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Chemical finger-printing, antioxidant activity and in silico validation of phytometabolites of Octhochloa compressa

Fast spectral solver for viscoelastic structures under oscillatory flow in free space or wall-bounded domains: Applications to quartz crystal microbalance and force spectroscopy

We present a fast spectral solver for the linear response of viscoelastic structures under oscillatory flow either in free space or close to a flat moving wall. The scheme works in the frequency domain (using phasors) and couples the oscillatory Stokes equation with rigid or flexible structures, modeled by viscoelastic networks of immersed boundary kernels. The fluid–structure coupling can be solved by two routes. One route calculates the hydrodynamic mobility matrix required to solve the equation for the structure deformation rate in matrix form. The second route iteratively solves the coupled fluid–structure equations: fluid-induced forces on the structures create a tension field, which is then transferred to the fluid, until convergence. The resulting fixed-point problem is solved iteratively using the Anderson acceleration method. The mobility route is optimal when dealing with one or a few structures, while the iterative scheme is preferred for denser dispersions. In any case, the flow resulting from the body forces is solved by a recently developed scheme [R. P. Peláez, P. Palacios-Alonso, and R. Delgado-Buscalioni, J. Fluid. Mech. 1010 A57 (2025)], which is spectral in space and time and deals with doubly periodic open domains (either free-space or wall-bounded) where meshing is restricted to the region of interest around the structures. We test the present scheme in two applied contexts: quartz-crystal-microbalance (QCM) of spheres, suspended, adsorbed, or tethered to viscoelastic linkers; and force spectroscopy (via atomic force microscopy) reproducing the power spectra of vibrating microparticles near a solid boundary. In all cases, comparisons with analytical, numerical, and experimental results show excellent agreement. We conclude by discussing new routes the scheme opens in force spectroscopy and QCM analyses of soft objects.

Cross-dataset pan-cancer detection by correlating cell-free DNA fragment coverage with open chromatin sites across cell types

Knowledge graph embedding for predicting and analyzing microbial interactions

Abstract Interactions between microorganisms play a major role in shaping the structure and function of microbial communities, yet their prediction remains a challenge in microbial ecology. While currently available machine learning methods have shown promising performance, they often rely on extensive input features that are obtained from labor-intensive experiments. Here, we propose a new framework to predict pairwise interactions that minimizes the need for in vitro experimentation. Our approach is based on knowledge graph embedding, which learns the representation of microorganisms and their interactions in an embedding space. Using a dataset of interactions between 20 soil bacterial strains cocultured in 40 different carbon source environments, we demonstrate the effectiveness of our framework in accurately predicting pairwise interactions. Notably, we show that our model can predict interactions involving strains with missing culture data. We additionally show that the obtained embeddings can reveal similarities between carbon source environments, enabling the prediction of interactions in one environment based on the outcomes in a similar environment between the same pair of microorganisms. Furthermore, our approach allows the design of a recommendation system that can be used to guide microbial community engineering. These findings demonstrate that knowledge graph embedding is a promising modeling strategy in microbial ecology.

Key factors in semi-generic coarse-grained modeling of solid polymer electrolytes

Given the long length and time scales of interest and strong interactions present in solid polymer electrolytes, coarse-grained molecular models can be useful in understanding the molecular basis of their structure and transport properties. Rather than representing atoms individually, coarse-grained models use beads representing groups of atoms, making the system simpler and more efficient. Generic coarse-grained models, which are not built based on matching a particular atomistic system, can provide insight into the important physical considerations that apply across different chemical systems, though it can be unclear how to best match experimental systems and capture relevant experimental behaviors with as simple a model as possible. Here, we build on generic bead-spring models but use stiff angle potentials, set different bead properties for different polymer types, and include additional ion parameters, creating a semi-generic coarse-grained model that can map more specifically to polymers and copolymers with different chain architectures, component glass transition temperatures, and ion solvation behaviors. We set most parameters with basic homopolymer data, such as glass transition temperatures, Kuhn length, density, and dielectric constant, with further adjustment based on data from the polymer electrolyte system. We specifically model polystyrene-block-poly(oligo-oxyethylene methyl ether methacrylate) (PS-b-POEM) with lithium triflate salt, considering the POEM to be made of a poly(methylmethacrylate) backbone with poly(ethylene oxide) side chains. Solvation of ions is accounted for by additional polymer–ion interactions of the form –S/r4, plus additional lithium–polymer Lennard-Jones interactions. We find that these potentials have different effects and discuss strategies for setting these parameters.

Multi-scale Interaction Mechanism for Edge-Localized-Mode Suppression in the Tokamak Edge

Abstract A central challenge in fusion energy is reconciling the high-confinement mode required for reactor performance with the intense intermittent relaxation events it produces, known as edge-localized modes. These instabilities arise in the steep pressure pedestal at the plasma edge when magnetohydrodynamic thresholds are crossed, inflicting damaging heat loads on reactor components. Here, we show that multiscale interactions between microscopic turbulence and macroscopic magnetohydrodynamic modes provide encouraging prospects for self-organized edge-localized modes regulation. Using direct quantitative measurements of multiscale modes, eddy dynamics, and turbulent flux, we show that small-scale electron drift wave turbulence actively scatters the large-scale peeling-ballooning modes. This scattering decorrelates the pressure and velocity fields of the instability, so arresting its growth. Our modeling and theoretical analysis confirm this suppression mechanism is effective even when conventional linear stability thresholds are exceeded. This work establishes a nonlinear principle for edge-localized modes stability, revealing how ambient micro-turbulence can be leveraged to maintain a macro-stable, high-performance pedestal for future fusion reactors.

Sustainable synthesis and characterization of Zn–Al doped nanocomposites for removal of brilliant blue dye: optimization using a response surface methodology

Magnetic Co-tip control of quantum states in a triple-decker sandwich molecule: Mechanistic insights from DFT/HEOM simulations

The manipulation of quantum states in triple-decker organometallic molecules remains challenging due to their complex many-body interactions. In this study, we combine density functional theory (DFT) and the hierarchical equations of motion (HEOM) to map, for the first time, the evolution of quantum states in a triple-decker dinuclear complex under mechanical manipulation by a magnetic cobalt tip. DFT calculations demonstrate that the tip approach induces substantial structural distortion of the molecular framework, which triggers a reconstruction of the internal magnetic coupling network. This process is accompanied by an evolution of the electronic structure that includes modifications to the local density of states, magnetic moment, spin-state populations, and molecular orbital hybridization characteristics. By solving the spin-polarized Anderson model using the HEOM method, we have revealed the dynamic evolution of strongly correlated Kondo effects. When the system enters the contact regime, the Kondo resonance peak exhibits asymmetric splitting, where the splitting characteristics exhibit a simultaneous dependence on the spin polarization degree of the electrodes and the coupling strength between the impurity and the electrodes. These atomic-scale insights into the external control of molecular quantum states provide a robust framework for the future design of molecular spintronic devices.

A high signal-to-noise ratio and high-frequency seesaw cantilever for high-speed atomic force microscopy

Cannabidiol inhibits TGF-β1-induced epithelial-mesenchymal transition in human conjunctival epithelial cells by interrupting TGF-β/Smad signaling

Non-equilibrium lifetimes of DNA under electronic current in a molecular junction

We investigate the non-equilibrium mechanical motion of double-stranded DNA in a molecular junction under electronic current using Keldysh–Langevin molecular dynamics. Non-equilibrium electronic force reshapes the effective potential energy surface and along with electronic viscosity force and stochastic force, governs voltage-dependent dynamics of DNA’s collective mechanical coordinate. We compute mean first-passage times to quantify the non-equilibrium lifetime of the DNA junction. At low voltage biases, electron–mechanical motion coupling destabilizes DNA by shifting the potential minimum toward critical displacement and suppressing barriers, thus shortening lifetimes by several orders of magnitude. Unexpectedly, at higher voltages, the trend reverses: the potential minimum shifts away from instability and the barrier re-emerges, producing re-stabilization of the junction. In addition, we demonstrate the Landauer blowtorch effect in this system: coordinate-dependent fluctuations generate a spatially varying effective temperature, changing current-induced dynamics of mechanical degrees of freedom. Apparent temperatures of DNA mechanical motion increase far above ambient due to current-induced heating, correlating with suppressed electronic current at stronger couplings. Our results reveal a non-equilibrium interplay between current-driven forces, dissipation, and fluctuations in DNA junctions, establishing mechanisms for both destabilization and recovery of DNA stability under electronic current.

Domestication shaped the chromatin landscape of grain amaranth

Abstract Plant domestication has had profound impacts on the morphology and genetic diversity of crops. Beyond sequence diversity, changes in chromatin structure can play an important role in plant adaptation. However, the interplay between the chromatin landscape and plant domestication remains unclear. Here, we present a high-quality genome assembly and chromatin landscape map of the ancient pseudo-cereal, amaranth. ATAC-sequencing of multiple accessions of three grain amaranth species and two wild relatives, shows that the overall amount of accessible chromatin is highly conserved, but about 2.5% of all chromatin switched states, with a higher fraction of the genome repeatedly opening during domestication processes. These differentially accessible chromatin regions, between the crops and their wild ancestor, are species-specific and significantly associated with selective sweeps - reflecting the repeated independent domestication of amaranth. Our findings reveal the dynamic interplay between domestication and the chromatin landscape, highlighting an additional layer of diversity in crops.

Innovative vaginal wash formulation with Chitosan nanoparticles targets microbial pathogens, ovarian cancer and inflammation

Dielectric permittivity of water confined in stacks of charged lipid layers: Extracting profiles from molecular dynamics simulations using a modified Poisson–Boltzmann equation

Most organic and inorganic surfaces (e.g., glass or lipid membranes) become charged in aqueous solutions. The resulting ionic distribution induces effective interactions between the charged surfaces, which depend on the permittivity of the confined aqueous solution. To explore this phenomenon in very confined systems, we perform all-atom molecular dynamics (MD) simulations of charged lipid membranes separated by a salted water layer of varying thickness. To extract an effective permittivity from the atomistic model, we compare the ion distributions of these simulations with the ones of a continuous, mesoscopic model: a modified Poisson–Boltzmann (mPB) equation taking into account a spatially varying dielectric permittivity and an explicit Born solvation energy for ions. Such mPB/MD comparisons, applied to lipid membranes at various hydration levels, reveal a sharp decrease of the permittivity upon dehydration, converging to a plateau value that we attribute to lipid headgroups. We discuss the limitations of the mPB model in the dehydrated lipid membranes, in particular through the appearance of ion/ion correlations, and compare our results to alternative computational methods. In our tension-free simulations of the fluid membranes, an increase in the area per lipid indicates that the permittivity decrease is accompanied by intermembrane attraction. Our approach could be generalized to estimate a mesoscopic permittivity of liquids confined by other interfaces, provided ions follow Boltzmann statistics.

Atomic structure and in situ visualization of native PMEL lamellae in melanosomes

Functional connectivity between non-motor and motor networks predicts motor recovery changes after stroke

Thermochemical properties of small rhenium molecules: ReC, ReN, ReO, ReS, and ReC2

The rhenium-containing molecules ReC, ReN, ReO, ReS, and ReC2 have been investigated using a pulsed laser ablation supersonic beam molecular source in resonant two-photon ionization experiments with time-of-flight mass spectrometric detection. Sharp predissociation thresholds have been observed, allowing precise bond dissociation energies (BDEs) to be measured as D0(ReC) = 5.731(3) eV, D0(ReN) = 5.635(3) eV, D0(ReO) = 5.510(3) eV, D0(ReS) = 3.947(3) eV, and D0(Re–C2) = 5.359(3) eV. The threshold for two-photon ionization was also measured for ReC, ReN, and ReO, providing ionization energies (IEs) of IE(ReC) = 8.425(12) eV, IE(ReN) = 8.193(20) eV, and IE(ReO) = 8.561(11) eV. These are the first measurements of these thermochemical quantities to be reported in the literature. The combination of BDEs and IEs allowed the BDEs of the cations ReC+, ReN+, and ReO+ to be determined via a thermochemical cycle as D0(Re+-C) = 5.140(12) eV, D0(Re+-N) = 5.275(20) eV, and D0(Re+-O) = 4.783(11) eV. In addition, computations of these thermochemical values were performed using density functional theory [B3LYP/aug-cc-pVQZ(-PP)] to determine the ground states and their geometric parameters. These were further studied at the CCSD(T) level with extrapolation to the complete basis set limit using aug-cc-pVXZ(-PP) basis sets (X = 3, 4, 5) to obtain computational values of the BDEs and IEs as well. The high-level super correlation consistent composite approach (s-ccCA) was also utilized, providing an additional approach for the prediction of thermochemical values. The electronic structure of the molecules is discussed, along with the periodic trends as the ligand is varied.

TGFβ-Smad3 signaling restores cell-autonomous Srsf1-mediated splicing of fibronectin in aged skeletal muscle stem cells

Abstract Loss of Fibronectin (FN) from the skeletal muscle stem cell (MuSC) niche represents a root cause of regenerative failure in aging. While FN has pleiotropic functions during healthy skeletal muscle regeneration, it remains unclear how aging affects its spatiotemporal specificity for MuSCs. Here, we demonstrate that activated MuSCs secrete an autoregulatory FN splice variant containing the EDB extra domain (EDB(+) FN), which is not expressed by accessory cells in the niche. EDB(+) FN splicing in MuSCs depends on serine/arginine-rich splicing factor 1 (Srsf1) whose promoter is controlled by Smad3. EDB(+) FN knockdown or downregulation in aging affects MuSC proliferation through aberrant integrin signaling and impairs skeletal muscle regeneration. During a defined regeneration interval in aged mice, Smad3 activation using transforming growth factor-beta 1 (TGFβ1) improves MuSC function and skeletal muscle repair by stimulating EDB(+) FN secretion. Altogether, we identify and characterize the TGFβ1-Smad3-Srsf1-EDB(+) FN pathway as a therapeutic target for age-associated regenerative failure.

Quantum color image encryption using a novel 4D hyperchaotic Lorenz system and Fibonacci transform

An internally contracted multireference coupled cluster treatment of the CO ground state in a wide range of internuclear distances

The internally contracted multireference coupled cluster (ic-MRCC) method was applied for large-scale calculations of the potential energy curve and the permanent dipole moment function (DMF) for the ground X1Σ+ state of the CO molecule in the range of internuclear distances R from 0.7 to 3.0 Å, covering the energy range significantly higher than the last spectroscopically observed vibrational level v = 41. The ic-MRCCSD(T){4} approach, perturbatively accounting for contributions of triple excitation cluster amplitudes with up to four active indices, results in ab initio vibrational term values with a maximum deviation from their experimental counterparts not exceeding 10–15 cm−1 for v ∈ [0, 41]. The respective DMF obtained by the present ic-MRCC calculation agrees within ±0.005 D with its most accurate theoretical and semi-empirical counterparts in the interval R ∈ [0.8, 1.5] Å, but systematically diverges for R > 1.8 Å up to 0.1 D. It highlights the necessity for the revised intensity measurements between high-lying (v > 7) vibrational levels of the CO ground state since the observed discrepancy is unlikely to be attributed to the lack of higher excitations in the cluster expansion or the incompleteness of basis sets employed. The ic-MRCC method can be recommended for highly accurate calculations of electronic structure and properties of other small atmospheric molecules.