Browse Articles

TRIM39 aggravates hepatocellular carcinoma growth through targeting the p62-KEAP1-NRF2 axis

Kinetic rate of methane hydrate film growth from microsecond molecular dynamics simulations

Microsecond molecular dynamics (MD) simulations are employed in the isobaric–isothermal ensemble for the determination of the growth rate of sI methane hydrate. Statistically meaningful measurements of the growth rate are given for a wide range of pressures and temperatures. The reported growth rates are measured from the MD trajectories with two different methods. The first method is based on the time evolution of the potential energy of the system by correlating the rate of potential energy decrease to the speed of the moving hydrate interface. The second method that was originally introduced in the current study uses Voronoi tessellation to characterize the molecules depending on their neighborhood and thus allows the identification for each time step of the exact position of the interface. Both methods yield practically identical results. At the low pressure regime, the MD results are compared to available experimental data with highly satisfactory agreement. A useful correlation for engineering applications is suggested, which offers prediction of the methane growth rate as a function of the concentration of methane in the aqueous phase between the supersaturated and the isobaric equilibrium conditions. The calculated hydrate growth rates are also compared to reported experimental and MD simulations data.

Missense variant in TTBK2 kinase domain causes loss of function and impaired protein phosphorylation

Abstract Tau tubulin kinase 2 (TTBK2) is a ubiquitous serine-threonine protein kinase implicated in diverse cellular processes, including microtubule regulation, ciliogenesis, synaptic signaling, and the phosphorylation of key proteins like TDP-43. Despite its relevance, many aspects of TTBK2 function in both physiological and pathological conditions remain poorly understood. Truncating variants in TTBK2 gene cause s pinocerebellar ataxia type 11 (SCA11), a rare form of autosomal dominant cerebellar ataxia. However, the functional consequences and pathogenic potential of missense variants have yet to be elucidated. In this study, we developed a CRISPR/Cas9 knock-in cell model harboring a missense variant in TTBK2 kinase domain (NM_173500.4:c.625 C > T; p.Leu209Phe) to evaluate its impact on TTBK2 expression, associated protein levels, and phosphoproteomic profiles. TTBK2 missense variant (TTBK2-L209F) was associated with reduced TTBK2 protein levels, altered levels of cytoskeleton-related proteins, and impaired kinase activity, namely toward TDP-43. Phosphoproteomic analyses identified dysregulation in pathways linked to gene regulation, protein degradation, cytoskeletal organization, and TGF-β signaling. These findings provide valuable insights into the biological roles of TTBK2 in cellular signaling. Moreover, this study underscores the importance of functional studies to better understand the consequences of TTBK2 missense variants, particularly those affecting the kinase domain, and their potential contribution to disease.

Chalcogenated biazulenediimides: A promising class of triplet harvesters

Visible-light absorbing planar perylenediimide and its chalcogenated congeners (X-PDIs; X = O, S, Se) showed huge promise in triplet harvesting. Analogous biazulenediimides (X-BAzDIs) may also hold great opportunity owing to the expected large spin–orbit coupling (SOC) via internal structural-twist and the heavy-atom effect due to chalcogen substituents. Herein, the rich photophysics of X-BAzDIs are explored and well understood by implementing time-dependent optimally tuned range separated hybrid density functional theory, achieving a reliable and accurate description of the excited electronic states. Increased SOC down the chalcogen group in X-BAzDIs due to the heavy-atom effect results in greater intersystem crossing (ISC) rates, ranging from ∼108 to 1013 s−1. Furthermore, ∼6–7 orders smaller fluorescence rates than the ISC of S/Se-BAzDIs suggest their excellent triplet harvesting efficacy. Unlike the planar O-PDI, an appreciable ISC rate of ∼108 s−1 is found for O-BAzDI, resulting from the inherent structural-twist. However, comparable ISC rates of ∼1011–1013 s−1 are found for both S/Se-BAzDIs and S/Se-PDIs. Inherently twisted-structures of X-BAzDIs are expected to surpass the self-aggregation. In addition, the high energy lowest excited triplet, and a modest lifetime, together with large ISC rates, position them as better triplet photosensitizers than X-PDIs. These findings will be helpful for understanding the molecular photophysics and also designing analogous azulene-based twisted organic systems to efficiently harvest high energy and long-lived triplets.

Mitochondrial genome assembly of the Peruvian Paso horse through PacBio long-read sequencing

Erratum: “Noniterative triple excitations contributions in equation-of-motion coupled-cluster theory for singlet and triplet excitation energies of closed-shell systems” [J. Chem. Phys. 163, 134117 (2025)]

Hybrid micromagnetic and atomistic modeling of magnetization dynamics induced by engineered defects

Abstract This study presents a 3D version of multiscale approach for investigating magnetization dynamics in multiscale, hybrid micromagnetic-atomistic simulations. The present work introduces engineered discontinuities (i) a double-slit structure, which enables the study of domain wall and spin wave interference, and (ii) a tetrahedron shaped cluster of atoms with tunable anisotropy, which provides insights into how localized anisotropic perturbations influence domain wall pinning and skyrmion stability in fully three-dimensional (3D) hybrid simulations. We considered the dynamics of spin waves, domain walls, as well as 3D skyrmions, in the presence of these defects. The magnonic double-slit experiment demonstrates interference patterns analogous to electronic wave phenomena, offering potential applications in wave-based computing. Additionally, the results reveal the impact of the local anisotropy that leads to distinct transformations, including domain wall deformations, tubular and spherical structures, skyrmion annihilation, and breathing mode. The findings underscore the critical role of defect-induced anisotropic interactions in controlling domain wall motion, skyrmion topology, and spin wave propagation.

Absorption, scattering, and extinction cross sections of a nanosphere with adjacent molecule

While the electromagnetic interaction between noble metal nanoparticles with adjacent molecules has been known for some time, the exact expression of the scattering, absorption, and extinction cross sections of such a system has long remained unspecified. Herein, these cross sections are analytically derived for a molecule–nanoparticle system in which the molecule is excited to a radiating dipole by monochromatic incident radiation. These analytic cross sections were used in numerical calculations to model the UV–vis spectrum of a 20 nm gold nanoparticle colloid with attached IR-808 variant dye molecules. The numerical results compared favorably with experimental spectra.

Association of glycemic variability with short- and long-term mortality in critically ill patients with trauma

Rectification of vibrational energy transfer in driven chiral molecules

We show that the combination of molecular chirality and phase-controlled driving can lead to rectification of vibrational energy transfer. We demonstrate this effect using (1) a harmonic model of a single helical chain and (2) a more realistic model of a polyethylene double helix. We examine the effect of driving frequency, polarization, and temperature on this phenomenon. Notably, we find that the direction and magnitude of the observed directionality preference depend on the driving frequency and phase and that the effect persists at room temperature.

Identification of new interactors of eIF3f by endogenous proximity-dependent biotin labelling in human muscle cells

Abstract Regulation of protein synthesis is central to maintaining skeletal muscle integrity and its understanding is important for the treatment of muscular and neuromuscular pathologies. The eIF3f subunit of the translation initiation factor eIF3 has a key role, as it stands at the crossroad between protein-synthesis-associated hypertrophy and MAFbx/atrogin-1-dependent atrophy. To decipher the molecular mechanisms underpinning the role of eIF3f in regulating muscle mass, we established a cellular model that enables interrogation of eIF3f functionality via identification of proximal interactors. Using CRISPR-Cas9 molecular scissors, we generated single cell clones of immortalised human muscle cells expressing eIF3f fused to the BirA biotin ligase (eIF3f-BioID1 chimera) from the endogenous EIF3F locus. Biotinylated proteins, representing interactors of eIF3f in nanometer range distance, were identified by streptavidin pull-downs and mass spectrometry. In both proliferating and differentiated muscle cells, the eIF3f-BioID1 chimera co-sedimented with ribosomal complexes in polysome profiles and interacted mainly with components of the eIF3 complex, and with the eIF4E, eIF4G, and eIF5 initiation factors. Surprisingly, we identified several nucleus-localised interactors of eIF3f, and the immunofluorescence analyses revealed a previously unknown nuclear localization of eIF3f in both myoblasts and myotubes. We also identified novel cytoplasmic partners of eIF3f, responsible for the maintenance of skeletal muscle ultrastructure (sarcomeric/Z-disc (SYNPO2) bound proteins) and proteins of the lysosomal compartment (LAMP1). The established tagging system should be useful to further advance studies of eIF3f function in hypertrophic and atrophic conditions in skeletal muscle.

Coarse-grained simulations of pairs of polymer-grafted nanoparticles in implicit solvent

By grafting polymer chains to nanoparticles, one can create inorganic–organic hybrid materials whose structure and properties can be tuned by controlling graft density, chain length, and other molecular features. These polymer-grafted nanoparticles (PGNs) are usually synthesized and processed in solution, and then are often deposited and dried to create films or bulk materials with uniform spacings of particles in a mechanically robust matrix. Understanding interparticle interactions in solvated PGN systems is crucial to controlling the structure and properties of PGNs during and after deposition. Here, we use molecular dynamics simulations with a generic coarse-grained model to study polymer conformations and effective interparticle interactions of PGN systems in implicit solvent, for systems at two graft densities and a range of solvent strengths. As expected, higher graft density and good solvent correspond to more extended graft chain conformations, which are analyzed via mean-squared internal distances. We calculate the potentials of mean force between pairs of PGNs and find a relatively sudden onset of a deep attractive well with increasing solvent strength, which occurs at nearly the same solvent strength regardless of graft density. The implications of our results for solution phase behavior are discussed.

A novel method for acoustic modeling of cranial bone based on the porosity index

The scattering function of ideal two-dimensional asymmetric pom–pom polymers

The properties of ideal two-dimensional asymmetric pom–pom polymers containing 601–1263 units are investigated with a Monte Carlo growth method. The mean-square radii of gyration, various g-ratios, and scattering functions are calculated. A graph theory approach is employed to obtain exact scattering functions using a novel technique for counting paths in the graph representation of the polymers. All the simulation results are in very good agreement with theoretical predictions. Asymmetric pom–poms are more compact than symmetric ones and this is reflected in various g-ratios and the structure factor.

From monochromatic waves to realistic tides: deep learning for short-term forecasting of coastal ocean

Abstract In this study, a hybrid architecture combining convolutional neural networks for spatial reconstruction and long short-term memory networks for temporal forecasting is used to predict sea-level variations in the German Bight. This new framework is applied to a series of sea level data ranging from academic to realistic data. Experiments with monochromatic waves demonstrate the model’s ability to deliver accurate short-term forecasts with minimal errors. Forecasts of real tidal constituents, including M2 and the sum of M2 and M4 tides, confirm robust model performance over lead times up to 48 h. A key result is that deep learning can reconstruct basin-wide sea level from a limited number of coastal gauge stations. Therefore, in the forecast experiments, adding data from coastal observations (mimicking data assimilation) significantly improves prediction accuracy. The study highlights the potential of deep learning to supplement traditional numerical models, particularly in regions with dense observational coverage. Key factors influencing model performance are identified, among them spatial signal complexity and steepness of gradients. An overall result is that deep learning can complement numerical models in operational ocean forecasting and provide a valuable tool for evidence-based coastal management in data-rich regions.

Resolving the “CO puzzle”: Disentangling electronic structure and dynamic effects via an <i>operando</i> dynamics framework

The adsorption and activation of carbon monoxide (CO) on catalytic surfaces are fundamental steps in heterogeneous catalytic processes relevant to energy conversion, environmental remediation, and fine chemical synthesis. A notable theoretical challenge in this context is the “CO puzzle,” wherein conventional density functional theory methods incorrectly predict a hollow-site preference for CO adsorption on Pt(111), contrary to experimental observations favoring the top site. This discrepancy has been primarily attributed to limitations in describing the electronic structure; however, recent studies have highlighted the potential role of dynamical effects. The respective contributions of electronic structure and dynamics to site preference remain unresolved. In this study, we systematically examine the interplay between electronic structure and dynamics by employing high-dimensional neural network potential energy surfaces (NN-PESs) integrated with molecular dynamics simulations, using both PBE and vdW-DF functionals. Our results demonstrate that dynamic effects, particularly entropic contributions, are crucial for accurately capturing temperature-dependent adsorption behavior. PBE-based PES simulations predict a preference for hollow-site adsorption at low temperatures but shift toward top-site adsorption at elevated temperatures, aligning with experimental trends. In comparison, vdW-DF-based simulations consistently favor the top site across all temperatures. In addition, comparison with lower-dimensional (6D) rigid PES simulations underscores the importance of adsorbate–surface atoms coupling in accurately modeling thermodynamic properties and site preferences. These findings disentangle the roles of electronic structure and dynamics in resolving the CO puzzle, establishing a robust framework for modeling catalytic processes under operando conditions.

Microwave-assisted synthesis of new triangulenium dyes for lifetime imaging microscopy (FLIM)

Abstract We introduce a novel microwave-assisted method for the rapid and efficient synthesis of triangulenium dyes, enabling the creation of a broader range of these fluorophores, which are characterized by very long fluorescence lifetimes. We prepared different azadioxatriangulenium (ADOTA) and diazaoxatriangulenium (DAOTA) derivatives and thoroughly characterized their photophysical properties. We investigated their solvatochromic properties and the effects of the solvent, aided by computational chemistry results. The new ADOTA and DAOTA dyes were applied in multiple in cellulo microscopy modalities, including confocal, fluorescence lifetime imaging microscopy (FLIM), and super-resolution imaging. ADOTA derivatives predominantly accumulated in mitochondria, while DAOTAs showed pronounced nuclear staining and participation in endocytic pathways. Notably, these dyes enable clear discrimination of subcellular compartments via lifetime contrast in FLIM: mitochondria, where ADOTAs undergo electron transfer-driven quenching and display short lifetimes; nuclei and DNA, where lifetimes remain long; and endocytic vesicles, where partial dye aggregation leads to lifetime reduction.

Non-Gaussian rotational diffusion and swing motion of dumbbell probes in two-dimensional colloids

Two-dimensional (2D) colloids exhibit intriguing phase behaviors distinct from those in three dimensions, as well as dynamic heterogeneity reminiscent of glass-forming liquids. Here, using discontinuous molecular dynamics simulations, we investigate the reporting dynamics of dicolloidal dumbbell probes in 2D colloids across the liquid–hexatic phase transition, where hexagonal bond-orientational order (HBOO) extends to a quasi-long-ranged one. The rotational dynamics of dumbbell probes faithfully captures the structural and dynamical features of the host: Brownian in the isotropic liquid and non-Gaussian in the hexatic and solid phases, reflecting both HBOO and dynamic heterogeneity of the medium. In the 2D hexatic and solid phases, probe rotation reflects heterogeneity as the dumbbells sample multiple dynamical domains of the host system: in mobile domains, they undergo rotational jumps of π/3 in accordance with HBOO, whereas in immobile domains, they librate within cages formed by surrounding disks. Such non-Gaussianity disappears upon re-entrant melting of the host medium driven by size polydispersity, highlighting a close connection between HBOO and probe dynamics. Furthermore, the probe dynamics exhibits translation–rotation decoupling through the breakdown of the Debye–Stokes–Einstein relation, regardless of how the rotational diffusion coefficient is defined. We identify swing motion as the dominant microscopic diffusion mechanism of the dumbbell probes, consistent with the observed decoupling.

Biosorption potential and plant growth promoting activities of zinc tolerant novel Chitinophaga niastensis HMR31 from zinc-infested zone

Molecular arrangement planarization induces a high-pressure polymorphism transition of the hydrogen-bonded organic crystal maltol

The high-pressure behavior of maltol (3-hydroxy-2-methyl-4H-pyran-4-one, C6H6O3) molecular crystals has been investigated using in situ high-pressure Raman spectroscopy and synchrotron angular dispersive x-ray diffraction. The results of the high-pressure experiments indicate that the transition from phase II (monoclinic, P21/c) to phase III (monoclinic, P21/c) occurs at pressures above 2.0 GPa and is completed at pressures above 6.4 GPa. The mechanism of the phase transition is that the fastest compression along the c-axis at high pressures leads to a planarization tendency of supramolecular layers, which triggers the rearrangement of O–H⋯O and C–H⋯O hydrogen bonds. This study provides a theoretical basis for the development of supramolecular materials with layered hydrogen-bonded networks.