bluuebunny/crossref_metadata_2025 huggingface dataset:
The noise of the charge density waves in quasi-1D NbSe3 nanowires — contributions of electrons and quantum condensate
Authors: Ghosh Subhajit , Rumyantsev Sergey , Balandin Alexander A.
Published: April 2024

Low-frequency electronic noise in charge-density-wave van der Waals materials has been an important characteristic, providing information about the material quality, phase transitions, and collective current transport. However, the noise sources and mechanisms have not been completely understood, particularly for the materials with a non-fully gapped Fermi surface where the electrical current includes components from individual electrons and the sliding charge-density wave. We investigated noise in nanowires of quasi-one-dimensional NbSe3, focusing on a temperature range near the Pearls transition TP1 ∼ 145 K. The data analysis allowed us to separate the noise produced by the individual conduction electrons and the quantum condensate of the charge density waves before and after the onset of sliding. The noise as a function of temperature and electric bias reveals several intriguing peaks. We explained the observed features by the depinning threshold field, the creep and sliding of the charge density waves, and the possible existence of the hidden phases. It was found that the charge density wave condensate is particularly noisy at the moment of depinning. The noise of the collective current reduces with the increasing bias voltage in contrast to the noise of the individual electrons. Our results shed light on the behavior of the charge density wave quantum condensate and demonstrate the potential of noise spectroscopy for investigating the properties of low-dimensional quantum materials.
The effects of curvature and
β
on zonally invariant f-plane dynamics
Authors: Yacoby Itamar , Gildor Hezi , Paldor Nathan
Published: April 2024

The modification of the dynamics on the f-plane due to the inclusion of the latitudinal variation of the Coriolis frequency, quantified by β, is examined by comparing steady and time-dependent solutions for different values of β, including 0. The comparisons are made for analytic expressions and numerical simulations of the solutions of two physical problems: geostrophic adjustment and Ekman transport. By varying the extent of the meridional domain, L, and the value of β, while keeping the same value of the deformation radius, Rd, we find that the relative change of the Coriolis frequency across L is not a uniformly valid predictor of the effect of β on the dynamics. Instead, the magnitude of this effect varies with the physical problem, the type of dynamics, i.e., steady or time dependent, and with the particular values of β and L. In contrast to the effect of β, the effect of curvature on the zonally invariant f-plane dynamics is negligible in all cases for L≤1200 km and Rd=30 km employed here.
Thermally stable high carrier mobility nanocomposite infrared photodetector
Authors: Xue Xiaomeng , Lv Hongyu , Qiu Yanyan , Hao Qun , Chen Menglu
Published: April 2024

Quantum dots (QDs) show excellent optical properties, such as a high extinction coefficient, tunable colors, and superior photostability. However, the transport properties of QDs, such as carrier mobility, are quite limited, which hinder optoelectronic applications. On the other hand, carbon nanotubes (CNTs) generally have high carrier mobility and thermal stability with a weak optical response. These features inspire us to couple QDs with CNTs to achieve improved optoelectronics. We take infrared HgTe QDs and multi-walled CNTs as examples. With appropriate coupling between QD and CNT matrices, carrier mobility could reach 34.6–54.1 cm2/Vs in the nanocomposite, a 1000-fold increase compared with the reference. The nanocomposite benefits external quantum efficiency up to 12 500% and detectivity 1012 Jones on the 2500 nm infrared photodetectors. The CNT matrix also helps relaxing thermally generated carriers, improving the photodetector thermal stability. We also demonstrate that the device maintains high detectivity at a high operating temperature.
Effect of water film evaporation on the shale gas transmission in inorganic nanopores under viscosity
Authors: Wang Haoyi , Peng Weihong , Hu Liangyu , Zhang Wei
Published: April 2024

Shale gas reservoirs generally have ultra-low water saturation, and the water in reservoirs is closely bound to the walls of inorganic nanopores, forming a water film structure on the hydrophilic surface. When shale gas enters the inorganic nanopores, the water films in the inorganic pores will be removed by evaporation instead of being driven away by the gas, which increases the difficulty of predicting production during shale gas extraction. Based on molecular dynamics simulations, a water film evaporation model is proposed, considering the evaporation of water films during shale gas transport and the influence of water film evaporation on the shale gas transport mechanism. The Green–Kubo method is employed to calculate the viscosity of the water film. The evaporation flux of the water film under the influence of viscosity is discussed in the evaporation model. The transport mechanisms of shale gas in nanopores and the effect of water film evaporation on shale gas transport mechanisms are analyzed in detail. The result indicates that the water films in the inorganic nanopores are constrained on the hydrophilic surface, and the viscosity normal to the surface of the water film of 4 Å is 0.005 26 Pa⋅S, which is 6.12 times the reference value of viscosity at 298 K. In the process of water film evaporation, the evaporation flux of the water film is influenced by viscosity. In the study of the shale gas transport mechanism, water films in inorganic nanopores can hinder the surface diffusion of the methane molecules adsorbed on boundary and significantly reduce the mass flux of shale gas.
A dual-ring network design for the fast orbit feedback system of the storage ring
Authors: Liang Yu , Zhu Wenchao , Xie Chunjie , Wei Zhengyu , Luo Qing , Sun Baogen , Zhou Zeran
Published: April 2024

Building reliable fast orbit feedback (FOFB) systems to offer high stability of the beam orbit becomes more challenging for the diffraction-limited storage ring due to the smaller beam size. The beam position measurement and control (BPMC) processor has been developed to streamline the FOFB system architecture by integrating BPM (Beam Position Monitor) electronics and an orbit feedback controller. This paper designs a hierarchical dual-ring network topology based on BPMC processors using parameters derived from the storage ring of the Hefei Advanced Light Facility. To reduce latency and prevent data transmission collisions, we propose a multi-forwarding communication scheme and a communication controller design in a field-programmable gate array. Experimental results verify that this topology operates reliably with the multi-forwarding scheme, providing an approximate communication latency as low as 17.336 μs to support the 30 kHz orbit feedback update rate.
Effects of structural variations to x-ray absorption spectra of g-C3N4: Insight from DFT and TDDFT simulations
Authors: Zhang Jun-Rong , Wang Sheng-Yu , Wei Minrui , Fu Qiang , Hua Weijie
Published: April 2024

X-ray absorption spectroscopy (XAS) is widely employed for structure characterization of graphitic carbon nitride (g-C3N4) and its composites. Nevertheless, even for pure g-C3N4, discrepancies in energy and profile exist across different experiments, which can be attributed to variations in structures arising from diverse synthesis conditions and calibration procedures. Here, we conducted a theoretical investigation on XAS of three representative g-C3N4 structures (planar, corrugated, and micro-corrugated) optimized with different strategies, to understand the structure–spectroscopy relation. Different methods were compared, including density functional theory (DFT) with the full core-hole (FCH) or equivalent core-hole (ECH) approximation as well as the time-dependent DFT (TDDFT). FCH was responsible for getting accurate absolute absorption energy; while ECH and TDDFT aided in interpreting the spectra, through ECH-state canonical molecular orbitals (ECH-CMOs) and natural transition orbitals (NTOs), respectively. With each method, the spectra at the three structures show evident differences, which can be correlated with different individual experiments or in between. Our calculations explained the structural reason behind the spectral discrepancies among different experiments. Moreover, profiles predicted by these methods also displayed consistency, so their differences can be used as a reliable indicator of their accuracy. Both ECH-CMOs and NTO particle orbitals led to similar graphics, validating their applicability in interpreting the transitions. This work provides a comprehensive analysis of the structure-XAS relation for g-C3N4, provides concrete explanations for the spectral differences reported in various experiments, and offers insight for future structure dynamical and transient x-ray spectral analyses.
Influence of surface work function and neutral gas temperature on mechanism of H− production in negative hydrogen ion sources
Authors: He Zhou-Qi , Yang Wei , Gao Fei , Du Cheng-Ran , Wang You-Nian
Published: April 2024

Negative hydrogen ion sources (NHISs) based on surface production with cesium (Cs) seeded can fulfill the demanded parameters for neutral beam injection systems for ITER. In this study, the Global Model for Negative Hydrogen Ion Source based on volume-produced H− ions is developed to include surface-produced H− ions and is validated against experimental data obtained in a planar inductively coupled plasma discharge used for study of Cs effect on H− production. The H− density predicted by the model decreases three times with surface work function from 2.1 to 4.5 eV, achieving good agreement with the experimental results, as surface conversion yield of particles to H− ions shows exponential decline with surface work function. The model predicts the rise in neutral gas temperature remarkably enhances surface production but reduces volume production of H− ions, because of increase in surface conversion yield of H atoms to H− ions and in electron temperature, respectively. The dependences of H− production on surface work function and neutral gas temperature are analyzed by evaluating creation rates of the H− ions from different reaction pathways. The developed model can be applied for prediction of H− production in NHISs and ultimate parameter optimization of negative ion beams for fusion reactors.
High-pressure and high-temperature modulation of one-dimensional infinite chain in SeO2
Authors: Lu Wencheng , Liu Siyu , Cai Jinqun , Ning Ping , Ma Chuanheng , Liu Guangtao , Wang Hongbo , Guo Qing , Zhou Mi , Wang Yanchao , Ma Yanming
Published: April 2024

The structural evolution of lone-pair compounds under high-pressure and high-temperature conditions has been a subject of fundamental interest in revealing modulated polymorphs. As one of the archetypal lone-pair compounds, selenium dioxide (SeO2) has attracted much attention due to the pressure modulation of its one-dimensional infinite W-shaped chain arrangement. Here, through swarm intelligence algorithm in conjunction with the first-principles simulation, we propose the existence of an orthorhombic Pnma-SeO2 structure, characterized by V-shaped chains interconnected via vertex-sharing SeO3 pyramids. These V-shaped chains demonstrate reduced compressibility along their chain direction compared to the W-shaped chains. Calculations indicate that Pnma-SeO2 is a semiconductor with a large indirect bandgap of 2.39 eV. Remarkably, we synthesized the predicted Pnma-SeO2 in a laser-heated diamond anvil cell at a pressure of 48.5 or 87 GPa as identified by in situ synchrotron x-ray diffraction data. Our findings lead to a significant extension of the phase diagram and transition path of SeO2 and provide key insights into understanding the pressure modulation in lone-pair compounds.
Encapsulating perovskite solar cells for long-term stability and prevention of lead toxicity
Authors: Dipta Shahriyar Safat , Rahim Md. Arifur , Uddin Ashraf
Published: April 2024

Lead halide perovskite solar cells (PSCs) have achieved remarkable efficiencies comparable to those of their established silicon counterparts at a very fast pace. Moreover, solution-processable facile technologies offer low-cost, low-temperature, scalable fabrication of these solar cells. Numerous studies have focused on improving the performance, stability, and processing of PSCs. However, potential lead toxicity and poor long-term stability impede their commercialization. In recent years, several studies have developed novel encapsulants for PSCs that can simultaneously improve stability and impede potential lead leakage. Although improvements have been made on both fronts, no solution to date could achieve a level of stability and leakage prevention that could result in a market breakthrough. Here, we analyze PSC encapsulation and lead leakage prevention techniques undertaken in recent years. While most of the related studies focused on improving either stability or toxicity, we note that both can be solved together with a suitable encapsulant that is impermeable to both moisture and Pb2+ ions. In addition, the lack of a unified standard stability testing protocol has led to stability testing under a variety of temperatures, humidities, and environmental conditions. Therefore, the urgency for a standard protocol for stability and lead toxicity testing cannot be overlooked.
Confinement effect on the microcapillary flow and shape of red blood cells
Authors: Nouaman Mohammed , Darras Alexis , Wagner Christian , Recktenwald Steffen M.
Published: April 2024

The ability to change shape is essential for the proper functioning of red blood cells (RBCs) within the microvasculature. The shape of RBCs significantly influences blood flow and has been employed in microfluidic lab-on-a-chip devices, serving as a diagnostic biomarker for specific pathologies and enabling the assessment of RBC deformability. While external flow conditions, such as the vessel size and the flow velocity, are known to impact microscale RBC flow, our comprehensive understanding of how their shape-adapting ability is influenced by channel confinement in biomedical applications remains incomplete. This study explores the impact of various rectangular and square channels, each with different confinement and aspect ratios, on the in vitro RBC flow behavior and characteristic shapes. We demonstrate that rectangular microchannels, with a height similar to the RBC diameter in combination with a confinement ratio exceeding 0.9, are required to generate distinctive well-defined croissant and slipper-like RBC shapes. These shapes are characterized by their equilibrium positions in the channel cross section, and we observe a strong elongation of both stable shapes in response to the shear rate across the different channels. Less confined channel configurations lead to the emergence of unstable other shape types that display rich shape dynamics. Our work establishes an experimental framework to understand the influence of channel size on the single-cell flow behavior of RBCs, providing valuable insights for the design of biomicrofluidic single-cell analysis applications.
Freezing density scaling of transport coefficients in the Weeks–Chandler–Andersen fluid
Authors: Khrapak S. A. , Khrapak A. G.
Published: April 2024

It is shown that the transport coefficients (self-diffusion, shear viscosity, and thermal conductivity) of the Weeks–Chandler–Andersen (WCA) fluid along isotherms exhibit a freezing density scaling (FDS). The functional form of this FDS is essentially the same or closely related to those in the Lennard-Jones fluid, hard-sphere fluid, and some liquefied noble gases. This proves that this FDS represents a quasi-universal corresponding state principle for simple classical fluids with steep interactions. Some related aspects, such as a Stokes–Einstein relation without a hydrodynamic diameter and gas-to-liquid dynamical crossover, are briefly discussed. Simple fitting formulas for the transport coefficients of the dense WCA fluid are suggested.
Methacrylated gelatin hydrogel conjugated with ε-polylysine and enriched with platelet-rich plasma for chronically infected wounds
Authors: Yan Peiyu , Chen Xiangru , He Xin , Liu Zhaoyang , Sun Jing
Published: April 2024

While numerous hydrogel dressings are available for treating chronically infected wounds, their clinical application is impeded by intricate preparation processes, low mechanical strength, and frequent reliance on exogenous antimicrobial agents. The latter often leads to antibiotic misuse and compromises the bioactivity of cell growth-promoting substances. Therefore, the field of therapeutic treatment is faced with a pressing need to prepare high-mechanical-strength hydrogels through a facile procedure, achieving endogenous antibacterial characteristics and long-term healing abilities for chronically infected wounds. In this study, employing the Michael addition reaction principle, we conducted the conjugate addition of the natural antimicrobial poly amino acid, ε-polylysine (ε-PL), to gelatin methacrylate. This not only augmented the hydrogel’s mechanical strength but also preserved its antimicrobial efficacy. Subsequently, platelet-rich plasma (PRP), capable of releasing diverse growth factors, was introduced. Injectable and degradable hydrogels with high mechanical strength and water absorption were prepared through UV curing while retaining PRP bioactivity. The combination of PRP and ε-PL substantiated the enhanced antimicrobial properties and promotion of human umbilical vein endothelial cell growth, as validated through bacterial inhibition experiments, such as live-dead bacterial staining and cellular assays, including cell proliferation. Therefore, the as-developed PL-PRP hydrogel presents as a promising hydrogel dressing for the treatment of chronically infected wounds.
Fast fluid–structure interaction simulation method based on deep learning flow field modeling
Authors: Hu Jiawei , Dou Zihao , Zhang Weiwei
Published: April 2024

The rapid acquisition of high-fidelity flow field information is of great significance for engineering applications such as multi-field coupling. Current research in flow field modeling predominantly focuses on low Reynolds numbers and periodic flows, exhibiting weak generalization capabilities and notable issues with temporal inferring error accumulation. Therefore, we establish a reduced order model (ROM) based on Convolutional Auto-Encoder (CAE) and Long Short-Term Memory (LSTM) neural network and propose an unsteady flow field modeling method for the airfoil with a high Reynolds number and strong nonlinear characteristics. The attention mechanism and weak physical constraints are integrated into the model architecture to improve the modeling accuracy. A broadband excitation training strategy is proposed to overcome the error accumulation problem of long-term inferring. With only a small amount of latent codes, the relative error of the flow field reconstructed by CAE can be less than 5‰. By training LSTM with broadband excitation signals, stable dynamic evolution can be achieved in the time dimension. CAE-LSTM can accurately predict the forced response and complex limit cycle behavior of the airfoil in a wide range of amplitude and frequency under subsonic/transonic conditions. The relative errors of predicted variables and integral force are less than 1%. The fluid–structure interaction framework is built by coupling the ROM and motion equations of the structure. CAE-LSTM predicts the time series response of pitch displacement and moment coefficient at different reduced frequencies, which is in good agreement with computational fluid dynamics, and the simulation time savings exceed one order of magnitude.
Unveiling the underappreciated: The bonding features of C–H⋯S–S interactions observed from rotational spectroscopy
Authors: Lv Wenqi , Xu Yugao , Yang Tingting , Wang Liuting , Huang Jinxi , Huang Haiying , Feng Gang
Published: April 2024

The C–H⋯S–S interactions are fundamentally important to understand the stability of biomacromolecules and their binding with small molecules, but they are still underappreciated. Herein, we characterized the C–H⋯S–S interactions in model molecular complexes. The rotational spectra of the complexes of diethyl disulfide with CH2CH2 and CH2CHF were measured and analyzed. All the detected structures are mainly stabilized by a C–H⋯S–S hydrogen bond, providing stabilization energies of 2.3–7.2 kJ mol−1. Incidental C–H⋯π or C–H⋯F interactions enhance the stabilization of the complexes. London dispersion, which accounts for 54%–68% of the total attractions, is the main driving force of stabilization. The provided bonding features of C–H⋯S–S are crucial for understanding the stabilizing role of this type of interaction in diverse processes such as supramolecular recognition, protein stability, and enzyme activity.
Low-cost and convenient fabrication of polymer micro/nanopores with the needle punching process and their applications in nanofluidic sensing
Authors: Liu Rui , Liu Zhe , Li Jianfeng , Qiu Yinghua
Published: April 2024

Solid-state micro/nanopores play an important role in the sensing field because of their high stability and controllable size. Aiming at problems of complex processes and high costs in pore manufacturing, we propose a convenient and low-cost micro/nanopore fabrication technique based on the needle punching method. The thin film is pierced by controlling the feed of a microscale tungsten needle, and the size variations of the micropore are monitored by the current feedback system. Based on the positive correlation between the micropore size and the current threshold, the size-controllable preparation of micropores is achieved. The preparation of nanopores is realized by the combination of needle punching and chemical etching. First, a conical defect is prepared on the film with the tungsten needle. Then, nanopores are obtained by unilateral chemical etching of the film. Using the prepared conical micropores, resistive-pulse detection of nanoparticles is performed. Significant ionic current rectification is also obtained with our conical nanopores. It is proved that the properties of micro/nanopores prepared by our method are comparable to those prepared by the track-etching method. The simple and controllable fabrication process proposed here will advance the development of low-cost micro/nanopore sensors.
Dissociative photoionization of phenyl triflate, a photoacid generator for photolithography, at 92 eV
Authors: Laffert V. , Sajjadian F. S. , Richter R. , van Setten M. J. , Holzmeier F.
Published: April 2024

The dissociative photoionization of phenyl triflate (C6H5OSO2CF3), a neutral photoacid generator used in photolithography, was investigated in a gas phase experiment employing extreme ultraviolet (EUV) synchrotron radiation at 92 eV and photoelectron–photoion coincidence detection. The interaction of EUV photons with the molecule leads almost exclusively to dissociation, which is dominated by a sequential fragmentation mechanism, in which SO2, CF3, CO, and C2H2 are lost. For lithographic purposes, the lack of the observation of a fragment that could serve as a precursor for the formation of triflic acid means that the effective photoacid generator concentration in a photoresist is reduced, impacting its patterning performance in EUV lithography. A better understanding of the dissociative photoionization of photoresist components and proxies thereof can provide a crucial handle that guides the design of photoresists for the upcoming technology nodes with ever decreasing feature sizes for more powerful computer chips.
The march of change
Authors: Fitzgerald Richard J.
Published: April 2024

I’ve been at Physics Today for 25 1/2 years. When I joined the staff, the Physics Today website—indeed, the Web as we know it today—was in its infancy. Google was newly incorporated. Webpages were static. “Physics Today” meant Physics Today the magazine, its sole incarnation.
Highly charged uranium tests the limits of quantum electrodynamics
Authors: Lopatka Alex
Published: April 2024

Technical advances and clever correction schemes separated signals of quantum effects in heavy atoms from the noise.
Twisted bilayer graphene’s gallery of phases
Authors: Bernevig B. Andrei , Efetov Dmitri K.
Published: April 2024

The simultaneous occurrence of exotic phases, and the ability to easily tune them, has positioned magic-angle twisted bilayer graphene as one of the richest materials platforms in condensed-matter physics.
The many lives of an 11th-century astrolabe
Authors: Dahn Ryan
Published: April 2024

An art historian uncovers an astronomical device that exposes centuries of cross-cultural exchange.
Impact of specific electromagnetic radiation on wakefulness in mice
Authors: Deng Hu , Liu Lingyu , Tang Xiaping , Lu Yingxian , Wang Xiaofei , Zhao Yanyu , Shi Yigong
Published: April 2024

Electromagnetic radiation (EMR) in the environment, particularly in the microwave range, may constitute a public health concern. Exposure to 2.4 GHz EMR modulated by 100 Hz square pulses was recently reported to markedly increase wakefulness in mice. Here, we demonstrate that a similar wakefulness increase can be induced by the modulation frequency of 1,000 Hz, but not 10 Hz. In contrast to the carrier frequency of 2.4 GHz, 935 MHz EMR of the same power density has little impact on wakefulness irrespective of modulation frequency. Notably, the replacement of the 100 Hz square-pulsed modulation by sinusoidal-pulsed modulation of 2.4 GHz EMR still allows a marked increase of wakefulness. In contrast, continuous sinusoidal amplitude modulation of 100 Hz with the same time-averaged power output fails to trigger any detectable change of wakefulness. Therefore, alteration of sleep behavior by EMR depends upon not just carrier frequency but also frequency and mode of the modulation. These results implicate biological sensing mechanisms for specific EMR in animals.
The wooden artifacts from Schöningen’s Spear Horizon and their place in human evolution
Authors: Leder Dirk , Lehmann Jens , Milks Annemieke , Koddenberg Tim , Sietz Michael , Vogel Matthias , Böhner Utz , Terberger Thomas
Published: April 2024

Ethnographic records show that wooden tools played a pivotal role in the daily lives of hunter-gatherers including food procurement tools used in hunting (e.g., spears, throwing sticks) and gathering (e.g. digging sticks, bark peelers), as well as, domestic tools (e.g., handles, vessels). However, wood rarely survives in the archeological record, especially in Pleistocene contexts and knowledge of prehistoric hunter-gatherer lifeways is strongly biased by the survivorship of more resilient materials such as lithics and bones. Consequently, very few Paleolithic sites have produced wooden artifacts and among them, the site of Schöningen stands out due to its number and variety of wooden tools. The recovery of complete wooden spears and throwing sticks at this 300,000-y-old site (MIS 9) led to a paradigm shift in the hunter vs. scavenger debate. For the first time and almost 30 y after their discovery, this study introduces the complete wooden assemblage from Schöningen 13 II-4 known as the Spear Horizon. In total, 187 wooden artifacts could be identified from the Spear Horizon demonstrating a broad spectrum of wood-working techniques, including the splitting technique. A minimum of 20 hunting weapons is now recognized and two newly identified artifact types comprise 35 tools made on split woods, which were likely used in domestic activities. Schöningen 13 II-4 represents the largest Pleistocene wooden artifact assemblage worldwide and demonstrates the key role woodworking had in human evolution. Finally, our results considerably change the interpretation of the Pleistocene lakeshore site of Schöningen.
Analysis of pea mutants reveals the conserved role of
FRUITFULL
controlling the end of flowering and its potential to boost yield
Authors: Martínez-Fernández Irene , Fourquin Chloe , Lindsay Donna , Berbel Ana , Balanzà Vicente , Huang Shaoming , Dalmais Marion , LeSignor Christine , Bendahmane Abdelhafid , Warkentin Thomas D. , Madueño Francisco , Ferrándiz Cristina
Published: April 2024

Monocarpic plants have a single reproductive phase in their life. Therefore, flower and fruit production are restricted to the length of this period. This reproductive strategy involves the regulation of flowering cessation by a coordinated arrest of the growth of the inflorescence meristems, optimizing resource allocation to ensure seed filling. Flowering cessation appears to be a regulated phenomenon in all monocarpic plants. Early studies in several species identified seed production as a major factor triggering inflorescence proliferative arrest. Recently, genetic factors controlling inflorescence arrest, in parallel to the putative signals elicited by seed production, have started to be uncovered in Arabidopsis, with the MADS-box gene
FRUITFULL (FUL)
playing a central role in the process. However, whether the genetic network regulating arrest is also at play in other species is completely unknown. Here, we show that this role of
FUL
is not restricted to Arabidopsis but is conserved in another monocarpic species with a different inflorescence structure, field pea, strongly suggesting that the network controlling the end of flowering is common to other plants. Moreover, field trials with lines carrying mutations in pea
FUL
genes show that they could be used to boost crop yield.
Regulation of adaptive growth decisions via phosphorylation of the TRAPPII complex in Arabidopsis
Authors: Wiese Christian , Abele Miriam , Al Benjamin , Altmann Melina , Steiner Alexander , Kalbfuß Nils , Strohmayr Alexander , Ravikumar Raksha , Park Chan Ho , Brunschweiger Barbara , Meng Chen , Facher Eva , Ehrhardt David W. , Falter-Braun Pascal , Wang Zhi-Yong , Ludwig Christina , Assaad Farhah F.
Published: April 2024

Plants often adapt to adverse or stress conditions via differential growth. The trans-Golgi network (TGN) has been implicated in stress responses, but it is not clear in what capacity it mediates adaptive growth decisions. In this study, we assess the role of the TGN in stress responses by exploring the previously identified interactome of the Transport Protein Particle II (TRAPPII) complex required for TGN structure and function. We identified physical and genetic interactions between AtTRAPPII and shaggy-like kinases (GSK3/AtSKs) and provided in vitro and in vivo evidence that the TRAPPII phosphostatus mediates adaptive responses to abiotic cues. AtSKs are multifunctional kinases that integrate a broad range of signals. Similarly, the AtTRAPPII interactome is vast and considerably enriched in signaling components. An AtSK–TRAPPII interaction would integrate all levels of cellular organization and instruct the TGN, a central and highly discriminate cellular hub, as to how to mobilize and allocate resources to optimize growth and survival under limiting or adverse conditions.
p24 family Tango(1) at the endoplasmic reticulum exit site to organize cargo exit
Authors: Saito Kota , Maeda Miharu
Published: April 2024

The p24 family of proteins have been regarded as cargo receptors for endoplasmic reticulum (ER) to Golgi transport; however, their precise functions have yet to be revealed. In this issue, Pastor-Pareja and colleagues (https://doi.org/10.1083/jcb.202309045) show that the interaction of these proteins with Tango1 is critical for their localization at the ER exit site (ERES) and efficient transport of secretory proteins in Drosophila.
Rotating effects on the thermophysical properties of a two-dimensional GaAs quantum ring
Authors: Ghanbari Ahmad
Published: April 2024

In this work, we have investigated the rotating effect on the thermodynamic properties of a 2D quantum ring. Accordingly, we have considered the radial potential of a 2D quantum ring and solved the Schrödinger equation in the presence of the Aharonov–Bohm effect and a uniform magnetic field for the considered potential. According to the solution of the equation, we calculated the eigenvalues and eigenfunctions of the considered system. Using the calculated energy spectrum, we obtained the partition function and thermodynamic properties of the system, such as the mean energy, specific heat, entropy and free energy. Our results show that the rotating effect has a significant influence on the thermophysical properties of a 2D quantum ring. We also study other effects of the rotating term: (1) the effect of different values of rotating parameters, and (2) the effect of negative rotation on the thermodynamic properties of the system. Our results are discussed in detail.
Capture Efficiency Analysis in the Circular Restricted Three-body Problem
Authors: Miao Yu-Xuan , Hou Xi-Yun
Published: April 2024

Temporary capture efficiency is studied in the framework of the circular restricted three-body problem in two steps. First, a non-uniform distribution of test particles around the secondary’s orbit is obtained by fully accounting the secondary’s gravitational influence. Second, the capture efficiency is computed based on the non-uniform distribution. Several factors influencing the result are discussed. By studying the capture efficiency in the circular restricted three-body problem of different mass ratios, a power-law relation between the capture efficiency (p) and the mass ratio (μ) is established, which is given by p ≈ 0.27 × μ
0.53, within the range of 3.0035 ×10−6 ≤ μ ≤ 3.0034 × 10−5. Taking the Sun–Earth system as an example, the influence from the orbit eccentricity of the secondary on the non-uniform distribution and the capture efficiency is studied. Our studies find that the secondary’s orbit eccentricity has a negative influence on the capture efficiency.
The penetration depth of atomic radicals in tubes with catalytic surface properties
Authors: PAUL Domen , MOZETIČ Miran , ZAPLOTNIK Rok , VESEL Alenka , PRIMC Gregor , ÐONLAGIČ Denis
Published: April 2024

Catalysis of molecular radicals is often performed in interesting experimental configurations. One possible configuration is tubular geometry. The radicals are introduced into the tubes on one side, and stable molecules are exhausted on the other side. The penetration depth of radicals depends on numerous parameters, so it is not always feasible to calculate it. This article presents systematic measurements of the penetration depth of oxygen atoms along tubes made from nickel, cobalt, and copper. The source of O atoms was a surfatron-type microwave plasma. The initial density of O atoms depended on the gas flow and was 0.7×1021 m−3, 2.4×1021 m−3, and 4.2×1021 m−3 at the flow rates of 50, 300, and 600 sccm, and pressures of 10, 35, and 60 Pa, respectively. The gas temperature remained at room temperature throughout the experiments. The dissociation fraction decreased exponentially along the length of the tubes in all cases. The penetration depths for well-oxidized nickel were 1.2, 1.7, and 2.4 cm, respectively. For cobalt, they were slightly lower at 1.0, 1.3, and 1.6 cm, respectively, while for copper, they were 1.1, 1.3, and 1.7 cm, respectively. The results were explained by gas dynamics and heterogeneous surface association. These data are useful in any attempt to estimate the loss of molecular fragments along tubes, which serve as catalysts for the association of various radicals to stable molecules.
IMPRINTS.CETSA and IMPRINTS.CETSA.app: an R package and a Shiny application for the analysis and interpretation of IMPRINTS-CETSA data
Authors: Gerault Marc-Antoine , Granjeaud Samuel , Camoin Luc , Nordlund Pär , Dai Lingyun
Published: April 2024

IMPRINTS-CETSA (Integrated Modulation of Protein Interaction States—Cellular Thermal Shift Assay) provides a highly resolved means to systematically study the interactions of proteins with other cellular components, including metabolites, nucleic acids and other proteins, at the proteome level, but no freely available and user-friendly data analysis software has been reported. Here, we report IMPRINTS.CETSA, an R package that provides the basic data processing framework for robust analysis of the IMPRINTS-CETSA data format, from preprocessing and normalization to visualization. We also report an accompanying R package, IMPRINTS.CETSA.app, which offers a user-friendly Shiny interface for analysis and interpretation of IMPRINTS-CETSA results, with seamless features such as functional enrichment and mapping to other databases at a single site. For the hit generation part, the diverse behaviors of protein modulations have been typically segregated with a two-measure scoring method, i.e. the abundance and thermal stability changes. We present a new algorithm to classify modulated proteins in IMPRINTS-CETSA experiments by a robust single-measure scoring. In this way, both the numerical changes and the statistical significances of the IMPRINTS information can be visualized on a single plot. The IMPRINTS.CETSA and IMPRINTS.CETSA.app R packages are freely available on GitHub at https://github.com/nkdailingyun/IMPRINTS.CETSA and https://github.com/mgerault/IMPRINTS.CETSA.app, respectively. IMPRINTS.CETSA.app is also available as an executable program at https://zenodo.org/records/10636134.
SpatialcoGCN: deconvolution and spatial information–aware simulation of spatial transcriptomics data via deep graph co-embedding
Authors: Yin Wang , Wan You , Zhou Yuan
Published: April 2024

Spatial transcriptomics (ST) data have emerged as a pivotal approach to comprehending the function and interplay of cells within intricate tissues. Nonetheless, analyses of ST data are restricted by the low spatial resolution and limited number of ribonucleic acid transcripts that can be detected with several popular ST techniques. In this study, we propose that both of the above issues can be significantly improved by introducing a deep graph co-embedding framework. First, we establish a self-supervised, co-graph convolution network–based deep learning model termed SpatialcoGCN, which leverages single-cell data to deconvolve the cell mixtures in spatial data. Evaluations of SpatialcoGCN on a series of simulated ST data and real ST datasets from human ductal carcinoma in situ, developing human heart and mouse brain suggest that SpatialcoGCN could outperform other state-of-the-art cell type deconvolution methods in estimating per-spot cell composition. Moreover, with competitive accuracy, SpatialcoGCN could also recover the spatial distribution of transcripts that are not detected by raw ST data. With a similar co-embedding framework, we further established a spatial information–aware ST data simulation method, SpatialcoGCN-Sim. SpatialcoGCN-Sim could generate simulated ST data with high similarity to real datasets. Together, our approaches provide efficient tools for studying the spatial organization of heterogeneous cells within complex tissues.
Graphormer supervised de novo protein design method and function validation
Authors: Mu Junxi , Li Zhengxin , Zhang Bo , Zhang Qi , Iqbal Jamshed , Wadood Abdul , Wei Ting , Feng Yan , Chen Hai-Feng
Published: April 2024

Protein design is central to nearly all protein engineering problems, as it can enable the creation of proteins with new biological functions, such as improving the catalytic efficiency of enzymes. One key facet of protein design, fixed-backbone protein sequence design, seeks to design new sequences that will conform to a prescribed protein backbone structure. Nonetheless, existing sequence design methods present limitations, such as low sequence diversity and shortcomings in experimental validation of the designed functional proteins. These inadequacies obstruct the goal of functional protein design. To improve these limitations, we initially developed the Graphormer-based Protein Design (GPD) model. This model utilizes the Transformer on a graph-based representation of three-dimensional protein structures and incorporates Gaussian noise and a sequence random masks to node features, thereby enhancing sequence recovery and diversity. The performance of the GPD model was significantly better than that of the state-of-the-art ProteinMPNN model on multiple independent tests, especially for sequence diversity. We employed GPD to design CalB hydrolase and generated nine artificially designed CalB proteins. The results show a 1.7-fold increase in catalytic activity compared to that of the wild-type CalB and strong substrate selectivity on p-nitrophenyl acetate with different carbon chain lengths (C2–C16). Thus, the GPD method could be used for the de novo design of industrial enzymes and protein drugs. The code was released at https://github.com/decodermu/GPD.
ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles
Authors: Wei Junkang , Xiao Jin , Chen Siyuan , Zong Licheng , Gao Xin , Li Yu
Published: April 2024

The rapid growth in the number of experimental and predicted protein structures and more complicated protein structures poses a significant challenge for computational biology in leveraging structural information and accurate representation of protein surface properties. Recently, AlphaFold2 released the comprehensive proteomes of various species, and protein surface property representation plays a crucial role in protein-molecule interaction predictions, including those involving proteins, nucleic acids and compounds. Here, we proposed the first extensive database, namely ProNet DB, that integrates multiple protein surface representations and RNA-binding landscape for 326 175 protein structures. This collection encompasses the 16 model organism proteomes from the AlphaFold Protein Structure Database and experimentally validated structures from the Protein Data Bank. For each protein, ProNet DB provides access to the original protein structures along with the detailed surface property representations encompassing hydrophobicity, charge distribution and hydrogen bonding potential as well as interactive features such as the interacting face and RNA-binding sites and preferences. To facilitate an intuitive interpretation of these properties and the RNA-binding landscape, ProNet DB incorporates visualization tools like Mol* and an Online 3D Viewer, allowing for the direct observation and analysis of these representations on protein surfaces. The availability of pre-computed features enables instantaneous access for users, significantly advancing computational biology research in areas such as molecular mechanism elucidation, geometry-based drug discovery and the development of novel therapeutic approaches.

Database URL:  https://proj.cse.cuhk.edu.hk/aihlab/pronet/.
Effects of different dietary lipid levels on physiological metabolism and odor quality of hepatopancreas in adult female Chinese mitten crab (Eriocheir sinensis)
Authors: Wu Jingjing , Zhang Long , Jiang Xiaodong , Wu Xugan , Wang Xichang
Published: April 2024

Objectives

This study aimed to investigate the impact of different dietary lipid levels on the physiological metabolism and odor quality of adult female Eriocheir sinensis during the fattening phase.

Materials and Methods

Five dietary schemes, each containing different total lipid levels (4%, 7%, 10%, 13%, and 16%), were administered over a 60-d fattening period for adult female crab (approximately 50 g, n=60). Chromatography and spectroscopy techniques were used for the detection of aroma and key aroma precursors.

Results

Dietary lipids had no significant effect on growth performance and hepatopancreas index (P<0.05). The carotenoid content showed an increasing and then decreasing trend, with a significant increase to 1312.51 mg/kg (P<0.05) at 7% lipid content of the diet. In contrast, a diet with a 13% lipid level led to a significant increase in total unsaturated fatty acids (115.3 mg/g, P<0.05), which maximized the contents of major fatty acids (oleic, linoleic, and linolenic, among others), and presented a fluctuating trend. A diet with higher lipid levels (16%) inhibited fatty acid accumulation. Moreover, a 13% dietary lipid level enhanced characteristic aroma compounds (for example, nonanal, octanal, hexanal, 3-methylbutanal, and 2-heptanone) in E. sinensis cooked hepatopancreas. Through an orthogonal partial least squares discriminant analysis model, it becomes evident that lipids and carotenoids together promote aroma formation in hepatopancreas.

Conclusions

Based on the current findings, the optimal dietary lipid level for enhancing the odor quality of hepatopancreas in adult female E. sinensis during the fattening phase was 13%. This study provides more precise options for the high-quality cultivation of E. sinensis.
Quantitative genetic analysis of attractiveness of yeast products to Drosophila
Authors: Yan Weiru , Li Yishen , Louis Edward J , Kyriacou Charalambos P , Hu Yue , Cordell Rebecca L , Xie Xiaodong
Published: April 2024

An attractive perfume is a complex mixture of compounds, some of which may be unpleasant on their own. This is also true for the volatile combinations from yeast fermentation products in vineyards and orchards when assessed by Drosophila. Here, we used crosses between a yeast strain with an attractive fermentation profile and another strain with a repulsive one and tested fly responses using a T-maze. QTL analysis reveals allelic variation in four yeast genes, namely PTC6, SAT4, YFL040W, and ARI1, that modulated expression levels of volatile compounds [assessed by gas chromatography–mass spectrometry (GC–MS)] and in different combinations, generated various levels of attractiveness. The parent strain that is more attractive to Drosophila has repulsive alleles at two of the loci, while the least attractive parent has attractive alleles. Behavioral assays using artificial mixtures mimicking the composition of odors from fermentation validated the results of GC–MS and QTL mapping, thereby directly connecting genetic variation in yeast to attractiveness in flies. This study can be used as a basis for dissecting the combination of olfactory receptors that mediate the attractiveness/repulsion of flies to yeast volatiles and may also serve as a model for testing the attractiveness of pest species such as Drosophila suzukii to their host fruit.
Inhibition of DAPK3 Suppresses Radiation-Induced Cellular Senescence by Activation of a PGC1α-Dependent Metabolism Pathway in Brain Endothelial Cells
Authors: Park Ji-Eun , Park Jeong Woo , Sim Myong-Kyu , Kim So Ra , Kim Kwang Seok
Published: April 2024

In the brain, environmental changes, such as neuroinflammation, can induce senescence, characterized by the decreased proliferation of neurons and dendrites and synaptic and vascular damage, resulting in cognitive decline. Senescence promotes neuroinflammatory disorders by senescence-associated secretory phenotypes and reactive oxygen species. In human brain microvascular endothelial cells (HBMVECs), we demonstrate that chronological aging and irradiation increase death-associated protein kinase 3 (DAPK3) expression. To confirm the role of DAPK3 in HBMVEC senescence, we disrupted DAPK3 activity using small interfering RNA (siRNA) or a dominant-negative mutant (DAPK3-P216S), which reduced cellular senescence phenotypes, as assessed by changes in tube formation, senescence-associated beta-galactosidase activity, and cell proliferation. In endothelial cells, DAPK3 promotes cellular senescence by regulating the phosphorylation and inactivation of peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC1α) via the protein kinase B pathway, resulting in the decreased expression of mitochondrial metabolism-associated genes, such as ATP5G1, BDNF, and COX5A. Our studies show that DAPK3 is involved in cellular senescence and PGC1α regulation, suggesting that DAPK3 regulation may be important for treating aging-related brain diseases or the response to radiation therapy.