bluuebunny/crossref_metadata_2025 huggingface dataset:
SPH code development for X-pinch plasma simulation
Authors: Park Su-San , Kim Deok-Kyu , Ham Seunggi , Chung Kyoung-Jae , Na Yong-Su , Kim Eung Soo
Published: March 2024

We have developed the first smoothed particle hydrodynamics code for investigating X-pinch plasmas driven by pulsed power generators. To achieve the required code performance, we incorporated and discussed appropriate physics models capable of simulating the X-pinch phenomenon across various domains, encompassing equation of state, plasma transport, and radiation effects. The simulations were conducted in full three dimensions using our newly developed code, and we have compared and evaluated the results with experimental data obtained from the X-pinch device at Seoul National University. As a result, our simulations effectively captured the implosion behavior of X-pinch plasma, faithfully reproducing the four-step evolution process commonly observed in typical X-pinch configurations. Furthermore, it provided comprehensive spatiotemporal data on various plasma parameters, including density, temperature, velocity field, and radiated power. Notably, the electron temperature and density at the hot spot well agree with the experimental measurements, validating the accuracy and reliability of the developed simulation code. Additionally, the radiation data exhibited significantly improved accuracy compared to previous simulation results, confirming the effectiveness of the proposed radiation model, and it provides valuable insights into the X-pinch hot spot formation.
A diamond anvil microassembly for Joule heating and electrical measurements up to 150 GPa and 4000 K
Authors: Geballe Zachary M. , Vitale Suzy M. , Yang Jing , Miozzi Francesca , Dobrosavljevic Vasilije V. , Walter Michael J.
Published: March 2024

When diamond anvil cell (DAC) sample chambers are outfitted with both thermal insulation and electrodes, two cutting-edge experimental methods are enabled: Joule heating with spectroradiometric temperature measurement and electrical resistance measurements of samples heated to thousands of kelvin. The accuracy of temperature and resistance measurements, however, often suffers from poor control of the shape and location of the sample, electrodes, and thermal insulation. Here, we present a recipe for the reproducible and precise fabrication of DAC sample, electrodes, and thermal insulation using a three-layer microassembly. The microassembly contains two potassium chloride thermal insulation layers, four electrical leads, a sample, and a buttressing layer made of polycrystalline alumina. The sample, innermost electrodes, and buttress layer are fabricated by focused-ion-beam milling. Three iron samples are presented as proof of concept. Each is successfully compressed and pulsed Joule heated while maintaining a four-point probe configuration. The highest pressure-temperature condition achieved is ∼150 GPa and 4000 K.
Dynamical vaccination behavior with risk perception and vaccination rewards
Authors: Wang Xueying , Li Juyi , Liu Jie , Wu Xiaoqun
Published: March 2024

Vaccination is the most effective way to control the epidemic spreading. However, the probability of people getting vaccinated changes with the epidemic situation due to personal psychology. Facing various risks, some people are reluctant to vaccinate and even prefer herd immunity. To encourage people to get vaccinated, many countries set up reward mechanisms. In this paper, we propose a disease transmission model combining vaccination behaviors based on the SIR (Susceptible-Infected-Recovered) model and introduce three vaccination mechanisms. We analyze the impact of the infection rate and the recovery rate on the total cost and the epidemic prevalence. Numerical simulations fit with our intuitive feelings. Then, we study the impact of vaccination rewards on the total social cost. We find that when vaccination rewards offset vaccination costs, both the total cost and the epidemic prevalence reach the lowest levels. Finally, this paper suggests that encouraging people to get vaccinated at the beginning of an epidemic has the best effect.
Deep learning-based state prediction of the Lorenz system with control parameters
Authors: Wang Xiaolong , Feng Jing , Xu Yong , Kurths Jürgen
Published: March 2024

Nonlinear dynamical systems with control parameters may not be well modeled by shallow neural networks. In this paper, the stable fixed-point solutions, periodic and chaotic solutions of the parameter-dependent Lorenz system are learned simultaneously via a very deep neural network. The proposed deep learning model consists of a large number of identical linear layers, which provide excellent nonlinear mapping capability. Residual connections are applied to ease the flow of information and a large training dataset is further utilized. Extensive numerical results show that the chaotic solutions can be accurately forecasted for several Lyapunov times and long-term predictions are achieved for periodic solutions. Additionally, the dynamical characteristics such as bifurcation diagrams and largest Lyapunov exponents can be well recovered from the learned solutions. Finally, the principal factors contributing to the high prediction accuracy are discussed.
Loss cone effects and monotonic sheath conditions of a partially magnetized plasma sheath
Authors: Castillo Andres M. , Hara Kentaro
Published: March 2024

In this Letter, we propose the conditions for monotonic plasma sheaths adjacent to a floating wall in the presence of an applied, oblique magnetic field. The electron velocity distribution function (VDF) at the sheath edge obtained from a kinetic model exhibits a loss cone shaped truncation. Using an approximation of the truncated VDF, we derive an analytical framework of the sheath edge condition (i.e., Bohm condition), namely, the relation of ion injection velocity and sheath potential drop as a function of the magnetic field angle. The results show that the sheath edge velocity and total potential drop decrease for a steady-state sheath, which eventually collapses when the magnetic field lines become parallel to the wall.
Dissipation-based proper orthogonal decomposition of turbulent Rayleigh–Bénard convection flow
Authors: Olesen P. J. , Soucasse L. , Podvin B. , Velte C. M.
Published: March 2024

We present a formulation of proper orthogonal decomposition (POD) producing a velocity–temperature basis optimized with respect to an H1 dissipation norm. This decomposition is applied, along with a conventional POD optimized with respect to an L2 energy norm, to a dataset generated from a direct numerical simulation of Rayleigh–Bénard convection in a cubic cell (Ra=107, Pr=0.707). The dataset is enriched using symmetries of the cell, and we formally link symmetrization to degeneracies and to the separation of the POD bases into subspaces with distinct symmetries. We compare the two decompositions, demonstrating that each of the 20 lowest dissipation modes is analogous to one of the 20 lowest energy modes. Reordering of modes between the decompositions is limited, although a corner mode known to be crucial for reorientations of the large-scale circulation is promoted in the dissipation decomposition, indicating suitability of the dissipation decomposition for capturing dynamically important structures. Dissipation modes are shown to exhibit enhanced activity in boundary layers. Reconstructing kinetic and thermal energy, viscous and thermal dissipation, and convective heat flux, we show that the dissipation decomposition improves overall convergence of each quantity in the boundary layer. Asymptotic convergence rates are nearly constant among the quantities reconstructed globally using the dissipation decomposition, indicating that a range of dynamically relevant scales is efficiently captured. We discuss the implications of the findings for using the dissipation decomposition in modeling and argue that the H1 norm allows for a better modal representation of the flow dynamics.
Magnon spin current from a non-collinear magnetic phase in a compensated rare earth ferrimagnet
Authors: Wu Kang-Kuo , Lee Hsin-Man , Xu Jinsong , Yang Pei-Ying , Chien C. L. , Huang Ssu-Yen , Qu Danru
Published: March 2024

The rare earth iron garnets have been commonly treated like ferromagnets due to the strong exchange coupling between the Fe3+ sublattices. However, the exchange coupling between the rare earth (RE) and transition metal (TM) in the RE-TM compounds is relatively weak and cannot hold the magnetic moments rigidly in a collinear state upon effective anisotropy energy. In this work, we show that a non-collinear magnetic phase is readily presented for a rare earth ferrimagnetic insulator, gadolinium iron garnet (GdIG), when a small magnetic field (H) is applied in the hard axis. We excite magnons from both the collinear and non-collinear magnetic configuration in GdIG via the spin Seebeck effect and detect these magnons in the adjacent normal metal. The comparison between the collinear and non-collinear magnetic configurations reveals a comparable magnon compensating temperature (TMM) for both cases. Moreover, as temperature decreases, the in-plane component of the magnon from the non-collinear case enhances and becomes comparable with that of the collinear case at TMM, representing the dominant role Gd3+ 4f spin plays at low T. Our study shows a wide magnetic tunability in the compensated ferrimagnetic insulator, which offers a myriad of opportunities for magnonic applications.
The approximate coupled-cluster methods CC2 and CC3 in a finite magnetic field
Authors: Kitsaras Marios-Petros , Grazioli Laura , Stopkowicz Stella
Published: March 2024

In this paper, we report on the implementation of CC2 and CC3 in the context of molecules in finite magnetic fields. The methods are applied to the investigation of atoms and molecules through spectroscopic predictions and geometry optimizations for the study of the atmosphere of highly magnetized White Dwarf stars. We show that ground-state finite-field (ff) CC2 is a reasonable alternative to CCSD for energies and, in particular, for geometrical properties. For excited states, ff-CC2 is shown to perform well for states with predominant single-excitation character. Yet, for cases in which the excited state wavefunction has double-excitation character with respect to the reference, ff-CC2 can easily lead to completely unphysical results. Ff-CC3, however, is shown to reproduce the CCSDT behavior very well and enables the treatment of larger systems at a high accuracy.
Data-driven discovery of turbulent flow equations using physics-informed neural networks
Authors: Yazdani Shirindokht , Tahani Mojtaba
Published: March 2024

In the field of fluid mechanics, traditional turbulence models such as those based on Reynolds-averaged Navier–Stokes (RANS) equations play a crucial role in solving numerous problems. However, their accuracy in complex scenarios is often limited due to inherent assumptions and approximations, as well as imprecise coefficients in the turbulence model equations. Addressing these challenges, our research introduces an innovative approach employing physics-informed neural networks (PINNs) to optimize the parameters of the standard k−ω turbulence model. PINNs integrate physical loss functions into the model, enabling the adaptation of all coefficients in the standard k−ω model as trainable parameters. This novel methodology significantly enhances the accuracy and efficiency of turbulent flow simulations, as demonstrated by our application to the flow over periodic hills. The two coefficients that have been modified considerably are σω and α, which correspond to the diffusion and production terms in the specific dissipation rate equation. The results indicate that the RANS simulation with PINNs coefficients (k−ω−PINNs simulation) improves the prediction of separation in the near-wall region and mitigates the overestimation of turbulent kinetic energy compared to the base RANS simulation. This research marks a significant advancement in turbulence modeling, showcasing the potential of PINNs in parameter identification and optimization in fluid mechanics.
Understanding layered compounds under high pressure
Authors: Pellicer-Porres J.
Published: March 2024

This Tutorial focuses on the physics of layered compounds under high pressure. We have chosen h-BN and III–VI layered materials as representative materials. h-BN layers are strictly two-dimensional. Layers in III–VI compounds are more complex, and subtle details in their structural behavior play an important role in the evolution of high pressure properties. They are also interesting because they contain a different number of layers in their primitive unit cell and/or have a different ionic character. We begin describing the structural evolution. We discuss the experimental challenges encountered as well as the main findings related to intra- and interlayer compressibility, polytype influence, and geometrical modifications induced by pressure inside the layers. We then describe lattice vibrations. The origin of the modes is reviewed, paying attention to the relationships between atom motions in different layers. We discuss the convenience of redefining the Grüneisen parameter and describe the behavior of rigid layer modes, soft modes, and Davidov pairs. The last section is devoted to the electronic properties. We show that the changes observed when passing from a single layer to a three-dimensional BN are qualitatively similar to those induced by high pressure. The pressure behavior of electronic transitions in III–VI layered compounds is very rich, revealing the subtle balance between intra- and inter-layer interactions. Finally, we take advantage of high pressure studies to explain the formation of the Mexican hat type of valence band at ambient conditions in single layers of InSe and GaSe, but not in three-dimensional compounds.
Transport properties and electronic phase transitions in two-dimensional tellurium at high pressure
Authors: Zou Boyu , Wang Shu , Wang Qinglin , Wang Guangyu , Zhang Guozhao , Jiang Jialiang , Cui Jie , He Jiarui , Xi Hongzhu , Fu Hailong , Wang Zhongchang , Wang Cong , Wang Qiushi , Liu Cailong
Published: March 2024

Utilizing in situ Raman spectroscopy, resistivity, and Hall-effect measurements, we conducted an extensive investigation on the continuous electronic phase transitions and transport properties of two-dimensional (2D) tellurium (Te) under high pressure at room and low temperature (80–300 K). The distinguishable decrease in the A1 Raman mode's full width at half maximum in the trigonal phase (Te-I) indicated an electronic phase transition at 2.2 GPa. The following Hall-effect experiments located the Lifshitz transition and the semiconductor-semimetal transition at 0.9 and 1.9 GPa, respectively, and the semiconductor-semimetal transition was also confirmed by resistivity variation through temperature. The charge carrier types of the Te changed from hole to electron during the phase transition from Te-I to Te-II (triclinic phase) at low temperature, while the transport parameters remained almost unchanged during the phase transition from Te-II to Te-III (monoclinic phase). The results offered complete and thorough electronic phase transitions and transport characteristics of 2D Te, hence great advancing the potential application of Te in electronic devices.
Taylor–Couette flow and heat transfer in an elliptical enclosure with a rotating inner cylinder
Authors: Unnikrishnan Akash , Narayanan Vinod , Chamorro Leonardo P. , Vanka Surya Pratap
Published: March 2024

We numerically investigate Taylor–Couette flows within a system consisting of an elliptical outer cylinder and a rotating inner circular cylinder, with particular emphasis on the behavior of Taylor cells. The three-dimensional unsteady Navier–Stokes equations are solved under the assumption of axial periodicity. Also, a scalar transport equation is solved for the heat transfer. Our methodology employs a Fourier-spectral meshless discretization technique, which interpolates variables at scattered points using polyharmonic splines and appended polynomials. A pressure-projection algorithm achieves the time advancement of the flow equations. We present findings for an elliptical enclosure with an aspect ratio of two, examining a range of Reynolds numbers (Re) from subcritical to 300. Our analysis includes streamlines, axial velocity contours, pressure, vorticity, and temperature profiles. The results indicate that the flow remains steady up to Re≈300 before transitioning to an unsteady state at Re≈350.
Measurement of residual elastic strain in rolled-up amorphous nanomembranes using nanobeam electron diffraction
Authors: Zheng Zhi , Liu Chang , He Wenhao , Huang Jiayuan , He Jiachuo , Huang Gaoshan , Mei Yongfeng , Zheng Changlin
Published: March 2024

Amorphous nanomembranes play a crucial role in flexible electronics due to their ability to create intricate 3D structures through strain engineering. To better understand the formation of these structures, accurately mapping the local elastic strain distribution is essential. In this study, we conducted position-sensitive nanobeam electron diffraction investigations on various rolled-up amorphous nanomembranes. By analyzing the diffraction rings obtained from different locations on the amorphous samples, we extracted anisotropic structure information in reciprocal space and determined the local strain distributions in real space. Our analysis revealed that particle-assisted dry-released samples exhibited higher strain values than pure amorphous samples. This suggests that nanoparticles introduce additional strain through dewetting effects, thereby facilitating the formation of self-rolling 3D structures.
Vibration effect on Rayleigh–Taylor instability of sedimenting suspension
Authors: Zhu Senlin , Tao Jianjun
Published: March 2024

In this paper, the effect of vertical vibration on the Rayleigh–Taylor instability at the lower interface of a sedimenting suspension layer sandwiched between viscous fluids is studied numerically and theoretically. It is shown numerically that the vibration suppresses the amplitudes of interface perturbations and enlarges the widths of granular fingers, postponing the nonlinear growth stage. By modeling the suspension as a fluid with its effective density and viscosity, stability analyses are carried out, and the dominant growth rate and the dominant wave number predicted by the dispersion relation agree with the numerical results, especially for cases with strong vibrations. Because of the small-scale flow induced by the particles, high vibration acceleration amplitude and low vibration frequency, which correspond to a large vibration power input, increase the kinetic energy spectra at the high wave number regime, a phenomenon contrary to the vibration effect for pure fluid cases.
MHD stability of spherical tokamak equilibria with non-monotonic q-profiles
Authors: Jardin S. C. , Munaretto S. , Ferraro N. M. , Kaye S. M. , Kleiner A. , Lyons B. C.
Published: March 2024

We use the 3D magnetohydrodynamic (MHD) code M3D-C1 [Jardin et al., Comput. Sci. Discovery 5, 014002 (2012)] to examine the MHD stability and subsequent evolution of NSTX shot 129169. This discharge had a period with a non-monotonic safety factor profile, q (reversed shear), which was terminated by a MHD event that abruptly lowered the central safety factor, q0, and greatly reduced the peakedness of the pressure profile. We show that the equilibrium just before the MHD event occurred was linearly unstable to many pressure-driven infernal modes. Modes with toroidal mode number n≥3 all had rational surfaces very close to the minimum value of q. However, a non-resonant pressure-driven (1, 1) mode was also present, and this dominated the nonlinear evolution. The final state in the simulation, after the MHD activity subsided, had a reduced and flattened pressure profile and a nearly monotonic q-profile, in qualitative agreement with experimental results. The initial state was also unstable to the resistive interchange criteria in the reversed-shear region, but the final state was stable everywhere. The “double tearing mode” (DTM) does not appear to play a role in the MHD activity of this discharge. In Appendix A, we show that in a torus, the DTM is strongly stabilized by pressure, but it is destabilized in cylindrical geometry (which has been the most extensively analyzed in the literature).
Photosensitization of TiO2 electrodes immobilized with chiral plasmonic Au nanocolloids by circularly polarized light irradiation
Authors: Kameyama Tatsuya , Isogawa Shuji , Akiyoshi Kazutaka , Kashida Hiromu , Asanuma Hiroyuki , Torimoto Tsukasa
Published: March 2024

Photosensitization of semiconductors by excitation of chiral plasmonic metallic nanostructures has attracted much attention, not only for the analysis and detection of circularly polarized light but also for its potential applications in chiral photosynthesis. Although there have been reports on the detection of semiconductor-sensitized current in chiral nanostructures precisely fabricated by physical vapor deposition and/or lithography techniques, there have been no studies using plasmonic metal nanocolloids synthesized by chemical processes. In this study, we report the establishment of a fabrication method for large-area chiral photoelectrodes and the semiconductor photosensitization phenomenon realized using chiral plasmonic nanoparticles. Chiral plasmonic Au nanoparticles prepared by previously reported colloidal methods were immobilized onto a TiO2 thin film electrode by electrophoresis. When TiO2 electrodes loaded with chiral Au nanoparticles synthesized using L-cysteine were irradiated with circularly polarized light, left circularly polarized light irradiation at a wavelength of 500–600 nm generated a larger anodic photocurrent than right circularly polarized light irradiation at the same wavelength. This trend was reversed for TiO2 electrodes immobilized with colloidal Au nanoparticles synthesized with D-cysteine. From these results, we conclude that the efficiency of photocurrent generation by chiral plasmon excitation can be controlled by the polarization direction of the incident light.
Corner states and particle trapping in waterborne acoustic crystals
Authors: Liang Jialuo , Zheng Riyi , Lu Zhenyi , Pan Jincheng , Lu Jiuyang , Deng Weiyin , Ke Manzhu , Huang Xueqin , Liu Zhengyou
Published: March 2024

Higher-order topological insulators exhibit intriguing capacity to confine energy on lower-dimensional boundaries owing to the unique bulk-boundary correspondence. Many potential practical applications of the higher-order states in classical wave systems have been proposed and achieved. In this work, we implement a second-order topological insulator in a waterborne acoustic crystal by drilling and grooving a copper plate based on a two-dimensional Su–Schrieffer–Heeger lattice with different intracell and intercell couplings. The far-field transmission spectrum and near-field pressure field distributions verify the existence of the one-dimensional edge states and zero-dimensional corner states in the bulk bandgap. Due to the highly localized edge and corner states, the polystyrene particles are trapped at the edges and corners by the acoustic gradient force. Our findings provide a good platform to manipulate underwater acoustic wave and may inspire topological acoustic applications.
Early warning indicators via latent stochastic dynamical systems
Authors: Feng Lingyu , Gao Ting , Xiao Wang , Duan Jinqiao
Published: March 2024

Detecting early warning indicators for abrupt dynamical transitions in complex systems or high-dimensional observation data are essential in many real-world applications, such as brain diseases, natural disasters, and engineering reliability. To this end, we develop a novel approach: the directed anisotropic diffusion map that captures the latent evolutionary dynamics in the low-dimensional manifold. Then three effective warning signals (Onsager–Machlup indicator, sample entropy indicator, and transition probability indicator) are derived through the latent coordinates and the latent stochastic dynamical systems. To validate our framework, we apply this methodology to authentic electroencephalogram data. We find that our early warning indicators are capable of detecting the tipping point during state transition. This framework not only bridges the latent dynamics with real-world data but also shows the potential ability for automatic labeling on complex high-dimensional time series.
Connecting microscopic and mesoscopic mechanics in model structural glasses
Authors: Richard David
Published: March 2024

We present a novel formalism to characterize elastic heterogeneities in amorphous solids. In particular, we derive high-order strain-energy expansions for pairwise energies under athermal quasistatic dynamics. We then use the presented formalism to study the statistical properties of pairwise expansion coefficients and their link with the statistics of soft, quasilocalized modes, for a wide range of formation histories in both two- and three-dimensional systems. We further exploit the presented framework to access local yield stress maps by performing a non-linear stress–strain expansion within a cavity embedded in a frozen matrix. We show that our “bond micromechanics” compare well with the original “frozen matrix” method, with the caveat of overestimating large stress activations. We additionally show how local yield rules can be used as an input for a scalar elasto-plastic model (EPM) to predict the stress response of materials ranging from ductile to brittle. Finally, we highlight some of the limits of simple mesoscale models in capturing the aging dynamics of post-yielding systems. Intriguingly, we observe subdiffusive and diffusive shear band growths for particle-based simulations and EPMs, respectively.
Fundamental detectability of Raman scattering: A unified diagrammatic approach
Authors: Min Wei , Gao Xin
Published: March 2024

Both spontaneous Raman scattering and stimulated Raman scattering (SRS) are cornerstones of modern photonics, spectroscopy, and imaging. However, a unified understanding of the ultimate detectability of Raman scattering is lacking, due to both historical and technical reasons. Starting from quantum electrodynamics, we formulate the fundamental detectability for both spontaneous Raman scattering and SRS. The key concept is recognizing spontaneous Raman scattering as stimulated Raman process driven by vacuum field fluctuation. A simple and unified expression, Eq. (17), is derived, which can be depicted on a two-dimensional phase-diagram-like graph with inherent symmetry. It turns out that the particle nature of light dictates the ultimate detectability of spontaneous Raman scattering, which can be represented by a line on this detectability diagram. Importantly, if provided with a reasonably strong Stokes photon flux, SRS can breach this fundamental limit and open uncharted territory of drastically accelerated measurement speed and much lower detection concentration relevant to biological imaging. Such new territory in the detectability diagram is otherwise forbidden by the spontaneous counterpart. Diagrammatical analysis explains the empirical observations, provides quantitative insights, and makes new predictions. Notably, recent experimental applications of SRS microscopy can almost entirely be captured by this diagram, further supporting the explanatory power of the theory. Thus, this unified diagrammatic approach outlines a framework to understand all Raman-based measurement and provides a theoretical explanation for the remarkable utility of the emerging SRS microscopy.
Detection of principal and higher harmonic frequencies using stochastic resonance phenomenon in PBTTT-C14-based organic field-effect transistor
Authors: Mandal Bishwajit , Kumar Santosh , Singh Samarendra Pratap
Published: March 2024

Stochastic resonance (SR) is an intriguing phenomenon in which noise, typically considered a detrimental aspect of electronic communication systems, assumes a beneficial role in the detection of undetectable signals. The SR phenomenon for detecting low-intensity optical signals using PBTTT-C14-based organic field-effect transistors (OFETs) is being reported. In this discourse, we explicate the sensing of an undetectable periodic optical signal with a frequency of 5 Hz, using a PBTTT-C14-based OFETs in the presence of a finite and optimal quantity of Gaussian noise (noise bandwidth of 1 Hz and noise amplitude of 2.0, 4.0, 6.0, and 7.5 V). The detection of higher harmonics for optical signals using the SR phenomenon has not been hitherto explored for OFETs. This report presents a noteworthy finding elucidating the detection of the principal frequency and also higher harmonics of the optical signal. This simplistic methodology for examining the SR phenomenon holds great promise in identifying its robust utility in diverse real-world contexts.
Timed receptor tyrosine kinase signaling couples the central and a peripheral circadian clock in
Drosophila
Authors: Cavieres-Lepe Javier , Amini Emad , Zabel Maia , Nässel Dick R. , Stanewsky Ralf , Wegener Christian , Ewer John
Published: March 2024

Circadian clocks impose daily periodicities to behavior, physiology, and metabolism. This control is mediated by a central clock and by peripheral clocks, which are synchronized to provide the organism with a unified time through mechanisms that are not fully understood. Here, we characterized in
Drosophila
the cellular and molecular mechanisms involved in coupling the central clock and the peripheral clock located in the prothoracic gland (PG), which together control the circadian rhythm of emergence of adult flies. The time signal from central clock neurons is transmitted via small neuropeptide F (sNPF) to neurons that produce the neuropeptide Prothoracicotropic Hormone (PTTH), which is then translated into daily oscillations of Ca
2+
concentration and PTTH levels. PTTH signaling is required at the end of metamorphosis and transmits time information to the PG through changes in the expression of the PTTH receptor tyrosine kinase (RTK), TORSO, and of ERK phosphorylation, a key component of PTTH transduction. In addition to PTTH, we demonstrate that signaling mediated by other RTKs contributes to the rhythmicity of emergence. Interestingly, the ligand to one of these receptors (Pvf2) plays an autocrine role in the PG, which may explain why both central brain and PG clocks are required for the circadian gating of emergence. Our findings show that the coupling between the central and the PG clock is unexpectedly complex and involves several RTKs that act in concert and could serve as a paradigm to understand how circadian clocks are coordinated.
DNA methylation signatures of early-life adversity are exposure-dependent in wild baboons
Authors: Anderson Jordan A. , Lin Dana , Lea Amanda J. , Johnston Rachel A. , Voyles Tawni , Akinyi Mercy Y. , Archie Elizabeth A. , Alberts Susan C. , Tung Jenny
Published: March 2024

The early-life environment can profoundly shape the trajectory of an animal’s life, even years or decades later. One mechanism proposed to contribute to these early-life effects is DNA methylation. However, the frequency and functional importance of DNA methylation in shaping early-life effects on adult outcomes is poorly understood, especially in natural populations. Here, we integrate prospectively collected data on fitness-associated variation in the early environment with DNA methylation estimates at 477,270 CpG sites in 256 wild baboons. We find highly heterogeneous relationships between the early-life environment and DNA methylation in adulthood: aspects of the environment linked to resource limitation (e.g., low-quality habitat, early-life drought) are associated with many more CpG sites than other types of environmental stressors (e.g., low maternal social status). Sites associated with early resource limitation are enriched in gene bodies and putative enhancers, suggesting they are functionally relevant. Indeed, by deploying a baboon-specific, massively parallel reporter assay, we show that a subset of windows containing these sites are capable of regulatory activity, and that, for 88% of early drought-associated sites in these regulatory windows, enhancer activity is DNA methylation-dependent. Together, our results support the idea that DNA methylation patterns contain a persistent signature of the early-life environment. However, they also indicate that not all environmental exposures leave an equivalent mark and suggest that socioenvironmental variation at the time of sampling is more likely to be functionally important. Thus, multiple mechanisms must converge to explain early-life effects on fitness-related traits.
4Pi MINFLUX arrangement maximizes spatio-temporal localization precision of fluorescence emitter
Authors: Rickert Julian D. , Held Marcus O. , Engelhardt Johann , Hell Stefan W.
Published: March 2024

We introduce MINFLUX localization with interferometric illumination through opposing objective lenses for maximizing the attainable precision in 3D-localization of single inelastic scatterers, such as fluorophores. Our 4Pi optical configuration employs three sequentially tilted counter-propagating beam pairs for illumination, each providing a narrow interference minimum of illumination intensity at the focal point. The localization precision is additionally improved by adding the inelastically scattered or fluorescence photons collected through both objective lenses. Our 4Pi configuration yields the currently highest precision per detected photon among all localization schemes. Tracking gold nanoparticles as non-blinking inelastic scatterers rendered a position uncertainty <0.4 nm
3
in volume at a localization frequency of 2.9 kHz. We harnessed the record spatio-temporal precision of our 4Pi MINFLUX approach to examine the diffusion of single fluorophores and fluorescent nanobeads in solutions of sucrose in water, revealing local heterogeneities at the nanoscale. Our results show the applicability of 4Pi MINFLUX to study molecular nano-environments of diffusion and its potential for quantifying rapid movements of molecules in cells and other material composites.
Exceptions to Fourier’s law at the macroscale
Authors: Zheng Kaikai , Ghosh Shankar , Granick Steve
Published: March 2024

The usual basis to analyze heat transfer within materials is the equation formulated 200 years ago, Fourier’s law, which is identical mathematically to the mass diffusion equation, Fick’s law. Revisiting this assumption regarding heat transport within translucent materials, performing the experiments in vacuum to avoid air convection, we compare the model predictions to infrared-based measurements with nearly mK temperature resolution. After heat pulses, we find macroscale non-Gaussian tails in the surface temperature profile. At steady state, we find macroscale anomalous hot spots when the sample is topographically rough, and this is validated by using two additional independent methods to measure surface temperature. These discrepancies from Fourier’s law for translucent materials suggest that internal radiation whose mean-free-path is millimeters interacts with defects to produce small heat sources that by secondary emission afford an additional, non-local mode of heat transport. For these polymer and inorganic glass materials, this suggests unique strategies of heat management design.
Rubisco is evolving for improved catalytic efficiency and CO
2
assimilation in plants
Authors: Bouvier Jacques W. , Emms David M. , Kelly Steven
Published: March 2024

Rubisco is the primary entry point for carbon into the biosphere. However, rubisco is widely regarded as inefficient leading many to question whether the enzyme can adapt to become a better catalyst. Through a phylogenetic investigation of the molecular and kinetic evolution of Form I rubisco we uncover the evolutionary trajectory of rubisco kinetic evolution in angiosperms. We show that
rbcL
is among the 1% of slowest-evolving genes and enzymes on Earth, accumulating one nucleotide substitution every 0.9 My and one amino acid mutation every 7.2 My. Despite this, rubisco catalysis has been continually evolving toward improved CO
2
/O
2
specificity, carboxylase turnover, and carboxylation efficiency. Consistent with this kinetic adaptation, increased rubisco evolution has led to a concomitant improvement in leaf-level CO
2
assimilation. Thus, rubisco has been slowly but continually evolving toward improved catalytic efficiency and CO
2
assimilation in plants.
Fatty acid–binding proteins 3, 7, and 8 bind cholesterol and facilitate its egress from lysosomes
Authors: Fang Xian-Xiu , Wei Pengcheng , Zhao Kai , Sheng Zhao-Chen , Song Bao-Liang , Yin Lei , Luo Jie
Published: March 2024

Cholesterol from low-density lipoprotein (LDL) can be transported to many organelle membranes by non-vesicular mechanisms involving sterol transfer proteins (STPs). Fatty acid–binding protein (FABP) 7 was identified in our previous study searching for new regulators of intracellular cholesterol trafficking. Whether FABP7 is a bona fide STP remains unknown. Here, we found that FABP7 deficiency resulted in the accumulation of LDL-derived cholesterol in lysosomes and reduced cholesterol levels on the plasma membrane. A crystal structure of human FABP7 protein in complex with cholesterol was resolved at 2.7 Å resolution. In vitro, FABP7 efficiently transported the cholesterol analog dehydroergosterol between the liposomes. Further, the silencing of FABP3 and 8, which belong to the same family as FABP7, caused robust cholesterol accumulation in lysosomes. These two FABP proteins could transport dehydroergosterol in vitro as well. Collectively, our results suggest that FABP3, 7, and 8 are a new class of STPs mediating cholesterol egress from lysosomes.
Cholesterol 25-hydroxylase mediates neuroinflammation and neurodegeneration in a mouse model of tauopathy
Authors: Toral-Rios Danira , Long Justin M. , Ulrich Jason D. , Yu Jinsheng , Strickland Michael R. , Han Xianlin , Holtzman David M. , Cashikar Anil G. , Paul Steven M.
Published: March 2024

Alzheimer’s disease (AD) is characterized by amyloid plaques and neurofibrillary tangles, in addition to neuroinflammation and changes in brain lipid metabolism. 25-Hydroxycholesterol (25-HC), a known modulator of both inflammation and lipid metabolism, is produced by cholesterol 25-hydroxylase encoded by Ch25h expressed as a “disease-associated microglia” signature gene. However, whether Ch25h influences tau-mediated neuroinflammation and neurodegeneration is unknown. Here, we show that in the absence of Ch25h and the resultant reduction in 25-HC, there is strikingly reduced age-dependent neurodegeneration and neuroinflammation in the hippocampus and entorhinal/piriform cortex of PS19 mice, which express the P301S mutant human tau transgene. Transcriptomic analyses of bulk hippocampal tissue and single nuclei revealed that Ch25h deficiency in PS19 mice strongly suppressed proinflammatory signaling in microglia. Our results suggest a key role for Ch25h/25-HC in potentiating proinflammatory signaling to promote tau-mediated neurodegeneration. Ch25h may represent a novel therapeutic target for primary tauopathies, AD, and other neuroinflammatory diseases.
Revolutionizing plasmonic platform via magnetic field-assisted confined ultrafast laser deposition of high-density, uniform, and ultrafine nanoparticle arrays
Authors: Xu Jin , Wang Lingfeng , Yang Peilin , Jiang Haoqing , Zheng Huai , An Licong , Liu Xingtao , Cheng Gary J
Published: March 2024

The remarkable capabilities of 2D plasmonic surfaces in controlling optical waves have garnered significant attention. However, the challenge of large-scale manufacturing of uniform, well-aligned, and tunable plasmonic surfaces has hindered their industrialization. To address this, we present a groundbreaking tunable plasmonic platform design achieved through magnetic field (MF) assisted ultrafast laser direct deposition in air. Through precise control of metal nanoparticles (NPs), with cobalt (Co) serving as the model material, employing an MF, and fine-tuning ultrafast laser parameters, we have effectively converted coarse and non-uniform NPs into densely packed, uniform, and ultrafine NPs (∼3 nm). This revolutionary advancement results in the creation of customizable plasmonic ‘hot spots,’ which play a pivotal role in surface-enhanced Raman spectroscopy (SERS) sensors. The profound impact of this designable plasmonic platform lies in its close association with plasmonic resonance and energy enhancement. When the plasmonic nanostructures resonate with incident light, they generate intense local electromagnetic fields, thus vastly increasing the Raman scattering signal. This enhancement leads to an outstanding 2–18 fold boost in SERS performance and unparalleled sensing sensitivity down to 10−10 M. Notably, the plasmonic platform also demonstrates robustness, retaining its sensing capability even after undergoing 50 cycles of rinsing and re-loading of chemicals. Moreover, this work adheres to green manufacturing standards, making it an efficient and environmentally friendly method for customizing plasmonic ‘hot spots’ in SERS devices. Our study not only achieves the formation of high-density, uniform, and ultrafine NP arrays on a tunable plasmonic platform but also showcases the profound relation between plasmonic resonance and energy enhancement. The outstanding results observed in SERS sensors further emphasize the immense potential of this technology for energy-related applications, including photocatalysis, photovoltaics, and clean water, propelling us closer to a sustainable and cleaner future.
Comments about comments: peer review and the amazing editorial board of Brain Communications
Authors: Spires-Jones Tara L
Published: March 2024

Our editor discusses our editorial board members, who come from eight countries on four continents, and wider issues of the peer review system.
Heteroclinic dynamics in network dynamical systems with higher-order interactions
Authors: Bick Christian , von der Gracht Sören
Published: March 2024

Heteroclinic structures organize global features of dynamical systems. We analyse whether heteroclinic structures can arise in network dynamics with higher-order interactions which describe the nonlinear interactions between three or more units. We find that while commonly analysed model equations such as network dynamics on undirected hypergraphs may be useful to describe local dynamics such as cluster synchronization, they give rise to obstructions that allow to design of heteroclinic structures in phase space. By contrast, directed hypergraphs break the homogeneity and lead to vector fields that support heteroclinic structures.
Surgical ventricular reconstruction and intraoperative cryoablation in a patient with drug-refractory ventricular tachycardia and left ventricular thrombus: a case report
Authors: Lopez Maryuri Delgado , Vogler Julia , Aboud Anas , Heeger Christian-Hendrik , Tilz Roland Richard
Published: March 2024

Background

Despite modern techniques for ablation of ventricular tachycardia (VT), the procedure faces challenges such as deep intramural substrates or inaccessibility of the pericardial space. We aim to present a case of successful surgical treatment of a patient with drug-refractory VT, an apical aneurysm, large left ventricular (LV) thrombus, and recurrent implantable cardioverter defibrillator (ICD) shocks following failed epicardial catheter ablation.

Case summary

A 67-year-old male with a history of ischaemic cardiomyopathy was brought to the emergency room after a syncope because of VT. The VT was terminated by an external cardioversion prior to admission. The ICD interrogation showed an episode of sustained monomorphic VT with eight appropriate but mostly ineffective ICD shocks. An echocardiogram revealed an apical aneurysm with a thrombus. Anticoagulation and antiarrhythmic drug therapy were initiated. Days later, the patient suffered recurrent episodes of sustained VTs, refractory to pharmacological therapy, and epicardial ablation; therefore, following aneurysmectomy and thrombus removal, a reconstruction of the LV and surgical endocardial cryoablation were performed. In addition, ICD extraction was done due to recurrent bacteraemia with Staphylococcus aureus. A subcutaneous ICD was later implanted. After surgery, the patient remained free of any VT episodes during 44 months of follow-up.

Conclusion

Combined surgical ventricular reconstruction and intraoperative cryoablation may be considered as an alternative, highly effective therapy in patients with drug-refractory VTs in the setting of a LV thrombus.
Heart failure pharmacotherapy and cancer: pathways and pre-clinical/clinical evidence
Authors: Sayour Nabil V , Paál Ágnes M , Ameri Pietro , Meijers Wouter C , Minotti Giorgio , Andreadou Ioanna , Lombardo Antonella , Camilli Massimiliano , Drexel Heinz , Grove Erik Lerkevang , Dan Gheorghe Andrei , Ivanescu Andreea , Semb Anne Grete , Savarese Gianluigi , Dobrev Dobromir , Crea Filippo , Kaski Juan-Carlos , de Boer Rudolf A , Ferdinandy Péter , Varga Zoltán V
Published: March 2024

Heart failure (HF) patients have a significantly higher risk of new-onset cancer and cancer-associated mortality, compared to subjects free of HF. While both the prevention and treatment of new-onset HF in patients with cancer have been investigated extensively, less is known about the prevention and treatment of new-onset cancer in patients with HF, and whether and how guideline-directed medical therapy (GDMT) for HF should be modified when cancer is diagnosed in HF patients. The purpose of this review is to elaborate and discuss the effects of pillar HF pharmacotherapies, as well as digoxin and diuretics on cancer, and to identify areas for further research and novel therapeutic strategies. To this end, in this review, (i) proposed effects and mechanisms of action of guideline-directed HF drugs on cancer derived from pre-clinical data will be described, (ii) the evidence from both observational studies and randomized controlled trials on the effects of guideline-directed medical therapy on cancer incidence and cancer-related outcomes, as synthetized by meta-analyses will be reviewed, and (iii) considerations for future pre-clinical and clinical investigations will be provided.
The genetic basis of apple shape and size unraveled by digital phenotyping
Authors: Keller Beat , Jung Michaela , Bühlmann-Schütz Simone , Hodel Marius , Studer Bruno , Broggini Giovanni A L , Patocchi Andrea
Published: March 2024

Great diversity of shape, size, and skin color is observed among the fruits of different apple genotypes. These traits are critical for consumers and therefore interesting targets for breeding new apple varieties. However, they are difficult to phenotype and their genetic basis, especially for fruit shape and ground color, is largely unknown. We used the FruitPhenoBox to digitally phenotype 525 genotypes of the apple reference population (apple REFPOP) genotyped for 303,148 single nucleotide polymorphism (SNP) markers. From the apple images, 573 highly heritable features describing fruit shape and size as well as 17 highly heritable features for fruit skin color were extracted to explore genotype–phenotype relationships. Out of these features, seven principal components (PCs) and 16 features with the Pearson’s correlation r < 0.75 (selected features) were chosen to carry out genome-wide association studies (GWAS) for fruit shape and size. Four PCs and eight selected features were used in GWAS for fruit skin color. In total, 69 SNPs scattered over all 17 apple chromosomes were significantly associated with round, conical, cylindrical, or symmetric fruit shapes and fruit size. Novel associations with major effect on round or conical fruit shapes and fruit size were identified on chromosomes 1 and 2. Additionally, 16 SNPs associated with PCs and selected features related to red overcolor as well as green and yellow ground color were found on eight chromosomes. The identified associations can be used to advance marker-assisted selection in apple fruit breeding to systematically select for desired fruit appearance.