Browse Articles

Simulation of vibronic strong coupling and cavity-modified hydrogen tunneling dynamics

Polaritons have gained significant attention for the tantalizing possibility of modifying chemical properties and dynamics by coupling molecules to resonant cavity modes to create hybrid light–matter quantum states. Herein, we implement the semiclassical nuclear–electronic orbital time-dependent configuration interaction (NEO-TDCI) approach, which treats electrons and specified nuclei on the same quantum mechanical level, while treating the cavity mode classically. This ab initio dynamics approach can describe both the electronic strong coupling and the vibrational strong coupling regimes at the same level of theory without invoking the Born–Oppenheimer separation between the quantum nuclei and the electrons. This approach is used to simulate resonant and off-resonant vibronic strong coupling, where the cavity mode couples to one or many vibronic transitions associated with joint electronic–nuclear excitations within a vibronic progression. In this case, the cavity mode couples to nuclear motions even for cavity frequencies typically associated with electronic strong coupling. This approach is also used to illustrate that coupling a molecule to a cavity mode can alter hydrogen tunneling dynamics. The semiclassical NEO-TDCI approach provides the foundation for investigating how polaritons may be able to influence chemical reactions involving tunneling and nonadiabatic effects.

Correction for Wurman et al., Supercell tornadoes are much stronger and wider than damage-based ratings indicate

Correction: Environmentally sustainable epoxy nanocomposite coating reinforced with chitosan derived nitrogen doped graphene for enhanced corrosion resistance and mechanical performance

Line shape parameters of the first pure rotational R lines of CO in H2 baths down to a few kelvins

Line shape parameters of the first pure rotational R(j = 0 − 4) lines of carbon monoxide in hydrogen baths, between 1 and 500 K, have been calculated using the close coupling method. The theoretical thermally averaged collisional widths and shifts between 30 and 500 K agree well with the values reported in the literature. However, below this temperature range, we confirm the long-standing substantial disagreement between experimental and theoretical values for the R(0) and R(1) lines. In addition to the usual collisional widths and shifts, we provide the complex optical frequency of the velocity-changing collisions. We also study the speed dependence of the line shape parameters and investigate their double power law temperature representation. We conclude that beyond-Voigt effects, including the collision duration, cannot reconcile theory and experiments at low temperatures.

Overcoming the space clamp effect: Reliable recovery of local and effective synaptic conductances of neurons

Neurons process information by integrating thousands of synaptic inputs along their dendrites. Understanding the computational principles underlying neuronal information processing requires a reliable measure of synaptic conductance dynamics that accurately represents the input sources before signal integration and processing. Prevailing approaches to measuring synaptic conductances typically employ a voltage clamp at the soma of a neuron and assume the neuron as an isopotential point when processing electrical signals. However, owing to the presence of the well-known space clamp effect, the measurement of synaptic conductances through these methods often leads to significant errors, impeding the elucidation of dendritic signal features and subsequent signal integration processes. To address this issue, here we first develop a two-step clamp method at the soma that separately recovers the mean and time constant information of local synaptic conductance on the dendrite with high accuracy when a neuron receives a single synaptic input. Furthermore, under in vivo conditions of multiple synaptic inputs, we propose an intercept method to extract effective net excitatory and inhibitory synaptic conductances from measurements of synaptic currents at the soma. Both methods are grounded in mathematical perturbation analyses of a conductance-based passive cable model and are validated across multiple biologically detailed multicompartment neuron models with active channels, including Purkinje neuron, pyramidal neuron, and fast-spiking interneuron. Results demonstrate that our methods effectively circumvent the space clamp effect, offering reliable means to assess the role of measured conductances and synaptic activity in neuronal information processing.

A novel turmeric drying approach based on supercritical carbon dioxide

The role of confinement and surface charge on electrical and diffusio-osmotic conductivity of electrolyte solutions from <i>ab initio</i> methods

We perform extensive ab initio molecular dynamics simulations to compute transport properties of a KCl solution at high concentration using Green–Kubo relations based on Onsager’s system of linear equations. Our results show an increase in the electrical conductivity under confinement, with a further enhancement in the case of a positive charge on graphene. The presence of surface charges also determines the direction of electro-osmotic flow and of the diffusio-osmotic electrical current in the nanofluidic systems. Structural analysis reveals that in the case of positively charged graphene sheets, chloride ions accumulate at the surface. This promotes a spatial separation of anions and cations, thereby reducing their correlations and leading to an increased electrical conductivity in this system. We show how accounting for electronic structure by means of ab initio molecular dynamics is essential in the calculation of the transport properties. While quantitative results can be obtained for the diagonal terms of the Onsager transport matrix, only a qualitative impact can be gauged for the off-diagonal terms due to limitations in sampling. Nevertheless, our results reveal that surface charges significantly alter ionic conductivity and determine the direction of the electro-osmotic flow and of the diffusio-osmotic current, thereby advancing the understanding of transport at the nanoscale.

Fiber recruitment drives a phase transition of cell polarization at a critical cell spacing in matrix-mediated tissue remodeling

Biological tissues exhibit sharp phase transitions where cells collectively transition from disordered to ordered states at critical densities. We demonstrate through bio-chemo-mechanical modeling that this emergent behavior arises from a nonmonotonic dependence on nonlinear extracellular matrix (ECM) mechanics: mechanical communication between cells is optimized at intermediate stiffness values where cells can both generate sufficient forces and create strain-stiffened tension bands in the ECM. This balance establishes a critical cell spacing threshold for cell–cell communication ( ∼ 100 to 200 μ m) that is conserved across experimental observations for a broad range of cell types and collagen densities. Our model reveals that the critical stretch ratio at which fibrous networks transition from compliant to strain-stiffening governs this threshold through the formation of tension bands between neighboring cells. These mechanical communication networks drive collective phase transition in tissue condensation when cell density exceeds an effective percolation threshold. Our model explains how microscale cell–ECM interactions control emergent mechanical properties in biological systems and offers insight both into the physics of inhomogeneous materials under active stress, and into potential mechanical interventions for wound healing and fibrotic disorders.

Insights from Atangana-Baleanu fractional derivatives modeling of influenza epidemics and sensitivity analysis

Mechanism of ferromagnetism and valley properties in monolayer TiSeCl

We introduce a novel two-dimensional ferromagnetic valley material, TiSeCl, and confirm its potential to enable valley-related multichannel Hall effects within a stable two-dimensional ferromagnetic semiconductor. The intrinsic lack of spatial inversion symmetry and time-reversal symmetry in the TiSeCl structure allows for spontaneous valley polarization, making it highly advantageous for practical valley manipulation since its intrinsic valley polarization values can reach 95 meV. The strong spin–orbit coupling effects in the TiSeCl monolayer result in distinct Berry curvatures and opposing signals in the +K and −K valleys, leading to an anomalous valley Hall effect. Furthermore, under a 1.25% tensile strain, the TiSeCl monolayer undergoes band inversion, leading to a topological phase transition from the ferromagnetic valley state to the semivalley metal state and subsequently to a valley-polarized quantum anomalous Hall phase. This study expands our understanding of valley properties in two-dimensional materials and provides theoretical guidance for valley manipulation in valley electronics.

Global constraint principle for microbial growth laws

Understanding complex living systems requires identifying universal phenomenological laws that are independent of species and molecular-biological details. The Monod equation is a cornerstone of phenomenological microbial growth laws, depicting the growth rate as a saturating function of a single substrate. Because of its similarity in functional form to the Michaelis–Menten equation, cellular growth is often thought to be limited by a single reaction. However, cellular growth generically results from the coordination of thousands of metabolic reactions and diverse intracellular limited resources. Consequently, the mechanistic origins of the Monod equation remain controversial, and its extension has encountered limitations. Here, we propose the global constraint principle for cellular growth: As one nutrient becomes more available, other intracellular resources become limiting, driving transitions to distinct modes of resource allocation. Based on a general framework of constraint-based modeling and its dual formulations, we mathematically prove that, in general, microbial growth kinetics curves are monotonically increasing and concave with respect to nutrient availability. Numerical simulations using genome-scale Escherichia coli models with proteome allocation, molecular crowding, and membrane capacity constraints reproduce these features in a multiphasic manner. In contrast to the original Monod’s growth law, the global constraint principle also captures the dependence of microbial growth on the availability of multiple nutrients, by generalizing the Liebig’s law of the minimum, another phenomenological growth law for higher organisms, into a terraced landscape of diminishing returns. It thus integrates the classical phenomenological laws proposed by Monod and Liebig into a comprehensive theory of cellular growth.

Brassinosteroids negatively regulate barley deacclimation tolerance via modulation of chloroplast gene expression and cell hydration

Abstract Global warming may cause overwintering plants to lose tolerance to low temperatures owing to de-acclimation caused by winter temperature fluctuations. The effect of elevated temperatures is regulated by the endogenous levels of phytohormones, including brassinosteroids, which allow the maintenance of high productivity under stressful conditions This study examined barley (Hordeum vulgare) de-acclimation tolerance using two mutant lines: BW084, harbouring a mutation in the HvCPD gene, and BW312, harbouring a mutation in the HvBRI1 gene. Both mutants were more tolerant to de-acclimation than the reference cultivar and displayed downregulation of chloroplast genes expression in response to de-acclimation, but differed in physiological traits related to photosynthesis and soluble carbohydrates metabolism. After 1 day of de-acclimation, biosynthesis mutant BW084 was characterized by a greater increase in the net photosynthesis rate than signalling mutant BW312. In turn after 10 days of de-acclimation, signalling mutant BW312 was characterized by the largest decrease in the fructan pool and degree of polymerization in leaves and crowns while biosynthesis mutant BW084 showed a significantly smaller decrease. In both mutants, de-acclimation tolerance was associated with maintenance of optimal tissue hydration, as evidenced by lower osmotic potential and higher cell hydration compared to the reference cultivar.

A new form of particle number conserving fermionic coherent states for electronic structure theory and electron dynamics

We propose a new form of Particle Number Conserving Fermionic Coherent States (PNCFCSs) that provide an efficient basis for calculating electronic wave functions. We demonstrate that a simple algorithm based on combinatorial analysis can be used for calculations of PNCFCS overlaps and matrix elements. We show an example where a basis of such coherent states with randomly selected parameters can converge quickly to the full configuration interaction result. In the future, PNCFCS can be used in dynamics just like other types of coherent states and in electronic structure theory.

Correction for Jin et al., Autocrine signaling by an <i>Aplysia</i> neurotrophin forms a presynaptic positive feedback loop

Characterizing the cage state of glassy systems and its sensitivity to frozen boundaries

Understanding the role that structure plays in the dynamical arrest observed in glassy systems remains an open challenge. Over the past decade, machine learning (ML) strategies have emerged as an important tool for probing this structure–dynamics relationship, particularly for predicting heterogeneous glassy dynamics from local structure. A recent advancement is the introduction of the cage state, a structural quantity that captures the average positions of particles while rearrangements are forbidden. During the caging regime, linear models trained on the cage state have been shown to outperform more complex ML methods trained on initial configurations only. In this paper, we explore the properties associated with the cage state in more detail to better understand why it serves as such an effective predictor for the dynamics. In particular, we examine how the cage state in a binary hard-sphere mixture is influenced by both packing fraction and boundary conditions. Our results reveal that, as the system approaches the glassy regime, the cage state becomes increasingly influenced by long-range structural effects. This influence is evident both in its predictive power for particle dynamics and in the internal structure of the cage state, suggesting that the CS might be associated with some form of an amorphous growing structural length scale.

High rates of polygyny do not lock large proportions of men out of the marriage market

There is a widespread belief, in both the scholarly literature and the popular press, that polygyny prevents large numbers of men from marrying by skewing the sex ratio of the marriage market. In turn, the exclusion of men from marriage is thought to lead to negative outcomes, e.g., by fueling crime and armed conflict. In this paper, we investigate systematically the relationship between polygyny and men’s marriage prospects. First, using a demographic model, we show that marriage markets are skewed sufficiently feminine, under a range of realistic demographic scenarios, to sustain some level of polygyny without locking any men out of marriage. Second, through analysis of 84.1 million census records from 30 countries across Africa, Asia, and Oceania between 1969 and 2016, we show that the subnational association between the prevalence of polygyny and the prevalence of unmarried men is negative or null, rather than positive, for almost all countries in the sample. Third, through analysis of the full-count 1880 US federal census, we show that the average prevalence of unmarried men is lower, not higher, across counties of the West with Mormon polygyny, compared to other counties of the West, and to counties of the Midwest and the Northeast; it is higher only compared to counties of the South. Overall, these findings challenge a dominant narrative linking polygyny to negative social outcomes. Drawing on existing evidence, we suggest that the observed patterns may be explained by an underlying association between the prevalence of polygyny and the strength of promarriage norms.

Phonon-mediated relaxation in nanomaterials using Boltzmann transport equation by combining density functional theory based non-adiabatic molecular dynamics with many-body perturbation theory

Boltzmann transport equation (BE) is a potent approach to dynamics of a photoexcited (nano)material. BE collision integrals for different relaxation channels can be systematically computed using the Kadanoff–Baym–Keldysh formalism (also called NEGF) utilizing the density functional theory (DFT) simulation output. However, accurate description of phonon-mediated relaxation in a general class of (nano)materials that includes exciton effects is still an outstanding problem. The approach proposed here is based on the observation that the non-adiabatic couplings of the DFT-based non-adiabatic molecular dynamics play the role of a time-dependent external potential coupled to the electrons. This allows application of the Keldysh approach resulting in the exciton–phonon BE collision integral, which incorporates exciton wave functions and energies obtained from the Bethe–Salpeter equation. As an application, we augment BE with radiative recombination and photon-mediated exciton–exciton transition terms and then use it to calculate photoluminescence spectrum for several 1.5 nm semiconductor chalcogenide nanocrystals, such as Cd37Pb31Se68, Cd31Pb37Se68, which are Janus-type, and for Pb68Se68.

Targeting the 3D genome by anthracyclines for chemotherapeutic effects

The chromatin is folded into three-dimensional (3D) structures, and aberrant 3D chromatin folding has been implicated in cancer. We performed ATAC-seq and TOP2A ChIP-seq to assess the potential effects of various anthracycline drugs on the chromatin architecture. We found that specific anthracycline variants selectively disrupt chromatin looping anchors by interfering with CTCF binding, suggesting an additional therapeutic mechanism of anthracycline drugs targeting the 3D genome. Hi-C experiments in K562 cells treated with anthracycline drugs revealed widespread disruption of 3D chromatin organization, including altered long-range regulation at the Myc locus. Furthermore, AML patients treated with anthracycline drugs exhibited changes in chromatin structures near possible looping anchors, which were associated with distinct clinical outcomes. Together, our findings indicate that anthracycline drugs function as potent and selective epigenomic modulators, with the capacity to further target the 3D genome to exert anticancer effects, highlighting their potential for personalized therapy in tumors with aberrant 3D chromatin architecture.

Intrinsic chiral discrimination via terahertz absorption circular dichroism

Identifying chiral molecules and accurately resolving their enantiomeric characteristics in the terahertz (THz) regime remains challenging due to intrinsically weak circular dichroism (CD) signals. Most existing THz-CD studies have relied on transmission amplitude differences, which are susceptible to severe signal attenuation and spectral distortion in lossy or strongly absorbing media. In this work, we present an alternative approach that retrieves helicity-dependent absorption coefficients from the complex transmission function, obtained through polarization-resolved THz time-domain spectroscopy. By analyzing the difference between the extracted absorption spectra for right and left circularly polarized THz waves, we obtain an absorption-resolved CD signal that reflects the intrinsic chiroptical asymmetry of the sample. We validate this method using two representative chiral molecules, glucose and tartaric acid, whose enantiomers exhibit bisignate CD spectral features centered at 1.45 and 1.1 THz, respectively, corresponding to their molecular resonances. These spectral signatures, which are obscured in transmission-based CD measurements, become distinctly observable through our absorption-based analysis. This label-free and quantitative approach provides a robust platform for chiral sensing and is applicable to pharmaceutical analysis, biochemical diagnostics, and molecular spectroscopy.

Electronic origin of the anomalous melting of sodium under pressure

Despite extensive experimental and theoretical investigations, the fundamental electronic origin of compressed sodium’s melting temperature reversal under pressure, characterized by a maximum and a minimum in its melting curve, remains unclear. A recent two-state model proposed for high-pressure potassium, which exhibits a similar melting anomaly, attributes this behavior to changes in the distribution of non-nuclear localized electrons (electrides), resulting in distinct liquid phases. To test this hypothesis for sodium, we conducted ab initio molecular dynamics simulations to examine its atomic dynamics and electronic properties under high pressure. Our results reveal no discontinuities in atomic or electronic transport properties, nor any evidence of multiple inherent structural forms. Furthermore, the electronic screening potential governing liquid structure remains largely unchanged above 50 GPa. Instead, we find that the key parameter responsible for the melting anomaly arises from differences in the average number of electrons per non-nuclear maximum, which affects the relative packing densities of the liquid and solid phases.