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At least 1,513 records · Page 84

The need for standardization and improved open (meta)data practices in metaproteomics

Metaproteomics enables functional insight into microbial communities by identifying and quantifying proteins in complex samples. Yet, heterogeneous analytical workflows and the lack of standardization across experimental and bioinformatics stages hinder reproducibility and comparability, limiting integration with other omics data. We here present a community-developed reporting checklist tailored to the specific needs of metaproteomics. We also outline current efforts to enable structured and interoperable metadata capture, drawing on standards from proteomics and microbiome research wherever possible. By promoting transparent reporting and advancing metadata practices, our recommendations aim to align metaproteomics more closely with FAIR principles and support reproducible and interoperable research practices.

Armengaud, Jean [Universite Paris-Saclay, France]↗

Unveiling the mechanism of remote epitaxy of crystalline semiconductors on 2D materials-coated substrates

Abstract Remote epitaxy has opened novel opportunities for advanced manufacturing and heterogeneous integration of two-dimensional (2D) materials and conventional (3D) materials. The lattice transparency as the fundamental principle of remote epitaxy has been studied and challenged by recent observations defying the concept. Understanding remote epitaxy requires an integrated approach of theoretical modeling and experimental validation at multi-scales because the phenomenon includes remote interactions of atoms across an atomically thin material and a few van der Waals gaps. The roles of atomically thin 2D material for the nucleation and growth of a 3D material have not been integrated into a framework of remote epitaxy research. Here, we summarize studies of remote epitaxy mechanisms with a comparison to other epitaxy techniques. In the end, we suggest the crucial topics of remote epitaxy research for basic science and applications. Graphical Abstract

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Improving Mathematical Exposition of an Industrial-Scale Linear Program

Industrial-scale models require considerable setup time; hence, once built, they are used in myriad ways to consider closely related cases. In practice, the code for these models frequently evolves without appropriate notational choices, largely as a result of the lengthy development time of, and the number of individuals contributing to, their formulation. This leads to inefficiencies and obfuscates model structures that might be leveraged to expedite solutions. In this paper, we advocate for an emerging literature on model formulation “best practices” and present the reformulation of a widely used industrial-scale linear program. The efficient mathematical expression of this linear program, used to plan capacity expansion in the energy sector, allows for greater transparency of model structures and enhanced ability to identify computational performance improvements, as well as a lucid interpretation of its solutions. This type of formulation is employed in several mathematical programming courses at our university as an example of the advantages of best practices; the model more broadly is used widely to inform policy in the U.S. energy sector.

97 MATHEMATICS AND COMPUTING↗

COHERENT Collaboration data release from the measurements of CsI[Na] response to nuclear recoils

The data release from the measurements of the CsI[Na] response to low energy nuclear recoils by the COHERENT collaboration. The release corresponds to the results published in 'D. Akimov et al 2022 JINST 17 P10034.' We share the data in the form of raw ADC waveforms, provide benchmark subselections and event reconstruction scripts to enhance the transparency and reproducibility of our results.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Thermodynamic Modeling of Intrinsic Defects in MnBi₂Te₄

This repository contains the computational data supporting the manuscript titled “The critical role of intrinsic defects and many-body interactions on the stability of MnBi₂Te₄.” It includes: 1. DFT data generated using VASP, used for training and benchmarking electronic structure models. 2. Quantum Monte Carlo (QMC) data produced with QMCPACK, used to apply many-body corrections and validate the electronic and magnetic properties of MnBi₂Te₄. 3. Relevant scripts used to run, analyze, and process the calculations, enabling reproducibility and transparency of the workflows.

36 MATERIALS SCIENCE↗

Dataset for manuscript "Equipartition and the temperature of maximum density of TIP4P/2005 water"

We simulate TIP4P/2005 water in the temperature range of 257 K to 318 K with time-steps 0.25, 0.50, 1.00, 2.00, and 4.00 fs. The density-temperature behavior obtained using 0.25 or 0.50 fs are in excellent agreement with each other but differ from those obtained using time-steps that have been shown earlier to lead to a breakdown of equipartition. The temperature of maximum density (TMD) is 277.15 K with time-step 0.25 or 0.50 fs, but is shifted to progressively lower values for longer time-steps, a trend that holds for different thermostat/barostat combinations. Enhancing the water-water dispersion interaction, as has been recommended for simulating disordered proteins in TIP4P/2005, degrades the description of the liquid-vapor phase envelope. We present a simple physically transparent reasoning to highlight the separation of the time-scales between translational and rotational motion. We also develop a metric, Chi, that we term the equipartition anomaly, to detect equipartition violations in simulations that include molecules that are treated as rigid objects. Calculating Chi is shown to be straightforward and sensitive to equipartition violations. A key takeaway from this study is that using sufficiently short time-steps (less than or equal to 0.5 fs) to preserve equipartition is essential for obtaining meaningful liquid water properties and for producing reliable simulation data, as correct-ensemble sampling is fundamental to ensure reproducibility across codes and simulation alogrithms. The included dataset provides the raw data used in the preparation of the graphs noted in the manuscript.

36 MATERIALS SCIENCE↗

STM/S Grid LDOS Data and Analysis Code for Deciphering Majorana Zero Modes in Topological Superconductor

This dataset provides raw millikelvin scanning tunneling microscopy/spectroscopy (STM/S) grid spectroscopy data and Python analysis scripts supporting the manuscript “Deciphering Majorana Zero Modes in Topological Superconductor FeTe0.55Se0.45 with Machine-Learning-Assisted Spectral Deconvolution.” The dataset includes a raw grid spectroscopy file acquired on FeTe0.55Se0.45 at 40 mK under magnetic field, together with Python/Jupytext analysis scripts used for STM/S data processing, visualization, spectral deconvolution, Lorentzian peak fitting, feature extraction, machine-learning-assisted clustering, and figure generation. These files support the analysis of vortex-core local density of states and the identification of zero-bias-peak-related spectral components from complex in-gap states. The dataset is intended to provide a citable archival record of the data and analysis code associated with the published manuscript and to support transparency and reproducibility of the reported STM/S and machine-learning workflow.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

OPERATING EXPERIENCE AND ITS RELATIONSHIP TO EMBEDDED DIGITAL DEVICES IN SAFETY SYSTEMS

Interest in embedded digital devices (EDDs) for monitoring and providing control of components is increasing and the added functionality digital brings such as diagnostics, displays, control functions is welcomed in both the nuclear and other industries. As a result, pure analog-based components continue to disappear from the industrial I&C marketplace. Equipment with EDDs, also known by related terms such as smart devices, intelligent devices, and digital devices of limited functionality, can include sensors, breakers, priority logic modules, time delay relays, pumps, valve actuators, motor control centers, and uninterruptible power supplies. Not only is equipment consisting of analog and older digital technology being replaced with commercial grade products containing EDDs, but EDDs can also be retrofitted to work with existing components. EDDs may be installed physically within a component, such as in a relay. There are also external devices that some would not consider an EDD, but that operate in almost all technical ways identically to one internal to a component such as in a valve controller. In fact, the digital portions may be located hundreds of feet from the actual component.Due to the potential of being used in an identical manner and without alteration from their application in other industries, operating experience (OpE) for EDDs may be much more applicable than in the case of other more system level devices. Clear separation and independence of functionality provided with EDDs may also allow greater applicability of existing OpE from industry for changes that can be shown not to affect its safety function. However, OpE also demonstrates issues with different conditions between other industries and nuclear power plants, such as issues with undeclared changes or undeclared digital devices and the new failure modes they may introduce, issues with the reporting of OpE in industry, and a lack of transparency into OpE for EDDs.Understanding and addressing these issues will be key in the future use of EDDs in nuclear power plants, but failure rate data is difficult to obtain for EDDs, and lessons learned from the use of EDDs are difficult to collect and identify.Key words: embedded digital device, smart device, operating experience, failure modes

Muhlheim, Michael↗

Intense infrared lasers for strong-field science

The advent of chirped-pulse amplification in the 1980s and femtosecond Ti:sapphire lasers in the 1990s enabled transformative advances in intense laser–matter interaction physics. Whereas most of experiments have been conducted in the limited near-infrared range of 0.8–1 μm, theories predict that many physical phenomena such as high harmonic generation in gases favor long laser wavelengths in terms of extending the high-energy cutoff. Significant progress has been made in developing few-cycle, carrier-envelope phase-stabilized, high-peak-power lasers in the 1.6–2 μm range that has laid the foundation for attosecond X ray sources in the water window. Even longer wavelength lasers are becoming available that are suitable to study light filamentation, high harmonic generation, and laser–plasma interaction in the relativistic regime. Long-wavelength lasers are suitable for sub-bandgap strong-field excitation of a wide range of solid materials, including semiconductors. In the strong-field limit, bulk crystals also produce high-order harmonics. In this review, we first introduce several important wavelength scaling laws in strong-field physics, then describe recent breakthroughs in short- (1.4–3 μm), mid- (3–8 μm), and long-wave (8–15 μm) infrared laser technology, and finally provide examples of strong-field applications of these novel lasers. Furthermore, some of the broadband ultrafast infrared lasers will have profound effects on medicine, environmental protection, and national defense, because their wavelengths cover the water absorption band, the molecular fingerprint region, as well as the atmospheric infrared transparent window.

43 PARTICLE ACCELERATORS↗

Serving Verifiable, Device-Independent Randomness to the Public

Device-independent random number generators can be certified unhackable simply by the impossibility of superluminal signaling. We demonstrate a novel protocol to transparently operationalize this security through a public randomness beacon service.

Kavuri, Gautam A.↗

Plasmonic gold-cellulose nanofiber aerogels

Assembly of plasmonic nanomaterials into a low refractive index medium, such as an aerogel, holds a great promise for optical metamaterials, optical sensors, and photothermal energy converters. However, conventional plasmonic aerogels are opaque and optically isotropic composites, impeding them from being used as low-loss or polarization-dependent optical materials. Here we demonstrate a plasmonic-cellulose nanofiber composite aerogel that comprises of well-dispersed gold nanorods within a cellulose nanofiber network. The cellulose aerogel host is highly transparent owing to the small scattering cross-section of the nanofibers and forms a nematic liquid crystalline medium with strong optical birefringence. We find that the longitudinal surface plasmon resonance peak of gold nanorods shows a dramatic shift when probed for the cellulose aerogel compared with the wet gels. Simulations reveal the shift of surface plasmon resonance peak with gel drying can be attributed to the change of the effective refractive index of the gels. This composite material may provide a platform for three- dimensional plasmonic devices ranging from optical sensors to metamaterials.

36 MATERIALS SCIENCE↗

Toward high laser power beam manipulation with nanophotonic materials: evaluating thin film damage performance

Nanophotonic materials enable unprecedented control of light-matter interactions, including the ability to dynamically steer or shape wavefronts. Consequently, nanophotonic systems such as metasurfaces have been touted as promising candidates for free-space optical communications, directed energy and additive manufacturing, which currently rely on slow mechanical scanners or electro-optical components for beam steering and shaping. However, such applications necessitate the ability to support high laser irradiances (> kW/cm 2 ) and systematic studies on the high-power laser damage performance of nanophotonic materials and designs are sparse. Here, we experimentally investigate the pulsed laser-induced damage performance (at λ ∼ 1 µm) of model nanophotonic thin films including gold, indium tin oxide, and refractory materials such as titanium nitride and titanium oxynitride. We also model the spatio-thermal dissipation dynamics upon single-pulse illumination by anchoring experimental laser damage thresholds. Our findings show that gold exhibits the best laser damage resistance, but we argue that alternative materials such as transparent conducting oxides could be optimized to balance the tradeoff between damage resistance and optical tunability, which is critical for the design of thermally robust nanophotonic systems. We also discuss damage mitigation and ruggedization strategies for future device-scale studies and applications requiring high power beam manipulation.

36 MATERIALS SCIENCE↗

Tamper performance for confined laser drive applications

The shock imparted by a laser beam striking a metal surface can be increased by the presence of an optically transparent tamper plate bonded to the surface. We explore the shock produced in an aluminum slab, for a selection of tamper materials and drive conditions. The experiments are conducted with a single-pulse laser of maximum fluence up to 100 J/cm 2 . The pressure and impulse are measured by photon doppler velocimetry, while plasma imaging is used to provide evidence of nonlinear tamper absorption. We demonstrate a pressure enhancement of 50x using simple commercially available optics. We compare results from hard dielectric glasses such as fused silica to soft plastics such as teflon tape. We discuss the mechanism of pressure saturation observed at high pulse fluence, along with some implications regarding applications. Below saturation, overall dependencies on pulse intensity and material parameters such as mechanical impedances are shown to correlate with a model by Fabbro et al .

36 MATERIALS SCIENCE↗

Polarization-independent photonic Bragg grating filter with cladding asymmetry

A photonic Bragg grating is a fundamental building block that reflects the direction of wave propagation through spatial phase modulation and can be implemented using sidewall corrugation. However, due to the asymmetric aspect ratio of a waveguide cross section, typical Bragg gratings exhibit a strong polarization sensitivity. Here, we show that photonic Bragg gratings with cladding asymmetry can enable polarization-independent notch filters by rotating input polarizations. Such Bragg gratings strongly couple transverse electric (TE) and transverse magnetic (TM) modes propagating in opposite directions, filtering the input signal and reflecting the rotated mode. We analyzed this polarization-rotating Bragg grating using the coupled-mode theory and experimentally demonstrated it on a silicon-on-insulator platform. Our device concept is simple to implement and compatible with other platforms, readily available as polarization transparent Bragg components.

Pimbi, Daniel (ORCID:000000025933203X)↗

Impact of raw material surface oxide removal on dual band infrared optical properties of As 2 Se 3 chalcogenide glass

The manufacturing of low loss chalcogenide glasses (ChGs) for optoelectronic applications is ultimately defined by the concentration of impurities present in starting materials or imparted via processing. We describe a rapid method for purifying metallic starting materials in As 2 Se 3 glass where oxide reduction is correlated to optical and physical properties. Specifically, As-O reduction enhances the glass’ dual-band optical transparency proportional to the extent (13-fold reduction) of oxide reduction, and is accompanied by a change in density and hardness associated with changes in matrix bonding. A significant modification of the glass’ index and LWIR Abbe number is reported highlighting the significant impact purification has on material dispersion control required in optical designs.

36 MATERIALS SCIENCE↗

Mid-infrared luminescence properties of erbium and dysprosium doped lanthanum titanate glasses

Glasses of composition x RE 2 O 3 -(17− x ) La 2 O 3 -83 TiO 2 were prepared by levitation melting from x = 0.1 to 9 for RE=Er and at x =0.1 and 1 for RE=Dy. The glasses have high transition temperature, exhibit low OH, and 1 mm thick discs are transparent out to 6 μ m. Mid-infrared emission lineshapes and lifetimes are comparable to what is seen in tellurite glasses containing Er 3+ and Dy 3+ . For x fixed at 1, the Er 3+ : 4 I 11/2 → 4 I 13/2 transition at 2716 nm has a fluorescence lifetime of 254 μ s and the Dy 3+ : 6 H 13/2 → 6 H 15/2 transition at 2957 nm has a fluorescence lifetime of 9.09 μ s. The results indicate that doped lanthanum titanate glasses offer the thermal stability of a ’hard’ glass with the host properties typically associated with ’soft’ glasses. Problems with the measurement of spectral features in the mid-infrared that could erroneously be assigned as resulting from rare-earth ion emissions are presented and discussed.

36 MATERIALS SCIENCE↗

Nonlinear refraction and absorption properties of optical materials for high-peak-power long-wave-infrared lasers

Optical materials transparent in the CO 2 laser wavelength range have been evaluated regarding their suitability for components in ultrashort-pulse (≤ a few ps), high-peak-power (≥ a few TW) long-wave infrared (LWIR) lasers. We provide values for the nonlinear refractive index ( n 2 ) for seventeen materials, and onsets for nonlinear absorption for eleven materials. Characterizations were performed using a 2 ps laser pulse at λ =9.2 μ m. This paper methodically presents the newly acquired data in conjunction with existing literature on linear optical properties, establishing it as a comprehensive reference for designing high-peak-power LWIR laser systems.

43 PARTICLE ACCELERATORS↗

Adiabatic frequency shifting in epsilon-near-zero materials: the role of group velocity

The conversion of a photon’s frequency has long been a key application area of nonlinear optics. It has been discussed how a slow temporal variation of a material’s refractive index can lead to the adiabatic frequency shift (AFS) of a pulse spectrum. Such a rigid spectral change has relevant technological implications, for example, in ultrafast signal processing. Here, we investigate the AFS process in epsilon-near-zero (ENZ) materials and show that the frequency shift can be achieved in a shorter length if operating in the vicinity of R e { ε <#comment/> r } = 0 . We also predict that, if the refractive index is induced by an intense optical pulse, the frequency shift is more efficient for a pump at the ENZ wavelength. Remarkably, we show that these effects are a consequence of the slow propagation speed of pulses at the ENZ wavelength. Our theoretical predictions are validated by experiments obtained for the AFS of optical pulses incident upon aluminum zinc oxide thin films at ENZ. Our results indicate that transparent metal oxides operating near the ENZ point are good candidates for future frequency conversion schemes.

36 MATERIALS SCIENCE↗