAL SCIENCES↗

Deuterium retention in Be-D co-deposits formed over an ITER relevant parameter space

Be-D co-deposit samples are produced over an extended range of plasma-material interaction parameters reflective of the conditions expected in ITER deposition dominant locations. Deposition temperature, D impact energy, atomic Be deposition rate, and D2 neutral pressure were varied in the ranges 373–623 K, ~2–100 eV, 1–10 × 10 19 m 2 s –1 , and 0.27–13.3 Pa respectively. Thermal desorption spectrometry was carried out on samples, subsequently, to measure the D release profile and retention. In this work, it was found that the D retention in samples agrees well with the existing GDT D/Be scaling over the extended parameter space, and that increased D impact energy and D2 pressure can lead to the observation of a sharp low-temperature release peak at ~440 K in desorption data. Desorption data without the presence of the sharp release mechanism are modeled with TMAP-7 utilizing three traps of de-trapping energies, 0.8, 0.9 and 1.0 eV.

36 MATERIALS SCIENCE↗

Investigation of two-dimensional radio-frequency sheath properties using a microscale fluid model

Abstract In previous work (Kohno and Myra 2023 Comput. Phys. Commun. 291 108841), we developed a numerical scheme based on a two-dimensional microscale radio-frequency (RF) sheath model with periodically curved wall boundaries. Here, we expand the capability of this scheme through modification of the boundary conditions (BCs) on the conducting walls, which allows the ion flow to turn back to the plasma at locations on the walls where the electromagnetic force on the ions is reversed from its usual direction. Numerical simulations are carried out to investigate the dependences of the surface-integrated admittances on the wall bump height, ion magnetization, ion mobility, and the magnetic field angle, and to visualize the sheath structures in several cases. One of the main results is the ion cyclotron admittance resonance observed under the condition of low ion mobility (high normalized frequency). It is shown that the amplitude of the resonance peak depends on the wall bump height and the ion velocity is reversed on the sides of the bump in an RF cycle for the resonance cases. Furthermore, the differences in the admittances between the one- and two-dimensional microscale models are assessed for the purpose of understanding non-locality of the sheath near the wall surface for the parameters considered in this study. This information will be essential for improving the sheath BC for macroscale calculations in the future.

Kohno, H. (ORCID:0000000332690010)↗

The matrix product approximation for the dynamic cavity method

Stochastic dynamics of classical degrees of freedom, defined on vertices of locally tree-like graphs, can be studied in the framework of the dynamic cavity method which is exact for tree graphs. Such models correspond for example to spin-glass systems, Boolean networks, neural networks, and other technical, biological, and social networks. The central objects in the cavity method are edge messages—conditional probabilities of two vertex variable trajectories. In this paper, we discuss a rather pedagogical derivation for the dynamic cavity method, give a detailed account of the novel matrix product edge message (MPEM) algorithm for the solution of the dynamic cavity equation as introduced, and present optimizations and extensions. Matrix product approximations of the edge messages are constructed recursively in an iteration over time. Computation costs and precision can be tuned by controlling the matrix dimensions of the MPEM in truncations. Without truncations, the dynamics is exact. Data for Glauber–Ising dynamics shows a linear growth of computation costs in time. In contrast to Monte Carlo simulations, the approach has a much better error scaling. Hence, it gives for example access to low probability events and decaying observables like temporal correlations. Here, we discuss optimized truncation schemes and an extension that allows to capture models which have a continuum time limit.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Kiloparsec-scale AGN outflows and feedback in merger-free galaxies

ABSTRACT Recent observations and simulations have challenged the long-held paradigm that mergers are the dominant mechanism driving the growth of both galaxies and supermassive black holes (SMBH), in favour of non-merger (secular) processes. In this pilot study of merger-free SMBH and galaxy growth, we use Keck Cosmic Web Imager spectral observations to examine four low-redshift (0.043 < z < 0.073) disc-dominated ‘bulgeless’ galaxies hosting luminous active galactic nucleus (AGN), assumed to be merger-free. We detect blueshifted broadened [O iii] emission from outflows in all four sources, which the $\mathrm{[O\, \small {III}]}$/$\rm {H}\beta$ ratios reveal are ionized by the AGN. We calculate outflow rates in the range $0.12{-}0.7~\rm {M}_{\odot }~\rm {yr}^{-1}$, with velocities of $675{-}1710~\rm {km}~\rm {s}^{-1}$, large radial extents of $0.6{-}2.4~\rm {kpc}$, and SMBH accretion rates of $0.02{-}0.07~\rm {M}_{\odot }~\rm {yr}^{-1}$. We find that the outflow rates, kinematics, and energy injection rates are typical of the wider population of low-redshift AGN, and have velocities exceeding the galaxy escape velocity by a factor of ∼30, suggesting that these outflows will have a substantial impact through AGN feedback. Therefore, if both merger-driven and non-merger-driven SMBH growth lead to co-evolution, this suggests that co-evolution is regulated by feedback in both scenarios. Simulations find that bars and spiral arms can drive inflows to galactic centers at rates an order of magnitude larger than the combined SMBH accretion and outflow rates of our four targets. This work therefore provides further evidence that non-merger processes are sufficient to fuel SMBH growth and AGN outflows in disc galaxies.

Smethurst, R. J. (ORCID:0000000164177196)↗

Dynamic properties of a polaron coupled to dispersive optical phonons

We study static and dynamic properties of an electron coupled to dispersive quantum optical phonons in the framework of the Holstein model defined on a one-dimensional lattice. Calculations are performed using the Lanczos algorithm based on a highly efficient construction of the variational Hilbert space. Even small phonon dispersion has a profound effect on the low-energy optical response. While the upward phonon dispersion broadens the optical spectra due to single-phonon excitations, the downward dispersion has the opposite effect. With increasing dispersion, a multiphonon excitation (MPE) state becomes the lowest excited state of the system at zero momentum and determines the low-frequency response of the optical conductivity where the threshold for optical absorption moves below the single-phonon frequency. Multiphonon states form a well-defined bandlike feature just above the polaron band as clearly seen in the electron spectral function. Low-energy MPEs should be observable in systems with strong optical phonon dispersion in optical as well as angle-resolved photoemission experiments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Magnetic structure and magnetoelectric properties of the spin-flop phase in LiFePO 4

We investigate the magnetic structure and magnetoelectric(ME) effect in the high-field phase of the antiferromagnet LiFePO 4 above the critical field of 31 T. A neutron diffraction study in pulsed magnetic fields reveals the propagation vector to be q = 0 for the high-field magnetic structure. Pulsed-field electric polarization measurements show that, at the critical field, the low-field off-diagonal ME coupling α ab is partially suppressed, and the diagonal element α bb emerges. These results are consistent with a spin-flop transition where the spin direction changes from primarily being along the easy b axis below the transition to being along a above. The persistence of off-diagonal ME tensor elements above the critical field suggests a lowering of the magnetic point-group symmetry and hence a more complex magnetic structure in the high-field phase. In addition, neutron diffraction measurements in low magnetic fields show no observable field-induced spin canting, which indicates a negligible Dzyaloshinskii-Moriya interaction. The observed spin-flop field supports the Hamiltonian recently deduced from inelastic neutron studies and indicates that the system is less frustrated and with a larger single-ion anisotropy than originally thought. Our results demonstrate the effectiveness of combining pulsed-field neutron diffraction and electric polarization measurements to elucidate the magnetic structures and symmetries at the highest attainable field strengths.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

High-field/high-frequency electron spin resonances of Fe-doped β − Ga 2 O 3 by terahertz generalized ellipsometry: Monoclinic symmetry effects

We demonstrate detection and measurement of electron paramagnetic spin resonances (EPR) of iron defects in β − Ga 2 O 3 utilizing generalized ellipsometry at frequencies between 110 and 170 GHz. The experiments are performed on an Fe-doped single crystal in a free-beam configuration in reflection at 45 ∘ and magnetic fields between 3 and 7 T. In contrast with low-field, low-frequency EPR measurements, we observe all five transitions of the s = 5 / 2 high-spin state Fe 3 + simultaneously. We confirm that ferric Fe 3 + is predominantly found at octahedrally coordinated Ga sites. We obtain the full set of fourth-order monoclinic zero-field splitting parameters for both octahedrally and tetrahedrally coordinated sites by employing measurements at multiple sample azimuth rotations. The capability of high-field EPR allows us to demonstrate that simplified second-order orthorhombic spin Hamiltonians are insufficient, and fourth-order terms as well as consideration of the monoclinic symmetry are needed. These findings are supported by computational approaches based on density-functional theory for second-order and on ligand-field theory for fourth-order parameters of the spin Hamiltonian. Terahertz ellipsometry is a way to measure spin resonances in a cavity-free setup. Its possibility of varying the probe frequency arbitrarily without otherwise changing the experimental setup offers unique means of truly disentangling different components of highly anisotropic spin Hamiltonians. Published by the American Physical Society 2024

Materials Science↗

Electronic structure of the honeycomb iridate Cu 2 ⁢IrO 3 at high pressure

Cu 2 IrO 3 has attracted recent interest due to its proximity to the Kitaev quantum spin liquid state and the complex structural response observed at high pressures. We use x-ray spectroscopy and scattering as well as electrical transport techniques to unveil the electronic structure of Cu 2 IrO 3 at ambient and high pressures. Despite featuring a Ir 4+ J eff = 1/2 state at ambient pressure, Ir L 3 -edge resonant inelastic x-ray scattering reveals broadened electronic excitations that point to the importance of Ir 5d-Cu 3d interaction. High pressure first drives an Ir-Ir dimer state with collapsed < L · S > and < L z >/< S z >, signaling the formation of 5d molecular orbitals. A novel Cu → Ir charge transfer is observed above 30 GPa at low temperatures, leading to an approximate Ir 3+ and Cu 1.5+ valence, with persistent insulating electrical transport seemingly driven by charge segregation of Cu 1+ /Cu 2+ ions into distinct sites. Concomitant x-ray spectroscopy and diffraction measurements through different thermodynamic paths demonstrate a strong electron-lattice coupling, with J eff = 1/2 and Ir 3+ /Cu 1.5+ electronic states occurring only in phases 1 and 5, respectively. Remarkably, the charge-transfer state can only be reached if Cu 2 IrO 3 is pressurized at low temperature, suggesting that phonons play an important role in the inhibiting this phase. Furthermore, these results point to the choice of thermodynamic path across interplanar collapse transition as a key parameter to access novel states in intercalated iridates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Extended Interacting Boson Model with Configuration Mixing Description For 98 Mo

An extended version of the interacting boson model (IBM), encompassing two-particle–two-hole (2p-2h) excitations originating from below a valence shell and one-particle–one-hole (1p-1h) excitations extending to the upper next-nearest major shell, is developed to investigate cross-shell excitation effects in the transitional nucleus 98 Mo. This extended IBM framework is utilized to reproduce experimentally observed properties such as low-lying positive-parity level energies, 𝐵⁡(𝐸⁢2) values, and the electric quadrupole moment of the 2$^{+}_{1}$ state, 𝜌 2 ⁡(𝐸⁢0, 0$^{+}_{2}$ → 0$^{+}_{g}$), as well as the strength functions of the isoscalar giant monopole resonance (ISGMR) and the isoscalar giant quadrupole resonance (ISGQR) in 98 Mo. It is shown that the extended consistent-𝑄 IBM, incorporating configuration mixing of both 2p-2h excitations from below the valence shell and 1p-1h excitations to the upper next-nearest major shell, describes the low-lying structural properties and the ISGMR and ISGQR strength distributions of 98 Mo quite well, with the ISGMR and the ISGQR strength distributions comparable to the results of the self-consistent quasiparticle random-phase approximation with Skyrme interactions.

90 ≤ A ≤ 149↗

Light new physics in XENON1T

We examine the recently-reported low-energy electron recoil spectrum observed at the XENON1T underground dark matter direct detection experiment, in the context of new interactions with solar neutrinos. In particular we show that scalar and vector mediators with masses $\lesssim 50$ keV coupled to leptons could already leave a visible signature in the XENON1T experiment, similar to the observed peak below 7 keV. This signals that dark matter detectors are already competing with neutrino scattering experiments such as GEMMA, CHARM-II and Borexino. If these results from XENON1T are interpreted as a new signal of such physics, the parameters which fit the excess face challenges from astrophysics which seem very difficult to overcome. If they are rather viewed as a constraint on new couplings, they herald the start of an era of novel precise probes of physics beyond the standard model with dark matter detectors.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Demonstration of new MeV-scale capabilities in large neutrino LArTPCs using ambient radiogenic and cosmogenic activity in MicroBooNE

Large neutrino liquid argon time projection chamber (LArTPC) experiments can broaden their physics reach by reconstructing and interpreting MeV-scale energy depositions, or blips, present in their data. We demonstrate new calorimetric and particle discrimination capabilities at the MeV energy scale using reconstructed blips in data from the MicroBooNE LArTPC at Fermilab. We observe a concentration of low-energy (<3 MeV) blips around fiberglass mechanical support struts along the time projection chamber edges with energy spectrum features consistent with the Compton edge of 2.614 MeV 208 Tl decay 𝛾 rays. These features are used to verify proper calibration of electron energy scales in MicroBooNE’s data to few percent precision and to measure the specific activity of 208 Tl in the fiberglass composing these struts, (11.7 ± 0.2⁢(stat) ± 3.1⁢(syst)) Bq/kg. Cosmogenically produced blips above 3 MeV in reconstructed energy are used to showcase the ability of large LArTPCs to distinguish between low-energy proton and electron energy depositions. An enriched sample of low-energy protons selected using this new particle discrimination technique is found to be smaller in data than in dedicated corsika cosmic-ray simulations, suggesting either incorrect corsika modeling of incident cosmic fluxes or particle transport modeling issues in geant4.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Tuning the critical Li intercalation concentrations for MoX 2 (X = S, Se, or Te) bilayer phase transitions

Transition metal dichalcogenides (TMDs), such as MoS 2 , are known to undergo a structural phase transformation as well as a change in the electronic conductivity upon Li intercalation. These properties make them candidates for charge-tunable ion-insertion materials that could be used in electro-chemical devices. In this work we study the phase stability and electronic structure of H and T’ Li-intercalated MoX 2 bilayers with X=S, Se, or Te. Here, using first-principles calculations in combination with classical and machine learning modeling approaches, we find that the H phase is more stable at low Li concentration for all X, and the critical Li concentration at which the T’→H transition occurs decreases with increasing mass of X. Furthermore the relative free energy of the two phases becomes less sensitive to Li insertion with increasing atomic mass of the chalcogen atom X. While the electronic conductivity increases with increasing ion concentration at low concentrations, we do not observe a (positive) conductivity jump at the phase transition from H to T’.

36 MATERIALS SCIENCE↗

Upland forest retreat lags behind sea‐level rise in the mid‐Atlantic coast

Abstract Ghost forests consisting of dead trees adjacent to marshes are striking indicators of climate change, and marsh migration into retreating coastal forests is a primary mechanism for marsh survival in the face of global sea‐level rise. Models of coastal transgression typically assume inundation of a static topography and instantaneous conversion of forest to marsh with rising seas. In contrast, here we use four decades of satellite observations to show that many low‐elevation forests along the US mid‐Atlantic coast have survived despite undergoing relative sea‐level rise rates (RSLRR) that are among the fastest on Earth. Lateral forest retreat rates were strongly mediated by topography and seawater salinity, but not directly explained by spatial variability in RSLRR, climate, or disturbance. The elevation of coastal tree lines shifted upslope at rates correlated with, but far less than, contemporary RSLRR. Together, these findings suggest a multi‐decadal lag between RSLRR and land conversion that implies coastal ecosystem resistance. Predictions based on instantaneous conversion of uplands to wetlands may therefore overestimate future land conversion in ways that challenge the timing of greenhouse gas fluxes and marsh creation, but also imply that the full effects of historical sea‐level rise have yet to be realized.

Biodiversity & Conservation↗

Development and evaluation of a Novel RT‐PCR system for reliable and rapid SARS‐CoV ‐2 screening of blood donations

Abstract Background The ongoing outbreak of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has caused great global concerns. In contrast to SARS, some SARS‐CoV‐2–infected people can be asymptomatic or have only mild nonspecific symptoms. Furthermore, there is evidence that SARS‐CoV‐2 may be infectious during an asymptomatic incubation period. With the discovery that SARS‐CoV‐2 can be detected in plasma or serum, blood safety is worthy of consideration. Study Design and Methods We developed a nucleic acid test (NAT) screening system for SARS‐CoV‐2 targeting nucleocapsid protein (N) and open reading frame 1ab (ORF 1ab) gene that could screen 5076 samples every 24 hours. The 2019 novel coronavirus RNA standard was used to evaluate linearity of standard curves. Diagnostic sensitivity and reproducibility were evaluated using artificial SARS‐CoV‐2. Specificity was evaluated with 61 other respiratory pathogens. Diagnostic performance was evaluated by testing two sputum and nine oropharyngeal swab specimens. The reverse transcription polymerase chain reaction (RT‐PCR) assay was used to screen SARS‐CoV‐2 RNA in blood donor specimens collected during the outbreak of SARS‐CoV‐2 in Chengdu. Results Limits of detection of the SARS‐CoV‐2 RT‐PCR assay for N and ORF 1ab gene were 12.5 and 27.58 copies/mL, respectively. Intra‐assay and interassay for the SARS‐CoV‐2 RT‐PCR assay based on cycle threshold were acceptably low. No cross‐reactivity was observed with other respiratory virus and bacterial isolates. The overall agreement value between the SARS‐CoV‐2 RT‐PCR assay and clinical diagnostic results was 100%. A total of 16 287 blood specimens collected from blood donors during SARS‐CoV‐2 surveillance were tested negative. Conclusions A high‐throughput NAT screening system was developed for SARS‐CoV‐2 screening of blood donations during the outbreak of SARS‐CoV‐2.

Li, Meng↗

Reversible structural transformations in supercooled liquid water from 135 to 245 K

Water has many anomalous properties compared to “simple” liquids, and these anomalies are typically enhanced in supercooled water.1-3 While numerous models have been proposed, including the liquid-liquid critical point,4,5 the singularity-free scenario,6 and the stability limit conjecture,1 a molecular-level understanding remains elusive. The main difficulty in determining which, if any, of these models is correct is the limited amount of data in the relevant temperature and pressure ranges. For water at ambient pressures, which is the focus of this work, data is largely missing from 160 – 232 K (“No Man’s Land”) due to rapid crystallization.2,3 Whether rapid crystallization is just an experimental obstacle, or a fundamental problem signaling the inability of water to thermally equilibrate prior to crystallization is also a major unanswered question.5,7 Here, we investigate the structural transformations of transiently-heated, supercooled water with nanosecond time resolution using infrared vibrational spectroscopy. The experiments demonstrate three key results. First, water’s structure relaxes from its initial configuration to a “steady-state” configuration prior to the onset of crystallization over a wide temperature range. Second, water’s steady-state structure can be reproduced by a linear combination of two, temperature-independent structures that correspond to a “high-temperature liquid” and a “low-temperature liquid.” Third, the observed structural changes are reversible over the full temperature range. Taken together, these results show that supercooled water can equilibrate prior to crystallization for temperatures from the homogeneous nucleation temperature, TH ~232 K,3 down to the glass transition temperature (Tg ~ 136 K). Second, the results provide support for the hypothesis that supercooled water can be described as a mixture of two, structurally-distinct, interconvertible liquids from 135 K to 245 K.5,8-18

Kringle, Loni M.↗

In Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13 C and 2 H Tracers

Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are thermophilic anaerobic bacteria with complementary metabolic capabilities that utilize distinct glycolytic pathways for the conversion of cellulosic sugars to biofuels. We integrated quantitative metabolomics with 2 H and 13 C metabolic flux analysis to investigate the in vivo reversibility and thermodynamics of the central metabolic networks of these two microbes. We found that the glycolytic pathway in C. thermocellum operates remarkably close to thermodynamic equilibrium, with an overall drop in Gibbs free energy 5-fold lower than that of T. saccharolyticum or anaerobically grown Escherichia coli . The limited thermodynamic driving force of glycolysis in C. thermocellum could be attributed in large part to the small free energy of the phosphofructokinase reaction producing fructose bisphosphate. The ethanol fermentation pathway was also substantially more reversible in C. thermocellummthan in T. saccharolyticum. These observations help explain the comparatively low ethanol titers of C. thermocellum and suggest engineering interventions that can be used to increase its ethanol productivity and glycolytic rate. In addition to thermodynamic analysis, we used our isotope tracer data to reconstruct the T. saccharolyticum central metabolic network, revealing exclusive use of the Embden-Meyerhof-Parnas (EMP) pathway for glycolysis, a bifurcated tricarboxylic acid (TCA) cycle, and a sedoheptulose bisphosphate bypass active within the pentose phosphate pathway. Thermodynamics constitutes a key determinant of flux and enzyme efficiency in metabolic networks. Here, we provide new insights into the divergent thermodynamics of the glycolytic pathways of C. thermocellum and T. saccharolyticum, two industrially relevant thermophilic bacteria whose metabolism still is not well understood. We report that while the glycolytic pathway in T. saccharolyticum is as thermodynamically favorable as that found in model organisms, such as E. coli or Saccharomyces cerevisiae , the glycolytic pathway of C. thermocellum operates near equilibrium. The use of a near-equilibrium glycolytic pathway, with potentially increased ATP yield, by this cellulolytic microbe may represent an evolutionary adaptation to growth on cellulose, but it has the drawback of being highly susceptible to product feedback inhibition. The results of this study will facilitate future engineering of high-performance strains capable of transforming cellulosic biomass to biofuels at high yields and titers.

59 BASIC BIOLOGICAL SCIENCES↗

Online MCMC Thinning with Kernelized Stein Discrepancy

A fundamental challenge in Bayesian inference is efficient representation of a target distribution. Many nonparametric approaches do so by sampling a large number of points using variants of Markov chain Monte Carlo (MCMC). Here, we propose an MCMC variant that retains only those posterior samples which exceed a kernelized Stein discrepancy (KSD) threshold, which we call KSD thinning. We establish the convergence and complexity trade-offs for several settings of KSD thinning as a function of the KSD threshold parameter, sample size, and other problem parameters. We provide experimental comparisons against other online nonparametric Bayesian methods that generate low-complexity posterior representations. We observe superior consistency/complexity trade-offs across a range of settings including MCMC sampling on two Bayesian inference problems from the biological sciences, and 10 × inference speedup and storage reduction for Bayesian neural networks with no loss of accuracy and no increase in training time. Our code is available at https://github.com/colehawkins/KSD-Thinning.

Bayesian inference↗