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At least 703 records · Page 39

DXO/Rai1 enzymes remove 5′-end FAD and dephospho-CoA caps on RNAs

Abstract In eukaryotes, the DXO/Rai1 enzymes can eliminate most of the incomplete and non-canonical NAD caps through their decapping, deNADding and pyrophosphohydrolase activities. Here, we report that these enzymes can also remove FAD and dephospho-CoA (dpCoA) non-canonical caps from RNA, and we have named these activities deFADding and deCoAping. The crystal structures of mammalian DXO with 3′-FADP or CoA and fission yeast Rai1 with 3′-FADP provide elegant insight to these activities. FAD and CoA are accommodated in the DXO/Rai1 active site by adopting folded conformations. The flavin of FAD and the pantetheine group of CoA contact the same region at the bottom of the active site tunnel, which undergoes conformational changes to accommodate the different cap moieties. We have developed FAD-capQ to detect and quantify FAD-capped RNAs and determined that FAD caps are present on short RNAs (with less than ∼200 nucleotides) in human cells and that these RNAs are stabilized in the absence of DXO.

59 BASIC BIOLOGICAL SCIENCES↗

Bolometric Superconducting Optical Nanoscopy (BOSON)

Superconducting transition-edge sensors are renowned for their extraordinary photon sensitivity and energy resolution, finding applications spanning quantum information, astronomy, and nanophotonics. Here, we report the development of bolometric superconducting optical nanoscopy (BOSON), a novel platform that integrates bolometric detection at the superconducting transition edges with near-field optical techniques. BOSON enables the mapping of photoinduced changes in superconductivity with unprecedented spatial resolution and photon sensitivity. By incorporating BOSON with low-dimensional materials, we achieved polariton imaging at nanowatt excitation levels—at least 4 orders of magnitude lower than the power typically required in prior near-field nanoscopy experiments. Our findings highlight the potential for BOSON to advance scanning-probe-based optical platforms to enable the detection of photons, polaritons, and Cooper pair dynamics at the nanoscale. This paves the way for quantum sensing applications using single-polariton detection and can offer deeper insights into quasiparticle dynamics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Excitons and trions in monolayer semiconductors with correlated electrons

We revisit low-temperature optical spectra of transition-metal dichalcogenide monolayers and point to a possible crystallization of electrons (or holes) at low to moderate charge densities. To calculate the excitonic spectra under such conditions, we introduce the recursion method and compute how the charge density affects the energies, linewidths, and oscillator strengths of exciton and trion complexes. Equally important, we study how excitons and trions in the monolayer evolve when the charge particles gradually transition to a periodic Wigner lattice. The results provide valuable information on the ability to detect whether the particles are ordered through the exciton spectrum. Finally, we calculate the change in exciton energy in cases where the added charge particles have similar and dissimilar quantum numbers (spin and valley) to those of the electron or hole in the exciton. Here, the results of this work shed new light on the important optical properties of monolayer semiconductors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Steady-State Ultrasonic Non-Destructive Evaluation for Aerospace & Additive Manufacturing Applications [Slides]

How does ultrasonic inspection work? Rich phenomenology of interactions between ultrasonic waves and features in plate-like structures. Hidden defects/discontinuities create measurable changes in the surface wavefield. Based on these measurements, we can build tools that detect the presence of different kinds of defects and estimate structural/material properties (e.g. local thickness).

42 ENGINEERING↗

High-dimensional Data-driven Energy optimization for Multi-Modal Transit Agencies (HD-EMMA) (Final Technical Report)

Public bus transit services in the U.S. are responsible for at least 19.7 million metric tons of CO 2 emission annually. Electric vehicles (EVs) can have a much lower environmental impact than comparable internal combustion engine vehicles (ICEVs), especially in urban areas. Unfortunately, EVs are also much more expensive than ICEVs. As a result, many public transit agencies can afford only mixed fleets of transit vehicles, consisting of EVs, hybrids (HEVs), and ICEVs. Transit agencies that operate such mixed fleets of vehicles face a challenging optimization problem: these agencies need to decide which vehicles are assigned to serving which transit trips. Since the advantage of EVs over ICEVs varies depending on the route and time of day (e.g., the benefit of EVs is higher in slower traffic with frequent stops and lower on highways), the assignment can have a significant effect on energy use and, hence, environmental impact. Through this project, we have developed reference data about energy collections and constructed a set of machine learning models that can accurately predict the energy consumption for the whole fleet at the level of each trip. We have used these models to develop a scheduling and assignment strategy that can rotate the different vehicle types across the transit agencies’ routes. The optimization algorithm ensures that the vehicles are matched to trips considering weather patterns, expected congestion, and road gradients to minimize the overall energy usage. We list the key observations from our project for other practitioners below. Details are available in the report, and the list of source code and our publications are included in the appendix. 1. We have demonstrated the feasibility of collecting, merging and analyzing large volumes of high-resolution real-world telemetry data from a mixed vehicle fleet. To mitigate the inherent noise of the recorded GPS points, the team developed an algorithm that filters data and maps the points onto a street. The algorithm considers previous and subsequent location measurements and different characteristics of nearby streets to determine how likely the vehicle travels on them. Then, the team segmented the time series into disjoint contiguous samples based on adjacent road segments and repeated the outlier detection and removal. For each data point, the team added features corresponding to elevation changes within the samples, weather features, such as temperature, and traffic data, such as speed ratio between actual speed and free-flow speed. 2. We have developed two forms of machine learning models that be used to understand and analyze the energy operations of a mixed vehicle transit fleet. The micro prediction model provides estimates of instantaneous energy prediction for all types of buses (diesel, hybrid, and electric). Such a model is important in evaluating the energy impacts of real-time bus operation strategies, but it is challenging due to diversified driving cycles of transit buses. The model can help the drivers understand the impact of their driving behaviors and short-term congestions. The macro prediction models estimate average energy consumption across the whole trip considering the features: distance traveled, various road-type features, elevation change, day of the week, time of day, various weather features (temperature, humidity, etc.), and traffic features (speed ratio and jam factor). 3. We have demonstrated that it is possible to transfer the machine learning models we have developed in this project to other teams and cities by using inductive transfer learning. We also showed that the performance of the macro energy prediction models can be improved using a multi-task learning approach where the learning parameters are shared between the models being developed for different vehicle types. The advantage of this approach is improved learning performance as the models can exploit common spatio-temporal and environmental characteristics. 4. Finally, we have developed trip and vehicle assignment and scheduling algorithms that use the energy prediction models and develop a trip to vehicle type (diesel, electric, hybrid) assignment for the whole operation to reduce overall emissions and cost. We have shown through simulations that the proposed algorithms can save $\$$ 48,910 in energy costs and 175 metric tons of CO 2 emission annually for CARTA.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

ARES I: WASP-76 b, A Tale of Two HST Spectra

We analyze the transmission and emission spectra of the ultra-hot Jupiter WASP-76 b, observed with the G141 grism of the Hubble Space Telescope’s (HST) Wide Field Camera 3 (WFC3). We reduce and fit the raw data for each observation using the open-source software Iraclis before performing a fully Bayesian retrieval using the publicly available analysis suite TauREx 3. Previous studies of the WFC3 transmission spectra of WASP-76 b found hints of titanium oxide (TiO) and vanadium oxide (VO) or non-gray clouds. Accounting for a fainter stellar companion to WASP-76, we reanalyze this data and show that removing the effects of this background star changes the slope of the spectrum, resulting in these visible absorbers no longer being detected, eliminating the need for a non-gray cloud model to adequately fit the data but maintaining the strong water feature previously seen. However, our analysis of the emission spectrum suggests the presence of TiO and an atmospheric thermal inversion, along with a significant amount of water. Given the brightness of the host star and the size of the atmospheric features, WASP-76 b is an excellent target for further characterization with HST, or with future facilities, to better understand the nature of its atmosphere, to confirm the presence of TiO and to search for other optical absorbers.

79 ASTRONOMY AND ASTROPHYSICS↗

Spin Change of Asteroid 2012 TC4 Probably by Radiation Torques

Asteroid 2012 TC4 is a small (∼10 m) near-Earth object that was observed during its Earth close approaches in 2012 and 2017. Earlier analyses of light curves revealed its excited rotation state. We collected all available photometric data from the two apparitions to reconstruct its rotation state and convex shape model. We show that light curves from 2012 and 2017 cannot be fitted with a single set of model parameters; the rotation and precession periods are significantly different for these two data sets, and they must have changed between or during the two apparitions. Nevertheless, we could fit all light curves with a dynamically self-consistent model assuming that the spin states of 2012 TC4 in 2012 and 2017 were different. To interpret our results, we developed a numerical model of its spin evolution in which we included two potentially relevant perturbations: (i) gravitational torque due to the Sun and Earth and (ii) radiation torque, known as the Yarkovsky–O’Keefe–Radzievskii–Paddack (YORP) effect. Despite our model simplicity, we found that the role of gravitational torques is negligible. Instead, we argue that the observed change of its spin state may be plausibly explained as a result of the YORP torque. To strengthen this interpretation, we verify that (i) the internal energy dissipation due to material inelasticity and (ii) an impact with a sufficiently large interplanetary particle are both highly unlikely causes of its observed spin state change. If true, this is the first case where the YORP effect has been detected for a tumbling body.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A Gaussian Process Regression Reveals No Evidence for Planets Orbiting Kapteyn’s Star

Radial–velocity (RV) planet searches are often polluted by signals caused by gas motion at the star’s surface. Stellar activity can mimic or mask changes in the RVs caused by orbiting planets, resulting in false positives or missed detections. Here we use Gaussian process regression to disentangle the contradictory reports of planets versus rotation artifacts from Kapteyn’s star. To model rotation, we use joint quasiperiodic kernels for the RV and Hα signals, requiring that their periods and correlation timescales be the same. We find that the rotation period of Kapteyn’s star is 125 days, while the characteristic active-region lifetime is 694 days. Adding a planet to the RV model produces a best-fit orbital period of 100 yr, or 10 times the observing time baseline, indicating that the observed RVs are best explained by star rotation only. We also find no significant periodic signals in residual RV data sets constructed by subtracting off realizations of the best-fit rotation model and conclude that both previously reported “planets” are artifacts of the star’s rotation and activity. Our results highlight the pitfalls of using sinusoids to model quasiperiodic rotation signals.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Constraining Kick Signals Through Advanced Multi-Phase Data

<ul><li>Re-designed ambient experimental apparatus constructed and operational</li><li>Finalized design of elevated experiments w/ LSU</li><li>Shakedown reveals that current sensors do not respond to changes in gas content</li><li>Designing surrogate sensor(s) w/ LSU</li><li>Implemented a sequence anomaly detection algorithm to identify kicks</li></ul>

Carney, Janine↗

Detecting multi‐scale riverine topographic variability and its influence on Chinook salmon habitat selection

Abstract Quantifying geomorphic conditions that impact riverine ecosystems is critical in river management due to degraded riverine habitat, changing flow and thermal conditions, and increasing anthropogenic pressure. Geomorphic complexity at different scales directly impacts habitat heterogeneity and affects aquatic biodiversity resilience. Here we showed that the combination of continuous spatial survey at high resolution, topobathymetric light detection and ranging (LiDAR), and continuous wavelet analysis can help identify and characterize that complexity. We used a continuous wavelet analysis on 1‐m resolution topobathymetry in three rivers in the Salmon River Basin, Idaho (USA), to identify different scales of topographic variability and the potential effects of this variability on salmonid redd site selection. On each river, wavelet scales characterized the topographic variability by portraying repeating patterns in the longitudinal profile. We found three major representative spatial wavelet scales of topographic variability in each river: a small wavelet scale associated with local morphology such as pools and riffles, a mid‐wavelet scale that identified larger channel unit features, and a large wavelet scale related to valley‐scale controls. The small wavelet scale was used to identify pools and riffles along the entire lengths of each river as well as areas with differing riffle‐pool development. Areas along the rivers with high local topographic variability (high wavelet power) at all wavelet scales contained the largest features (i.e., deepest or longest pools) in the systems. By comparing the wavelet power for each wavelet scale to Chinook salmon redd locations, we found that higher small‐scale wavelet power, which is related to pool‐riffle topography, is important for redd site selection. The continuous wavelet methodology objectively identified scales of topographic variability present in these rivers, performed efficient channel‐unit identification, and provided geomorphic assessment without laborious field surveys.

Duffin, Jenna↗

Estimating coccidioidomycosis endemicity while accounting for imperfect detection using spatio - temporal occupancy modeling

Coccidioidomycosis, or Valley fever, is an infectious disease caused by inhaling Coccidioides fungal spores. Incidence has risen in recent years, and it is believed the endemic region for Coccidioides is expanding in response to climate change. While Valley fever case data can help us understand trends in disease risk, using case data as a proxy for Coccidioides endemicity is not ideal because case data suffers from imperfect detection, including false positives (e.g., travel-related cases reported outside of endemic area) and false negatives (e.g., misdiagnosis or underreporting). Here we proposed a Bayesian, spatio-temporal occupancy model to relate monthly, county-level presence/absence data on Valley fever cases to latent endemicity of Coccidioides, accounting for imperfect detection. We used our model to estimate endemicity in the western United States. We estimated high probability of endemicity in southern California, Arizona, and New Mexico, but also in regions without mandated reporting, including western Texas, eastern Colorado, and southeastern Washington. We also quantified spatio-temporal variability in detectability of Valley fever, given an area is endemic to Coccidioides. We estimated an inverse relationship between lagged 3- and 9-month precipitation and case detection, and a positive association with agriculture. This work can help inform public health surveillance needs and identify areas that would benefit from mandatory case reporting.

60 APPLIED LIFE SCIENCES↗

High-Pressure Investigation of 2,4,6-Trinitro-3-bromoanisole (TNBA): Structural Determination and Piezochromism

Understanding phase transitions in energetic materials is crucial for developing predictive models of detonation. 2,4,6-Trinitro-3-bromoanisole (TNBA), an energetic material, was studied in its single-crystal form up to pressures of 45 GPa in a diamond anvil cell. The material was characterized by using X-ray, Raman, and optical transmission measurements. From single-crystal X-ray diffraction, the ambient structure of TNBA was determined which crystallizes in the P2 1 /c space group having four molecular units per unit cell. The X-ray data up to 9.2 GPa were fitted to a third-order Birch–Murnaghan equation of state by using the parameters K o = 13.2(2.4) GPa and K p = 5.1(1.4). Between 6.8 and 7.3 GPa, a phase transition was inferred in TNBA from concurrent fading of X-ray diffraction, disappearance of Raman peaks, increase in sample fluorescence, and discontinuous color change. The new phase was consistent with an amorphous state of at least partially intact molecules judging from the presence of higher-order Raman modes and irreversibility of the Raman spectra upon release. Piezochromism was observed with the translucent yellow TNBA gradually darkening and becoming opaque black at ~25 GPa. This correlated to the absorption edge gradually shifting to the red in the visible spectrum. Signs of two possible additional structural transitions were detected in the 32.4–41.0 GPa range as suggested by a jump in the absorption edge, the irreversible changes in the absorption spectrum upon release to ambient pressure, and by the lack of Raman modes in recovered samples. Here, the crystal and electronic structures of TNBA were also investigated up to 10 GPa by using DFT calculations and crystal structure prediction (CSP) simulations. In agreement with the experimentally observed transition at 7 GPa, the simulations at 10 GPa found a bevy of polymorphs lower in enthalpy and higher in density than P2 1 /c. The lowest calculated enthalpy structure was determined to be P2 1 2 1 2 1 , being in a different space group than the ambient experimental result.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The role of ambient gas confinement, plasma chemistry, and focusing conditions on emission features of femtosecond laser-produced plasmas

Ultrafast laser ablation coupled with optical emission spectroscopy is currently under development for standoff detection of elements and their isotopes for a wide range of application areas. In this work, we explore the role of ambient air pressure during the interaction of an ultrafast laser beam with two metallic targets (brass and uranium) with significantly different oxygen gas-phase reactivity. Plasma plumes were generated by focusing ~800 nm, ~35 fs pulses from an ultrafast laser system using a long focal length lens with f = 1 m. Two-dimensional spectral imaging was performed over the pressure range of 30 mTorr-700 Torr air to evaluate emission dynamics, plasma chemistry, signal-to-background ratio, and characteristic parameters (i.e. excitation temperature, electron density). An increase in ambient air pressure during ultrafast laser ablation leads to plume confinement and subsequent changes in the emission dynamics due to plasma chemistry as well as changes in plasma generation conditions (i.e. focused fs laser ablation versus filament ablation). Ablation crater morphologies were also investigated via scanning electron microscopy. Results indicate atomic emission intensity and signal-to-background ratios peak at moderate pressure levels (~50-100 Torr air) for both targets studied, although plasma chemistry influences uranium emission signatures. The emission features of the uranium plasma at pressures = 10 Torr showed the presence of atoms and oxide molecules which are co-located within the plume. We also find filament ablation leads to wider, more shallow craters compared to focused laser ablation. Our study provides unique insight into the interplay between plume dynamics, confinement, and oxygen chemistry of fs laser-produced plasmas and how these phenomena evolve with changing ambient air pressure.

Laser-produced plasma↗

Expansive open Fermi arcs and connectivity changes induced by infrared phonons in ZrTe 5

Expansive open Fermi arcs covering most of the surface Brillouin zone (SBZ) are desirable for detection and control of many topological phenomena, but they have generally been reported for Kramers-Weyl points, or unconventional chiral fermions, pinned at time-reversal invariant momentum in chiral materials. Here using first-principles band structure calculations, we show that for conventional Weyl points in ZrTe 5 with the chirality of +1/–1 near the BZ center at general momentum induced by one of the infrared phonons—the second lowest $B_{1u}$ mode for breaking inversion symmetry—they can also form expansive open Fermi arcs across the SBZ boundary to occupy most of the SBZ when projected on the (001) surface. In this work, we reveal that such expansive open Fermi arcs are evolved from the topological surface states that connect multiple surface Dirac points on the (001) surface of the topological insulator phases without lattice distortion in ZrTe 5 . Furthermore, we find that the connectivity of the induced open Fermi arcs can be changed by the magnitude of the lattice distortion of this infrared phonon mode. Thus, we propose that using coherent optical phonons to modulate lattice parameters can offer ways to induce unique topological features including expansive open Fermi arcs and to dynamically control Fermi arc connectivity in ZrTe 5 .

36 MATERIALS SCIENCE↗

A Data-Driven Passive Islanding Detection Scheme

This paper proposes a novel statistical parameters based data driven approach for passive islanding detection. The proposed scheme relies in the voltage data, measured at the point of common coupling, and is comprised of three stages. The Stage-1 quickly detects what is termed as coarse islanding, Stage-2 computes the decaying DC detector (DDCD), and 3) finally, the digital relay logic (DRL) is devised in Stage-3. The proposed scheme is tested as per the IEEE-1547, UL 1741 and IEC-62116 standards. Various tests are investigated on the modified IEEE-13 bus system, modeled in PSCAD/EMTDC, under stringent test scenarios such as power mismatch, induction motor starting effect, capacitor bank switching and various level of loads changes, considered for both single and multiple DG systems. The test results reveal that the proposed scheme can detect islanding in less than 2 cycles, and results in nearly zero non detection zone (NDZ). Also, the scheme can very well be used for single-phase microgrids too as it relies only on the single phase voltage information.

anti-islanding protection↗

Changing effects of external forcing on Atlantic–Pacific interactions

Recent studies have highlighted the increasingly dominant role of external forcing in driving Atlantic and Pacific Ocean variability during the second half of the 20th century. This paper provides insights into the underlying mechanisms driving interactions between modes of variability over the two basins. We define a set of possible drivers of these interactions and apply causal discovery to reanalysis data, two ensembles of pacemaker simulations where sea surface temperatures in either the tropical Pacific or the North Atlantic are nudged to observations, and a pre-industrial control run. We also utilize large-ensemble means of historical simulations from the Coupled Model Intercomparison Project Phase 6 (CMIP6) to quantify the effect of external forcing and improve the understanding of its impact. A causal analysis of the historical time series between 1950 and 2014 identifies a regime switch in the interactions between major modes of Atlantic and Pacific climate variability in both reanalysis and pacemaker simulations. A sliding window causal analysis reveals a decaying El Niño–Southern Oscillation (ENSO) effect on the Atlantic as the North Atlantic fluctuates towards an anomalously warm state. The causal networks also demonstrate that external forcing contributed to strengthening the Atlantic's negative-sign effect on ENSO since the mid-1980s, where warming tropical Atlantic sea surface temperatures induce a La Niña-like cooling in the equatorial Pacific during the following season through an intensification of the Pacific Walker circulation. The strengthening of this effect is not detected when the historical external forcing signal is removed in the Pacific pacemaker ensemble. The analysis of the pre-industrial control run supports the notion that the Atlantic and Pacific modes of natural climate variability exert contrasting impacts on each other even in the absence of anthropogenic forcing. The interactions are shown to be modulated by the (multi)decadal states of temperature anomalies of both basins with stronger connections when these states are “out of phase”. We show that causal discovery can detect previously documented connections and provides important potential for a deeper understanding of the mechanisms driving changes in regional and global climate variability.

54 ENVIRONMENTAL SCIENCES↗