Browse Articles

Optimization of fragment state spaces within the excitonic renormalization framework

The recently proposed excitonic renormalization framework presents an alternative ansatz to the electronic structure theory of weakly interacting fragments. It makes use of absolutely localized orbitals and correlated states evaluated on isolated fragments, which are then used to recover the interaction in an ab initio manner based on a biorthogonal framework. The correlated monomer information can be heavily truncated, and the Hamiltonian can be expanded in a rapidly converging series, allowing the Hamiltonian to be built and diagonalized in a scalable fashion. However, the methodology still lacks an efficient bottom-up procedure, capable of producing optimized model state spaces for the isolated fragments, without ever building the Hamiltonian in the full monomer state spaces. In order to address this issue, this work presents an algorithm utilizing monomer gradients at three different levels as well as an efficient pre-screening of the determinant space, ensuring compact model state spaces and intermediates. Numerical results are presented for the beryllium dimer, showing that the algorithm is indeed capable of building compact model state spaces, yielding results that closely resemble those of the optimal model state spaces. Furthermore, it is shown that model state spaces, optimized at the zeroth order of the Hamiltonian expansion, can also be used to accurately recover first order results, enabling very efficient optimization, as the optimization can be conducted at a lower order than the targeted final level. Hence, the presented solver completes the excitonic renormalization methodology, forming a polynomially scaling framework.

Continuous frost causes a greater reduction in forest growth than isolated frost in the Northern Hemisphere

siRNA-mediated inhibition of NTT-MMP-2 reduces oxidative stress and apoptotic signaling in an ex vivo model of ischemia/reperfusion injury

Properties of the simplest localized molecular orbitals: The P-LMOs

The columns of the LCAO density matrix, P, obtained in a standard Hartree–Fock or Kohn–Sham calculation, can be interpreted as coefficients of occupied localized molecular orbitals (LMOs). Requiring no extra calculations once P is available, they constitute the simplest possible set of occupied LMOs. They are nonorthogonal, moreover redundant, and are related to the usual projected atomic orbitals that emerge as the columns of matrix PS, where S is the overlap matrix of atomic orbitals. Both P-LMOs and PS-LMOs may serve as molecular orbitals even for procedures that determine P directly, i.e., avoiding the construction of molecular orbitals. To enhance localization, the LMOs resulting from the square root of P are also investigated. Properties of P-LMOs and P1/2-LMOs are discussed, and they are compared to PS-LMOs and to other well-known types of localized orbitals.

Exploring single-cell biosynthetic noise and dynamics for enhanced betaxanthin production in Escherichia coli

Neurally adjusted ventilatory assist vs pressure support ventilation: short-term effects on shunt and dead space after cardiac surgery

Abstract Postoperative pulmonary complications, particularly atelectasis, are common after cardiac surgery and may contribute to impaired gas exchange or acute lung injury (ALI). Neurally Adjusted Ventilatory Assist (NAVA) delivers ventilatory support proportional to the patient’s respiratory drive, offering theoretical advantages over Pressure Support Ventilation (PSV), including improved synchrony, enhanced diaphragmatic efficiency, and reduced risk of ventilator-induced lung injury. However, comparative data on gas exchange, dead space, and regional ventilation during weaning after cardiac surgery remain limited. This prospective crossover study evaluated 12 mechanically ventilated patients with mild ALI following cardiac surgery across three ventilation phases: two PSV phases (PSV1 and PSV2) separated by a phase of NAVA. Intrapulmonary shunt fraction was calculated from measurements obtained via a Swan-Ganz catheter. Physiological dead space fraction (V D /V T ) was assessed using three methods: the Bohr–Enghoff equation, end-tidal CO₂-derived alveolar dead space fraction (AVDSf-ET), and a novel time-to-volume converted capnographic approach (V CAP-CALC ). Regional ventilation was assessed using electrical impedance tomography (EIT), and neuroventilatory efficiency (NVE) was calculated from diaphragmatic electrical activity (EAdi). Data were analyzed using linear mixed-effects models to account for repeated measures and within-subject variability. V D /V T was significantly lower during NAVA compared with PSV1 and PSV2 when assessed by V CAP-CALC (58.5% vs. 63.8% and 61.3%, respectively;  p  < 0.001). The PaO₂/FiO₂ ratio and NVE were significantly higher during NAVA ( p  = 0.01 and  p  = 0.037, respectively). No significant difference in pulmonary shunt fraction was observed. EIT revealed a modest increase in dorsal end-expiratory lung volume during NAVA, without redistribution of tidal volume or Center of Ventilation. The V CAP-CALC method showed strong agreement with established dead space measures (R2 = 0.77–0.82) and demonstrated high repeatability (mean coefficient of variation 3.5%). NAVA is a safe and feasible ventilatory mode following cardiac surgery, associated with reduced dead space fraction, improved oxygenation and enhanced neuroventilatory efficiency. Given that shunt fraction remained unchanged, the observed improvement in ventilation–perfusion (V/Q) matching reflects a reduction in V D /V T . The potential implications for postoperative recovery and long-term outcomes merit evaluation in larger clinical studies. ClinicalTrials.gov: NCT03217305. Initial Release 21/06/2017.

Assessment of density functional theory methods on atomic and electronic structure of <i>β</i> -NiOOH structural models

A reliable determination of the atomic and electronic structure of nickel (oxy)hydroxide (NiOOH) is crucial for understanding its application as an oxygen evolution reaction (OER) electrocatalyst. However, discrepancies across experimental and computational studies have left the structure–composition–activity relationship of β-NiOOH poorly defined. In this work, we reassess the atomic and electronic structure of β-NiOOH using first-principles density functional theory calculations, emphasizing the influence of exchange–correlation functional and choice of ground-state structure on predicted structural and electronic properties. Simulated Raman is employed as an additional validation metric to inform structural assignments. Building on the optimized bulk β-NiOOH model, we construct and analyze a Fe-doped β-NiFeOOH (001) surface to explore the electronic and catalytic consequences of 25% Fe incorporation. Our comparative computational framework enables consistent evaluation of bulk and surface properties, offering deeper insights into the role of structural motifs in governing OER activity and guiding the design of improved earth-abundant electrocatalysts.

Tracing the origin of myofibroblasts in kidney fibrosis

Dynamic structure driven image scrambling technique for data protection

Abstract Today, communication using digital media has increased rapidly. In this digital communication era, providing security to sensitive images is essential at the time of transmission. The images are mostly focused nowadays because they are used directly or indirectly in every field of information sharing, for example, healthcare, military, intellectual property, and many more areas. In this paper a new approach to image scrambling is proposed to secure the sensitive image information. The proposed method is focused on the core concept of data structure. It involves the use of binary trees and the efficiency of hash tables, which enhances image security during transmission. The dynamic data structure properties enhanced the scrambling and descrambling process. In the scrambling method, the image pixels are first stored in the binary tree using the hash table. After the binary tree arrangement, pixels are collected into a one-dimensional array using the tree traversing process. Now, the one-dimensional array is converted into the two-dimensional array to match the size of the original image. The descrambling method is the inverse of the scrambling method. The proposed method maintains the quality of the image for both sender and receiver; different quality assessment parameters like PSNR, MSE, NCC, AD, SC, MD, Corr, HC, VC, DC, NPCR, UACI and Entropy are used to check the outcome. The outcome of PSNR between the original image and the scrambled image is less than 4 dB. For the descrambled image and the original image, the PSNR is infinite. According to the obtained results, there is a 100% similarity between the original image and the descrambled image. The proposed method was also compared with the existing methods, and it showed a negative or near to ‘0’ correlation between the scrambled image and the original image. In future work the proposed scrambling method can be used in image watermarking or image steganography techniques.

Machine-learning potentials for efficient simulations of anisotropic colloids

Simulating interactions between non-spherical colloidal particles is computationally challenging due to the complex dependency of forces and energies on their geometry. Instead of a position and orientation, we represent each shape by a small set of points with the same symmetry, which allows the use of descriptor-based and end-to-end models for predicting interaction energies and forces of atomistic systems. Then, we compare various descriptors coupled with different regression models, such as Behler–Parrinello descriptors, smooth overlap of atomic positions, and neuroevolution potential (NEP), as well as multiple end-to-end models, namely, SchNet, DimeNet, and DimeNet++. Among these, the NEP offers an optimal balance between accuracy and computational efficiency. NEP, originally developed for atomistic systems, represents interactions between rigid anisotropic bodies using point clouds, which enables the representation of any arbitrary shape. Molecular dynamics simulations using NEP accurately reproduced structural properties across diverse particle shapes, including cubes, tetrahedra, pentagonal bipyramids, and twisted cylinders, while achieving roughly an order-of-magnitude speedup over other methods. In addition, we show that the extension of the method to multi-face shapes with different interactions on their surface is straightforward. We used a twisted cylinder, which lacked any point group symmetry, to demonstrate the flexibility and accuracy of NEP. Our approach enables scalable simulations of complex colloidal systems and can potentially help to facilitate efficient studies on shape dependent interactions and phase behavior in the future.

Investigating action topography in visual cortex and deep artificial neural networks

Abstract High-level visual cortex contains category-selective areas embedded within larger-scale topographic maps like animacy and real-world size. Here, we propose action as a key organizing factor shaping visual cortex topography and assess the ability of topographic deep artificial neural networks (DANNs) in capturing this organization. Using fMRI, we examined responses to images of body-parts and objects with different degrees of action properties. In left lateral occipitotemporal cortex, we identified a topographically-organized action gradient, with overlapping activations for bodies, hands, tools, and manipulable objects along a dorsal-posterior to ventral-anterior axis, culminating at the intersection of body parts and objects exhibiting higher action properties. Multivariate analyses confirmed action as a crucial organizing principle, while shape and animacy dominated ventral occipitotemporal cortex and DANNs, which exhibited no action-based organization. Our proposed action dimension serves as a further organizing principle of object categories, advancing understanding of visual cortex organization and its divergence from DANN-based models.

Optimization of comprehensive wheat growth index system and monitoring model based on LAI

Key roles of conical intersections in the photolysis of phosphine and diphosphine

The photochemical reactions of phosphine (PH3) and diphosphine (P2H4) play important roles in interstellar chemical evolution. Herein, the multistate complete active space second-order perturbation theory has been employed to investigate the photolysis mechanisms of PH3 and P2H4 in gas phase. Our results show that upon light irradiation, the PH3 molecule splits to form the PH2 and H radicals, with PH2 dimerizing to P2H4. The excited-state P2H4 either isomerizes to PH3 and PH or undergoes dehydrogenation to yield P2H3 and H radicals involving an unusual three-state crossing point (S1/T2/T1)x. Importantly, we found that the isomerization is governed by an extended (S1/S0)x conical intersection seam, first observed in phosphorus-containing compounds. These mechanisms explain the early experimental observation about the changing trend of P2H4 yield in the photolysis of PH3 [Ferris and Benson, Nature 285, 156–157 (1980)], advance phosphorus hydride photochemistry, and provide a theoretical framework for interstellar phosphorus molecule evolution.

The cryo-EM structure of Photosystem I from Chromera velia with a bound superoxide dismutase heterodimer

Solar forcing on elemental and nanomechanical variations in Late Cretaceous lacustrine deposits

Abstract Decennial to annual-scale paleoclimate proxy variations are often attributed to solar forcing and/or unforced internal climate oscillations, but recognition of such variations in nanomechanical properties is extremely rare. Here we present a well-preserved, millimeter-scale laminated shale-carbonate couplet from Late Cretaceous petroliferous Qingshankou Formation in the Songliao Basin, NE China (ca. 90.53 Ma). Cyclicity analyses of elemental and nanomechanical data reveal periods of 47.7 ± 5.2–20.3 ± 2.2 year and 15.1 ± 1.6–7.4 ± 0.8 year attributed to Hale and Schwabe solar cycles, respectively; a 5.3 ± 0.6–2.5 ± 0.3 year period probably reflecting ENSO-like climatic fluctuations. Solar activities govern climatic changes that reshape aquatic environment, which further controls the laminated sedimentary composition and mechanical properties. The mechanically weak interfaces between solar-forced biogenic soft carbonates and terrigenous hard detritus are susceptible to crack propagation, affecting horizontal hydraulic fracturing in shale oil exploitation. This study introduces an integrated science-engineering research paradigm in shale oil field.

Photoionization dynamics of O2 and O3 for atmospheric and astrophysical applications

The photoionization dynamics of molecular oxygen (O2) and ozone (O3) are investigated using the ab initio R-matrix method, incorporating explicit electron correlation and resonance effects. These two oxygen-bearing species are of fundamental importance in atmospheric photochemistry and astrophysical environments; however, quantitative data for their total and valence shell photoionization cross-sections remain incomplete. For O2, we computed the total and channel-resolved cross-sections associated with ionization from the 1πg, 1πu, and 3σg valence orbitals, leading to the X2Πg, a4Πu, A2Πu, b4Σg−, and B2Σg− ionic states, as well as additional Πu states (22Πu, 32Πu) that arise from mixed contributions, including ionization and excitation effects linked to their strong multiconfigurational character. The calculated cross-sections and their resonance structures show excellent agreement with available experimental measurements, accurately reproducing the near-threshold and autoionization features. For O3, high-resolution total and partial photoionization cross-sections corresponding to the 2A1(6a1−1), 2B2(4b2−1), and 2A2(1a2−1) ionic states are reported for the first time. The results reveal pronounced Rydberg series and resonance enhancements dominating the low-energy region, providing a comprehensive picture of the O3 photoionization continuum. The present benchmark dataset establishes a consistent framework for modeling O2 and O3 photoionization across atmospheric and astrophysical conditions and serves as a reference for future theoretical and experimental investigations.

Synovial sarcoma reprograms transcription by GBAF activation of polycomb targets and loss of CBAF enhancers

Abstract Synovial sarcoma is a cancer driven by a fusion oncoprotein, SS18::SSX, that links SS18, a subunit of BAF-family chromatin remodeling complexes, to the carboxy terminus of SSX, which avidly binds nucleosomes with the histone post-translational modification H2AK119ub. Here, we show in mice that SS18::SSX expression redistributes non-canonical GBAF complexes broadly to promoters and distal enhancers marked by H2AK119ub, which causes developmental loci to lose H3K27me3 and become transcriptionally active. Canonical BAF containing SS18::SSX abandons its typical binding sites, is largely absent from H2AK119ub-marked sites, and instead distributes narrowly to transcription start sites with PBAF. Disruption of Arid1a or Arid1b (both CBAF-specific) retains synovial sarcoma character, while Smarcb1 (PBAF- and CBAF-specific) or Pbrm1 (PBAF-specific) disruption does not, although all accelerate SS18::SSX-driven tumorigenesis in mice. Thus, the synovial sarcomagenesis mechanism involves SS18::SSX reprogramming transcription positively through GBAF redistribution to activate polycomb-targeted developmental genes, and negatively by loss of normal CBAF localization and function.

Oxindole based sulfonyl derivatives synthesized as potent inhibitors of alpha amylase and alpha glucosidase along with their molecular docking study

A unified framework for semiclassical reaction rate theory

A general semiclassical theory for the calculation of reaction rate constants is developed. The theory can be understood as a formal framework that encompasses existing semiclassical methods: instanton theory and semiclassical transition state theory (SCTST). Unlike SCTST, the present formalism does not start from the concept of “good” action-angle variables. Instead, it is based on a conjectured connection between the cumulative reaction probability and the instanton contribution to the formally exact generalization of Gutzwiller’s formula for the trace of the Green’s function. The formalism effectively generalizes the “imaginary free-energy” formulation of instanton theory to microcanonical scattering rates and all orders in ℏ. In one dimension, explicit expressions are derived for the generalized reduced action up to O(ℏ4) using exact WKB/quantum Hamilton–Jacobi theory. The connection between the present formalism and the standard second-order vibrational perturbation theory (VPT2) version of SCTST is explored. It is also shown that the standard thermal instanton rate theory, as well as higher order (dividing surface independent) “perturbative” corrections, can be straightforwardly derived from the framework. Above the crossover temperature, first-order corrections in ℏ to the parabolic barrier (“sphaleron”) rate are also derived. A simple anharmonic transition state theory and anharmonic version of the Wigner tunneling correction are presented. Finally, the potential for the development of new and improved semiclassical methods for modeling reaction kinetics is discussed.

Decrypting spatiotemporal code of human endometrial receptivity