bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrable heat conduction model
Authors: Franceschini Chiara , Frassek Rouven , Giardinà Cristian
Published: April 2023

We consider a stochastic process of heat conduction where energy is redistributed along a chain between nearest neighbor sites via an improper beta distribution. Similar to the well-known Kipnis–Marchioro–Presutti (KMP) model, the finite chain is coupled at its ends with two reservoirs that break the conservation of energy when working at different temperatures. At variance with KMP, the model considered here is integrable, and one can write in a closed form the n-point correlation functions of the non-equilibrium steady state. As a consequence of the exact solution one, can directly prove that the system is in “local equilibrium,” which is described at the macro-scale by a product measure. Integrability manifests itself through the description of the model via the open Heisenberg chain with non-compact spins. The algebraic formulation of the model allows us to interpret its duality relation with a purely absorbing particle system as a change of representation.
Nonlinear nonlocal metasurfaces
Authors: Kolkowski Radoslaw , Hakala Tommi K. , Shevchenko Andriy , Huttunen Mikko J.
Published: April 2023

Optical metasurfaces have recently emerged as the game changer in light manipulation and opened up new perspectives in many subfields of optics and photonics. Recent developments in nonlocal metasurfaces, in which the nanoscale building blocks respond to the incoming light collectively rather than as individual objects, are especially promising for enhancing and controlling the nonlinear optical phenomena. In this article, we provide a brief overview of the basic principles of nonlocal metasurfaces in the context of their nonlinear optical functionalities. We discuss the origin and the regimes of the nonlocal response, covering the aspects of multiple scattering, radiation damping, quality factor, local-field enhancement, and temporal dynamics. Some important aspects are illustrated by computational examples. We also give our personal viewpoint on the selected ideas and research directions in nonlocal and nonlinear metasurfaces, including the role of spatial symmetry in nonlocal interactions, the effects of phase and momentum matching in frequency conversion, as well as the possibilities offered by new material platforms and novel concepts, such as bound states in the continuum, parity–time symmetry, and time-variant metasurfaces.
Signatures of diradicals in x-ray absorption spectroscopy
Authors: Marin Kevin , Huang Meng , Evangelista Francesco A.
Published: April 2023

Theoretical simulations are critical to analyze and interpret the x-ray absorption spectrum of transient open-shell species. In this work, we propose a model of the many-body core-excited states of symmetric diradicals. We apply this model to analyze the carbon K-edge transitions of o-, m-, and p-benzyne, three organic diradicals with diverse and unusual electronic structures. The predictions of our model are compared with high-level multireference computations of the K-edge spectrum of the benzynes obtained with the driven similarity renormalization group truncated to third order. Our model shows the importance of a many-body treatment of the core-excited states of the benzynes and provides a theoretical framework to understand which properties of the ground state of these diradicals can be extracted from their x-ray spectrum.
Drag increase and turbulence augmentation in two-way coupled particle-laden wall-bounded flows
Authors: Battista F. , Gualtieri P. , Mollicone J.-P. , Salvadore F. , Casciola C. M.
Published: April 2023

The exact regularized point particle method is used to characterize the turbulence modulation in two-way momentum-coupled direct numerical simulations of a turbulent pipe flow. The turbulence modification is parametrized by the particle Stokes number, the mass loading, and the particle-to-fluid density ratio. The data show that in the wide region of the parameter space addressed in the present paper, the overall friction drag is either increased or unaltered by the particles with respect to the uncoupled case. In the cases where the wall friction is enhanced, the fluid velocity fluctuations show a substantial modification in the viscous sub-layer and in the buffer layer. These effects are associated with a modified turbulent momentum flux toward the wall. The particles suppress the turbulent fluctuations in the buffer region and concurrently provide extra stress in the viscous sub-layer. The sum of the turbulent stress and the extra stress is larger than the Newtonian turbulent stress, thus explaining the drag increase. The non-trivial turbulence/particles interaction turns out in a clear alteration of the near-wall flow structures. The streamwise velocity streaks lose their spatial coherence when two-way coupling effects are predominant. This is associated with a shift of the streamwise vortices toward the center of the pipe and with the concurrent presence of small-scale and relatively more intense vortical structures near the wall.
An uncertainty-aware strategy for plasma mechanism reduction with directed weighted graphs
Authors: Venturi S. , Yang W. , Kaganovich I. , Casey T.
Published: April 2023

In this work, we present a framework for the analysis and reduction of plasma mechanisms by means of weighted directed graphs, in which reactions and species are both treated as nodes. The methodology consists of two distinct analyses. The first, which is qualitative, relies on graph spatializations via force-directed algorithms to discover the predominant global patterns in the chemical model. The second ranks the reactions based on their shortest paths' lengths from/to the species of interest and their relative contributions to the power balance. This quantitative investigation enables a strategy for mechanism reduction that is fully automatized, as it does not require any expert knowledge, highly effective, as it generates reduced mechanisms that are highly accurate while relying on a small number of processes, and easily interpretable, as the algorithm justifies the importance of the retained reactions by outputting their related chemical pathways. Additionally, the work proposes a methodology extension that employs ensembles of graphs to improve the robustness of the reduced mechanism to reaction parameter uncertainties. The approach, here tested for steady-state predictions of a plasma system characterizing negative hydrogen ion sources, is general and can be used in a wide variety of applications outside the particular nuclear fusion context demonstrated in this work.
Electrical tuning of robust layered antiferromagnetism in MXene monolayer
Authors: Yang Xinyu , Ding Ning , Chen Jun , Wang Ziwen , An Ming , Dong Shuai
Published: April 2023

A-type antiferromagnetism, with an in-plane ferromagnetic order and the interlayer antiferromagnetic coupling, owns inborn advantages for electrical manipulations but is naturally rare in real materials except in those artificial antiferromagnetic heterostructures. Here, a robust layered antiferromagnetism with a high Néel temperature is predicted in a MXene Cr2CCl2 monolayer, which provides an ideal platform as a magnetoelectric field effect transistor. Based on first-principles calculations, we demonstrate that an electric field can induce the band splitting between spin-up and spin-down channels. Although no net magnetization is generated, the inversion symmetry between the lower Cr layer and the upper Cr layer is broken via electronic cloud distortions. Moreover, this electric field can be replaced by a proximate ferroelectric layer for non-volatility. The magneto-optic Kerr effect can be used to detect this magnetoelectricity, even if it is a collinear antiferromagnet with zero magnetization.
Gamma-radiation hardness and long-term stability of
ALD-Al2O3 surface passivated Si
Authors: Getz Michael N. , Povoli Marco , Koybasi Ozhan , Slavicek Tomas , Monakhov Eduard
Published: April 2023

Al2O3 has emerged as the surface passivation material of choice for p-type silicon in photovoltaics and has also become a candidate for passivating Si-based radiation sensors. However, the surface passivation of Al2O3 has been shown to degrade when exposed to gamma-radiation, making it of interest to determine methods of depositing Al2O3 that minimize the radiation-induced degradation on the surface passivation. In this study, we investigate the long-term stability and gamma-radiation hardness of Al2O3 prepared using the TMA+H2O+O3 precursor combination and how the pretreatment, the deposition temperature, and the film thickness affect the density of interface states, Dit, and fixed oxide charge, Qfix, before and after gamma-irradiation. We find that the surface saturation current density, J0s, of silicon passivated by Al2O3 increases after annealing but stabilizes over time depending on the Al2O3 thickness. Samples with thicknesses of <20 nm stabilize within hours, while those with >60 nm stabilize over days. J0s stabilizes at lower values with increased Al2O3 thickness. After exposure to 1 Mrad gamma-radiation, the samples still exhibit low Dit and high Qfix, with the best performing sample having a Dit of 1.5 × 1010 eV−1 cm−2 and a Qfix of −3.1 × 1012 cm−2. The deposition temperature appears to indirectly affect radiation hardness, owing to its impact on the hydrogen concentration in the film and at the Si–SiOx–Al2O3 interface. Lifetime measurements after irradiation indicate that Al2O3 still passivates the surface effectively. The carrier lifetime and Qfix can largely be recovered by annealing samples in O2 at 435 °C.
Environment friendly lead-free Cs3Sb2Br9 perovskite: Wide measure range, high sensitivity, and rapid sensing response for high-performance humidity sensor
Authors: You Han , Wu Daofu , Wang Jian , He Jiao , Kuang Xinyi , Li Chenlu , Guo Fawen , Zhang Dingke , Qi Qi , Tang Xiaosheng
Published: April 2023

Due to the superiority of easy manufacture, low cost, coupled with super optoelectronic attributes, the metal halide perovskites have appeared as an emerging class of semiconductors owning their considerable potential for assorted utilization in humidity sensors. Nevertheless, the toxicity problem along with inherent instability of lead (Pb) halide perovskites is grimly impeding the large-scale manufacturing as well as commercialization. Herein, lead-free Cs3Sb2Br9 perovskites were successfully synthesized using a modified ligand-assisted reprecipitation approach and the humidity sensing properties relevant for humidity sensor applications were investigated. The as-fabricated Cs3Sb2Br9 humidity sensors display a super-high impedance variation of more than 105, and the testing range can be extended to a very low humidity (2% relative humidity, RH). The value of hysteresis is as low as 2.9%, and the response/recovery time is discovered to reach ∼0.9/3 s from 11% to 95% RH, which owns a large potential in the detection of the real-time moisture. Moreover, the Cs3Sb2Br9 humidity sensor boasts good reversibility and a remarkable level of stability. Our results demonstrate the potential for lead-free Cs3Sb2Br9 perovskites in a real-time and high-performance humidity sensor.
Lattice distortion in FCC HEAs and its effect on mechanical properties: Critical analysis and way forward
Authors: Kumar Jitesh , Linda Albert , Biswas Krishanu
Published: April 2023

Lattice distortion is considered to be one of the four core effects in a multicomponent high-entropy alloy. However, their effect is least understood from experiment and theoretical standpoints. The present investigation revealed a unique way to understand this effect by combining experiments with density functional theory (DFT) calculations. A small amount of Al and Si were carefully added to the whole-solute matrix of Cantor alloys. The different-sized atomic species introduces a huge lattice distortion in the matrix, leading to a simultaneous improvement in yield strength (YS), ultimate tensile strength (UTS), and percent elongation. An extensive DFT simulation indicates that a lattice distortion is prominent in an Al-containing alloy, whereas Si does not induce a lattice distortion. However, Si leads to severe interlayer lattice distortion, caused by the displacement of Si, during twinning. This leads to the improvement of YS, UTS, and ductility. Lattice distortion and its variants play significant effects on the mechanical properties of high-entropy alloys (HEAs) in terms of local lattice distortion, providing an uneven energy landscape for the movement of line defects or interlayer distortion. The inherent nature of local lattice distortion in HEAs leads to the wavy or tortuous dislocation, unlike a straight dislocation in conventional alloys. The movement of the wavy type of dislocation through a distorted or defective lattice requires large stress, resulting in a pronounced effect on solid solution strengthening. This local lattice distortion also dictates the degree of the interlayer distance distortion in the vicinity of atoms, leading to an increase or decrease in stable stacking fault energy that decides the deformation mode via slip or twinning.
Anomalous impact of thermal fluctuations on spin transfer torque induced ferrimagnetic switching
Authors: Yuan Zhengping , Long Jingwei , Xu Zhengde , Xin Yue , An Lihua , Ren Jie , Zhang Xue , Yang Yumeng , Zhu Zhifeng
Published: April 2023

The dynamics of a spin torque-driven ferrimagnetic (FiM) system is investigated using the two-sublattice macrospin model. We demonstrate ultrafast switching in the picosecond range. However, we find that the excessive current leads to magnetic oscillation. Therefore, faster switching cannot be achieved by unlimitedly increasing the current. By systematically studying the impact of thermal fluctuations, we find that the dynamics of FiMs can also be distinguished into the precessional region, the thermally activated region, and the crossover region. However, in the precessional region, there is a significant deviation between FiM and ferromagnet (FM), i.e., the FM is insensitive to thermal fluctuations since its switching is only determined by the amount of net charge. In contrast, we find that the thermal effect is pronounced even when a very short current pulse is applied to the FiM. We attribute this anomalous effect to the complex relation between the anisotropy and overdrive current. By controlling the magnetic anisotropy, we demonstrate that the FiM can also be configured to be insensitive to thermal fluctuations. This controllable thermal property makes the FiM promising in many emerging applications such as the implementation of tunable activation functions in the neuromorphic computing.
Investigation of carbon incorporation in laser-assisted MOCVD of GaN
Authors: Zhang Yuxuan , Thirupakuzi Vangipuram Vijay Gopal , Zhang Kaitian , Zhao Hongping
Published: April 2023

Background carbon (C) impurity incorporation in metalorganic chemical vapor deposition (MOCVD) grown gallium nitride (GaN) represents one of the major issues in further improving GaN vertical power device performance. This work presents a laser-assisted MOCVD (LA-MOCVD) technique to address the high-C issue in MOCVD homoepitaxial GaN under different growth rate (Rg) regimes and studies the correlations between [C] and Rg. [C] in LA-MOCVD GaN is reduced by 50%–90% as compared to the conventional MOCVD GaN for a wide growth rate range between 1 and 16 μm/h. A mass-transport based model is developed to understand the C incorporation at different Rg regimes. The results obtained from the developed model are in good agreement with experimental data. The model further reveals that LA-MOCVD effectively suppresses C incorporation by reducing the active C species in the gas phase. Moreover, high step velocity in step flow growth mode can facilitate C incorporation at fast Rg, exhibiting steeper C increase. The theoretical model indicates that [C] can be suppressed below 1016 cm−3 with a fast growth rate (Rg) of 10 μm/h by utilizing higher power LA-MOCVD and freestanding GaN substrates with larger off-cut angles.
Efficient calculation of derivatives of integrals in a basis of non-separable Gaussians
Authors: Desmarais Jacques K. , De Frenza Alessandro , Erba Alessandro
Published: April 2023

A computational procedure is developed for the efficient calculation of derivatives of integrals over non-separable Gaussian-type basis functions, used for the evaluation of gradients of the total energy in quantum-mechanical simulations. The approach, based on symbolic computation with computer algebra systems and automated generation of optimized subroutines, takes full advantage of sparsity and is here applied to first energy derivatives with respect to nuclear displacements and lattice parameters of molecules and materials. The implementation in the Crystal code is presented, and the considerably improved computational efficiency over the previous implementation is illustrated. For this purpose, three different tasks involving the use of analytical forces are considered: (i) geometry optimization; (ii) harmonic frequency calculation; and (iii) elastic tensor calculation. Three test case materials are selected as representatives of different classes: (i) a metallic 2D model of the Cu(111) surface; (ii) a wide-gap semiconductor ZnO crystal, with a wurtzite-type structure; and (iii) a porous metal-organic crystal, namely the ZIF-8 zinc-imidazolate framework. Finally, it is argued that the present symbolic approach is particularly amenable to generalizations, and its potential application to other derivatives is sketched.
Design of graphene spin beam splitter based on Brewster’s law
Authors: Yang Xiyin , Chen Xin , Zhang Rui , Jian Siyu , Song Yu
Published: April 2023

Spin beam splitter is one of the building blocks of graphene spintronics. Here, we adopt the concept of electron optics and design a new type of spin beam splitter by analogy with Brewster’s law. The device is a pristine/ferromagnetic/pristine (P/M/P) graphene junction, where the M region is formed by a proximity effect of ferromagnetic insulators, such as EuO, and acts as an “optically thinner medium” relative to the P region. It is found that, when standing waves are formed in the M region with a length of integral multiple of the half longitudinal wavelength of electrons, electrons with the corresponding spin can pass completely through the junction and only electrons with the other spin are reflected by the P/M interface. This manifests Brewster’s law and a spin beam splitter. It is also demonstrated that, due to the strong electric field effect of graphene, the Brewster angles for both spins can be monotonically modulated by a gate voltage in the M region in the whole range of − π / 2 to π / 2. Thus, our proposed spin beam splitter is not only an easily implemented and widely tunable build block for spintronics but also an interesting demonstration of electron optics.
Adiabatic extraction of nonlinear optical properties from real-time time-dependent electronic-structure theory
Authors: Ofstad Benedicte Sverdrup , Kristiansen Håkon Emil , Aurbakken Einar , Schøyen Øyvind Sigmundson , Kvaal Simen , Pedersen Thomas Bondo
Published: April 2023

Real-time simulations of laser-driven electron dynamics contain information about molecular optical properties through all orders in response theory. These properties can be extracted by assuming convergence of the power series expansion of induced electric and magnetic multipole moments. However, the accuracy relative to analytical results from response theory quickly deteriorates for higher-order responses due to the presence of high-frequency oscillations in the induced multipole moment in the time domain. This problem has been ascribed to missing higher-order corrections. We here demonstrate that the deviations are caused by nonadiabatic effects arising from the finite-time ramping from zero to full strength of the external laser field. Three different approaches, two using a ramped wave and one using a pulsed wave, for extracting electrical properties from real-time time-dependent electronic-structure simulations are investigated. The standard linear ramp is compared to a quadratic ramp, which is found to yield highly accurate results for polarizabilities, and first and second hyperpolarizabilities, at roughly half the computational cost. Results for the third hyperpolarizability are presented along with a simple, computable measure of reliability.
The turbulence development at its initial stage: A scenario based on the idea of vortices decay
Authors: Talalov S. V.
Published: April 2023

In this paper, a model of the development of a quantum turbulence in its initial stage is proposed. The origin of the turbulence in the suggested model is the decay of vortex loops with an internal structure. We consider the initial stage of this process, before an equilibrium state is established. As result of our study, the density matrix of developing turbulent flow is calculated. The quantization scheme of the classical vortex rings system is based on the approach proposed by the author earlier.
A compact and highly collimated atomic/molecular beam source
Authors: Bhardwaj Geetika , Singh Saurabh Kumar , Shirhatti Pranav R.
Published: April 2023

We describe the design, characterization, and application of a simple, highly collimated, and compact atomic/molecular beam source. This source is based on a segmented capillary design, constructed using a syringe needle. Angular width measurements and free molecular flow simulations show that the segmented structure effectively suppresses atoms traveling in off-axis directions, resulting in a narrow beam of Helium atoms having a width of 7 mrad (full width half maximum). We demonstrate an application of this source by using it for monitoring real-time changes in surface coverage on a clean Cu(110) surface exposed to oxygen by measuring the specular reflectivity of the Helium beam generated using this source.
The effects of pulsed blowing jets on power gain of vortex-induced vibrations of a circular cylinder
Authors: Guo Yujie , Huang Zhengui , Zheng Chun , Chen Zhihua
Published: April 2023

To enhance the power gain of vortex-induced vibration of a circular cylinder, the active control method of pulsed blowing jets located at θ = 90° is utilized to intensify its oscillation with the two-dimensional simulation of Reynolds-averaged Navier–Stokes at 2.0 × 104 ≤ Re ≤ 9.6 × 104. Different from traditional continuous jets, the blowing jets used in this paper start once the cylinder moves to the upper limited position and last for a certain duration. Based on the combination of nine momentum coefficients and four pulse durations of the jets, the oscillation responses of the cylinder at a series of reduced velocities are calculated and distinct responses are observed in three branches. In the initial branch (U* ≤ 4.27), no matter what the values of Cμ and n are, the vortex patterns keep 2S accompanied by the amplitude ratios vibrating around the benchmarks. In the fore part of the upper branch (4.27 < U* ≤ 6.17), as Cμ ≤ 0.1005, the control effect is similar to that at U* ≤ 4.27; as Cμ > 0.1005, both slight enhancement and suppression in amplitude ratios are observed, as well as the small values of power gain ratios. In the rear part of the upper branch and lower branch (U* > 6.17), the enlarged disturbance of the jets to wake results in enhanced amplitude ratios for most cases. Galloping is observed at n = 1/4 and 1/2 with a maximum amplitude ratio 13 times the benchmark, except for some suppressed cases at Cμ > 0.1005, n = 1/16, and 1/8. Though large amplitude ratios are achieved, considering more energy consumed as Cμ increases, the better control strategy with η ranging from 5.45% to 19.78% falls in U* > 6.17 and Cμ < 0.1005.
Shadow energy functionals and potentials in Born–Oppenheimer molecular dynamics
Authors: Niklasson Anders M. N. , Negre Christian F. A.
Published: April 2023

In Born–Oppenheimer molecular dynamics (BOMD) simulations based on the density functional theory (DFT), the potential energy and the interatomic forces are calculated from an electronic ground state density that is determined by an iterative self-consistent field optimization procedure, which, in practice, never is fully converged. The calculated energies and forces are, therefore, only approximate, which may lead to an unphysical energy drift and instabilities. Here, we discuss an alternative shadow BOMD approach that is based on backward error analysis. Instead of calculating approximate solutions for an underlying exact regular Born–Oppenheimer potential, we do the opposite. Instead, we calculate the exact electron density, energies, and forces, but for an underlying approximate shadow Born–Oppenheimer potential energy surface. In this way, the calculated forces are conservative with respect to the approximate shadow potential and generate accurate molecular trajectories with long-term energy stabilities. We show how such shadow Born–Oppenheimer potentials can be constructed at different levels of accuracy as a function of the integration time step, δt, from the constrained minimization of a sequence of systematically improvable, but approximate, shadow energy density functionals. For each energy functional, there is a corresponding ground state Born–Oppenheimer potential. These pairs of shadow energy functionals and potentials are higher-level generalizations of the original “zeroth-level” shadow energy functionals and potentials used in extended Lagrangian BOMD [Niklasson, Eur. Phys. J. B 94, 164 (2021)]. The proposed shadow energy functionals and potentials are useful only within this extended dynamical framework, where also the electronic degrees of freedom are propagated as dynamical field variables together with the atomic positions and velocities. The theory is quite general and can be applied to MD simulations using approximate DFT, Hartree–Fock, or semi-empirical methods, as well as to coarse-grained flexible charge models.
Experimental setup for measuring the dispersion forces by the adhered cantilever method
Authors: Postnikov Alexander V. , Uvarov Ilia V. , Svetovoy Vitaly B.
Published: April 2023

Dispersion forces start to play role in modern micro/nanoelectromechanical devices, but the methods to measure these forces at distances close to contact (<50 nm) suffer from pull-in instability. The method of adhered cantilever proposed recently has no instability and is able to make measurements at short separations. To measure the force at the average distance between surfaces in contact, one has to know the shape of an elastic beam with one end fixed at a height of 1–10 μm and the other end adhered to the substrate. The maximum contribution to this shape from the dispersion forces is in a range of 30–100 nm, which is well measurable by the interferometric methods. This paper describes the instrument, measurements, and data processing that make possible the reconstruction of the beam shape with an accuracy of 1 nm in a height range of at least 5000 nm. Critical steps of the fabrication procedure of cantilevers that are 12 mm long, 200 μm wide, and 10 μm thick are described. The interferometer measures the shape based on the differential interference-contrast method; the scanning is realized by a stage with a step of 0.1 μm. The signal recorded from the adhered cantilever has a noise level of 0.33 nm at a maximum sensitivity in a frequency band of 20 MHz. It is concluded that the instrument and data processing algorithm can be used to measure the dispersion forces and adhesion energies between rough surfaces in unloaded contact.
Ferroelectric dipole-MAPbI3 coupled x-ray detector
Authors: Zhu Ziyao , Chen Huiwen , Zhao Bo , Huang Weixiong , Lin Qianqian , Yu Xuefeng , Li Yunlong
Published: April 2023

Blade coating offers a low-cost production method for fabricating perovskite thick-film x-ray detectors. However, due to the preferential nucleation at the gas–liquid interface of a perovskite solution, high-quality perovskite thick films are in such a dilemma, sacrificing either the density of the thick film by forming a porous structure or the thickness of the film through depositing a compact structure. The porous structure will lead to carrier recombination and ion migration while low thickness will cause insufficient x-ray absorption, which will increase the dark current or reduce the sensitivity of the corresponding x-ray detector. In the present work, a scalable ferroelectric dipole–methylamine lead iodide (MAPbI3) coupled x-ray detector is proposed, where the x-ray photoconductor in situ formed on indium tin oxide shows a dense fibrous mesoscopic structure oriented along the charge-carriers transport direction. It is demonstrated that ferroelectric dipoles promise not only strong coupling effects with MAPbI3, driving better crystallinity and denser assemblies, but also excellent passivation to MAPbI3 interfaces, decreasing trap-state densities, leading to improved direct x-ray detection performance. In addition, the enhanced operational stability of the corresponding device suggests a strategy of introducing the localized polarization field for stable perovskite direct x-ray detectors.
Quantum transport and shot noise in two-dimensional semi-Dirac system
Authors: Chan Wei Jie , Ang L. K. , Ang Yee Sin
Published: April 2023

Two-dimensional (2D) semi-Dirac systems, such as 2D black phosphorus and arsenene, can exhibit a rich topological phase transition between insulating, semi-Dirac, and band inversion phases when subjected to an external modulation. How these phase transitions manifest within the quantum transport and shot noise signatures remains an open question thus far. Here, we show that the Fano factor converges to the universal F ≈ 0.179 at the semi-Dirac phase and transits between the sub-Poissonian ( F ≈ 1 / 3) and the Poissonian shot noise ( F ≈ 1) limit at the band inversion and the insulating phase, respectively. Furthermore, the conductance of a 2D semi-Dirac system converges to the contrasting limit of G / G 0 → 1 / d and G / G 0 → 0 at the band inversion and the insulating phases, respectively. The quantum tunneling spectra exhibits a peculiar coexistence of massless and massive Dirac quasiparticles in the band inversion regime, thus providing a versatile sandbox to study the tunneling behavior of various Dirac quasiparticles. These findings reveal the rich interplay between band topology and quantum transport signatures, which may serve as smoking gun signatures for the experimental studies of semi-Dirac systems near the topological phase transition.
Non-equilibrium molecular simulations of thin film rupture
Authors: Rahman Muhammad Rizwanur , Shen Li , Ewen James P. , Collard Benjamin , Heyes D. M. , Dini Daniele , Smith E. R.
Published: April 2023

The retraction of thin films, as described by the Taylor–Culick (TC) theory, is subject to widespread debate, particularly for films at the nanoscale. We use non-equilibrium molecular dynamics simulations to explore the validity of the assumptions used in continuum models by tracking the evolution of holes in a film. By deriving a new mathematical form for the surface shape and considering a locally varying surface tension at the front of the retracting film, we reconcile the original theory with our simulation to recover a corrected TC speed valid at the nanoscale.
Pentoxifylline promotes spermatogenesis via upregulation of the Nrf2-ARE signalling pathway in a mouse model of germ-cell apoptosis induced by testicular torsion–detorsion
Authors: Akanji Omotosho Dhulqarnain , Hassanzadeh Golamreza , Malekzadeh Mehrnoush , Khanmohammadi Nasrin , Khanezad Maryam , Sadeghiani Ghazaleh , Rastegar Tayebeh
Published: April 2023

Context Testicular torsion–detorsion results in loss of germ cells and infertility. Pentoxifylline has been shown to prevent tissue damage. Aims To determine the effect of pentoxifylline on germ cell survival in torsion–detorsion induced apoptosis Methods Twenty male mice were divided into four groups of five animals each: Control, T1 (Torsion–detorsion + single dose 100 mg/kg Pentoxifylline/IP), T2 (Torsion–detorsion + daily 20 mg/kg pentoxifylline/IP for 2 weeks, and T/D (Torsion–detorsion only). 35th day after torsion–detorsion, the left testes of all the animals were harvested for histological and biochemical analysis. Key results Histomorpholoical analysis showed significant increase (P < 0.05) in seminiferous tubule diameter, Johnsen’s score and germ cells of Control and T1 compared to T2 and T/D, with no significant difference (P > 0.05) in testis weight, sertoli, leydig and myoid cells. Tunnel assay showed significant increase (P < 0.05) in apoptotic cells of T/D and T2 animals compared to Control and T1. RT-PCR analysis showed significant high (P < 0.01) mRNA expression of Bax gene in T/D compared to T1 and T2 and significant increase (P < 0.05) of Bcl2 in Control, T1, T2 compared to T/D. Nrf2-ARE transcripts revealed significant increase (P < 0.05) in Control and T1 compared to T2 and T/D. Western blot showed significantly increased (P < 0.05) caspase-3 in T/D compared to Control, T1 and T2. Conclusion Pentoxifylline promotes spermatogenesis and suppressed apoptosis induced by testicular torsion–detorsion. Implication Pentoxifylline could serve as adjunct therapy to surgery in the treatment of torsion–detorsion induced germ cell apoptosis.
Fear circuit–based neurobehavioral signatures mirror resilience to chronic social stress in mouse
Authors: Ayash Sarah , Lingner Thomas , Ramisch Anna , Ryu Soojin , Kalisch Raffael , Schmitt Ulrich , Müller Marianne B.
Published: April 2023

Consistent evidence from human data points to successful threat–safety discrimination and responsiveness to extinction of fear memories as key characteristics of resilient individuals. To promote valid cross-species approaches for the identification of resilience mechanisms, we establish a translationally informed mouse model enabling the stratification of mice into three phenotypic subgroups following chronic social defeat stress, based on their individual ability for threat–safety discrimination and conditioned learning: the
Discriminating-avoiders
, characterized by successful social threat–safety discrimination and extinction of social aversive memories; the
Indiscriminate-avoiders
, showing aversive response generalization and resistance to extinction, in line with findings on susceptible individuals; and the
Non-avoiders
displaying impaired aversive conditioned learning. To explore the neurobiological mechanisms underlying the stratification, we perform transcriptome analysis within three key target regions of the fear circuitry. We identify subgroup-specific differentially expressed genes and gene networks underlying the behavioral phenotypes, i.e., the individual ability to show threat–safety discrimination and respond to extinction training. Our approach provides a translationally informed template with which to characterize the behavioral, molecular, and circuit bases of resilience in mice.
Shewanella oneidensis
MR-1 respires CdSe quantum dots for photocatalytic hydrogen evolution
Authors: Edwards Emily H. , Jelušić Jana , Kosko Ryan M. , McClelland Kevin P. , Ngarnim Soraya S. , Chiang Wesley , Lampa-Pastirk Sanela , Krauss Todd D. , Bren Kara L.
Published: April 2023

Living bio-nano systems for artificial photosynthesis are of growing interest. Typically, these systems use photoinduced charge transfer to provide electrons for microbial metabolic processes, yielding a biosynthetic solar fuel. Here, we demonstrate an entirely different approach to constructing a living bio-nano system, in which electrogenic bacteria respire semiconductor nanoparticles to support nanoparticle photocatalysis. Semiconductor nanocrystals are highly active and robust photocatalysts for hydrogen (H
2
) evolution, but their use is hindered by the oxidative side of the reaction. In this system,
Shewanella oneidensis
MR-1 provides electrons to a CdSe nanocrystalline photocatalyst, enabling visible light-driven H
2
production. Unlike microbial electrolysis cells, this system requires no external potential. Illuminating this system at 530 nm yields continuous H
2
generation for 168 h, which can be lengthened further by replenishing bacterial nutrients.
The mitochondrion of
Plasmodium falciparum
is required for cellular acetyl-CoA metabolism and protein acetylation
Authors: Nair Sethu C. , Munro Justin T. , Mann Alexis , Llinás Manuel , Prigge Sean T.
Published: April 2023

Coenzyme A (CoA) biosynthesis is an excellent target for antimalarial intervention. While most studies have focused on the use of CoA to produce acetyl-CoA in the apicoplast and the cytosol of malaria parasites, mitochondrial acetyl-CoA production is less well understood. In the current study, we performed metabolite-labeling experiments to measure endogenous metabolites in
Plasmodium falciparum
lines with genetic deletions affecting mitochondrial dehydrogenase activity. Our results show that the mitochondrion is required for cellular acetyl-CoA biosynthesis and identify a synthetic lethal relationship between the two main ketoacid dehydrogenase enzymes. The activity of these enzymes is dependent on the lipoate attachment enzyme LipL2, which is essential for parasite survival solely based on its role in supporting acetyl-CoA metabolism. We also find that acetyl-CoA produced in the mitochondrion is essential for the acetylation of histones and other proteins outside of the mitochondrion. Taken together, our results demonstrate that the mitochondrion is required for cellular acetyl-CoA metabolism and protein acetylation essential for parasite survival.
Dynamic responses of SO
2
pollution to China’s environmental inspections
Authors: Karplus Valerie J. , Wu Mengying
Published: April 2023

We evaluate the effect of rotating inspections carried out by China’s central government in 2016 to 2017 in response to the country’s air pollution crisis on the environmental performance of targeted cities and coal power plants. Using a staggered difference-in-differences (DID) design, we find that during one-month inspections concentrations of sulfur dioxide (SO
2
) at coal power plants in targeted cities are on average lower by 25 to 52% compared to not-yet-inspected cities but revert by 54 to 62% on average once scrutiny ends. Following inspections, SO
2
pollution increases more quickly at state-owned plants accountable to the central government, compared to state-owned plants accountable to the local (city or below) government. Our results suggest that for most plants SO
2
concentration changes during inspections may have been due primarily to the operation of end-of-pipe SO
2
removal devices, while following inspections local state-owned plants may have reduced output.
Bonded straight and helical flagellar filaments form ultra-low-density glasses
Authors: Yardimci Sevim , Gibaud Thomas , Schwenger Walter , Sartucci Matthew R. , Olmsted Peter D. , Urbach Jeffrey S. , Dogic Zvonimir
Published: April 2023

We study how the three-dimensional shape of rigid filaments determines the microscopic dynamics and macroscopic rheology of entangled semidilute Brownian suspensions. To control the filament shape we use bacterial flagella, which are microns-long helical or straight filaments assembled from flagellin monomers. We compare the dynamics of straight rods, helical filaments, and shape-diblock copolymers composed of seamlessly joined straight and helical segments. Caged by their neighbors, straight rods preferentially diffuse along their long axis, but exhibit significantly suppressed rotational diffusion. Entangled helical filaments escape their confining tube by corkscrewing through the dense obstacles created by other filaments. By comparison, the adjoining segments of the rod-helix shape-diblocks suppress both the translation and the corkscrewing dynamics. Consequently, the shape-diblock filaments become permanently jammed at exceedingly low densities. We also measure the rheological properties of semidilute suspensions and relate their mechanical properties to the microscopic dynamics of constituent filaments. In particular, rheology shows that an entangled suspension of shape rod-helix copolymers forms a low-density glass whose elastic modulus can be estimated by accounting for how shear deformations reduce the entropic degrees of freedom of constrained filaments. Our results demonstrate that the three-dimensional shape of rigid filaments can be used to design rheological properties of semidilute fibrous suspensions.
A PDLP-NHL3 complex integrates plasmodesmal immune signaling cascades
Authors: Tee Estee E. , Johnston Matthew G. , Papp Diana , Faulkner Christine
Published: April 2023

The plant immune system relies on the perception of molecules that signal the presence of a microbe threat. This triggers signal transduction that mediates a range of cellular responses via a collection of molecular machinery including receptors, small molecules, and enzymes. One response to pathogen perception is the restriction of cell-to-cell communication by plasmodesmal closure. We previously found that while chitin and flg22 trigger specialized immune signaling cascades in the plasmodesmal plasma membrane, both execute plasmodesmal closure via callose synthesis at the plasmodesmata. Therefore, the signaling pathways ultimately converge at or upstream of callose synthesis. To establish the hierarchy of signaling at plasmodesmata and characterize points of convergence in microbe elicitor-triggered signaling, we profiled the dependence of plasmodesmal responses triggered by different elicitors on a range of plasmodesmal signaling machinery. We identified that, like chitin, flg22 signals via RESPIRATORY BURST OXIDASE HOMOLOGUE D (RBOHD) to induce plasmodesmal closure. Further, we found that PLASMODESMATA-LOCATED PROTEIN 1 (PDLP1), PDLP5, and CALLOSE SYNTHASE 1 (CALS1) are common to microbe- and salicylic acid (SA)-triggered responses, identifying PDLPs as a candidate signaling nexus. To understand how PDLPs relay a signal to CALS1, we screened for PDLP5 interactors and found NON-RACE SPECIFIC DISEASE RESISTANCE/HIN1 HAIRPIN-INDUCED-LIKE protein 3 (NHL3), which is also required for chitin-, flg22- and SA-triggered plasmodesmal responses and PDLP-mediated activation of callose synthesis. We conclude that a PDLP–NHL3 complex acts as an integrating node of plasmodesmal signaling cascades, transmitting multiple immune signals to activate CALS1 and plasmodesmata closure.
Symbiosis between Cretaceous dinosaurs and feather-feeding beetles
Authors: Peñalver Enrique , Peris David , Álvarez-Parra Sergio , Grimaldi David A. , Arillo Antonio , Chiappe Luis , Delclòs Xavier , Alcalá Luis , Sanz José Luis , Solórzano-Kraemer Mónica M. , Pérez-de la Fuente Ricardo
Published: April 2023

Extant terrestrial vertebrates, including birds, have a panoply of symbiotic relationships with many insects and arachnids, such as parasitism or mutualism. Yet, identifying arthropod–vertebrate symbioses in the fossil record has been based largely on indirect evidence; findings of direct association between arthropod guests and dinosaur host remains are exceedingly scarce. Here, we present direct and indirect evidence demonstrating that beetle larvae fed on feathers from an undetermined theropod host (avian or nonavian) 105 million y ago. An exceptional amber assemblage is reported of larval molts (exuviae) intimately associated with plumulaceous feather and other remains, as well as three additional amber pieces preserving isolated conspecific exuviae. Samples were found in the roughly coeval Spanish amber deposits of El Soplao, San Just, and Peñacerrada I. Integration of the morphological, systematic, and taphonomic data shows that the beetle larval exuviae, belonging to three developmental stages, are most consistent with skin/hide beetles (family Dermestidae), an ecologically important group with extant keratophagous species that commonly inhabit bird and mammal nests. These findings show that a symbiotic relationship involving keratophagy comparable to that of beetles and birds in current ecosystems existed between their Early Cretaceous relatives.
Computational drug discovery for castration-resistant prostate cancers through in vitro drug response modeling
Authors: Zhang Weijie , Lee Adam M. , Jena Sampreeti , Huang Yingbo , Ho Yeung , Tietz Kiel T. , Miller Conor R. , Su Mei-Chi , Mentzer Joshua , Ling Alexander L. , Li Yingming , Dehm Scott M. , Huang R. Stephanie
Published: April 2023

Prostate cancer (PC) is the most frequently diagnosed malignancy and a leading cause of cancer deaths in US men. Many PC cases metastasize and develop resistance to systemic hormonal therapy, a stage known as castration-resistant prostate cancer (CRPC). Therefore, there is an urgent need to develop effective therapeutic strategies for CRPC. Traditional drug discovery pipelines require significant time and capital input, which highlights a need for novel methods to evaluate the repositioning potential of existing drugs. Here, we present a computational framework to predict drug sensitivities of clinical CRPC tumors to various existing compounds and identify treatment options with high potential for clinical impact. We applied this method to a CRPC patient cohort and nominated drugs to combat resistance to hormonal therapies including abiraterone and enzalutamide. The utility of this method was demonstrated by nomination of multiple drugs that are currently undergoing clinical trials for CRPC. Additionally, this method identified the tetracycline derivative COL-3, for which we validated higher efficacy in an isogenic cell line model of enzalutamide-resistant vs. enzalutamide-sensitive CRPC. In enzalutamide-resistant CRPC cells, COL-3 displayed higher activity for inhibiting cell growth and migration, and for inducing G1-phase cell cycle arrest and apoptosis. Collectively, these findings demonstrate the utility of a computational framework for independent validation of drugs being tested in CRPC clinical trials, and for nominating drugs with enhanced biological activity in models of enzalutamide-resistant CRPC. The efficiency of this method relative to traditional drug development approaches indicates a high potential for accelerating drug development for CRPC.
Genomic and structural basis for evolution of tropane alkaloid biosynthesis
Authors: Wang Yong-Jiang , Tain Tian , Yu Jia-Yi , Li Jie , Xu Bingyan , Chen Jianghua , D’Auria John C. , Huang Jian-Ping , Huang Sheng-Xiong
Published: April 2023

The tropane alkaloids (TAs) cocaine and hyoscyamine have been used medicinally for thousands of years. To understand the evolutionary origins and trajectories of serial biosynthetic enzymes of TAs and especially the characteristic tropane skeletons, we generated the chromosome-level genome assemblies of cocaine-producing
Erythroxylum novogranatense
(Erythroxylaceae, rosids clade) and hyoscyamine-producing
Anisodus acutangulus
(Solanaceae, asterids clade). Comparative genomic and phylogenetic analysis suggested that the lack of spermidine synthase/
N
-methyltransferase (
En
SPMT1) in ancestral asterids species contributed to the divergence of polyamine (spermidine or putrescine) methylation in cocaine and hyoscyamine biosynthesis. Molecular docking analysis and key site mutation experiments suggested that ecgonone synthases CYP81AN15 and CYP82M3 adopt different active-site architectures to biosynthesize the same product ecgonone from the same substrate in Erythroxylaceae and Solanaceae. Further synteny analysis showed different evolutionary origins and trajectories of CYP81AN15 and CYP82M3, particularly the emergence of
CYP81AN15
through the neofunctionalization of ancient tandem duplication genes. The combination of structural biology and comparative genomic analysis revealed that ecgonone methyltransferase, which is responsible for the biosynthesis of characteristic 2-substituted carboxymethyl group in cocaine, evolved from the tandem copies of salicylic acid methyltransferase by the mutations of critical E216 and S153 residues. Overall, we provided strong evidence for the independent origins of serial TA biosynthetic enzymes on the genomic and structural level, underlying the chemotypic convergence of TAs in phylogenetically distant species.