Browse Articles

Sound attenuation in glasses

Comprehending sound attenuation is integral to understanding the anomalous low temperature properties of glasses. Despite decades of studies, the underlying mechanism of sound attenuation in glasses is still debated. In this perspective, we review recent work on sound attenuation in amorphous solids. We focus on the role of defects and heterogeneous elasticity, and we also discuss attenuation in model amorphous solids without defects. We review our definition of attenuation defects and show that they strongly influence sound attenuation. However, we also find another contribution to sound attenuation that cannot be attributed to attenuation defects. We confirm an earlier result of Kapteijns et al. [Kapteijns et al., J. Chem. Phys. 154, 081101 (2021)] that heterogeneous elasticity theory predicts relative changes of sound attenuation in model two-dimensional glasses if the configuration-to-configuration elastic constants fluctuations are used to quantify the heterogeneity. We extend this finding to similar three-dimensional glasses. We end by discussing the Euclidean random matrix model, which exhibits Rayleigh scaling of sound attenuation but does not have quasi-localized excitations and, thus, probably does not have sound attenuation defects. We propose that the mechanisms behind sound attenuation can be more fully understood by approaching the problem from two directions: one where the strong influence of defects is studied and another where sound attenuation is studied in defect free, although disordered, materials.

Iterative SCRaMbLE for engineering synthetic genome modules and chromosomes

Abstract Saccharomyces cerevisiae is closing-in on the first synthetic eukaryotic genome with genome-wide redesigns, including LoxPsym site insertions that enable inducible genomic rearrangements in vivo via Cre recombinase through SCRaMbLE (Synthetic Chromosome Recombination and Modification by LoxPsym-mediated Evolution). Combined with selection, SCRaMbLE quickly generates phenotype-enhanced strains by diversifying gene arrangement and content. Here, we demonstrate how iterative cycles of SCRaMbLE reorganises synthetic genome modules and chromosomes to improve functions. We introduce SCOUT ( S CRaMbLE C ontinuous O utput and U niversal T racker), a reporter system that allows sorting of SCRaMbLEd cells into high-diversity pools. Paired with long-read sequencing, SCOUT enables high-throughput mapping of genotype abundance and genotype-phenotype relationships. Iterative SCRaMbLE is applied here to yeast strains with a full synthetic chromosome and histidine biosynthesis modules. Five HIS module designs are tested, and SCRaMbLE is used to optimise the poorest performer. Our results highlight iterative SCRaMbLE as a powerful tool for data driven modular genome design.

ALDH18A1 has carcinogenic functions and regulates alternative splicing events of DNA repair-related genes in esophageal carcinoma cells

Photodynamics simulation insights into excited-state relaxation mechanisms via Z/E isomerization in para-amino substituted GFP chromophores

The ability of green fluorescent protein (GFP) chromophore and its derivatives to undergo cis–trans photoswitching behavior has been widely acknowledged as of great interest because of its emerging applications in optogenetics and optoelectronics. However, key aspects of the internal conversion process in the GFP chromophore derivatives remain largely unclear. Based on quantum chemical methods and on-the-fly nonadiabatic dynamics simulations, we investigated the ultrafast photoinduced cis–trans isomerization phenomenon in the para-amino (NH2-HBDI) derivative of the GFP chromophore, which is intrinsically non-fluorescent. We demonstrate that upon excitation to the excited (S1) state, there occurs nonselective progression along the distortion of exocyclic methine-bridged imidazolinone (I) and phenylamine (P) bonds, leading to ultrafast nonradiative relaxation via S1(1ππ*)/S0 internal conversion. This internal conversion process is facilitated by multiple S1/S0 conical intersections with dominant imidazolinone (ΦI) dihedral rotations. Our results provide insight into the effect of the amino group on the dynamics of fluorescent probes. Therefore, these observations contribute to a valuable understanding of photoinduced switching phenomena and find a relation between structure and dynamics.

Mechanistic analysis and kinetic profiling of Soai’s asymmetric autocatalysis for pyridyl and pyrimidyl substrates

Abstract Nonlinear effects in chemical reactions, coupled with amplifying catalysis, can lead to remarkable phenomena like spontaneous symmetry breaking, central to the origin of biological homochirality. Soai’s asymmetric autocatalysis is a prototypical reaction for this, where the enantiomeric excess of the product alcohol is amplified during alkylation of pyridyl and pyrimidyl carbaldehydes by diisopropylzinc. However, the complex equilibria and elusive intermediates make the mechanism difficult to clarify. Here we unravel the intricate dynamics of this reaction by in situ high-resolution mass spectrometry, kinetic analysis, and reaction profile simulations. We identify for both the pyrimidyl and the pyridyl systems transient hemiacetalate isopropyl zinc complexes, formed by the addition of the alcoholate product to the aldehyde, as key catalytic intermediates. These diastereomeric complexes enable dual stereocontrol, explaining the observed enantioselectivity. Our analysis confirms the structures of all intermediates and validates the autocatalytic cycle, offering insights into how substituent and structural variations influence reaction performance. This understanding guides the design of new, efficient asymmetric autocatalytic systems.

Metabolic dynamics of human external urethral sphincter myoblast differentiation and the effects of tricarboxylic acid cycle inhibition

Abstract Stress urinary incontinence commonly arises with aging or following prostatectomy, yet its underlying mechanisms remain unclear. To address this, we investigated the role of metabolic pathways—particularly the tricarboxylic acid (TCA) cycle—in the differentiation of human external urethral sphincter myoblasts. Immortalized sphincter cells (US2-KD) were induced to differentiate over 192 h. Metabolomic profiling using gas chromatography–mass spectrometry, along with pathway enrichment analysis, identified key metabolic changes. Inhibition of mitochondrial pyruvate transport with UK5099 markedly suppressed TCA cycle metabolites, including citrate, α-ketoglutarate, fumarate, and malate. This inhibition also significantly reduced MYH7 expression and intracellular adenosine triphosphate levels throughout the differentiation period. These results demonstrate that the TCA cycle plays a critical role in both energy metabolism and the differentiation of urethral sphincter myoblasts. This study is the first to suggest that impaired TCA cycle activity may contribute to the pathogenesis of Stress urinary incontinence and represents a potential therapeutic target. Our findings offer new insight into age-related metabolic decline associated with Stress urinary incontinence and support the development of therapies that combine metabolic modulation with regenerative approaches.

Extension of the Fermi–Amaldi functional to fractional electron number

The Fermi–Amaldi correction is a conceptually significant density-functional approximation with explicit dependence on the electron number N. This dependence raises the question of whether N should be treated as the integral of the total electron density for systems with noninteger (fractional) N. We answer this question negatively by observing that the Fermi–Amaldi functional is identical with the exact exchange functional for any number of fermions or bosons occupying the same spatial orbital and in systems where occupied orbitals have zero differential overlap. This conclusion is consistent with previous reports that the preservation of certain properties of N-dependent functionals requires treating N as a parameter. Our analysis also suggests that the Fermi–Amaldi functional is discontinuous within a given spin-channel of the total electron density and continuous on the boundaries between different spin-channels at N = 1. This implies that the jump discontinuity of the exact exchange–correlation potential observed at N = 1 is a correlation effect. The last conclusion is illustrated with numerical calculations.

Integrative multi-omics reveals a regulatory and exhausted T-cell landscape in CLL and identifies galectin-9 as an immunotherapy target

Abstract T-cell exhaustion contributes to immunotherapy failure in chronic lymphocytic leukemia (CLL). Here, we analyze T cells from CLL patients’ blood, bone marrow, and lymph nodes, as well as from a CLL mouse model, using single-cell RNA sequencing, mass cytometry, and tissue imaging. T cells in CLL lymph nodes show the most distinct profiles, with accumulation of regulatory T cells and CD8+ T cells in various exhaustion states, including precursor (TPEX) and terminally exhausted (TEX) cells. Integration of T-cell receptor sequencing data and use of the predicTCR classifier suggest an enrichment of CLL-reactive T cells in lymph nodes. Interactome studies reveal potential immunotherapy targets, notably galectin-9, a TIM3 ligand. Inhibiting galectin-9 in mice reduces disease progression and TIM3+ T cells. Galectin-9 expression also correlates with worse survival in CLL and other cancers, suggesting its role in immune evasion and potential as a therapeutic target.

Exploring the relationship between circadian syndrome, serum uric acid levels, and hyperuricemia: evidence from NHANES 2005–2018

Classical dynamics in a quantum spirit: Refining semi-classical corrections for the scattering of H2 on W(100)

The collision dynamics of hydrogen on tungsten is studied using a combination of classical and quantum molecular dynamics approaches, making use of a multidimensional potential energy surface interpolated from density functional theory energies based on the vdW-DF2 functional. Corrections inspired by a semi-classical model are then introduced to improve the predictions of the classical description. In particular, a refined version of the adiabaticity correction (AC) is developed. This study demonstrates that, for H2 on W(100) in its ground state and in various rotationally excited states, applying both Gaussian binning and this refined AC to classical trajectories yields unparalleled agreement with time-dependent quantum wave packet results.

Photosynthate distribution determines spatial patterns in the rhizosphere microbiota of the maize root system

Abstract The spatial variation and underlying mechanisms of pattern formation in the rhizosphere microbiome are not well understood. We demonstrate that specific patterns in the distribution of recently fixed carbon within the plant root system influence the spatial organization of the rhizosphere microbiota. Non-invasive analysis of carbon allocation in the maize root system by 11C tracer-based positron emission tomography combined with magnetic resonance imaging reveals high spatial heterogeneity with highest 11C-signal accumulations at root tips and differences between root types. Strong correlations exist between root internal carbon allocation and rhizodeposition as evident from 13CO2 labeling. These patterns are reflected in the bacterial, fungal and protistan community structure in rhizosphere soil with differences depending on root structure and related spatial heterogeneities in carbon allocation. Especially the active consumers of 13C-labeled rhizodeposits are responsive to photosynthate distribution with differences in 13C-labeling according to their spatial localization within the root system. Thus, root photosynthate allocation supports distinct habitats in the plant root system and is a key determinant of microbial food web development, evident from 13C-labeling of diverse bacterial and protistan predators, especially at root bases, resulting in characteristic spatiotemporal patterns in the rhizosphere microbiome.

Epitaxial growth of monolayer white phosphorus on Cd(0001)

As a promising two-dimensional (2D) material, phosphorene has attracted tremendous research interest in both fundamental research and potential applications. Up to now, black phosphorene, blue phosphorene, violet phosphorene, and ultrathin nanosheets of red phosphorus have been successfully synthesized by mechanical exfoliation or epitaxial growth, while the synthesis of 2D white phosphorus (WP) has not been achieved. Here, we report the epitaxial growth of monolayer WP on Cd(0001) by means of low temperature (90 K) deposition. Scanning tunneling microscopy observation and first-principles calculations demonstrate that the monolayer WP is comprised of parallel dimer rows of P4 molecules, resembling the a–c plane of γ-phase WP. The monolayer WP is semiconducting with a bandgap of 1.5 eV. Increasing the substrate temperature to 120 K leads to the formation of a quasi-3 × 3 superstructure with building blocks of P4 nonamers. Voltage pulses from STM tip result in the structural transition from the quasi-3 × 3 superstructure to a 3 × 1 superstructure, of which the latter consists of alternating dimer rows and polymerized monomer rows. These observations demonstrate the essential role of dimerization, trimerization, and polymerization of P4 molecules in the formation of 2D white phosphorus.

Safety and Immunogenicity of aerosolized adenovirus-vectored COVID-19 vaccine and intramuscular mRNA vaccine bivalent boosters: a randomized open-label clinical trial

Ancient DNA reveals the prehistory of the Uralic and Yeniseian peoples

Thermodynamic analysis of heterogeneous nucleation on refractory nanoparticles

The present study investigates the influence of size effects and wettability on the process of heterogeneous nucleation of crystalline phase on refractory nanoparticles of different shapes. This work is based on the classical theory of nucleation. Formulas for the nucleation energy, incorporating linear tension as well as the influence of the nucleation surface curvature on surface tension, were employed for two distinct scenarios: the nucleation being formed on a convex (spherical) nanosubstrate or on a flat nanosubstrate. From the equilibrium condition of a spherical-cap nucleus on a convex surface, an equation defining the wetting contact angle by the standard angle of a large nucleus on a flat surface was obtained, and from the condition of the extremum of the nucleus energy, an equation for its critical radius was obtained. The method of successive approximations by the small parameter was utilized to solve these equations. A similar approach was adopted for the case of spherical-cap nucleation on a flat surface. This approach enabled the derivation of explicit expressions for the wetting function on both convex and flat substrates. The analysis of the obtained dependencies demonstrated that incorporating the linear tension and the Tolman effect resulted in a reduction of the energy required for heterogeneous nucleation. This effect is most significant on well-wetted convex nanosubstrates.

Frequency-selective actuation of liquid crystalline elastomer actuators with radio-frequency

Abstract Soft and miniaturized robots possess the capability to operate inside narrow, confined environments. However, powering soft robots inside these environments with on-board batteries or wired connections to external power supplies can significantly restrain their mobility. Similarly, wireless actuation approaches are constrained by near-field actuation, line-of-sight operation, or indiscriminate actuation of many actuators. To provide higher mobility for wireless soft robot to operate inside non-line-of-sight scenarios, we present a radio-frequency system that introduces frequency-selective actuation of liquid crystal elastomer actuators. We create liquid crystalline elastomer actuators with a low actuation temperature and embed them with conductive traces that resonate and heat by selected frequencies of radio-frequency excitation in the 2.40 GHz range. We further develop a wireless actuation platform that infers the wireless channel and beamforms towards the actuator to achieve efficient beamforming. Demonstrations show our system is capable of selectively actuating different actuators while the robot is in motion and obstructed by occlusions.

Molecular processes as quantum information resources

In this contribution to Abraham Nitzan’s Festschrift, we present a perspective of theoretical research over the years that has pointed to the potential of molecular processes to act as quantum information resources. Under appropriate control, homonuclear dimer (diatom) dissociation (half-collision) and the inverse process of atom-pair collisions are shown to reveal translational (EPR-like) entanglement that enables molecular wave packet teleportation. When such processes involve electronic-state excitation of the diatom, the fluorescence following dissociation can serve as an entanglement witness that unravels the molecular-state characteristics and evolution. Such entangling processes can also exhibit anomalous quantum thermodynamic features, particularly temperature enhancement of a cavity field that interacts with dissociated entangled diatoms.

The HM-TARGET personalised real-time haemodynamic targets in critical care

Algorithms and software for open quantum system dynamics

Interfaces govern the structure of angstrom-scale confined water solutions

Abstract Nanoconfinement of aqueous electrolytes is ubiquitous in geological, biological, and technological contexts, including sedimentary rocks, water channel proteins, and applications like desalination and water purification membranes. The structure and properties of water in nanoconfinement can differ significantly from bulk water, exhibiting, for instance, modified hydrogen bonds, altered dielectric constant, and distinct phase transitions. Despite the importance of nanoconfined water, experimentally elucidating the nanoconfinement effects on water, such as its orientation and hydrogen bond (H-bond) network, has remained challenging. Here, we study two-dimensionally nanoconfined aqueous electrolyte solutions with tunable confinement from nanoscale to angstrom-scale sandwiched between a graphene sheet and calcium fluoride (CaF2) achieved by capillary condensation. We employ heterodyne-detection sum-frequency generation (HD-SFG) spectroscopy, a surface-specific vibrational spectroscopy capable of directly and selectively probing water orientation and H-bond environment at interfaces and under confinement. The vibrational spectra of the nanoconfined water can be described quantitatively by the sum of the individual interfacial water signals from the CaF2/water and water/graphene interfaces until the confinement reduces to angstrom-scale (<~8 Å). Machine-learning-accelerated ab initio molecular dynamics simulations confirm our experimental observation. These results manifest that interfacial, rather than nanoconfinement effects, dominate the water structure until angstrom-level confinement for the two-dimensionally nanoconfined aqueous electrolytes.