Browse Articles

Proteomic analysis of 7-octenoic acid antifibrotic effects in TGF-β1 activated hepatic stellate cells

Communication: Modeling layered mosaic perovskite alloy microstructures across length scales via a packing algorithm

Layered “mosaic” metal-halide perovskite materials display a wide-variety of microstructures that span the order–disorder spectrum and can be tuned via the composition of their constituent B-site octahedral species. Such materials are typically modeled using computationally expensive ab initio methods, but these approaches are greatly limited to small sample sizes. Here, we develop a highly efficient hard-particle packing algorithm to model large samples of these layered complex alloys that enables an accurate determination of the geometrical and topological properties of the B-site arrangements within the plane of the inorganic layers across length scales. Our results are in good agreement with various experiments and, therefore, our algorithm bypasses the need for full-blown ab initio calculations. The accurate predictive power of our algorithm demonstrates how our minimalist hard-particle model effectively captures complex interactions and dynamics like incoherent thermal motion, out-of-plane octahedral tilting, and bond compression/stretching. We specifically show that the composition-dependent miscibility predicted by our algorithm for certain silver–iron and copper–indium layered alloys is consistent with previous experimental observations. We further quantify the degree of mixing in the simulated structures across length scales using our recently developed sensitive “mixing” metric. The large structural snapshots provided by our algorithm also shed light on previous experimentally measured magnetic properties of a copper–indium system. The generalization of our algorithm to model 3D perovskite alloys is also discussed. In summary, our packing model and mixing metric enable one to accurately explore the enormous space of hypothetical layered mosaic alloy compositions and identify materials with potentially desirable optoelectronic and magnetic properties.

Changes in spectrum of respiratory pathogens infections among hospitalized patients post COVID-19 pandemic in Jinan, Shandong Province

Structure of alkali magnesium, zinc, and calcium metasilicate glasses

The structure of the metasilicate composition glasses (A2O)x(XO)0.50−x(SiO2)0.50, with A = Na or K, X = Mg, Zn, or Ca, and x = 0.25 or 0.33, was investigated by combining neutron and high-energy x-ray diffraction with Raman scattering and 29Si and 25Mg magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy. The latter employed the rotor-assisted population transfer approach for signal enhancement. The diffraction results show a substantial population of four-coordinated X2+ cations in the majority of the magnesium- and zinc-bearing glasses. Based on the average degree of polymerization of the silicate networks obtained from the solid-state 29Si NMR results, and supported by the findings from Raman spectroscopy, no compelling evidence could be found for a network-forming role for the four-coordinated Mg2+ and Zn2+ species. The relationship between the Mg–O coordination numbers measured by diffraction and the mean isotropic chemical shifts found from 25Mg MAS NMR spectroscopy is considered for a variety of silicate glasses. A clear correlation between these parameters could not be found.

Constructing an implementation plan for integrating green BIM into undergraduate architecture programs

Simulating plastic ice VII with the data-driven many-body MB-pol potential

Computational studies using effective potentials that treat water as a rigid molecule were the first to predict the existence of a plastic phase of ice VII. Fifteen years later, this prediction was confirmed experimentally: in the plastic phase, water molecules retain the translational order of the body-centered cubic lattice while undergoing jump-like rotational motion typical of the liquid. Here, we show that this plastic phase also emerges in simulations employing the data-driven many-body MB-pol potential. The phase appears at high pressure, sandwiched between the liquid and ice VII phases. Our results confirm the first-order nature of both the ice VII–plastic and plastic–liquid transitions. Moreover, we find that ice VII exhibits rotational motion of hydrogen atoms on the nanosecond timescale near the melting line, although this motion is qualitatively distinct from that observed in the plastic phase. These results support the existence of the plastic phase beyond rigid-molecule models and provide new insight into the rotational dynamics of ice under extreme conditions.

Separation of the field source and characterization of the deep and shallow tectonics of the northwestern margin of the Sichuan-Yunnan rhombic massif

Abstract The Sichuan-Yunnan block, characterized by complex geological formations and persistent high-intensity seismicity, remains a focal domain for contemporary geodynamic research. To investigate the fracture depth of the northern Sichuan-Yunnan block and the southeastern part of the Qiangtang block, CRUST1.0 was employed to fit the trend items in the study area and to refine the gravity field model with measured data as control points. A two dimensional discrete wavelet transform analysis method is applied to separate the field sources from the obtained high-precision grid data. Additionally, radial logarithmic power spectrum analysis is utilized to estimate the average equivalent source depth of the abnormal geological bodies corresponding to each order wavelet, thereby extracting both transverse and longitudinal tectonic characteristics of the crust in the region. The results reveal that the Bouguer gravity anomaly within the study area exhibits a general pattern of low values in the northern region and high values in the southern areas. Major faults, including the Bianba-Luolong fault, Nujiang fault, Lancangjiang fault, Batang fault, Jinshajiang fault, Yushu-Ganzi fault and Ganzi-Litang fault are all deep and large faults, with respective depths of 38.9 km, 52.9 km, 52.9 km, 52.9 km, 38.9 km, 52.9 km, 52.9 km. This study provides physical insights into the crustal structure distribution of the northern Sichuan-Yunnan rhombohedral block.

Ultrafast non-adiabatic molecular energy conversion into photons induced by quantized electromagnetic fields

Molecular polaritons within the mid-infrared regime have emerged as a source for modifying and manipulating molecular and photonic properties. However, the development of new methodologies for photon generation is still a challenge in nanophotonics. We propose a molecular model based on the Holstein–quantum–Rabi Hamiltonian, which also incorporates realistic dipole moments and nonadiabatic couplings among electronic excited states, to study the ultrafast photodynamics of diatomic molecules in confined electromagnetic fields within quantized cavities. In addition to vibronic transitions due to intrinsic nonadiabatic couplings, two types of light-induced crossings emerge: one type is located at molecular nuclear geometries where the rotating wave approximation is fulfilled, and another type appears at different geometries where counter-rotating transitions may occur. We make a comprehensive study of polariton photodynamics within a time window of a few tens of femtoseconds, where dissipative mechanisms do not influence the polariton photodynamics. We stress the dramatic change of the polariton energy spectrum as a function of the Huang–Rhys factor when nonadiabatic couplings are included in the model. We conclude that both the molecular nonadiabatic couplings and, more specifically, the counter-rotating couplings in the cavity–molecule interaction play a crucial role in converting vibronic energy into photons through excited dressed states. We also show that the sign of the Huang–Rhys factor has a significant impact on this photon conversion. Our work paves the way for the development of many-photon generation powered by strong light–matter interaction, along with potential applications using alkaline earth monohydride molecules.

Loss of tropical moist broadleaf forest has turned Africa’s forests from a carbon sink into a source

Abstract Africa’s forests and woody savannas have historically acted as a carbon sink, removing atmospheric carbon and storing it as biomass. However, our novel analysis reveals a critical transition from a carbon sink to a carbon source between 2010 and 2017. Using new high-resolution satellite-derived biomass maps, validated with field plots and machine learning techniques, we quantified the aboveground biomass stocks across African biomes over a decade. Between 2007 and 2010, the continent gained 439 ± 66 Tg yr ⁻1 of aboveground biomass, but from 2010 to 2015 biomass declined by − 132 ± 20 Tg yr -1 and from 2015 to 2017 this decline continued with a loss of − 41 ± 6 Tg yr -1 , primarily driven by deforestation in tropical moist broadleaf forests. Gains in savanna biomass partially offset these losses, likely due to shrub encroachment. Our findings underline the urgent need for implementing policies to halt global deforestation as required by the Glasgow Leaders Declaration to close the global emissions gap. The current ongoing revisions of Nationally Determined Contributions to the Paris Agreement need to be even more ambitious to compensate for the ongoing loss of natural carbon sinks.

Optical signatures of coherence in molecular dimers

We calculate experimentally measurable signatures of quantum correlations in a coupled molecular dimer that strongly interacts with its vibrational environment. We investigate intensity and mode-resolved photon coincidences for different relative orientations of such dimers and observe spatio-temporal correlations for various configurations. We find that projective measurements can produce cooperative signatures even when emitters are arranged orthogonal to each other. To model effects of vibrational environments that are present in realistic experimental situations, we use the polaron framework. Furthermore, we also account for the effects of finite instrument response, varying temperature, and the presence of static disorder. We analyze the effect of disorder in both dimer orientation and measurement direction and find that photon coincidences remain well-resolvable using state-of-the-art detectors. This work enhances our understanding of cooperative emission from two coupled emitters and offers direction for future experiments on probing their coherent dynamics.

Remarkable adsorptive denitrogenation of indole and quinoline from model fuel oil by CuCl/UiO-66 metal-organic framework

Tuning effect of vanadium substitution on the structural and electronic properties of potassium hollandite surfaces

Metal oxide surfaces possess unique properties that are crucial for a wide variety of applications. Herein, density functional theory calculations are performed to study surfaces of potassium hollandite, KMn8O16, a promising cathode material for electrochemical energy storage, and the vanadium-substituted analog KMn7VO16. The results show that there is a clear increase in the stability of KMn8O16 with (001) < (110) < (100) or (010), apt to adopt an elongated rod-like morphology. The vanadium (V)-substitution lowers the crystal symmetry and prefers to occupy the surface sites, resulting in electron redistribution and selective tuning of surface energy depending on the surface structures. In particular, the higher stability of substituted V4+ compared with Mn4+ ions leads to stabilization of the (001) surface due to the direct interaction of reduced Mnδ+ ions on the surface, while such tuning effect decreases with the increase in surface stability, (110) > (100) and (010). As a result, the KMnO16 rod is shortened upon V-substitution as observed experimentally, effectively facilitating the ion transport during discharge. The V substituents also introduce stabilization to the defect surfaces resulting from Mn2+ dissolution during cycling, thereby hindering further structural decay. Our study demonstrates the potential tuning effect of V-substitution to promote the ion transport and mitigate the capacity degradation of α-MnO2-based materials.

Threshold-distance functions predict speech recognition with cochlear implants

Abstract Cochlear implantation shows unexplained outcome variability. Among the key factors affecting outcomes measured by speech understanding is the functional state of the auditory nerve and the amount of its degeneration due to hearing loss. In the present study we actively varied the distance of the stimulating electrodes from the modiolus (the spiral ganglion), quantified it using fluoroscopy and cone-beam computed tomography and related it to electrically-evoked compound action potentials (eCAPs) in human subjects. Stimulation was monopolar. The distance from modiolus could explain up to 91% of the variability in the thresholds of eCAPs. The threshold varied between participants. For individual electrodes of the implant in the given participant, a linear relationship between threshold (in current level) and distance from modiolar axis was found, with different slopes in different participants. The slopes of the eCAP thresholds to modiolus distance of the electrode across ears could explain up to 67% of the variability of speech understanding in these participants. We suggest that the slope of the threshold-distance function might serve as a marker for the functional state of the target neurons (spiral ganglion cells) and can be used to assess this in individual subjects.

Chirality-encoded molecular wavefunctions

For enantiomers, the ground-state charge densities are mapped into one another by spatial reflection, yet—when spin–orbit coupling (SOC) is present—their occupied spinors need not coincide beyond a global phase. SOC encodes spatially varying, intrinsic phase textures whose gradients leave the density unchanged but enter gauge-invariant response combinations. These phases provide a general mechanism for enantiospecific contributions in response tensors. We show that isotropic pseudoscalar signatures arise only from polar-axial couplings, while same-parity couplings remain mirror-even; in oriented samples, anisotropic tensor components can also flip sign. We derive analytical bounds linking SOC-driven spinor phases and amplitude distortions to measurable tensor differences and validate them with relativistic plane wave density-functional calculations on prototypical chiral molecules. Plane waves are chosen because they faithfully represent delocalized SOC phase textures that standard localized bases struggle to capture. Experiments that couple mirror-odd operators to SOC-induced phases in chiral samples can, in principle, yield enantiospecific responses.

Associations between systemic inflammation and cognitive trajectories post-stroke

Abstract Our objective was to explore whether plasma inflammatory biomarkers and related metabolites in acute phase and 3 months after stroke were associated with different cognitive trajectories and with changes in cognition post-stroke. The Norwegian Cognitive Impairment After Stroke (Nor-COAST) study was a prospective, multicentre cohort study of patients with acute stroke, followed up at 3, 18, and 36 months post-stroke. First, we modelled cognitive trajectory groups based on Montreal Cognitive Assessment (MoCA) scores and used multinominal logistic regression to study the associations between systemic inflammatory biomarkers/metabolites and group membership. Second, using mixed linear regression, we investigated whether the same biomarkers/metabolites were associated with changes in MoCA scores over time, stratified by pre-stroke cognitive status. The 466 participants had mean (SD) age 72 (12) years, 59% were males, and mean (SD) NIHSS score at admittance was 4 (4.8). Higher acute-phase values of the terminal complement complex, interleukin 6, macrophage inflammatory protein 1α, neopterin, quinolinic acid, and PA ratio = 4-pyridoxic acid / (pyridoxal + pyridoxal 5’-phosphate) and higher 3-month values of neopterin were associated with increased risk of being in the group characterized by low and declining MoCA score compared to the group of best MoCA score ( p  < 0.01). Higher acute-phase values of tumour necrosis factor and interleukin 8, were associated with progressive decline in the MoCA score ( p  < 0.01). Premorbid factors, and in particular pre-stroke frailty, had more impact on the models than stroke-related factors, and partly confounded several of these associations. Higher degrees of systemic inflammation in the acute phase were associated with worse cognitive trajectories and may reflect the response to the acute stroke, stroke-related complications and/or premorbid conditions. Trial registration: ClinicalTrials.gov: NCT02650531. Retrospectively registered January 8, 2016. First participant included May 18, 2015.

pyTTN: An open-source toolbox for open and closed system quantum dynamics simulations using tree tensor networks

We present the Python Tree Tensor Network (pyTTN) package for the evaluation of dynamical properties of closed and open quantum systems that makes use of Tree Tensor Network (TTN) based representations of wave functions. This package includes several features allowing for easy setup of zero- and finite-temperature calculations for general Hamiltonians using single and multi-set TTN ansätze with an adaptive bond dimension using subspace expansion techniques. In addition to these core features, pyTTN provides several tools for setting up efficient simulations of open quantum system dynamics, including the use of the TTN ansatz to represent the auxiliary density operator space for the simulation of the hierarchical equation of motion method and generalized quasi-Lindblad pseudomode methods. We present a set of applications for the package, starting with the widely used benchmark case of the photo-excitation dynamics of 24 mode pyrazine, after which we consider a more challenging model describing the exciton dynamics at the interface of an n-oligothiophene donor–C60 fullerene acceptor system. Finally, we consider applications to open quantum systems, including the spin-boson model, a set of extended dissipative spin models, and an Anderson impurity model. By combining ease of use and an efficient implementation, along with an extendable design that allows for the addition of future extensions, pyTTN can be integrated into a wide range of computational modeling software.

The mediating role of emotion regulation in the link between personality traits and self-regulated learning among low-achieving EFL learners

Vibrational spectra of materials and molecules from partially adiabatic elevated-temperature centroid molecular dynamics

Centroid molecular dynamics (CMD) incorporates nuclear quantum statistics into the calculation of vibrational spectra. However, when CMD is performed in Cartesian coordinates, it shows unphysical artifacts in certain vibrational bands, known as the curvature problem. Recent work showed that CMD spectra can be freed from the curvature problem by evolving the ring-polymer centroid on a potential of mean force (PMF) calculated at an elevated temperature (Te-CMD). Here, we present a partially adiabatic implementation of Te-CMD (PA-Te-CMD), which eliminates the need for precomputed PMFs and instead yields the centroid force on the fly. We introduce a two-temperature path-integral Langevin thermostat to achieve a temperature separation between the centroid and internal modes of the ring polymer. Because it is paramount that the elevated temperature be chosen as low as possible for a given physical temperature in this formulation, we present a general scheme for its determination. We benchmark PA-Te-CMD against exact vibrational spectra for the isolated water monomer and discuss its performance for challenging anharmonic systems: the carbonic acid fluoride molecule and the methylammonium lead iodide perovskite. We conclude that PA-Te-CMD mitigates the curvature problem and the steep increase in computational cost with decreasing temperature of conventional path-integral methods. We observe energy leakage from the hot internal modes to high-frequency centroid modes in some cases, which, nevertheless, only compromises the spectral line shapes at lower temperatures. While an adiabatic setup based on a coarse-grained centroid PMF is still preferable when a good pre-trained PMF can be easily obtained, PA-Te-CMD presents a low-barrier single-shot setup for any system.

Sustainable high-performance injection geopolymers, role of GGBFS and water-to-binder ratio in strength, microstructure, and predictive modeling

Minimum theoretical model of viral capsid self-assembly on a spherical scaffold

The formation of the protective shell, or capsid, of many large icosahedral viruses requires the aid of scaffold proteins to initiate nucleation, ensure correct size and shape, and facilitate interactions with the viral genome. Interestingly, SPs often preassemble into a template structure, upon which capsid proteins subsequently self-assemble. In this article, we present a minimum theoretical model, rooted in classical nucleation theory, that describes the in vitro self-assembly of a spherical capsid in the presence of a Preformed Spherical Scaffold (PSS). Within this framework, we examine the influence of the PSS on the size of the critical capsid, the nucleation barrier, and the steady-state nucleation rate. We contrast our findings with those of a recent extension of the original classical nucleation theory of viral capsids, which accounts for bending deformations. Furthermore, we present a detailed analysis of the physical conditions that lead to stable closed capsids. These are then represented in phase diagrams that highlight regions of favorable and unfavorable assembly on top of the template. Our model quantifies the necessary interactions between CPs and the PSS for optimal assembly and extends naturally to preformed scaffolds of diverse shapes.