bluuebunny/crossref_metadata_2025 huggingface dataset:
Which molecules can challenge density-functional tight-binding methods in evaluating the energies of conformers? investigation with machine-learning toolset
Authors: Terets Andrii , Nikolaienko Tymofii
Published: March 2024

Large organic molecules and biomolecules can adopt multiple conformations, with the occurrences determined by their relative energies. Identifying the energetically most favorable conformations is crucial, especially when interpreting spectroscopic experiments conducted under cryogenic conditions. When the effects of irregular surrounding medium, such as noble gas matrices, on the vibrational properties of molecules become important, semi-empirical (SE) quantum-chemical methods are often employed for computational simulations. Although SE methods are computationally more efficient than first-principle quantum-chemical methods, they can be inaccurate in determining the energies of conformers in some molecules while displaying good accuracy in others. In this study, we employ a combination of advanced machine learning techniques, such as graph neural networks, to identify molecules with the highest errors in the relative energies of conformers computed by the semi-empirical tight-binding method GFN1-xTB. The performance of three different machine learning models is assessed by comparing their predicted errors with the actual errors in conformer energies obtained via the GFN1-xTB method. We further applied the ensemble machine-learning model to a larger collection of molecules from the ChEMBL database and identified a set of molecules as being challenging for the GFN1-xTB method. These molecules hold potential for further improvement of the GFN1-xTB method, showcasing the capability of machine learning models in identifying molecules that can challenge its physical model.
Unusual bending patterns of spermidine3+ bound to DNA double helix
Authors: Perepelytsya Sergiy , Vasiliu Tudor , Laaksonen Aatto , Engelbrecht Leon De Villiers , Mocci Francesca
Published: March 2024

Natural polyamines play a fundamental role in the cell cycle. Despite being recognized as the most abundant organic counterions of DNA in the cell nucleus, their interactions with DNA have not been fully characterized. In a recent work [S. Perepelytsya, T. Vasiliu, A. Laaksonen, L. Engelbrecht, G. Brancato, and F. Mocci, J. Molec. Liq.389, 122828 (2023)], we have shown how the interactions between spermidine3+ and the DNA double helix induce significant conformational variations in the polyamine molecule. Specifically, we found that DNA induces conformations that are not observed in solution. Following that study, we present here a detailed investigation of the most compact conformation of the polyamine, analyzing its connection to the interaction with the DNA duplex. The analysis reveals that anomalous bent conformations of the spermidine3+ molecule result from the interaction of all three amino groups of the polyamine with the DNA phosphate groups on the minor groove side of the double helix. The changes in dihedral angles of the bent spermidine3+ molecule can be explained in terms of conformational transformations of six- and seven-membered rings, analogous to cyclohexane and cycloheptane. The analysis of the position of spermidine3+ molecule along the DNA surface reveals a sequence specificity of this binding mode with a marked preference for the narrow minor groove of A-tracts. The formation of the anomalous bent conformations of spermidine3+ in the complex with the DNA double helix is expected to be of paramount importance in understanding the mechanisms underlying DNA’s biological function.
Comparison of phase diagrams of H2O, D2O, and inert substances
Authors: Bulavin L. A. , Rudnikov Ye. G. , Lebovka N. I.
Published: March 2024

The phase diagrams for the light H2O, heavy D2O water, and inert substances (Ne, Ar, Kr, and Xe) have been compared. A method of choosing the starting point for entropy and internal energy was proposed. It allowed testing the principle of corresponding states using caloric variables. In the given coordinates of temperature, pressure, and chemical potential, the water isotopologues form one group of substances and have similar phase diagrams. The inert substances in the same coordinates form another group of substances with similar phase diagrams. The phase diagrams for inert Ne with significant de Boer quantum parameters differ to a certain extent from the phase diagrams of other inert substances.
Direct and inverse resonance problems for the massless Dirac operator on the half line
Authors: Xu Xiao-Chuan , Zuo Ting-Ting
Published: March 2024

For the direct problem, we give the asymptotic distribution of the resonances in the complex plane. For the inverse problem, we prove several uniqueness theorems of recovering the potential on the whole interval from partial resonances and the information of the potential on a subinterval.
Using machine learning with atomistic surface and local water features to predict heterogeneous ice nucleation
Authors: Soni Abhishek , Patey G. N.
Published: March 2024

Heterogeneous ice nucleation (HIN) has applications in climate science, nanotechnology, and cryopreservation. Ice nucleation on the earth’s surface or in the atmosphere usually occurs heterogeneously involving foreign substrates, known as ice nucleating particles (INPs). Experiments identify good INPs but lack sufficient microscopic resolution to answer the basic question: What makes a good INP? We employ molecular dynamics (MD) simulations in combination with machine learning (ML) to address this question. Often, the large amount of computational cost required to cross the nucleation barrier and observe HIN in MD simulations is a practical limitation. We use information obtained from short MD simulations of atomistic surface and water models to predict the likelihood of HIN. We consider 153 atomistic substrates with some surfaces differing in elemental composition and others only in terms of lattice parameters, surface morphology, or surface charges. A range of water features near the surface (local) are extracted from short MD simulations over a time interval (≤300 ns) where ice nucleation has not initiated. Three ML classification models, Random Forest (RF), support vector machine, and Gaussian process classification are considered, and the accuracies achieved by all three approaches lie within their statistical uncertainties. Including local water features is essential for accurate prediction. The accuracy of our best RF classification model obtained including both surface and local water features is 0.89 ± 0.05. A similar accuracy can be achieved including only local water features, suggesting that the important surface properties are largely captured by the local water features. Some important features identified by ML analysis are local icelike structures, water density and polarization profiles perpendicular to the surface, and the two-dimensional lattice match to ice. We expect that this work, with its strong focus on realistic surface models, will serve as a guide to the identification or design of substrates that can promote or discourage ice nucleation.
Data-driven modeling and forecasting of chaotic dynamics on inertial manifolds constructed as spectral submanifolds
Authors: Liu Aihui , Axås Joar , Haller George
Published: March 2024

We present a data-driven and interpretable approach for reducing the dimensionality of chaotic systems using spectral submanifolds (SSMs). Emanating from fixed points or periodic orbits, these SSMs are low-dimensional inertial manifolds containing the chaotic attractor of the underlying high-dimensional system. The reduced dynamics on the SSMs turn out to predict chaotic dynamics accurately over a few Lyapunov times and also reproduce long-term statistical features, such as the largest Lyapunov exponents and probability distributions, of the chaotic attractor. We illustrate this methodology on numerical data sets including delay-embedded Lorenz and Rössler attractors, a nine-dimensional Lorenz model, a periodically forced Duffing oscillator chain, and the Kuramoto–Sivashinsky equation. We also demonstrate the predictive power of our approach by constructing an SSM-reduced model from unforced trajectories of a buckling beam and then predicting its periodically forced chaotic response without using data from the forced beam.
Determining thermal activation parameters for ferroelectric domain nucleation in BaTiO3 from molecular dynamics simulations
Authors: Durdiev Dilshod , Zaiser Michael , Wendler Frank , Tsuzuki Takahiro , Azuma Hikaru , Ogata Shuji , Kobayashi Ryo , Uranagase Masayuki
Published: March 2024

Polarization switching in ferroelectric hysteresis of BaTiO3 proceeds by localized nucleation and subsequent growth of domains of reverse polarization. While this process is driven by the applied electric field, thermal activation can play an important role in domain nucleation. As a consequence of the stochastic nature of thermal activation, coercive fields in small systems exhibit a significant scatter. It is demonstrated that the statistics of coercive fields observed in molecular dynamics simulations is consistent with the statistical distribution expected for field-assisted thermally activated nucleation of reverse polarization domains. The excellent quantitative agreement between the simulation data and the theory of thermally activated processes provides strong evidence that polarization switching occurs by nucleation-and-growth rather than loss of the local minimum of the Gibbs free energy function. In a pristine crystal, switching is controlled by the field at which thermal fluctuations can create a critical nucleus in the bulk (homogeneous nucleation). The analysis of crystals with various vacancy-type defects demonstrates that such defects may enable heterogeneous nucleation at reduced fields. In both cases, the statistical analysis gives access to the respective activation energies, their field dependence, and the sizes of the critical nuclei.
Gas temperature measurements from ps-TALIF in highly collisional plasmas
Authors: Siby Abdoulaye , Stefas Dimitrios , Agha Yanis , Invernizzi Laurent , Gazeli Kristaq , Lombardi Guillaume , Hassouni Khaled , Prasanna Swaminathan
Published: March 2024

In this work, we present a straightforward approach to retrieve gas temperatures directly from the effective lifetime τH of the ps-laser excited species measured with picosecond Two Photon Absorption Laser Induced Fluorescence (ps-TALIF). This approach allows for simultaneous measurements of absolute atom densities and gas temperatures performed in moderate-pressure reactive plasmas using an advanced ps-TALIF diagnostic and has been demonstrated for highly collisional hydrogen microplasmas. Furthermore, this methodology was applied to obtain a 2D distribution of gas temperature and H-atom densities in the downstream region of the microplasma discharge.
Kinetic instability of whistlers in electron beam-plasma systems
Authors: Paul Anjan , Sharma Devendra
Published: March 2024

The whistlers in space plasmas and in magnetic fusion experiments are destabilized by beams of fast electrons. While the linear regime of instability is analytically tractable, in most practical cases, the instability operates at the saturated level during the stages of observation and measurement. The saturated states, however, involve nonlinear whistlers, which remain best accessible for analysis by kinetic simulations. Results of electromagnetic Vlasov simulations are presented, analyzing an anisotropic electron beam driven whistler instability. The simulations cover the initially unstable regime followed by a saturated or marginally stable regime. Both regimes are separated by an intermediate nonlinear regime during which the electron distribution undergoes a kinetically self-consistent modification. A linearly obtained generalized marginal stability condition is applied to the stabilized state. The condition obtained in its dispersive version shows the β|| at threshold and, in turn, the residual anisotropy, to be a function of the whistler mode number k.
Effects of Zr dopants on properties of PtNi nanoparticles for ORR catalysis: A DFT modeling
Authors: Farris Riccardo , Merinov Boris V. , Bruix Albert , Neyman Konstantin M.
Published: March 2024

Pt-based alloys, such as Pt3Ni, are among the best electrocatalysts for oxygen reduction reaction (ORR) in polymer electrolyte membrane fuel cells. Doping of PtNi alloys with Zr was shown to enhance the durability of the operating ORR catalysts. Rationalizing these observations is hindered by the absence of atomic-level data for these tri-metallic materials, even when not exposed to the fuel cell operation conditions. This study aims at understanding structure–property relations in Zr-doped PtNi nanoparticles as a key to their ORR function. In particular, we calculated, using a method based on density functional theory, the most stable chemical orderings of pristine and Zr-doped Pt3Ni particles containing over 400 atoms. We thus clarify (i) preferential location and charge states of Zr atoms in the Pt3Ni NPs; (ii) effect of doping Zr atoms on the stability of the Pt skin of the Pt3Ni NPs; (iii) charge redistribution induced by Zr dopants; (iv) layer-by-layer atomic ordering in the Pt3Ni/Zr NPs with the increasing Zr content; and (v) effect of Zr atoms on the adsorption energies of O and OH species as indicators of the ORR activity.
Electronic resonances in expanding non-neutral ultracold plasma
Authors: Bronin S. Ya. , Vikhrov E. V. , Saakyan S. A. , Zelener B. B. , Zelener B. V.
Published: March 2024

Calculations of the spectrum of eigen oscillations of an inhomogeneous ultracold plasma are presented both in the absence and in the presence of charge imbalance. The collective modes of these plasma oscillations are recorded in experiments as absorption resonances of a radio frequency electric field. It is shown that in the presence of friction of the electronic component, a discrete spectrum of plasma eigen oscillations is formed. The dependence of the frequency of these resonances on the plasma expansion time in the presence of a charge imbalance is obtained. There is good agreement with the experiments of different authors.
A study on dynamic pressure sensor based on Pitot tube structure
Authors: Yu Hao , Wang Xiaofeng , Liu Yan , Bai Fan
Published: March 2024

To meet the demand for the accurate measurements of the dynamic pressure of a shock wave, a composite dynamic pressure sensor design method is proposed based on the formation mechanism, propagation characteristics, special testing environment of the dynamic pressure, and Pitot tube structure. The dynamic pressure of the shock wave is evaluated by the total pressure and static pressure units installed in the composite sensor. FLUENT simulation software was used to analyze the aerodynamic characteristics of the dynamic pressure sensor, and parameters such as the structural size and inlet position of the sensor were determined. In response to the special experimental environment of the shock wave, the requirements for the dynamic pressure measurements under damage conditions were analyzed, and a dynamic pressure testing system was established. Dynamic pressure tests with four 2,4,6-trinitrotoluene [C7H5(NO2)3] equivalents of 1, 2, 15, and 20 kg were carried out. The experimental results show that the proposed sensor design method can accurately and effectively measure the dynamic pressure signal, and the dynamic pressure gain multiple decreases with an increase in the proportional distance. This provides an effective testing method for evaluating the dynamic pressure damage effect of ammunition systems.
Measurement of nonequilibrium vortex propagation dynamics in a nonlinear medium
Authors: Ford Patrick C. , Voitiv Andrew A. , Zhu Chuanzhou , Lusk Mark T. , Siemens Mark E.
Published: March 2024

We observe and measure the nonequilibrium dynamics of optical vortices as a function of propagation distance through a nonlinear medium. The precession of a tilted-core vortex is quantified as is vortex core sharpening, where the infinite width of a linear core subsequently shrinks and approaches the healing length of this nonlinear optical fluid. Experiments are performed with a variable-length nonlinear medium: a nonlinear fluid in a tank with an output window on a translating tube. This provides control over the distance the light propagates in the fluid and allows for the measurement of the dynamics throughout the propagation range. Results are compared with the predictions of a computational simulator to find the equivalent dimensionless nonlinear coefficient.
Corrosion of welding reinforcement height under dynamic conditions
Authors: Dou Xiaohui , Li Hu , Xiang Wei , Zhang Xinwei , He Zonghao , Zhang Dalei , Li Bin , Li Yan
Published: March 2024

The presence of welding reinforcement height (WRH) within oil and gas pipelines can lead to micro-turbulence in localized areas during transportation, resulting in corrosion failure. This study employed a modular reconstruction method to simulate and reconstruct X80 steel welded joints, and investigated the erosion-corrosion behavior at the WRH using wire beam microelectrode, electrochemical impedance spectroscopy, and computational fluid dynamics simulations. The results show that the galvanic current density (GCD) in the weld metal exhibits cathodic behavior, while the GCD in the base metal and heat-affected zone shows anodic behavior. The top of WRH is susceptible to corrosion failure. As the radius of WRH increases, the corrosion rate also increases. Additionally, the corrosion rate increases similarly with an increase in flow velocity. The galvanic corrosion intensity factor (g) is 0.24, and the local corrosion is moderate. This work has scientific significance in ensuring the long-term safe operation of pipelines and reducing the risk of corrosion failure.
Viscoplastic elliptical objects impacting a solid surface
Authors: Isukwem Kindness , Nemer Ramy , Hachem Elie , Pereira Anselmo
Published: March 2024

This theoretical and numerical study focuses on the physical mechanism driving the spreading of viscoplastic elliptical millimetric/centimetric objects after they impact a solid surface under no-slip conditions. The two-dimensional impacting objects are described as Bingham fluids. The two-dimensional numerical simulations are based on a variational multi-scale approach devoted to multiphase non-Newtonian fluid flows. The obtained results are analyzed considering the spreading dynamics, energy budgets and scaling laws. They show that, under negligible capillary effects, the impacting kinetic energy of the elliptical objects is dissipated through viscoplastic effects during the spreading process, giving rise to three flow regimes: inertio-viscous, inertio-plastic, and mixed inertio-visco-plastic. These regimes are strongly affected by the initial aspect ratio of the impacting objects, which reveals the possibility of using morphology to control spreading. Finally, the results are summarized in a diagram linking the object's maximum spreading and spreading time with different spreading regimes through a single dimensionless parameter called impact number.
The complex unsteady flow exploration of a contra-rotating rotor under inlet distortion
Authors: Zhang K. , Liu Y.
Published: March 2024

This article explores the relationship between stall types and speed ratios in contra-rotating boost stages, discovering stationary circumferential stall cells and dual stall cell phenomena, and examines the relationship between stall characteristics and inlet distortions. These stall characteristics of counter-rotating boost stages are markedly different from the single stall patterns of traditional compressor rotor-stator structures, highlighting the complexity of the flow field in counter-rotating stages. The study uses the experimental methods to investigate different speed ratios under both uniform and distorted inlet conditions, conducting both accelerating and decelerating stall tests, with each stall condition analyzed using data from 25 s. The main focus is on the stall types, frequencies, and development patterns under different distortion conditions at various speed ratios, filling a research gap in counter-rotating boost stages. It explores the unstable flow characteristics of counter-rotating boost stages under distorted conditions, particularly the stall disturbance characteristics and pressure fluctuation patterns at the blade tip during stall entry and recovery under distortions. Comparing distortions with uniform inlet conditions provides an intuitive understanding of the influence of various types of distortions on wall pressure and stall in the flow field. Researchers can use this knowledge to design casings or blowing devices to suppress stall disturbances, thereby achieving stall prevention and enhancing stability.
In situ annealing optimization by anomalous Hall effect for a high-entropy alloy
Authors: Min Huiqian , Wang Zhenhua , Wu Jianlong , Sun Hang , Wang Qing , Qiu Zhiyong
Published: March 2024

An in situ methodology was devised to refine the annealing parameters for a soft magnetic high-entropy alloy, Al0.7NiCoFe1.5Cr1.5. Anomalous Hall measurements were employed to elucidate the magnetic characteristics in real time during annealing. This approach facilitates the determination of an optimal annealing temperature range, centered approximately at 500 °C, within a single annealing process. After annealing, a notable 51.5% enhancement in the saturation magnetization was observed, accompanied by a significant 80.5% reduction in coercivity. Moreover, the methodology enables the acquisition of intricate insights into phase transitions occurring throughout the annealing process. The findings affirm the efficacy of the in situ technique for refining the annealing parameters and underscore its potential applicability in the exploration of microstructural and phase transformations in materials.
Turbulence generation in the transitional wake flow behind a sphere
Authors: Niu Lin , Dou Hua-Shu , Zhou Changquan , Xu Wenqian
Published: March 2024

Turbulence generation in the transitional flow in the wake behind a sphere is studied with numerical simulations. The filtered Navier–Stokes equation and the large eddy simulation method are employed as the governing equation and the numerical method, respectively. The ΩR̃ vortex identification method is used to trace the evolution of vortices in the wake flow. The energy gradient theory is used to analyze the spike formation in the wake flow. The simulation results show that the vortex structure in the wake flow is the type of hairpin vortices, which is similar to that in a boundary layer flow. Ejection and sweep motions exist around the hairpin vortices. There are two most unstable regions in the wake where turbulence “burst” is first produced, one is near the center of the vortex head and the other is between the two vortex legs. There is a high-pressure zone above the vortex head due to the decrease in the streamwise velocity, and a soliton-like coherent structure exists in this area. The mechanism of turbulence generation in the wake is the discontinuity of the streamwise velocity, which makes the Navier–Stokes equation be singular. This singularity leads to the formation of the “negative spike” in the streamwise velocity. The amplitude of the “negative spike” reaches up to 60% of the incoming velocity, which is close to the situation in a boundary layer flow on a flat plate. It is concluded that the mechanism of turbulence generation in the wake flow is the same as that in the boundary layer flow.
Microwave magnonic micro-oscillator based on a nm-thick YIG film
Authors: Nikitin Andrey A. , Tatsenko Ivan Yu. , Kostylev Mikhail P. , Ustinov Alexey B.
Published: March 2024

A numerical model describing a magnonic active ring oscillator (MARO) based on a microscopic spin-wave delay line is proposed. The model considers excitation, propagation, and reception of the magnetostatic surface waves in a yttrium iron garnet (YIG) magnetic film with a thickness in the nanometer range. The waves are excited and received with a microscopic coplanar antenna. We employed the model to analyze the influence of the YIG-film thickness and the distance between the antennas on the MARO performance characteristics. We showed that an increase in the delay time inserted by the delay line reduces the phase noise of the MARO and increases the auto-oscillation threshold. In addition, we found a relation between the auto-oscillation threshold, the thickness of the YIG film, and the distance between the antennas. The relation helps design miniature MAROs and suggests a way to reduce the phase noise of the device. The model predicts a phase noise level of −115 dBc/Hz at a 10 kHz offset from an oscillation frequency in the vicinity of 5 GHz for the MARO based on a 100 nm-thick YIG film and 56 μm of distance between the coplanar nano-antennas of the YIG-film based delay line. We believe that this is a clear way forward to microminiaturize the time-delay feedback microwave auto-oscillators. A further reduction in the phase noise down to −125 dBc/Hz at a 10 kHz offset is found in a model of cascaded connection of several microscopic spin-wave delay lines.
Counter-current spontaneous imbibition dynamics: Combined effects of wettability, fracture flow, and pore structure
Authors: Liu Yang , Zhu Rongjiu , Yu Ping , Wang Junhong , Zhao Jun
Published: March 2024

Spontaneous imbibition plays a crucial role in various engineering and industrial applications, with its efficiency significantly influenced by a range of factors. To unravel the intricate mechanisms behind these factors, our study employs pore-scale numerical simulations. Utilizing a color gradient model within the framework of the lattice Boltzmann method, we delve into how pore structure, wettability, and flow velocity within fractures collectively impact spontaneous imbibition. Our findings reveal that the dynamics of drainage and imbibition interfaces during countercurrent spontaneous imbibition are key determinants of imbibition efficiency. Specifically, the synergy between wettability and pore structure markedly affects the penetration depth and distribution characteristics of the imbibition interface, which, in turn, influences the imbibition's speed and duration. Moreover, the interaction between the flow velocity inside fractures and the configuration of adjacent pore structures significantly shapes the evolution of the drainage interface. This interplay is crucial as it can either enhance or hinder countercurrent spontaneous imbibition. These insights deepen our understanding of the pore-scale processes governing countercurrent spontaneous imbibition, laying a solid theoretical foundation for optimizing its application in engineering and industrial settings.
Low temperature sputtering deposition of Al1−xScxN thin films: Physical, chemical, and piezoelectric properties evolution by tuning the nitrogen flux in (Ar + N2) reactive atmosphere
Authors: Signore M. A. , Serra A. , Manno D. , Quarta G. , Calcagnile L. , Maruccio L. , Sciurti E. , Melissano E. , Campa A. , Martucci M. C. , Francioso L. , Velardi L.
Published: March 2024

This work investigates the physical properties of Al1−xScxN thin films sputtered at low temperatures by varying the process conditions. Specifically, the films were deposited at room temperature by applying a radio frequency power equal to 150 W to an AlSc alloy (60:40) target, varying the nitrogen flux percentage in the (Ar + N2) sputtering atmosphere (30%, 40%, 50%, and 60%) and keeping constant the working pressure at 5 × 10−3 mbar. The structural and chemical properties of the Al1−xScxN films were studied by x-ray diffraction and Rutherford backscattering spectrometry techniques, respectively. The piezoelectric response was investigated by piezoresponse force microscopy. In addition, the surface potential was evaluated for the first time for Sc-doped AlN thin films by Kelvin probe force microscopy, providing piezoelectric coefficients free from the no-piezoelectric additional effect to the mechanical deformation, i.e., the electrostatic force. By alloying AlN with scandium, the piezoelectric response was strongly enhanced (up to 200% compared to undoped AlN), despite the low deposition temperature and the absence of any other additional energy source supplied to the adatoms during thin film growth, which generally promotes a better structural arrangement of polycrystalline film. This is a strategic result in the field of microelectromechanical systems completely fabricated at low temperatures.
Key language markers of depression on social media depend on race
Authors: Rai Sunny , Stade Elizabeth C. , Giorgi Salvatore , Francisco Ashley , Ungar Lyle H. , Curtis Brenda , Guntuku Sharath C.
Published: March 2024

Depression has robust natural language correlates and can increasingly be measured in language using predictive models. However, despite evidence that language use varies as a function of individual demographic features (e.g., age, gender), previous work has not systematically examined whether and how depression’s association with language varies by race. We examine how race moderates the relationship between language features (i.e., first-person pronouns and negative emotions) from social media posts and self-reported depression, in a matched sample of Black and White English speakers in the United States. Our findings reveal moderating effects of race: While depression severity predicts I-usage in White individuals, it does not in Black individuals. White individuals use more belongingness and self-deprecation-related negative emotions. Machine learning models trained on similar amounts of data to predict depression severity performed poorly when tested on Black individuals, even when they were trained exclusively using the language of Black individuals. In contrast, analogous models tested on White individuals performed relatively well. Our study reveals surprising race-based differences in the expression of depression in natural language and highlights the need to understand these effects better, especially before language-based models for detecting psychological phenomena are integrated into clinical practice.
Phosphatidylserine regulates plasma membrane repair through tetraspanin-enriched macrodomains
Authors: Li Yang E. , Norris Dougall M. , Xiao Fanqian N. , Pandzic Elvis , Whan Renee M. , Fok Sandra , Zhou Ming , Du Guangwei , Liu Yang , Du Ximing , Yang Hongyuan
Published: March 2024

The integrity of the plasma membrane is critical to cell function and survival. Cells have developed multiple mechanisms to repair damaged plasma membranes. A key process during plasma membrane repair is to limit the size of the damage, which is facilitated by the presence of tetraspanin-enriched rings surrounding damage sites. Here, we identify phosphatidylserine-enriched rings surrounding damaged sites of the plasma membrane, resembling tetraspanin-enriched rings. Importantly, the formation of both the phosphatidylserine- and tetraspanin-enriched rings requires phosphatidylserine and its transfer proteins ORP5 and ORP9. Interestingly, ORP9, but not ORP5, is recruited to the damage sites, suggesting cells acquire phosphatidylserine from multiple sources upon plasma membrane damage. We further demonstrate that ORP9 contributes to efficient plasma membrane repair. Our results thus unveil a role for phosphatidylserine and its transfer proteins in facilitating the formation of tetraspanin-enriched macrodomains and plasma membrane repair.
Induction of immortal-like and functional CAR T cells by defined factors
Authors: Wang Lixia , Jin Gang , Zhou Qiuping , Liu Yanyan , Zhao Xiaocui , Li Zhuoyang , Yin Na , Peng Min
Published: March 2024

Long-term antitumor efficacy of chimeric antigen receptor (CAR) T cells depends on their functional persistence in vivo. T cells with stem-like properties show better persistence, but factors conferring bona fide stemness to T cells remain to be determined. Here, we demonstrate the induction of CAR T cells into an immortal-like and functional state, termed TIF. The induction of CARTIF cells depends on the repression of two factors, BCOR and ZC3H12A, and requires antigen or CAR tonic signaling. Reprogrammed CARTIF cells possess almost infinite stemness, similar to induced pluripotent stem cells while retaining the functionality of mature T cells, resulting in superior antitumor effects. Following the elimination of target cells, CARTIF cells enter a metabolically dormant state, persisting in vivo with a saturable niche and providing memory protection. TIF represents a novel state of T cells with unprecedented stemness, which confers long-term functional persistence of CAR T cells in vivo and holds broad potential in T cell therapies.
Cosmology in Lorentzian Regge calculus: causality violations, massless scalar field and discrete dynamics
Authors: Jercher Alexander F , Steinhaus Sebastian
Published: March 2024

We develop a model of spatially flat, homogeneous and isotropic cosmology in Lorentzian Regge calculus, employing four-dimensional Lorentzian frusta as building blocks. By examining the causal structure of the discrete spacetimes obtained by gluing such four-frusta in spatial and temporal direction, we find causality violations if the sub-cells connecting spatial slices are spacelike. A Wick rotation to the Euclidean theory can be defined globally by a complexification of the variables and an analytic continuation of the action. Introducing a discrete free massless scalar field, we study its equations of motion and show that it evolves monotonically. Furthermore, in a continuum limit, we obtain the equations of a homogeneous scalar field on a spatially flat Friedmann background. Vacuum solutions to the causally regular Regge equations are static and flat and show a restoration of time reparametrisation invariance. In the presence of a scalar field, the height of a frustum is a dynamical variable that has a solution if causality violations are absent and if an inequality relating geometric and matter boundary data is satisfied. Edge lengths of cubes evolve monotonically, yielding a contracting or an expanding branch of the Universe. In a small deficit angle expansion, the system can be deparametrised via the scalar field and a continuum limit of the discrete theory can be defined which we show to yield the relational Friedmann equation. These properties are obstructed if higher orders of the deficit angle are taken into account. Our results suggest that the inclusion of timelike sub-cells is necessary for a causally regular classical evolution in this symmetry restricted setting. Ultimately, this works serves as a basis for forthcoming investigations on the cosmological path integral within the framework of effective spin foams.
Shape of radiation dose response relationship for ischaemic heart disease mortality and its interpretation: analysis of the national registry for radiation workers (NRRW) cohort
Authors: Zhang Wei , Haylock Richard GE , Gillies Michael , Hunter Nezahat
Published: March 2024

Statistically significant increases in ischemic heart disease (IHD) mortality with cumulative occupational external radiation dose were observed in the National Registry for Radiation Workers (NRRW) cohort. There were 174 541 subjects in the NRRW cohort. The start of follow up was 1955, and the end of the follow-up for each worker was chosen as the earliest date of death or emigration, their 85th birthday or 31 December 2011. The dose-response relationship showed a downward curvature at a higher dose level >0.4 Sv with the overall shape of the dose-response relationship best described by a linear-quadratic model. The smaller risk at dose >0.4 Sv appears to be primarily associated with workers who started employment at a younger age (<30 years old) and those who were employed for more than 30 years. We modelled the dose response by age-at-first exposure. For the age-at-first exposure of 30+ years old, a linear dose-response was the best fit. For age-at-first exposure <30 years old, there was no evidence of excess risk of IHD mortality for radiation doses below 0.1 Sv or above 0.4 Sv, excess risk was only observed for doses between 0.1–0.4 Sv. For this age-at-first exposure group, it was also found that the doses they received when they were less than 35 years old or greater than 50 years old did not contribute to any increased IHD risk.
Quadrotor attitude control by improved snake optimizer based adaptive switching disturbance rejection approach
Authors: Zhou Tao , Chen Zhisheng , Jiao Junjun
Published: March 2024

In this paper, an adaptive switching anti-disturbance attitude control scheme based on improved snake optimizer (SO) is proposed for quadrotor attitude control when a quadrotor unmanned aerial vehicle is affected by measurement noise. The adaptive switching disturbance rejection controller (AWDRC) is composed of linear active disturbance rejection control and adaptive switching extended state observer which is used to achieve accurate signals reconstruction performance under measurement noise. Then, the improved SO (ISO) algorithm is developed with quadratic interpolation and comprehensive learning strategies to obtain the optimal parameters of the quadrotor attitude controller. The performance validity of ISO is demonstrated here by experiments on the CEC-2017 and the CEC-2020 benchmark functions with several state-of-the-art meta-heuristic algorithms. Secondly, the proposed ISO-based AWDRC algorithm is used in quadrotor attitude tracking control and compared with three other excellent active disturbance rejection controllers in a comparative experiment, and the experimental results show the effectiveness of the proposal. Finally, the robustness of the proposed method to parameters perturbation of the quadrotor attitude system is analyzed by Monte Carlo experiments.
Calibration of visual measurement system for excavator manipulator pose
Authors: Liu Guangxu , Wang Qingfeng , Li Bingcheng , Xi Xiangshuo
Published: March 2024

The automatic control of excavator operation trajectories is a pivotal technology for autonomous excavators, with the essential prerequisite being the real-time measurement of manipulator poses. Given the complexity of the operating environment, traditional sensor-based measurement methods face limitations, whereas visual measurement emerges as a promising technique. Accurately measuring excavator manipulator poses involves a crucial aspect: mapping the relationship between image information and poses. First, to address the significant errors in pose prediction encountered with machine learning techniques like artificial neural networks, this work introduces a mathematical model for mapping this relationship, referred to as the pose mapping mathematical model, which includes calibrating model parameters. Second, to address the sensitivity of initial values in the calibration process, we propose a residual-guided initialization algorithm. This algorithm aims to ensure that initial values closely approximate the ground truth values, thus preventing matrix singularity at the source and avoiding parameter estimation divergence. Third, to tackle challenges such as unstable lighting conditions and discrepancies between the dataset and the mathematical model, we introduce the random sample consensus-driven Levenberg–Marquardt parameter optimization algorithm to enhance parameter estimation accuracy. Experiments with static and dynamic online measurement demonstrate that our method reduces pose measurement errors compared to existing methods. This research lays a solid foundation for developing visual measurement techniques for excavators and automated manipulator control based on visual measurements, also serving as a valuable reference for research on mechanical arms.
Comparison of semi-automatic and manual segmentation methods for tumor delineation on head and neck squamous cell carcinoma (HNSCC) positron emission tomography (PET) images
Authors: Philip Mahima Merin , Watts Jessica , Moeini Seyedeh Niki Mir , Musheb Mohammed , McKiddie Fergus , Welch Andy , Nath Mintu
Published: March 2024

Objective. Accurate and reproducible tumor delineation on positron emission tomography (PET) images is required to validate predictive and prognostic models based on PET radiomic features. Manual segmentation of tumors is time-consuming whereas semi-automatic methods are easily implementable and inexpensive. This study assessed the reliability of semi-automatic segmentation methods over manual segmentation for tumor delineation in head and neck squamous cell carcinoma (HNSCC) PET images. Approach. We employed manual and six semi-automatic segmentation methods (just enough interaction (JEI), watershed, grow from seeds (GfS), flood filling (FF), 30% SUVmax and 40%SUVmax threshold) using 3D slicer software to extract 128 radiomic features from FDG-PET images of 100 HNSCC patients independently by three operators. We assessed the distributional properties of all features and considered 92 log-transformed features for subsequent analysis. For each paired comparison of a feature, we fitted a separate linear mixed effect model using the method (two levels; manual versus one semi-automatic method) as a fixed effect and the subject and the operator as the random effects. We estimated different statistics—the intraclass correlation coefficient agreement (aICC), limits of agreement (LoA), total deviation index (TDI), coverage probability (CP) and coefficient of individual agreement (CIA)—to evaluate the agreement between the manual and semi-automatic methods. Main results. Accounting for all statistics across 92 features, the JEI method consistently demonstrated acceptable agreement with the manual method, with median values of aICC = 0.86, TDI = 0.94, CP = 0.66, and CIA = 0.91. Significance. This study demonstrated that JEI method is a reliable semi-automatic method for tumor delineation on HNSCC PET images.
Statistical analysis on branching characteristics of positive streamer discharges in N2–O2 mixtures
Authors: Guo Yihao , Nijdam Sander
Published: March 2024

Streamers are fast-propagating ionization channels that can usually branch and form complex tree-like structures in dielectric media. In this paper, we perform experiments on positive streamers in different N2–O2 mixtures under varying conditions including voltage, pressure, and electrode geometry, with at least 125 discharge images captured for each condition. We present a statistical analysis on streamer branching characteristics from 3D models that are reconstructed by stereoscopic stroboscopic images and our dedicated semi-automatic 3D reconstruction method.

We found that by varying the concentration of O2, the morphology and branching characteristics are greatly changed. Specifically, the average branching angle decrease significantly from 90∘ in air to 66∘ in 1% O2, suggesting that photoionization plays an important role in streamer branching. The branching angles in our work are generally larger than previously reported results due to the resolved 3D structures of discharges by our method. A linear relation between the streamer diameter ratio and the branching direction difference of two daughter branches is found, which intersects the vertical axis almost at unity. It is also found that the average branching angles, streamer velocities and diameters increase as the voltage increases. This is again attributed to stronger photoionization effect under higher voltages. The velocities and diameters are similar at different pressures but at the same reduced electric field. The average branching angle decreases from 90∘ at 133 mbar to 79∘ at 200 mbar. This suggests that stochastic fluctuations become dominant over photoionization effect at higher pressures.
A model for a Langmuir sheath in a stagnating dense plasma with secondary ion formation
Authors: Martin Christopher R , Untaroiu Alexandrina , Rahman S M Mahbobur
Published: March 2024

This simplified model provides solutions for the current-voltage characteristics of a sheath in a dense flowing plasma when surface chemistry contributes secondary ions. The problem is motivated by the recent discovery that strong transient signals in industrial ion current sensors are caused by chemical reactions with carbon in the steel being cut or welded by oxyfuel processes. The one-dimensional model considers a quasi-uniform dense plasma flowing towards and stagnating on an absorbing surface, above which there is a source of secondary ions. Because the secondary ions are formed directly in the plasma sheath, they have strong impacts on the current-voltage characteristic. With ionic Reynolds number, R, and integral length scale, α, secondary ion formation rate, Ω, and length scale, β, saturation currents are simply R + βΩ until β ≪ 1, at which point, new electrons cannot escape the sheath, and secondary ions have no effect. Floating potential, ϕ
∞, scales like

exp
(

ϕ

∞

)
∝

R

−
3

/

4

, and secondary ions have little impact unless β
2Ω > 1. Even then, floating potential is only weakly affected by secondary ion formation. The integral length scale, α, is not found to strongly affect the results.
Self-organising phenomena in 2D complex plasma simulations withnon-mono dispersed dust size distributions
Authors: Holen G , Adhikari S , Mishra R , Miloch W J
Published: March 2024

Complex plasma with a variety of continuous and discrete dust grain size distributions are simulated in 2D with molecular dynamics simulations with radial geometry to determine differences in self-organizing phenomena to more realistically represent the actual in situ variations in dust-size. The standard deviation of particle size σ(a) strongly correlates with phase separation and coupling parameter Γ for all distribution types. We observe local differences in bond order parameters and Voronoi diagrams for different size distributions, and our results suggest that phase transition is affected by continuous size distributions, particularly in the binary distribution case. Simulations with discrete size result in artifacts and discontinuities that are not found in the continuous distributions. The use of continuous distributions is observed to be beneficial both for more realistic approximation of complex plasma experiments and to study systems of strongly coupled particles in general.
H-bonding interaction study for binary mixtures of methyl cellosolve and ethanol: a dielectric, FTIR spectroscopic and volumetric approach
Authors: Pabboj V S , Lakhamawad H N , Jinklor G T , Rander D N , Kanse K S , Joshi Y S , A C Kumbharkhane
Published: March 2024

The dielectric measurement of neat ethylene glycol monomethyl ether (EGMME), neat ethanol and their binary mixtures have been carried out using time domain technique in frequency range of 10 MHz to 50 GHz at the temperature range from 10 °C to 25 °C with a difference of 5 °C. The frequency domain technique within the frequency range of 20 Hz to 2 MHz is used to obtain complex dielectric permittivity ε*(ω), electrical modulus M*(ω), complex electrical conductivity σ*(ω) and loss tangent (tan δ) at 25 °C. The dielectric spectra obtained using TDR technique are fitted in Cole-Davidson model to extract the dielectric parameters such as static dielectric permittivity (ε
s), relaxation time (τ) and asymmetric distribution parameter (β). These relaxation parameter values are used to predict intermolecular hydrogen bonding between EGMME and ethanol molecules. Furthermore, the inter-molecular interactions through H-bonding between EGMME and ethanol molecules have been confirmed and discussed using Kirkwood correlation factor, excess permittivity, thermodynamic parameter, Bruggeman factor, excess molar volume, excess dielectric permittivity at high frequency and Fourier transform infrared (FTIR) spectra.