Browse Articles

Modeling surface and line tensions of nanoconfined water using a single atomistic simulation

In this work, the liquid–vapor (γlv), solid–liquid (γsl), and solid–vapor (γsv) surface tensions, as well as the line tension (τ) of water confined between planar rigid walls modeled as graphene sheets, are calculated from a single molecular dynamics simulation. While γlv and γsl are explicitly evaluated far from the contact lines between the liquid, vapor, and solid regions, γsv is deduced. Following a thermodynamic approach based on the description of the free energy, the line tension is determined from the three surface tensions, the pressures of the liquid and vapor phases, and the derivative of the free energy with respect to the length supporting the contact line. This analysis shows that the line tension cannot be reduced solely to the excess energy associated with line contact deformations. By relating the thermodynamic variables to the total stress along the x-direction, the mechanical and thermodynamic approaches are found to be consistent. We show that the line tension of confined water is negative and that neither temperature nor the degree of confinement affects its sign, which is consistent with other published results obtained using different methods. The main advantage of this approach lies in the ability to determine the three surface tensions and the line tension from a single atomistic simulation.

Proof-of-principle demonstration of epithermal neutron resonance spectroscopy utilizing a compact laser–driven electron accelerator

Epithermal neutron resonance spectroscopy is a key nondestructive approach for discerning material properties. However, the existing spallation and accelerator-based photonuclear neutron sources employed in this spectroscopy are huge and immobile, restricting their application in specialized scenarios. Here, we demonstrate a compact short-pulsed photonuclear neutron source driven by a terawatt femtosecond laser–based electron accelerator. After moderation, this neutron source maintains an outstanding time-resolution of 0.8 μ s at 5 eV, and its energy resolution can be less than 3% at a flight distance 1.72 m. When this compact neutron resonance spectroscopy facility is utilized to examine silver (Ag) and indium (In) metal sheets with a high signal-to-noise ratio, it distinctly reveals the shape of resonance absorption peaks for 115 In at 1.46 eV and 109 Ag at 5.19 eV. This laser-driven electron accelerator offers a solution, overcoming traditional source drawbacks and holding great potential for on-site nuclear material analysis and high-precision nuclear data acquisition.

Understanding energetics of bond formation and bond rotation with density functional theory and valence bond theory

Covalent bonding and noncovalent interactions are fundamental concepts in chemistry, biology, and related fields, yet the energetic factors driving bond formation and bond rotation remain a subject of ongoing debate in the literature because different theoretical frameworks might provide different insights. In this study, we examine the energetics of bond formation and bond rotation with both density functional theory and valence bond theory. Our analysis spans a wide range of systems, including 40 diatomic molecules; six energy profiles for Ar2, H2, F2, NaF, (H2O)2, and Na2 molecules; and six rotational barriers for CH3CH3, CH3NH2, CH3OH, H2O2, NH2NH2, and NH2OH. We find that (i) electrostatic energy is the dominant contributor in most cases; (ii) within the electrostatic terms, nuclear–electron attraction is often, but not always, the leading contributor; (iii) during bond formation, different interactions dominate at different stages; and (iv) in multi-electron systems, steric effects consistently contribute positively to the total energy decrease due to the spatial constraints imposed by the Pauli exclusion principle. These findings are consistently supported by both theories. Overall, this work should help bridge a critical knowledge gap by providing a unified perspective on the energetics of fundamental bonding processes.

Autoimmunity-associated DIORA1 binds the MRCK family of serine/threonine kinases and controls cell motility

Genetic association links disordered autoimmunity 1 (DIORA1) to numerous autoimmune rheumatic diseases, including systemic lupus erythematosus, Sjögren’s disease, rheumatoid arthritis, polymyositis, and systemic sclerosis. However, its cellular function has remained unknown. Here, we identify the Myotonic Dystrophy Kinase-Related Cdc42-Binding Kinases (MRCK kinases) family of serine/threonine kinases—key regulators of actomyosin contractility and cell motility—as direct interactors of DIORA1. Through interaction mapping, we show that DIORA1 binds three distinct modules of MRCK kinases, including the conserved kinase inhibitory motif, C1-PH, and citron homology domains. DIORA1 knockdown in human cells altered cellular phosphorylation patterns and reduced phosphorylation of known MRCK targets. RNA-sequencing and proteomic analyses revealed upregulation of epithelial–mesenchymal transition genes and proteins, and functional analyses confirmed increased cell invasion, following knockdown of DIORA1. Together, these findings identify the autoimmunity-associated DIORA1 protein as an interactor of MRCK kinases and a regulator of cell motility.

Unraveling the chemical nature of hydrides on doped ceria catalysts

Surface hydrogen, especially hydrides (H−), can serve as key active species in heterogeneous catalysis, yet the fundamental understanding of their nature and reactivity remains elusive. In this study, we systematically investigate the physico-chemical properties and hydrogenation reactivities of different hydrogen species at metal-doped CeO2(111) surfaces through density functional theory calculations. The results reveal that the properties of the hydride directly interacting with the doped metal (HM) are strongly correlated with the metal’s valence orbitals and exhibit periodic trends regarding the structures, stabilities, and ionicities, which in turn govern their catalytic behaviors. In particular, the HM species generated by s/p-valence dopants are strongly ionic and possess high-energy and weakly metal-coupled frontier orbitals that readily involve in C2H2 hydrogenation. In contrast, the HM species formed by d-valence dopants are generally less ionic, with the reactivity dominated by low-energy and strongly metal-coupled σ-bonding orbitals and thus exhibiting substantially reduced hydrogenation activity. By clarifying how the electronic character of dopants can dictate the frontier orbitals of active hydrides, our work provides effective strategies for controlling hydrogenation kinetics and selectivity through dopant engineering, thereby helping the design of advanced hydrogenation catalysts.

When crops fail, forests follow: Agricultural shocks and deforestation in Zambia

As climate change makes agricultural production shocks more frequent and severe, it is vital to understand their effect on farmer welfare, land use, and deforestation. Theoretically, a change in agricultural productivity could increase or decrease deforestation by changing demand for agricultural land and/or through the consumption of forests as a coping strategy. This paper uses the introduction of a crop pest to sub-Saharan Africa to estimate the effect of a negative agricultural productivity shock on deforestation. Using primary household data, we first find that farmers who were exposed to higher levels of fall armyworm saw substantial decreases in yield and food security. Using estimates of fall armyworm suitability in conjunction with machine-learning models of maize yields and deforestation, we find that the introduction of the fall armyworm induced a doubling of the deforestation rate in Zambia in the 3 y following the outbreak. This increase was driven both by increased agricultural land expansion and increased charcoal production as a coping strategy. These responses vary substantially over space. More remote areas experienced 23% lower FAW-induced deforestation compared with the sample average, suggesting that farmers with access to maize and charcoal markets may have increased deforestation as a response. Wealthier areas were also less likely to deforest in response to FAW pressure. In sum, our results suggest that negative agricultural productivity shocks may lead to a negative climate feedback, with farmers engaging in emissions-increasing strategies in response.

Off the beaten (catalytic) path: Charting the mechanistic space of enzyme reactions

Do enzymes always follow a single linear path of catalytic steps? Or is the catalytic process more like a maze of forest trails? Enzyme mechanisms are typically presented as a linear (or circular) sequence of chemical steps, and most mechanistic studies aim to identify “the” correct catalytic pathway. Alternative proposals are often pitted against one another and sometimes fiercely debated. In this paper, we consider the possibility that the reaction mechanism space accessible to enzyme active sites is more diverse than commonly recognized. This mechanistic space can be conveniently represented as a graph, where nodes correspond to active-site configurations (reactants, intermediates, or products) and edges denote catalytic steps transforming one configuration into another. We show that it is possible to generate alternative mechanism proposals, which take into account the 3D coordinates of the active site and known catalytic rules, for more than half of a test set of 25 enzymes. These findings hint at a previously unexplored facet of enzyme catalysis and underscore the need for the systematic exploration of the complete reactional space in computational studies of enzyme mechanisms.

Combined pesticide pollution enhances the dissemination of the phage-encoded antibiotic resistome in the soil under nitrogen deposition

Phage-mediated dissemination of antibiotic resistance genes (ARGs) intensifies health threat in the environment. Increasing amounts of pesticides are entering the soil ecosystem, yet their potential influence on phage-mediated ARG spread, particularly under conditions of global change, remains poorly understood. In this study, we performed a long-term field experiment simulating pesticide contamination under nitrogen deposition and examined the role of soil phages in ARG spread and host adaptation using metagenomic and viromic sequencing. Combined pesticide markedly elevated the abundance of phage-encoded ARGs under nitrogen deposition. By enhancing phage–host interactions and increasing the co-occurrence of auxiliary metabolic genes with ARGs, phages may further facilitate the transfer of ARGs to bacterial hosts, conferring hosts a competitive edge in intensified microbial competition driven by combined pesticide exposure under nitrogen deposition. The phage-driven mechanism was supported by in vitro cultivation experiments, demonstrating that phages harboring ARGs, shaped by long-term combined pesticide exposure under nitrogen deposition, can infect bacterial hosts and confer resistance. Collectively, our findings underscore the pivotal role of phages in ARG mobilization under environmental stressors, reinforcing the importance of accounting for phage activity in ARG risk assessments under global change.

Twist–bend nematic phase and heliconical superstructures of thioether-linked liquid crystal dimers

The twist–bend nematic (NTB) phase, characterized by a spontaneously formed nanoscale heliconical superstructure from achiral liquid crystal (LC) dimers, represents a fundamental advance in soft matter physics and photonic material design. Sulfur-containing LC dimers, with enhanced molecular flexibility and reduced bond angles, offer promising opportunities for functional NTB materials but remain limited by thermal instability and poorly characterized physical parameters. Herein, we comprehensively investigate a series of thioether-linked symmetric LC dimers (CBSnSCB, n = 3, 5, 7) and their mixtures, revealing how molecular architecture governs phase transition behavior. Judicious blending of multiple homologs significantly suppresses crystallization and extends the supercooled NTB phase stability to room temperature while preserving the phase sequence. Dielectric and elastic analyses demonstrate positive dielectric anisotropy and exceptionally low bend elastic constants, attributed to sulfur-mediated molecular flexibility, which can be further modified by incorporating conventional LCs. Leveraging these unique properties, electrically tunable oblique helicoidal cholesteric superstructures with continuously modulated photonic bandgaps across the entire visible spectrum are constructed. This study establishes a structure–property–function relationship in sulfur-containing LC dimers and offers a versatile platform for engineering stable, functional soft matter systems and adaptive photonic applications.

Density-dependent recruitment but not survival drives cyclic dynamics in a field vole population

Arguably, the most fundamental question in population ecology is what drives patterns in the abundance of populations? Small rodents exhibiting regular multiannual cycles in abundance have long been a test bed for addressing this question. The prevailing orthodoxy, the predation hypothesis, contends that nonmigratory, specialist predators are necessary, and specialist and generalist predators, combined, are both necessary and sufficient, for causing population cycles. Thus, variations in survival, from predation, are the key drivers of the cycles. However, this, and other competing theories, have hitherto lacked supportive demographic evidence and hence a solid evidential foundation. Here, we provide such evidence, analyzing 10 y of monthly data from a cyclic field vole population. We find, contrary to the prevailing orthodoxy, that recruitment, not survival, varied substantially from phase to phase in the cycles, made the major contribution to variations in population growth rate, and had cycle-phase-specific negative delayed density dependence. These results, their consistency with what is known from other systems, and the weak demographic foundations of the predation hypothesis, together suggest recruitment, specifically breeding-season length, not predation, as the cycles’ driving force. They therefore suggest that re-evaluation of the importance of the various determinants of population abundances, more generally, may be necessary.

Evidence for supramolecular dynamics of non-hydrogen bonding polar van der Waals liquids

Non-hydrogen bonding van der Waals liquids with dipole–dipole interactions are typically viewed as non-associative and not considered able to sustain large supramolecular structures. Combining broadband dielectric spectroscopy (BDS) and rheology, we demonstrate the supramolecular formation in a group of non-hydrogen bonding van der Waals liquids, i.e., 1-bromo-2-ethylhexane, 1-chloro-2-ethylhexane, and 1-bromo-3,7-dimethyloctane. BDS shows an emergence of a Debye-like process slower than their structural relaxation, which follows super-Arrhenius temperature dependence. Meanwhile, rheological measurements reveal a noticeable dynamical separation between the terminal relaxation and the structural rearrangements. Interestingly, the rheological terminal time agrees remarkably well with the dielectric Debye-like relaxation time, pointing to a strong coupling between the terminal flow and the supramolecular dynamics of these van der Waals liquids. These results highlight a key role of intermolecular dipole–dipole interaction in the supramolecular structure formation and the slow dynamics of van der Waals liquids.

Geometrical compartmentalization of trigger waves

Trigger waves, self-regenerating fronts of biochemical activity that spread without losing speed or amplitude, are widespread in cell signaling. Apoptosis is one example of a process that propagates through the cytoplasm via trigger waves. Curiously, in some contexts, like synaptic pruning, apoptotic caspase activation is confined to specific subcellular regions. We hypothesized that at junctions between a thin cytoplasmic extension, like a dendritic spine, and a thicker one, like a dendrite, trigger wave propagation may be blocked even though diffusion is not, as a result of the general properties of trigger waves and bistable systems. This hypothesis was explored theoretically through modeling studies and dimensional arguments, which confirmed that trigger wave compartmentalization was possible and that the critical channel width required for compartmentalization was likely to be biologically relevant. These predictions were then tested experimentally with undiluted Xenopus egg extracts that were induced to undergo apoptosis. We found that channels that are less than a few microns in diameter are small enough to compartmentalize apoptosis, and that the critical width is inversely proportional to trigger wave speed. Thus, cellular projections and tubules can allow for the compartmentalization of biochemical states within a spatially continuous cytoplasm, a fundamental yet previously overlooked mechanism for controlling biochemical signaling and cellular functions.

Publisher’s Note: “Modeling water using multipole response tensors fitted to the monomer geometry” [J. Chem. Phys. 163, 094103 (2025)]

Mouse X-linked microRNA cluster regulates the meiotic checkpoint and <i>Prdm9</i> -driven hybrid sterility in a copy number–dependent manner

One of the reproductive barriers between diverging populations during formation of a new species is the sterility of their hybrids. The Prdm9- driven hybrid male sterility of Mus musculus musculus × Mus musculus domesticus hybrids depends on the interaction between PRDM9, a histone methyltransferase that determines the positions of meiotic recombination hotspots, and an as yet unknown X-linked genetic factor within the Hybrid sterility X2 ( Hstx2 ) locus. Here, we report that the Mir465 microRNA (miRNA) gene cluster is the predicted Hstx2 hybrid sterility factor. We show that removal of the Mir465 genes restores the fertility of sterile hybrids and improves meiotic synapsis of homologous chromosomes. Mir465 knockout also restores spermatogenesis in sterile chromosomal translocation carriers, demonstrating that Mir465 acts as a meiotic checkpoint that can be activated independently of Prdm9 intersubspecific incompatibility. Furthermore, the Mir465 knockout increases the global recombination rate in hybrids and in parental Mus m. domesticus mice. This demonstrates that Mir465 is responsible for the phenotypes of the two overlapping genetic loci, the Hstx2 engaged in fertility of hybrids and the Meiotic recombination 1 ( Meir1 ) controlling the recombination rate. The finding of enlarged Mir465 clusters in all European Mus m. musculus samples tested and the identification of differentially expressed targets suggest that the reproductive barrier between the two subspecies is sensitive to copy number variation of Mir465 genes. Together, the underdominant interaction between Prdm9 and Mir465 provides a rare example of Dobzhansky–Muller incompatibility in hybrids of closely related species, making it accessible for further analysis at the molecular level.

Improved loss functions for machine-learned atomic potentials

Machine learning (ML) has become an invaluable tool across a wide array of domains in science as researchers find new ways to leverage its predictive power. This is especially true in chemistry, where ML is used to fit chemical properties or desirable attributes to the local structure of molecules and materials. In the pursuit of greater accuracy, it is relatively simple to increase the size or complexity of such models, although this often requires simultaneously seeking larger datasets in order to both fit and interpret the larger number of parameters. However, it is equally important to assess the quality and relative importance of the data and how these factors impact the training process. We, therefore, investigate the impact of using different loss functions for training neural network potentials (NNPs), as the loss function defines the error and parameter gradients used to train the NNP. In particular, we test the mean-squared error and Huber loss functions and, using insight from these functions, derive a new loss function based on the Asinh function, which yields significant improvement in the accuracy and generality of NNPs. We show that by discounting/minimizing errors and anomalies in the optimization process, both the Huber and Asinh loss functions improve the training of NNPs, leading to a final potential with a greater effective dimensionality.

Chemobiological synthesis of benzene, toluene, ethylbenzene, and xylene from glucose or glycerol

Benzene, toluene, ethylbenzene, and p -xylene (BTEX) are key aromatic hydrocarbons widely used in fuels, polymers, and industrial chemicals, yet their production remains heavily dependent on fossil resources, raising environmental and public health concerns. To promote de novo production of BTEX from renewable feedstocks, we developed a chemobiological platform that integrates microbial biosynthesis with chemical deoxygenation. Four metabolically engineered Escherichia coli strains were constructed to produce one of four oxygenated precursors of BTEX—phenol, benzyl alcohol, 2-phenylethanol, or 2,5-xylenol—from glucose or glycerol. After in situ two-phase extractive fermentation of the individual engineered strains using isopropyl myristate (IPM) as the organic solvent, the organic phase containing one of the oxygenated precursors was separated from the aqueous phase and subjected to distinct chemical deoxygenation reactions to reduce the precursor to the corresponding BTEX compound. This modular approach, based on the compatible organic solvent, streamlines biotransformation and consecutive chemical derivatization, providing a practical and viable route to sustainable BTEX production. The platform is extensible and provides a generalizable framework for integrating biosynthesis with chemical deoxygenation in hybrid bioprocessing.

A computationally efficient subspace harmonic relaxation algorithm for coarse-graining of molecular systems with nearly exact thermodynamic consistency

In a recent paper [Pimentel and Mandelshtam, J. Chem. Phys. 162, 214101 (2025)], a novel approach for the rigidification of a molecular cluster was proposed, in which, starting with an all-atom (AA) potential, a coarse-grained (CG) potential for the associated cluster of rigid monomers was constructed directly. The method is based on using the harmonic approximation for the fast intramolecular degrees of freedom. While conceptually primitive, the resulting CG model turned out to be surprisingly accurate for selected water and ammonia clusters. However, as originally formulated, a single evaluation of the CG potential turned out to be much more expensive than the evaluation of the AA potential, since the former required a subspace minimization followed by a subspace normal mode calculation. In this communication, we formulate the approach more broadly, making it applicable, e.g., to coarse-graining a large protein. We also introduce key algorithmic improvements, reducing the cost of the subspace minimization and normal mode calculation. Combined with the fact that the CG simulation requires roughly an order of magnitude fewer Monte Carlo steps to reach similar statistical accuracy for selected observables compared to the AA model, the overall computational cost becomes comparable. These improvements are demonstrated on a water cluster.

Enhanced PIEZO1 function contributes to the pathogenesis of sickle cell disease

Sickle cell disease (SCD), an inherited blood disorder caused by a mutation in the β-globin gene, is characterized by sickle erythrocytes that are prone to hemolysis, leading to anemia and vaso-occlusion crises. In sickle erythrocytes, hemoglobin aggregation is followed by altered cation permeability and subsequent dehydration. Interventions that restore cation permeability can decrease hemolysis and ameliorate the symptoms associated with SCD. PIEZO1 is a nonselective mechanosensitive cation channel that regulates erythrocyte volume. Gain-of-function (GOF) mutations in PIEZO1 cause hemolytic anemia by increasing cation permeability, leading to erythrocyte dehydration in humans and mice. Although PIEZO1 plays a key role in erythrocyte homeostasis, its role in SCD remains unknown. Here, we demonstrate that the function of the PIEZO1 channel is upregulated in sickle erythrocytes of humans and mice, and this enhancement can be restored through a dietary intervention. We found that PIEZO1 activity in sickle erythrocytes resembles that of the GOF mutation causing hemolytic anemia. A diet enriched in the ω -3 fatty acid eicosapentaenoic (EPA) acid decreases PIEZO1 activity in sickle erythrocytes, attenuates hemolysis, and reduces hypoxia-induced sickling. Furthermore, EPA reduces inflammatory markers. We propose that PIEZO1 contributes to the increase in nonselective cationic conductance (i.e., Psickle), which leads to dehydration downstream of hemoglobin polymerization. Our results suggest that reducing PIEZO1 function represents a promising therapeutic strategy to reestablishing normal cation permeability in SCD.

Effect of protein environment on the shape resonances of RNA pyrimidine nucleobases: Insights from a model system

In this work, we investigate the effect of an amino acid environment on nucleobase-centered anion radical shape resonances, using uracil as a model system for pyrimidine bases in RNA. Anionic uracil–glycine complexes were used to model the RNA–protein interactions. The resonance positions and widths of these complexes were simulated using the equation of motion coupled cluster method coupled with resonance via the Padé approach. Our results show that in the transient negative ion (TNI, i.e., the anion radical of glycine:uracil complex), glycine stabilizes nucleobase-centered resonances through hydrogen bonding, thereby increasing the lifetime of TNI. Simultaneously, a glycine-centered resonance demonstrates the ability of amino acids to capture the electron density and divert it away from the uracil nucleobase. At the micro-solvation level, this modeling indicates that amino acids would have more influence on nucleobase-centered resonances in the TNI than that displayed by the corresponding aqueous environment.

Reaction-induced departures from continuum Navier–Stokes turbulence

Reactive hydrodynamic turbulence is an inherently multiscale phenomenon, characterized by the separation between energy-containing, viscous, and molecular length and time scales. The separation between the viscous scale (the Kolmogorov scale) and the molecular mean free path ostensibly justifies a macroscopic description of reactive turbulence via the Navier–Stokes (NS) equations. However, here we use molecular-level simulations to demonstrate that exothermic bimolecular reactions can cause the NS description of turbulence to break down in the near-continuum regime. Sufficiently energetic heat-releasing reactive collisions strongly distort the Maxwell–Boltzmann velocity distribution function, modifying not only the macroscopic chemical rate law but the kinetic-energy-transfer processes as well. This translational nonequilibrium ultimately introduces significant departures from the NS description in the kinetic energy spectra at scales orders of magnitude larger than both the molecular mean free path and the Kolmogorov length scale. These departures prove substantial enough to meaningfully alter integrated quantities, including the overall turbulence kinetic energy itself.