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Multielectron dynamics, polarization, and Stark shifts for carbon monoxide molecule and molecular ions in a strong laser field
The ionization of CO, CO+, and CO2+ are quantified in an ultrafast, strong laser field. Measurements were performed over the intensity range from 1014 to 1017 W cm−2. Across this span, the intensity-dependent ionization yields were quantified over eight orders of magnitude in the dynamic range. Both sequential and (e, 2e) nonsequential ionization processes were observed. We calculate the electron states for CO and its molecular ions interacting with a strong laser field using a traditional field-free approach, the single active electron approximation, and present the results for the all-electron interaction of CO with the laser field. By comparing the calculated ionization with the experimental yields, we determined that the electron wave function polarization and Stark shifts were accurately treated with an all-electron Hartree–Fock calculation. The calculated field–molecule interaction included the core electron polarizability, which is not captured using field-free or frozen-core single-electron approximation.
Associations between serum JAML, nesfatin-1, and 25(OH)D and the risk of diabetic kidney disease in patients with type 2 diabetes
Infrared spectra of propargyl alcohol dimers in helium nanodroplets
Propargyl alcohol (HC≡C–C(H2)–OH) and its clusters have been isolated in helium nanodroplets and probed using infrared spectroscopy. The global energy minimum of the dimer, in which a strong hydrogen bond forms between the two OH groups, does not yield the most intense spectral features. Instead, bands from a higher energy structure are prominent and derive from dimers held together primarily by a single and far weaker –C≡C–H⋯O–H hydrogen bond. This suggests that helium nanodroplet encapsulation kinetically traps the dimers in a local minimum on account of the rapid cooling and low temperature. This provides access to an unusual part of the potential energy surface of the dimer and, more generally, allows the probing of weak hydrogen bonding interactions.
Multi-mode mobile mechanism based on anti-parallelogram and parallelogram mechanisms
Unifying measurement schemes in 2D terahertz spectroscopy
Two distinct measurement schemes have emerged for the new technique of two-dimensional terahertz spectroscopy (2DTS), complicating the literature. Here, we argue that the “conventional” measurement scheme derived from nuclear magnetic resonance and its optical-frequency analogs should be favored over the “alternative” measurement scheme implemented in the majority of 2DTS literature. It is shown that the conventional scheme avoids issues such as overlapping nonlinearities and facilitates physical interpretation of spectra, in contrast to the alternative scheme.
Cationic substitution, dynamical stability, thermal stability, electronic and thermoelectric properties in 2D dialkali metal monoxides via DFT and ML approach
Abstract Using the WIEN2k software, Density Functional Theory (DFT) was applied to analyse the impact of cationic substitution on the physical features of the 1T-K2O monolayer. Phonon dispersion analysis confirmed dynamical stability, Ab-initio Molecular Dynamics (AIMD) simulations validated thermal stability, and cohesive energy calculations ensured thermodynamic stability of 1T-K2O. Based on the phonon studies, both 1T-KNaO and 1T-KRbO are dynamically unstable with a slightly visible imaginary frequency. Specifically, for electronic property assessment, generalized gradient approximation (GGA) and hybrid exchange-correlation functionals were utilized. This study unveiled the 1T-KXO (X = Na, K, Rb) monolayers as an indirect band gap semiconductor, for 1T-K2O, 1T-KNaO and 1T-KRbO were 0.94 eV (1.84 eV), 1.03 eV (1.94 eV) and 0.84 eV (1.77 eV) obtained implementing GGA and hybrid functionals, respectively. Using a machine learning (ML) approach, the band gap was predicted as 1.45 eV (0.85 eV) for 1T-K2O, 1.79 eV (0.97 eV) for 1T-KNaO, and 1.17 eV (0.72 eV) for 1T-KRbO, with random forest regression (linear regression) method. The physical properties were tailored by the impact of cationic substitution on the 1T-K2O were studied. The variation in the physical properties were investigated. Optical analysis indicated a strong absorption coefficient, underscoring the 1T-KXO monolayers potential for photovoltaic applications in the UV region. The ZT value obtained at room temperature are 0.58, 0.86 and 0.69 for 1T-K2O, 1T-KNaO and 1TKRbO, respectively. Additionally, the 1T-KNaO demonstrated promising thermoelectric properties, at 400 K achieving a figure of merit (ZT) of 0.93, indicating its suitability for waste heat recovery. A ML model was trained to predict the ZT of 1T-KXO using random forest regression and linear regression.
Diffusion-mediated passing of molecular species in linear nanopores constrained by orientational alignment
For diffusion-mediated catalytic conversion reactions in materials with narrow linear nanopores, e.g., mesoporous silica MCM-41, a key parameter is the propensity for product species to be able to pass reactant species and thus to efficiently exit the pore. For elongated species, this can require orientational alignment with the pore axis. We perform benchmark analyses for such solution-phase systems where one of these species is elongated in order to quantify the dependence of this passing propensity, P, on pore diameter and on the rotational diffusion coefficient, Dr, of the elongated species. In particular, we consider the passing of a spherical and an elongated spherocylindrical shaped species in a cylindrical pore in an implicit solvent, where these species cannot overlap. Passing is mediated by diffusive Brownian motion of these species as described by strongly damped Langevin dynamics. We quantify scaling of P for pore width just above the threshold where passing is sterically blocked, and also reveal a significant decrease in P for lower Dr. We also consider the dependence of P on the aspect ratio of the elongated species and obtain an exact result in the limiting regime of large aspect ratio.
Protective effects of liraglutide on hypercholesterolemia-associated atherosclerosis involve attenuation of endothelial-monocyte adhesion through down-regulating the LOX-1/NF-κB signaling pathway
Free energy of self-avoiding polymer chain confined between parallel walls
Understanding and computing the entropic forces exerted by polymer chains under confinement is important for many reasons, from research to applications. However, extracting properties related to the free energy, such as the force (or pressure) on confining walls, does not readily emerge from conventional polymer dynamics simulations due to the entropic contributions inherent in these free energies. Here, we propose an alternative method to compute such forces and the associated free energies, based on empirically measuring the average force required to confine a polymer chain between parallel walls connected by an artificial elastic spring. This measurement enables us to interpolate the expression for the free energy of a confined self-avoiding chain and offers an analytical expression to complement the classical theory of ideal chains in confined spaces. Therefore, the significance of our method extends beyond the findings of this paper: it can be effectively employed to investigate the confinement free energy across diverse scenarios where all kinds of polymer chains are confined in a gap between parallel walls.
Field emission from vertically aligned graphene edges at the apex of the pencil lead
Microsecond-scale sucrose conformational dynamics in aqueous solution via molecular dynamics methods
Molecular dynamics methods have proven their applicability for the reproduction and prediction of molecular conformations during the past decades. However, most of works considered dilute solutions and relatively short trajectories that limit insights into conformational dynamics. In this study, we investigate the conformational dynamics of sucrose in aqueous solution using microsecond-scale molecular dynamics simulations. For the most of the calculations, we use the OPLS-AA/1.14*CM1A-LBCC force field, but we also utilize OPLS-AA/1.14*CM1A and GLYCAM06 for the comparison. We focused on the glycosidic linkage conformers and their lifetimes, glucopyranose and fructofuranose ring puckering. Our findings indicate that the 1C4 glucopyranose ring conformation can stabilize the sucrose conformer, appeared only in the GLYCAM06 and OPLS-AA/1.14*CM1A force fields. All the results are strengthened by comparison with the available experimental data on nuclear magnetic resonance J-coupling constants and ultrasonic spectra.
Pharmacokinetic, toxicological, and molecular interaction assessment of ginger-derived phenolics for SARS-CoV-2 main protease Inhibition
Physics-guided estimation of mean first-passage times from censored nucleation trajectories
Mean first-passage time (MFPT) analysis is a powerful tool for extracting thermodynamic and kinetic parameters of nucleation, including the critical nucleus size, nucleation barrier, and nucleation rate, from molecular dynamics (MD) simulations. However, accurate MFPT estimation typically requires extensive sampling and long simulation durations, making it computationally expensive, especially for rare nucleation events. Here, we present an efficient method to estimate MFPT from fixed-length MD simulations by leveraging the single-exponential tail (SET) behavior of first-passage time distributions in monomer-transition-based nucleation processes. Our approach allows for the estimation of MFPT for censored samples using information from uncensored ones via the characteristic decay rate of the SET, eliminating the need to observe complete nucleation trajectories. We validate this method using both artificial nucleation datasets and unbiased MD simulations of CO2 hydrate nucleation. The results demonstrate that, with an appropriate choice of simulation length and number of independent runs, the SET-based approach accurately recovers the full MFPT and nucleation parameters while substantially reducing computational costs. This work provides a practical and broadly applicable framework for accelerating nucleation studies in molecular simulations.
New robust two-parameter estimator for overcoming outliers and multicollinearity in Poisson regression model
Charge localization in diatomic ions investigated with a new dipole moment driven approach. Test for Ne2+ and (ArNe)+
A novel method is proposed to develop charge-localized representations of the electronic structure of singly ionized dimers of rare gases. The method is based on an orthogonal transformation of the adiabatic dimer dipole moment matrix to a new basis in which the matrix is as close as possible to its point charge approximation. Upon general considerations and derivations, the method is applied to two specific cases, a homonuclear dimer of Ne2+ and a heteronuclear dimer of (NeAr)+. High-level ab initio calculations have also been performed for both systems to get accurate input data and are reported.
Automated underwater image analysis reveals sediment patterns and megafauna distribution in the tropical Atlantic
Abstract The deep-sea comprises diverse habitats and species whose characterisation provides crucial insights into the health and resilience of our oceans. Whereas direct sampling enables investigation of the vertical variability of the seafloor at small spatial scales, optical imaging allows for multi-scale assessment of the spatial distribution of (mega)benthos and substrates. However, modern seafloor imaging surveys typically generate thousands of images that are infeasible to manual annotation. Consequently, transforming these terabyte-scale datasets into actionable insights requires automated workflows. Here, we deployed two A.I workflows to automate the annotation of substrates and megafaunal taxa in seafloor images from the tropical North Atlantic. Clustering, feature space visualisation and multivariate statistical analysis techniques were used to classify the seafloor into habitats, estimate megafaunal distribution patterns, and to identify environmental drivers that influence observed patterns. We found that the seabed here formed seven clearly distinct clusters, with visible sub-partitions observed in each cluster. Investigations revealed a gradient of sediment disturbance due to biogenic activity, with images showing little-to-no sediment disturbance mapping to one half of the feature space, whereas images exhibiting visibly vigorous sediment reworking mapping to the other half of the feature space. Also, megafaunal abundances were 14 times higher in the shallower Eastern region of the seabed, potentially due to higher Particulate Organic Carbon flux and relatively warmer temperatures. Moreover, geographic clustering of megafauna was observed in topographically complex features such as slopes of submarine canyons and on top of seamounts, where heterogeneity created diverse microhabitats and unique niches that megafauna could exploit.
Coarse-graining in quantum mechanics: Distinguishable and indistinguishable particles
Bottom-up coarse-grained (CG) modeling expands the spatial and temporal scales of molecular simulation by seeking a reduced, thermodynamically consistent representation of an atomistic model. Developments in CG theory have largely focused on CG modeling of atomistic systems that behave classically, while CG modeling of quantum systems has remained largely unexplored. We present in this work two fundamental advances in particle-based, bottom-up CG theory for systems obeying quantum statistical mechanics. We first expand the bottom-up CG formalism to include indistinguishable quantum particles, including bosons and fermions. We next introduce a variational optimization procedure for CG model parameterization, which is founded on the relative entropy minimization (REM) principle, and then bridge the classical and quantum REM methods through a semiclassical expansion in terms of the Feynman path centroid. We provide numerical examples of REM CG models of distinguishable and indistinguishable quantum systems, including as examples a harmonically trapped bosonic system and liquid water. The theoretical results presented here constitute a means to accelerate simulating thermal quantum systems, ranging from distinguishable particle systems at higher temperatures to quantum indistinguishable particle systems at lower temperatures.
Sustainable concrete production through the integration of waste foundry sand, fly ash, silica fume and metakaolin
Abstract This exploratory study investigates the use of waste foundry sand (WFS), combined with supplement cementitious materials (SCMs), in concrete production. The Preliminary Investigation is based on three groups, where the first group studies different percentages of natural sand replacement with WFS (i.e. 5%, 10%, 15% and 20%), the second group analyses the addition of 5% silica fume with WFS, and the third group observes 10% metakaolin inclusion with WFS. The studied parameters include density, nondestructive test (UPV), compressive and tensile strength, acid resistance, and environmental benefit analysis. According to the results, the compressive strength of the concrete mix is enhanced by 17% by adding 20% WFS and 5% silica fume, and this value increases by 23% when adding an additional 10% metakaolin. Furthermore, the use of 20% WFS leads to a 3.27% decrease in the cost of concrete as compared to the control mix, with a decrease of 2.1% and 5.1% for silica and metakaolin-containing mixes, respectively.
Liquid water under vibrational strong coupling: An extended cavity Born–Oppenheimer molecular dynamics study
A computational study of liquid water when the system is coupled with a (model) Fabry–Perot cavity is reported. At this end, the cavity Born–Oppenheimer molecular dynamics approach proposed recently [Li et al., Proc. Natl. Acad. Sci. U. S. A. 117, 18324–18331 (2020)] is employed and different properties of water under vibrational strong coupling are investigated. Different cavity frequencies are considered, corresponding to different modes in the IR spectrum of liquid water: high frequency (corresponding to O–H stretching modes), medium frequency (corresponding to water molecule bending), and low frequencies (corresponding to librational modes). Simulations were done using both classical and quantum nuclear dynamics, this last via ring polymer molecular dynamics. Similar effects of the cavity are obtained in both cases. Namely, whereas the infrared spectrum is observed to be split for all cavity frequencies, no effects on structural properties are detected. In addition, transport and dynamical properties, including the diffusion coefficient, molecular reorientation, and hydrogen bond jump exchange times, show no effect due to cavity coupling when an extended statistical analysis is performed.