Browse Articles
Discover research articles across all indexed journals
Bulk superinsulation and polar nematic orders in nanopatterned NbTiN
A computational study on effect of Cymbopogon citratu and Juniperus virginiana against Spodoptera litura
Abstract Spodoptera litura, commonly known as the leaf cutworm, is a destructive agricultural pest that poses significant threats to crop yields. In light of the growing resistance to conventional chemical insecticides, this study investigates the potential of lemongrass (Cymbopogon citratus) and cedarwood (Juniperus virginiana) essential oils as sustainable, eco-friendly alternatives for controlling S. litura. Using in-silico techniques, including homology modeling, protein structure validation, and protein-ligand docking, the binding affinities of lemongrass and cedarwood bioactive compounds against critical proteins in S. litura, such as cytochrome c oxidase, alpha-glucosidase, octopamine receptors, and chemosensory protein has been evaluated. The results showed that the compounds: chamazulene, robustoflavone, cynaroside, hinkoflavone, spathulenol, robustaflavone, and amentoflavone exhibited strong inhibitory potential, with superior binding stability and interaction energies compared to the chemical insecticide chlorpyrifos. Additionally, synergistic effects were observed when combining compounds from lemongrass and cedarwood, which improved binding stability and enhanced multi-target inhibition. This study highlights the promise of these natural compounds as viable, environmentally friendly pest control agents and provides a foundation for developing plant-based bioinsecticides to manage S. litura. Future experimental research is needed to validate these findings in field applications and assess their broader ecological impacts.
Dynamics of sterically hindered F− + <i>i</i>-C3H7Cl reaction: An enhancement of indirect mechanisms
It is essential but difficult to monitor the underlying atomistic mechanisms for the competitive nucleophilic substitution (SN2) and base-induced elimination (E2) reactions. Especially, the dynamic characters of bulky alkyl substitution halides remain unclear due to its complexity. Here, we present direct dynamics simulations of the fluoride anion reaction with isopropyl chloride, uncovering distinct dynamical behaviors compared to its ethyl chloride counterpart. Reaction dynamics simulation capture the key trends observed in differential scattering experiment, demonstrating predominant preference for the direct E2 pathway through stripping mechanisms at 1.9 eV of collision energy. Notably, an enhancement of indirect mechanisms emerges with increasing methyl substitution (from ethyl to isopropyl chloride), even at the high collision energy where such pathways are typically suppressed. This phenomenon arises from the synergistic effects of ion-induced dipole forces and van der Waals interactions between the reactants, coupled with the alkyl substitution-induced stabilization of the entrance-channel complex, which collectively prolong the interaction timescales. This work deepens an atomistic dynamics understanding of sterically hindered systems and highlights the role of the entrance channel on the chemical dynamics.
A FAN1 point mutation associated with accelerated Huntington’s disease progression alters its PCNA-mediated assembly on DNA
Abstract FAN1 is an endo- and exo-nuclease involved in DNA and interstrand crosslink repair. Genome-wide association studies of people with Huntington’s disease revealed a strong association between the FAN1 R507H mutation and early disease onset, however the underlying mechanism(s) remains unclear. FAN1 has previously been implicated in modulating triplet repeat expansion in a PCNA dependent manner. To examine the role of PCNA on FAN1 activation, we solved the cryo-EM structures of a PCNA–FAN1–DNA complex. Our findings reveal that the FAN1 R507 residue directly interacts with PCNA D232. Biophysical interaction studies demonstrated that FAN1 enhances the binding affinity of PCNA for DNA, a synergistic effect disrupted in mutants carrying the R507H mutation. In contrast, PCNA does not affect the affinity of FAN1 for DNA but does modulate FAN1 activity upon ternary complex formation. The weakened and functionally altered FAN1 R507H–PCNA–DNA complex may partly impair the FAN1-mediated repair of CAG extrahelical extrusions, providing a potential explanation for the mutation’s role in accelerating disease progression.
The serum evaluation of sex hormones including DHEAs, DHT, testosterone in oral lichen planus patients
Imaging the photochemistry of cyclobutanone using ultrafast electron diffraction: Experimental results
We investigated the ultrafast structural dynamics of cyclobutanone following photoexcitation at λ = 200 nm using gas-phase megaelectronvolt ultrafast electron diffraction. Our investigation complements the simulation studies of the same process within this special issue. It provides information about both electronic state population and structural dynamics through well-separable inelastic and elastic electron scattering signatures. We observe the depopulation of the photoexcited S2 state of cyclobutanone with n3s Rydberg character through its inelastic electron scattering signature with a time constant of (0.29 ± 0.2) ps toward the S1 state. The S1 state population undergoes ring-opening via a Norrish Type-I reaction, likely while passing through a conical intersection with S0. The corresponding structural changes can be tracked by elastic electron scattering signatures. These changes appear with a delay of (0.14 ± 0.05) ps with respect to the initial photoexcitation, which is less than the S2 depopulation time constant. This behavior provides evidence for the ballistic nature of the ring-opening once the S1 state is reached. The resulting biradical species react further within (1.2 ± 0.2) ps via two rival fragmentation channels yielding ketene and ethylene, or propene and carbon monoxide. Our study showcases the value of both gas-phase ultrafast diffraction studies as an experimental benchmark for nonadiabatic dynamics simulation methods and the limits in the interpretation of such experimental data without comparison with such simulations.
Structural basis of phosphorylation-independent nuclear import of CIRBP by TNPO3
Abstract Transportin 3 (TNPO3) is a nuclear import receptor known for its broad substrate specificity, often recognizing arginine-serine (SR/RS) repeat-rich nuclear localization signals (NLS) in SRSF proteins. While serine phosphorylation or glutamate presence has been associated with these NLSs, recent proteomic studies identified TNPO3 cargoes lacking SR/RS repeats. One such example is the cold-inducible RNA-binding protein (CIRBP), which contains a non-classical RSY-NLS. Using X-ray crystallography, here we investigate the TNPO3-CIRBP interaction and find that tyrosines within the RSY-NLS play a key role in binding, independent of phosphorylation. Surprisingly, serine and tyrosine phosphorylation in CIRBP’s NLS inhibits TNPO3 binding, suggesting a regulatory mechanism for nuclear import. Our study reveals a non-conventional nuclear import mechanism mediated by TNPO3, which may extend to other known or yet undiscovered TNPO3 cargoes.
Teacher adoption of digital education management systems through combined information systems and social cognitive frameworks during post-COVID era
The trimer paradox: The effect of stiff constraints on equilibrium distributions in overdamped dynamics
We reconsider the classical problem of a freely joined chain of Brownian particles connected by elastic springs and study its conformational probability distribution function in the overdamped regime in the limit of infinite stiffness of constraints. We show that the well-known solution by Fixman [Proc. Natl. Acad. Sci. U. S. A. 71, 3050 (1974)] is missing a shape-related term, later alluded to but not computed by Helfand [J. Chem. Phys 71, 5000 (1979)]. In our approach, the shape term, also termed zero-point energy, arises explicitly from a careful treatment of the distributional limit. We present a computationally feasible method for the calculation of the shape term and demonstrate its validity in a couple of examples.
Prolonging parathyroid hormone analog action in vitro and in vivo through peptide lipidation
Antibacterial and anticancer properties of Solanum mauritianum fruit components analyzed using LC-QTOF-MS/MS
Abstract This study evaluated the antibacterial and anticancer properties of S. mauritianum fruit components through LC-QTOF-MS/MS metabolomic profiling. The samples were extracted, and the antibacterial activity was conducted using a standard Resazurin microtiter assay. The minimum inhibitory concentrations (MICs) of the crude extracts were evaluated against reference pathogenic bacterial isolates. The anticancer activity of the extracts was tested against U-87 MG glioblastoma and A549 lung carcinoma cells (ATCC cancer cell lines). The real-time toxicity assay and comprehensive metabolomic profiling were evaluated for the crude extracts. Results revealed that the ripe fruit coat exhibited the richest chemical diversity, with 15 unique metabolites, while the unripe fruit had 5. Detailed classification of the identified metabolites showed that alkaloids accounted for 33.3%, followed by terpenoids (21.2%). The extracts of the fruit components had significant antibacterial activity against the referenced pathogens of public health importance. Extracts from the ripe fruit coat demonstrated significant cytotoxicity on U-87 MG glioblastoma cell viability, suggesting potential anticancer activity, while the effect on A549 lung carcinoma cells showed high viability across all treatments. The real-time cytotoxicity assays further highlighted the dose-dependent inhibition of glioblastoma cells by crude extracts from the ripe fruit coat, emphasizing its therapeutic potential.
A frequency-domain approach to molecular photoionization via driven Schrödinger equation
This work extends the formalism introduced in a previous publication [T. Marx and S. I. Bokarev, Phys. Rev. A 106, 032806 (2022)] and provides a comprehensive framework for predicting molecular photoelectron spectra. This method employs a frequency-domain approach, formulated as a driven inhomogeneous Schrödinger equation under first-order perturbation theory with outgoing boundary conditions. It is shown to be analytically equivalent to Fermi’s golden rule approach while offering a distinct physical interpretation tied directly to the measured photocurrent. The formalism incorporates detailed light–matter interactions, yielding unique solutions. The implementation strategy is discussed in depth, emphasizing computational efficiency and flexibility. The results are validated through comparisons with experimental data and other theoretical methods for atomic and small molecular systems and analytically solvable models.
Remote-controlled mechanical and directional motions of photoswitchable DNA condensates
Abstract Membrane-free synthetic DNA-based condensates enable programmable control of dynamic behaviors as shown by phase-separated condensates in biological cells. We demonstrate remote-controlled microflow using photocontrollable state transitions of DNA condensates, assembled from multi-branched DNA nanostructures via sticky-end (SE) hybridization. Introducing azobenzene into SEs enables their photoswitchable binding affinity, which underlies photoreversible fluidity of the resulting condensates that transition between gel/liquid/dissociated states in a wavelength-dependent manner. Leveraging base-sequence programmability, spatially coupled orthogonal DNA condensates with divergent photoresponsive capabilities perform multi-modal mechanical actions that depend on azobenzene insertion sites in the SE, including switching flows radially expanding and converging under photoswitching. Localizing photoswitching within a DNA liquid condensate generates two distinct directional motions, whose contrasting morphology, direction, and lifetime are determined by switching frequency. Numerical simulations reveal its regulatory role in weight-adjusting energy-exchanging and energy-dissipative interactions between the photoirradiated and unirradiated domains.
From river flow regime diversity to proxies for hydrologic homogeneity a Canada-wide case study
Photoelectron imaging spectroscopy of Ag3− in the S0 and S1 states
We explore laboratory-frame photoelectron angular distributions (LF-PADs) originating from the outermost two orbitals, σu [the highest occupied molecular orbital (HOMO)] and σg (HOMO−1), of the silver trimer anion (Ag3−) in the S0(1Σg+) state. The experiment was performed by our novel photoelectron imaging technique using a high-repetition-rate tunable laser [T. Horio et al., J. Chem. Phys. 162, 026101 (2025)]. The LF-PAD for σu is found to be highly energy-dependent in a photoelectron kinetic energy (PKE) range from 0 to 1.57 eV; an isotropic LF-PAD with an anisotropy parameter β ∼ 0 is observed at the detachment threshold, exemplifying the Wigner threshold law, whereas the β value decreases down to β = −0.4 at 0.46 eV, followed by an increase up to β = 0.6 at 1.57 eV, as PKE increases. A small dip discernible in the PKE range of 1.2–1.3 eV suggests an influence of the autodetachment process on the β value, which is via bound electronic state(s) embedded in the D0(2Σu+) + e− continuum. On the other hand, the LF-PAD for σg exhibits a strong anisotropy parallel to the laser polarization with β of ∼1 in 0–0.39 eV. These contrasted trends are qualitatively reproduced by theoretical modeling of LF-PAD that accounts for photoelectron partial waves allowed for each photodetachment process. Furthermore, two-photon detachment spectra via the excited S1(1Σu+) state are presented, where the relative band intensities for the two detachment channels, D0(2Σu+) + e− ← S1(1Σu+) and D1(2Σg+) + e− ← S1(1Σu+), are discussed in terms of their leading electronic configurations.
Blocking plasma cell fate enhances antigen-specific presentation by B cells to boost anti-tumor immunity
Advanced eco-friendly spectrophotometric analysis for Nebivolol, Valsartan, and related impurity with comprehensive environmental impact assessment
Abstract At present, one of the main priorities for analysts is creating more sustainable and environmentally friendly methods for pharmaceutical analysis. In this context, three innovative spectrophotometric techniques, using tri-colored (green, blue, and white), were optimized and developed to simultaneously assess two antihypertensive drugs, Nebivolol hydrochloride (NEB) and Valsartan (VAL), in the presence of synthetic precursor impurity of Valsartan (Valsartan Desvaleryl, VAL-D), which is the main acidic degradation product. The methods employed, including the double divisor-ratio spectra derivative spectrophotometric method, the dual-wavelength in ratio spectrum method, and the H-point derivative ratio method, displayed a good linear range of 2.5–70 µg/mL, 10–50 µg/mL, and 10–70 µg/mL for NEB, VAL, and VAL-D, respectively. Assessment of greenness was implemented to the established methods using the analytical Eco-Scale scoring, analytical greenness metric (AGREE), and the green analytical process index (GAPI). The concepts of blueness assessment using the recently introduced Blue Applicability Grade Index (BAGI tool) and whiteness assessment using the Red Green Blue 12 (RGB 12 tool) were also applied. The proposed methods were validated as per ICH guidelines and verified to be accurate. Statistical analysis was performed to ensure the validity of methods concerning published methods.
Simple and efficient computational strategies for calculating orbital energies and pair-orbital energies from pCCD-based methods
We introduce affordable computational strategies for calculating orbital and pair-orbital energies in atomic and molecular systems. Our methods are based on the pair Coupled Cluster Doubles (pCCD) ansatz and its orbital-optimized variant. The computed orbital and pair-orbital energies are then subsequently used to approximate ionization potentials (IPs), electron affinities (EAs), the resulting charge gaps, double ionization potentials (DIPs), and double electron affinities (DEAs). Our methodology builds on the standard Koopmans’ theorem and refines it for a pCCD-based wave function. Furthermore, we incorporate pCCD electron correlation effects into the model utilizing canonical Hartree–Fock or natural pCCD-optimized orbitals. The latter represents a diagonal approximation to the (D)IP/D(EA) equation of motion pCCD models. We benchmarked our newly developed models against theoretical and available experimental data for selected atoms in various basis set sizes and a set of 24 organic acceptor molecules. Our numerical results show that the Koopmans’ approach based on pCCD natural orbitals provides a balanced treatment of occupied and virtual orbital energies, resulting in reliable predictions of charge gaps at a low computational cost.