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Deubiquitinating enzyme USP42 promotes breast cancer progression by inhibiting JNK/p38-mediated apoptosis

Unveiling anisotropic and nonlinear electronic stopping in diamond under hydrogen irradiation: A real-time TDDFT study

Diamond’s exceptional radiation tolerance makes it ideal for aerospace electronics, yet the atomistic mechanisms governing its electronic stopping power (Se) remain elusive. Using real-time time-dependent density functional theory (rt-TDDFT), we simulate hydrogen irradiation in bulk diamond along channeling (<100>, <110>, <111>) and off-channeling trajectories. Our results reveal striking anisotropy in Se, with the <110> channel showing 35% lower stopping power at the Bragg peak (v = 1.8 a.u.) than the <100>/<111> channels, correlated with reduced radial charge density. Off-channeling simulations further uncover nonlinear Se scaling at low velocities (v < 0.5 a.u.), defying free electron gas predictions. We attribute this to hydrogen-induced impurity states that facilitate bandgap bridging via Zener-like tunneling, enabling electron excitation even at ultralow velocities. Electronic structure analysis confirms orbital-selective contributions: 2p electrons dominate below v = 0.4 a.u., while deeper 2s electrons activate above v = 0.5 a.u., driving nonlinear energy loss. These insights establish diamond’s unique electronic stopping behavior, critical for predicting radiation damage in extreme environments.

Temperature adaptation in structure and function in lactate dehydrogenase-A reflects convergent evolution in a few key protein regions

Adaptive differences in the thermal stabilities of enzyme structure and function play critical roles in establishing the thermal optima and limits of all organisms. Thus, understanding the mechanisms underlying these adaptations can yield insights into protein structure–function relationships, protein evolution, and the consequences of temperature shifts on species distributions. Past studies have suggested that only a small number of amino acid substitutions are needed for adaptive change, but whether similar sites in the sequence, which we term thermal adaptation–related sequence sites (TRSS), and similar changes in amino acid content at these TRSS occur across widely different taxa remains to be elucidated. For detecting TRSS among orthologs of species adapted to a wide range of temperatures, we investigated 277 lactate dehydrogenase-A (LDH-A) orthologs in marine fish from diverse habitats. We validated the importance of several TRSS variants using site-directed mutagenesis on zebrafish LDH-A, effectively recreating the variants in the zebrafish ortholog. Our results indicate that enzyme thermal adaptation arises primarily from a few substitutions that influence hydrophobicity in functionally important regions of secondary structures. These findings reveal striking convergence in the sites (the TRSS) of temperature-adaptive evolution of LDH-As and provide insights into the types of amino acid substitutions that foster adaptation to temperature. Furthermore, the patterns of convergent evolution identified in this study supported development of a deep learning model for predicting thermal limits. This model can provide an important tool for predicting thermal ranges of species and the potential effects of temperature change on distribution patterns.

Alpha-ketoglutarate mitigates insulin resistance and metabolic inflexibility in a mouse model of Ataxia-Telangiectasia

Abstract The maintenance of metabolic homeostasis relies on the ability to flexibly transit between catabolic and anabolic states in response to insulin signaling. Here we show insulin-activated ATM is a critical mediator of this process, facilitating the swift transition between catabolic-and-anabolic fates of glucose by regulating the functional status of PKM2 and HIF1α. In Ataxia-Telangiectasia (A-T), these mechanisms are disrupted, resulting in intrinsic insulin resistance and glucose intolerance. Consequently, cells exhibit a compensatory dependence on glutamine as an alternative metabolite for energy metabolism. Cerebellar degeneration, a hallmark of A-T, is characterized by the pronounced vulnerability of Purkinje cells, attributed to their unexpected sensitivity to insulin. Supplementation with α-ketoglutarate, the α-keto acid backbone of glutamine, has demonstrated potentials in alleviating glutamine dependence and attenuating Purkinje cell degeneration. These findings suggest that peripheral metabolic deficiencies may contribute to sustained neurodegenerative changes in A-T, underscoring the importance of screening, monitoring and addressing these metabolic disruptions in patients.

Multi-objective optimization of surface roughness and MRR in AISI 316L stainless steel processed by MQL end milling using taguchi, RSM, ANN, and RFR methods

Efficient quantum state preparation through seniority driven operator selection

Quantum algorithms require accurate representations of electronic states on a quantum device, yet the approximation of electronic wavefunctions for strongly correlated systems remains a profound theoretical challenge, with existing methods struggling to balance the competing demands of chemical accuracy and gate efficiency. Moreover, a critical limitation of most of the state-of-the-art methods developed to date lies in their substantial reliance on extensive pre-circuit measurements, which introduce significant overheads and contribute to inefficiencies in practical implementation. To address these interconnected challenges and establish a harmonious synergy between them, we propose an algorithmic framework that focuses on efficiently capturing the molecular strong correlation through an ordered set of computationally less demanding rank-one and seniority-zero paired excitations, yielding a parameterized Ansatz with shallow gate depth. Furthermore, to achieve minimal pre-circuit measurement overhead, we implement a selective pruning of excitations through a hybrid approach that combines chemically informed system-specific operator selection with parallel rank-one excitation driven uni-parameter circuit optimization guided energy-sorting strategy. With the incorporation of qubit-based excitations via particle-preserving exchange circuits, we demonstrate a further reduction in quantum complexities, enhancing the overall resource efficiency of the approach. With a range of challenging applications on strongly correlated systems, we demonstrate that our dynamic Ansatz not only significantly enhances computational efficiency but also delivers exceptional accuracy, robustness, and resilience to the noisy environments inherent in near-term quantum hardware.

Differential stability and dynamics of DNA-based and RNA-based coacervates affect non-enzymatic RNA chemistry

Abstract The RNA-peptide world hypothesis postulates the early co-evolution of RNA and peptides that led to the emergence of non-enzymatic RNA replication and peptide synthesis. Although nucleotides and amino acids have been shown to form and polymerise under prebiotic conditions, the origins of their synergy remain unclear. We propose that cooperation between DNA, RNA and peptides could have stemmed from their co-localisation in early biological compartments. Here, we show that heterogeneous mixtures of prebiotic oligonucleotides and peptides can spontaneously assemble into primitive coacervates. Experimental and computational studies reveal that peptide/nucleic acid coacervates are highly robust and form under a notably broad range of conditions. RNA-based coacervates are exceptionally stable and, in the presence of DNA, very fluid, which facilitates diffusion of reactive oligonucleotides and supports prebiotic RNA chemistry. Our findings suggest that coacervation may have occurred very early on the evolutionary timeline and fostered the emergence of a nucleic acid-peptide world. This study provides insights into the prebiotic role of coacervates and reconsiders their significance for the origins of life and the emergence of primitive replication and translation systems.

A bioluminescent deep-sea polychaete within the genus Aricidea (Paraonidae) from Minamidaito Island, Japan

Abstract The phylum Annelida encompasses a diverse group of animals, with bioluminescent species documented in 14 families. Despite this diversity and the scattered distribution of bioluminescent lineages, little is known about the molecular biology, chemistry, morphology, ecology, and evolution of bioluminescence in annelids. During a deep-sea exploration off Minamidaito Island in the western Pacific Ocean, we discovered that Aricidea sp. emits green light when stimulated. The specimens were identified with the limited key morphology as a species in the genus Aricidea. A molecular phylogenetic analysis suggests that the specimen belongs to the Aricidea/Paraonis clade but was not nested in the described species, of which sequences were publicly available. This study is the first to report bioluminescence within the family Paraonidae.

Numerical calculation of intrinsic viscosity of star and ring polymers using a modified Zimm model

In this study, the effect of structures of different polymers, i.e., ring and symmetrical star (with 3-6 arms), in a dilute solution (theta solvent) on their viscoelastic properties was theoretically investigated using a modified Zimm model. The shear relaxation modulus and the intrinsic viscosity of these polymer solutions can then be calculated. This theoretical approach offers a systematic way to infer the number of arms of a star polymer or the structure of the macromolecule in an unknown sample based on its corresponding viscoelastic properties, and it is applicable for polymers of any structure. Using star polymers and ring polymers as examples, it was generally found that, given the same molecular weight, the intrinsic viscosity of symmetrical star polymers decreases with increasing numbers of arms, and that a much more rapid decay is predicted in the shear relaxation modulus when the number of arms increases. In addition, the dynamics of the ring polymer in dilute solution are similar to those of the six-arm star polymer.

Low-emission cement clinker precursor production, enabled by electrolytic extraction of calcium from waste cement

An experimental demonstration of irreversible mesoscopic carrier transport phenomena in InGaN quantum wells

Abstract Light-induced carrier transport in mesoscopic systems exhibits a complex interplay between classical and quantum phenomena. Through direct spectroscopic measurements of optoelectronic energy transport in semiconductor quantum wells, we reveal the irreversible nature of carrier dynamics in the mesoscopic regime. A 2-probe near-field optical microscopy setup based on multiprobe scanning tunnelling microscopy detected the local excitation and emission at nanoscale resolution. By systematically exchanging the roles of the excitation and detection probes, we demonstrate a clear asymmetry in the spectroscopic response, indicating directional and irreversible transport behaviour. Our proposed approach directly reveals irreversible carrier transport in mesoscopic domains and can probe local excitonic dynamics, opening pathways for designing novel optoelectronic devices with irreversible transport mechanisms.

Transferability and interpretability of vibrational normalizing-flow coordinates

The choice of vibrational coordinates is crucial for the accuracy, efficiency, and interpretability of molecular vibrational dynamics and spectra calculations. We explore the recently proposed normalizing-flow vibrational coordinates, which are learned molecule-specific coordinate transformations optimized for a given basis set. Much like how spherical coordinates naturally simplify the hydrogen atom by embedding physical insight into the coordinate system, normalizing-flow coordinates offload complexity from the basis functions into the coordinate transformation itself. This shift not only improves basis-set convergence but also enhances the interpretability of vibrational motions. We provide an analysis of the utility, interpretation, and associated constraints of normalizing-flow vibrational coordinates. Moreover, we demonstrate that these coordinates can be generalized across different isotopologues and even structurally related molecules, achieved with minimal fine-tuning of selected output parameters.

Scaling laboratory results with machine learning is no silver bullet to strengthen global (micro)plastic mitigation policy

Systematic mapping of altermagnetic magnons by resonant inelastic X-ray circular dichroism

Abstract Altermagnets, a unique class of magnetic materials that combines features of both ferromagnets and antiferromagnets, have garnered attention for their potential in spintronics and magnonics. While the electronic properties of altermagnets have been well studied, characterizing their magnon excitations is essential for fully understanding their behavior and enabling practical device applications. In this work, we introduce a measurement protocol combining resonant inelastic X-ray scattering with circular polarization and azimuthal scanning to probe the chiral nature of the altermagnetic split magnon modes in CrSb. This approach circumvents the challenges posed by domain averaging in macroscopic samples, allowing for precise measurements of the polarization and energy of the magnons in individual antiferromagnetic domains. Our findings demonstrate a pronounced circular dichroism in the magnon peaks, with an azimuthal dependence that is consistent with the theoretical predictions and the g-wave symmetry. By establishing a reliable and accessible method for probing altermagnetic magnons, this work opens new avenues for fundamental studies of these collective excitations and for developing next-generation magnonic device applications.

Optimal tracking consensus for swarm systems with leader-following switching topologies

Evaluation of sulfur and selenium substituents to induce the heavy atom effect in metal-free porphyrins

The effects of the incorporation of oxygen, sulfur, selenium, and tellurium into the porphyrin core over nitrogen have been explored using density functional theory (DFT) and its time-dependent and quadratic response implementations (TDDFT and QR-TDDFT). The aim was to investigate how substitution affects the photophysical properties of these dyes and how such modifications could make them more suitable to be proposed as heavy-atom-free agents in photodynamic therapy (PDT). The photophysical properties assessed in our investigation, relevant for the PDT mechanism, allow us to establish that chalcogens trigger beneficial bathochromic shifts enabling the achievement of more biocompatible wavelengths while enhancing spin–orbit coupling and kinetic constants for intersystem crossings. Considering the higher safety profile of sulfur in biological systems and the numerous studies highlighting the role of Se-containing materials in inducing apoptosis in cancer cells with minimal side effects on normal cells, we believe that the results presented here on both the S- and Se-heterosubstitution strategies could be highly promising.

Different gametogenesis states uniquely impact longevity in Caenorhabditis elegans

Enhanced signal spaces assisted media-based modulation in index modulation-based MIMO networks

Abstract Index modulation, which develops the additional information using the antenna index (AI) domain, is a promising modulation technique for next wireless communications. In view of a rich radio scattering environment around transmit antennas (TAs), utilizing the indexes of channel fade realizations, media-based modulation (MBM), which develops the additional information using the channel index (CI) domain, is a recently potential channel modulation and viewed as a potential key technique for enhancing the reliability of communication systems. In this paper, to simultaneously carry the additional information including the AI and CI information bits, the integration of index modulation and MBM is investigated. Firstly of all, the application of the MBM technique to the extended space index modulation (ESIM) system, called as ESIM-MBM, is investigated to improve the spectral efficiency (SE) and error performance of the multiple-input multiple-output with index modulation (MIMO-IM) systems. Specifically, after obtaining one ESIM vector by modulating the real and imaginary parts of one mapped symbol on one or two active TAs using the selected AI vector, according to the number of active TAs, the real and imaginary parts of one mapped symbol are respectively performed Kronecker products by two selected CI vectors with two subparts of CI bits, result in the transmitted MBM vector. Secondly, in order to further extend the size of signal spaces to improve the AI information, with the combination of one or two signal points from QAM and secondary QAM constellations, a new design of enhanced signal spaces with two active TAs assisted the MBM system (ESS-TTAs-MBM) is proposed to enhance the throughput of the communication system. Furthermore, using the maximum likelihood (ML) at the receiver, the comparisons of detection complexities of the proposed ESIM-MBM and ESS-TTAs-MBM with different MBM-based IM schemes are analyzed, and the theoretical average bit error probability (BEP) is also formulated and shown to match well with the Monte-Carlo simulation results at different TAs and SEs in the high SNR region. Finally, a significant improvement in the SE and bit error performance of the proposed schemes is demonstrated with other classic MBM-based IM schemes such as quadrature spatial modulation assisted MBM (QSM-MBM) and quadrature channel modulation (QCM).

Coherent state field theory: A tool for inhomogeneous polymer dynamics and rheology

A non-equilibrium framework is introduced for recasting microscopic kinetic models of polymer dynamics into a compact field-theoretic form. Specifically, we adapt the Doi–Peliti formalism, which transforms a classical many-body problem into a second-quantized Schrödinger equation that is subsequently expressed as a real-time path integral using a boson coherent state basis. The framework is well-suited to the analysis of non-equilibrium, spatially inhomogeneous systems, which is illustrated using a simple Brownian dynamics model of dumbbell polymers in implicit solvent. By invoking a mean-field approximation, equations are derived that describe the coupled dynamics of polymer concentration and stress to second order in spatial gradients. New stress–concentration coupling and stress diffusion terms are found to arise from non-bonded interactions and serve to generalize previous theories beyond the dilute limit. Strategies are discussed for exploring fluctuation effects beyond the mean-field approximation, both analytically and numerically via field-theoretic simulation. The method can be extended to a wide variety of non-equilibrium polymer models, including those with reversible or irreversible chemical reactions.

Reply to Maleszka et al.: DNA methylation signals persist across insect metamorphosis