bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effective suppression of dark counts in superconducting microstructures with grid of pinholes in a magnetic field
Authors: Zhu Dong , Charaev Ilya , Schilling Andreas 
Published: August 2023

Abstract
In a magnetic field, vortices significantly contribute to the dark counts of single-photon detectors made of superconducting wires, and they are also limiting the critical current of such devices. To address this issue, we prepared superconducting microwires with a pinhole grid from WSi thin films and report on corresponding critical-current and count-rate measurements in an external magnetic field B. When compared to corresponding devices without pinholes, the critical current only weakly depends on the magnetic field at B < 16 mT and it is even larger already at B > 10 mT. Moreover, dark counts are not only suppressed in zero field, but particularly in magnetic fields B < 16 mT, while photon counts are virtually field insensitive in the same range of the magnetic field.
Investigation of dark count rate in NbRe microstrips for single photon detection
Authors: Ercolano P , Cirillo C , Ejrnaes M , Chianese F , Salvoni D , Bruscino C , Satariano R , Cassinese A , Attanasio C , Pepe G P , Parlato L 
Published: August 2023

Abstract
Superconducting microstrip single photon detectors (SMSPDs) received great interest since they are expected to combine the excellent performance of superconducting nanostrip single photon detectors with the possibility to cover large active areas using low-cost fabrication techniques. In this work, we fabricated SMSPDs based on NbRe to investigate the role of vortices in the dark counts events in this innovative material and in devices with micrometer size. We realized devices with different layouts, namely single microstrips and pairs of parallel microstrips. The energy barriers related to the motion of single vortices or vortex–antivortex pairs, responsible of detection events, have been determined and compared with the ones of similar devices based on different materials, such as MoSi, WSi and NbN. The analysis confirms the high potential of NbRe for the realization of superconducting single photon detectors with large areas.
Spin-fluctuation glue disfavors high-critical temperature of superconductivity?
Authors: Yamase Hiroyuki 
Published: August 2023

Abstract
Antiferromagnetic fluctuations are believed to be a promising glue to drive high-temperature superconductivity especially in cuprates. Here, we perform a close inspection of the superconducting mechanism from spin fluctuations in the Eliashberg framework by employing a typical one-band model on a square lattice. While spin fluctuations can eventually drive superconductivity as is well established, we find that the superconducting tendency is suppressed substantially by a seemingly negligible contribution from a small momentum transfer far away from

(
π
,
π
)

. This suppression comes from phase frustration of the pairing gap and is expected to be a general feature due to the repulsive pairing interaction of spin fluctuations. Furthermore, we find that the momentum dependence of the pairing gap largely deviates from the functional form of

cos

k
x

−
cos

k
y

, although this form is well established in cuprate superconductors. We argue that an instantaneous magnetic interaction plays the important role to understand high-critical temperature of superconductivity as well as the momentum dependence of the pairing gap.
The impact of Sm substitution on structural and optical properties of LaFeO3: their application as a photocatalyst for the degradation of methylene blue under visible light irradiation
Authors: Raslan W S , Makram N , Adam A 
Published: August 2023

Abstract
The objective of the present study is to enhance the photocatalytic activity of LaFeO3 by inserting Sm ions on the La site for the degradation of methylene blue. We employed citric sol–gel techniques to produce ultrafine powders of the La1-xSmxFeO3 (0.0 ≤ x ≤ 0.5) nanoperovskite samples. All samples confirmed the presence of a pure Pbnm orthorhombic phase structure. The decrease of lattice constants, crystallite sizes and cell volumes, and increase in microstrains suggest a deformation of the structure due to the addition of Sm ion on the La site of the La1-xSmxFeO3. The images of HR-TEM and FE-SEM for all samples revealed a homogeneous distribution of almost spherical nanoparticles, with decreasing average particle sizes ranging from 49.95 ± 3.12 to 34.28 ± 4.38 nm, as Sm ratios increases from 0.0 to 0.5%. The spectra of FTIR confirmed the formation of a Lax-1SmxFeO3 perovskite phase by the appearance of lower frequency bands Fe–O-Fe and La-O-La at ∼ 400 cm−1 and a higher absorption band Fe -O and La -O at ∼ 564 cm−1. The Raman spectra were employed to investigate the formation of phonon modes of La1-xSmxFeO3. Diffused reflectance spectroscopy (DRS) demonstrated the decrease of energy gap (Eg) values from 2.38 to 1.86 eV and the increase in Sm content from 0.0 to 0.5%. Since these Eg values fall within the visible light region, the photocatalytic activity of La1-xSmxFeO3 samples demonstrated a gradual increase in the degradation ratio of MB from 31.7 to 73.2% with increasing Sm content from 0.0 to 0.5%, respectively, under visible light illumination.
Conversion of waste PET into triazines-incorporated polyols and flame-retardant polyurethane foams
Authors: Kuang Rui , Duan Qian , Kuang Xuan 
Published: August 2023

Abstract
Preparation of flame retardant rigid polyurethane foams (RPUFs) from sustainable material sources like recycled polyethylene terephthalate (rPET) remains a challenge due to the difficulty in controlling the synthesis of polyols with flame retardant functionalities. Here, we propose a method for converting rPET into a polyester-amide-ether oligools incorporated flame retardant triazine-ring through the partial codepolymerization of rPET by 1,3,5-tris(hydroxymethyl isocyanurate (THMI), ethanolamine, and diethylene glycol, followed by linking oligools into polyols with phthalic anhydride. THMI was synthesized through nucleophilic additions of formaldehyde with isocyanuric acid. The codepolymerization and linking were carried out using a one-pot method. Single-factor experiments were implemented to optimize the process parameters such as reacting temperature and time. The L9 (43) orthogonal experiments were employed to systematically investigate the influence of the dosages of four raw materials on the performance of the synthesized polyols. Based on the range analysis of acid value, hydroxyl value, and viscosity of the synthesized polyols, the optimized polyol was synthesized as a candidate for preparing flame retardant RPUFs. Results demonstrated that the obtained RPUF derived from the optimized polyol could achieve a limiting oxygen index (LOI) value of 30.3% when mixed with phosphorous-containing flame-retardant DCPP, meeting the national standard of combustible stage B1.The high flame retardancy RPUF obtained from an rPET-based polyol with a triazine ring represents a novel and practical method of preparation, providing new insights into the optimization of synthesis parameters across multiple factors and levels.
Enhanced visible light photocatalytic activity of nanostructured SiO2-TiO2 thin films through optimizing thickness
Authors: Darvish Samira Mohammad , Masoudi Amir Ali , Mortezaali Abdollah , Hosseini Zahra Sadat 
Published: August 2023

Abstract
Thin films of silicon dioxide-titanium dioxide (SiO2-TiO2) with different thicknesses were deposited by a simple dip-coating method in a repetition behavior followed by heating processes. Choosing the optimum thickness is accounted as an approach for improving photocatalytic and hydrophilicity properties of a thin film. The obtained results from FESEM and AFM characterizations showed that with increasing thickness, the surface roughness increases from 3.089 nm to 132.8 nm. The XRD patterns indicate the presence of anatase phase for the SiO2-TiO2 thin film. Optical measurements were used to calculate thickness, generation rate of photocarriers, band gap, and refractive index of the samples. Decrease of band gap with increasing thickness makes the layer more proper for photocatalytic activity under visible light. It is obtained that the generation rate of carriers has the highest value (17.16 × 1024 m−3s−1) for the thickness of 336 nm. PL spectra for the thickness of 336 nm confirmed the presence of defects which reduce the recombination rate and improve charge carrier separation. XPS was used to distinguish the chemical composition. Variation of defect concentrations, number of grain boundaries, and surface roughness with thickness were considered as the main parameters affecting the photocatalytic performance. The highest photodegradation was obtained for 336 nm thick film under illumination of visible light (100% degradation of 40 ml solution of 10 mg l−1 methylene blue (MB)). This research provides a systematic study on the structural and optical properties of the different thick SiO2-TiO2 films with goal of enhancing photocatalytic activity in the visible light region.
Complete separation of variables in the geodesic Hamilton-Jacobi equation in four dimensions
Authors: Katanaev M O 
Published: August 2023

Abstract
We list all metrics of arbitrary signature in four dimensions which admit complete separation of variables in the Hamilton–Jacobi equation for geodesic Hamiltonians. There are only ten classes of separable metrics admitting Killing vector fields, indecomposable quadratic conservation laws, and coisotropic coordinates. Canonical separable metrics parameterized by several (up to twelve) arbitrary functions of single coordinates are written explicitly. The full set of independent conservation laws in involution for each canonical metrics is also found.
Parametric study of helicon wave current drive in CFETR
Authors: Wu Xianshu , Li Jingchun , Chen Jiale , Xu Guosheng , Dong Jiaqi , Wang Zhanhui , Sun Aiping , Zhong Wulv 
Published: August 2023

Abstract
This paper evaluates the feasibility of helicon current drive (HCD) in a hybrid scenario for the China Fusion Engineering Test Reactor (CFETR). Utilizing the GENRAY/CQL3D package, a large number of simulations (over 5000) were conducted, with parametric scans in the antenna’s poloidal position, launched parallel refractive index (n||
), and wave frequency. The analysis reveals that helicon has excellent accessibility under reactor-level conditions, and smaller n||
and higher wave frequency result in enhanced wave absorption. The simulations demonstrate an optimal launched n||
of approximately 1.6 for the CFETR hybrid scenario, with helicon achieving a maximum drive efficiency of 2.8 × 1019 A·W−1·m−2. The best launch position is found to be within a poloidal angle range of 25 degrees to 65 degrees. Additionally, it is preferable to have a narrow n||
spectrum for wave absorption when operating below the threshold value of Δn||
(∼0.6), beyond which the effect of Δn||
on wave absorption is negligible. This study provides valuable insights into the potential application of HCD in CFETR.
XUV plasmonic waveguides by near-zero index heterostructures
Authors: Assogna Luca , Ferrante Carino , Ciattoni Alessandro , Marini Andrea 
Published: August 2023

Abstract
The lack of transmissive photonic components in the extreme ultraviolet (XUV) constitutes a challenge for micro/nano-metric confinement. Here, we theoretically design a novel approach to attain XUV radiation guidance based on the electromagnetic properties of titanium–aluminum–titanium heterostructures in such a spectral domain. We show that, thanks to the near-zero-index properties of aluminum and titanium, XUV radiation can couple efficiently with plasma oscillations in such heterostructures, enabling the excitation of several distinct plasmon polariton modes. Our predictions, based on the semi-analytical solution of fully vectorial Maxwell’s equations, indicate that the dispersion profile of plasmon polariton modes can get efficiently modulated by the aluminum thickness, enabling nanometer confinement and micrometre propagation length. Moreover, we quantify the third-order nonlinearity enhancement factor, finding that it is resonant at the zero-index wavelength. Our results are promising for the development of future devices enabling advanced control and manipulation of XUV radiation.
Excitons in organic materials: revisiting old concepts with new insights
Authors: Valencia Ana M , Bischof Daniel , Anhäuser Sebastian , Zeplichal Marc , Terfort Andreas , Witte Gregor , Cocchi Caterina 
Published: August 2023

Abstract
The development of advanced experimental and theoretical methods for the characterization of excitations in materials enables revisiting established concepts that are sometimes misleadingly transferred from one field to another without the necessary disclaimers. This is precisely the situation that occurs for excitons in organic materials: different states of matter and peculiarities related to their structural arrangements and their environment may substantially alter the nature of the photo-induced excited states compared to inorganic semiconductors for which the concept of an exciton was originally developed. Adopting the examples of tetracene and perfluorotetracene, in this review, we analyze the nature of the excitations in the isolated compounds in solution, in the crystalline materials, and in melt. Using single crystals or films with large crystalline domains enables polarization-resolved optical absorption measurements, and thus the determination of the energy and polarization of different excitons. These experiments are complemented by state-of-the-art first-principles calculations based on density-functional theory and many-body perturbation theory. The employed methodologies offer unprecedented insight into the optical response of the systems, allowing us to clarify the single-particle character of the excitations in isolated molecules and the collective nature of the electron–hole pairs in the aggregated phases. Our results reveal that the turning point between these two scenarios is the quantum-mechanical interactions between the molecules: when their wave-function distributions and the Coulomb interactions among them are explicitly described in the adopted theoretical scheme, the excitonic character of the optical transitions can be captured. Semi-classical models accounting only for electrostatic couplings between the photo-activated molecules and their environment are unable to reproduce these effects. The outcomes of this work offer a deeper understanding of excitations in organic semiconductors from both theoretical and experimental perspectives.
Soft magnetic thin film deformation with a bistable electropermanent magnet
Authors: Keeys Nolen I. , Patel Dinesh K. , LeDuc Philip , Majidi Carmel 
Published: August 2023

Abstract
Physically soft magnetic materials (PSMMs) represent an emerging class of materials that can change shape or rheology in response to an external magnetic field. However, until now, no studies have investigated using an electropermanent magnet (EPM) and magnetic repulsion to magnetically deform PSMMs. Such capabilities would enable the ability to deform PSMMs without the need for continuous electrical input and produce PSMM film deformation without an air gap, as would be required with magnetic attraction. To address this, we introduce a PSMM-EPM architecture in which the shape of a soft deformable thin film is controlled by switching between bistable on/off states of the EPM circuit. We characterized the deflection of a PSMM thin film when placed at controlled distances normal to the surface of the EPM and compared its response for cases when the EPM is in the ‘on’ and ‘off’ states. This work is the first to demonstrate a magnetically repelled soft deformable thin film that achieves two electronically-controlled modes of deformation through the on and off states of an EPM. This work has the potential to advance the development of new magneto-responsive soft materials and systems.
Learning capacity and function of stochastic reaction networks
Authors: Ramezanpour Abolfazl , Mashaghi Alireza 
Published: August 2023

Abstract
Biochemical reaction networks are expected to encode an efficient representation of the function of cells in a variable environment. It is thus important to see how these networks do learn and implement such representations. The first step in this direction is to characterize the function and learning capabilities of basic artificial reaction networks. In this study, we consider multilayer networks of reversible reactions that connect two layers of signal and response species through an intermediate layer of hidden species. We introduce a stochastic learning algorithm that updates the reaction rates based on the correlation values between reaction products and responses. Our findings indicate that the function of networks with random reaction rates, as well as their learning capacity for random signal-response activities, are critically determined by the number of reactants and reaction products. Moreover, the stored patterns exhibit different levels of robustness and qualities as the reaction rates deviate from their optimal values in a stochastic model of defect evolution. These findings can help suggest network modules that are better suited to specific functions, such as amplifiers or dampeners, or to the learning of biologically relevant signal-response activities.
Establishment of transgenic epithelium-specific Cre-recombinase driving medaka (Oryzias latipes) by homology repair mediated knock-in
Authors: Watanabe Yuko , Katsumura Eri , Domon Tatsuki , Ishikawa Yuta , Oguri Rina , Takashima Minami , Meng Qi , Kinoshita Masato , Hashimoto Hisashi , Hitomi Kiyotaka 
Published: August 2023

ABSTRACT
Deletion of gene expression in the target tissues and cells is an effective strategy for elucidating the physiological functions of the protein of interest. For tissue-specific and/or inducible gene deletion, the Cre-loxP system has been widely used in various model organisms including medaka (Oryzias latipes). The epithelium is the key tissue, locating at the outermost area and playing a role in barrier to external stimuli. Despite a large genetic toolbox developed in medaka, there is no available Cre-driver line that works in an epithelium-specific manner. Here, we established epithelium-specific Cre-driver lines in medaka using a homology-directed repair mediated knock-in approach with CRISPR/Cas9, targeting each of periplakin and keratin genes. We show that Cre-recombinase is expressed exclusively in the epithelium in the knock-in lines and that it efficiently and specifically induces recombination in the tissues. These Cre-driver lines are useful for studying the functions of proteins expressed in the epithelium.
Dominance loss and tenure maintenance in Kalahari meerkats
Authors: Duncan Chris , Thorley Jack , Manser Marta B , Clutton-Brock Tim 
Published: August 2023

Abstract
In many social species, both the acquisition of dominance and the duration that individuals maintain their status are important determinants of breeding tenure and lifetime reproductive success. However, few studies have yet examined the extent and causes of variation in dominance tenure and the duration of breeding lifespans. Here, we investigate the processes that terminate dominance tenures and examine how they differ between the sexes in wild Kalahari meerkats (Suricata suricatta), a cooperative breeder where a dominant breeding pair produces most of the young recruited into each group. Mortality and displacement by resident subordinate competitors were important forms of dominance loss for both sexes. However, dominant males (but rarely females) were also at risk of takeovers by extra-group invading males. Dominant males also differed from dominant females in that they abandoned their group after the death of their breeding partner, when no other breeding opportunities were present, whereas dominant females that lost their partner remained and continued to breed in the same group. We show that a larger number of processes can terminate dominance tenure in males with the result that the average male tenure of breeding positions was shorter than that of females, which contributes to the reduced variance in the lifetime reproductive success in males compared to females. Our analysis suggests that sex differences in emigration and immigration may often have downstream consequences for sex differences in reproductive variance and for the selection pressures operating on females and males.
Optimal selection of suitable templates in protein interface prediction
Authors: Grudman Steven , Fajardo J Eduardo , Fiser Andras 
Published: August 2023

Abstract

Motivation
Molecular-level classification of protein–protein interfaces can greatly assist in functional characterization and rational drug design. The most accurate protein interface predictions rely on finding homologous proteins with known interfaces since most interfaces are conserved within the same protein family. The accuracy of these template-based prediction approaches depends on the correct choice of suitable templates. Choosing the right templates in the immunoglobulin superfamily (IgSF) is challenging because its members share low sequence identity and display a wide range of alternative binding sites despite structural homology.

Results
We present a new approach to predict protein interfaces. First, template-specific, informative evolutionary profiles are established using a mutual information-based approach. Next, based on the similarity of residue level conservation scores derived from the evolutionary profiles, a query protein is hierarchically clustered with all available template proteins in its superfamily with known interface definitions. Once clustered, a subset of the most closely related templates is selected, and an interface prediction is made. These initial interface predictions are subsequently refined by extensive docking. This method was benchmarked on 51 IgSF proteins and can predict nontrivial interfaces of IgSF proteins with an average and median F-score of 0.64 and 0.78, respectively. We also provide a way to assess the confidence of the results. The average and median F-scores increase to 0.8 and 0.81, respectively, if 27% of low confidence cases and 17% of medium confidence cases are removed. Lastly, we provide residue level interface predictions, protein complexes, and confidence measurements for singletons in the IgSF.

Availability and implementation
Source code is freely available at: https://gitlab.com/fiserlab.org/interdct_with_refinement.
crosshap: R package for local haplotype visualization for trait association analysis
Authors: Marsh Jacob I , Petereit Jakob , Johnston Brady A , Bayer Philipp E , Tay Fernandez Cassandria G , Al-Mamun Hawlader A , Batley Jacqueline , Edwards David 
Published: August 2023

AbstractSummaryGenome-wide association studies (GWAS) excels at harnessing dense genomic variant datasets to identify candidate regions responsible for producing a given phenotype. However, GWAS and traditional fine-mapping methods do not provide insight into the complex local landscape of linkage that contains and has been shaped by the causal variant(s). Here, we present crosshap, an R package that performs robust density-based clustering of variants based on their linkage profiles to capture haplotype structures in a local genomic region of interest. Following this, crosshap is equipped with visualization tools for choosing optimal clustering parameters (ɛ) before producing an intuitive figure that provides an overview of the complex relationships between linked variants, haplotype combinations, phenotype, and metadata traits.Availability and implementationThe crosshap package is freely available under the MIT license and can be downloaded directly from CRAN with R &gt;4.0.0. The development version is available on GitHub alongside issue support (https://github.com/jacobimarsh/crosshap). Tutorial vignettes and documentation are available (https://jacobimarsh.github.io/crosshap/).