Browse Articles

Photodynamics simulation insights into excited-state relaxation mechanisms via Z/E isomerization in para-amino substituted GFP chromophores

The ability of green fluorescent protein (GFP) chromophore and its derivatives to undergo cis–trans photoswitching behavior has been widely acknowledged as of great interest because of its emerging applications in optogenetics and optoelectronics. However, key aspects of the internal conversion process in the GFP chromophore derivatives remain largely unclear. Based on quantum chemical methods and on-the-fly nonadiabatic dynamics simulations, we investigated the ultrafast photoinduced cis–trans isomerization phenomenon in the para-amino (NH2-HBDI) derivative of the GFP chromophore, which is intrinsically non-fluorescent. We demonstrate that upon excitation to the excited (S1) state, there occurs nonselective progression along the distortion of exocyclic methine-bridged imidazolinone (I) and phenylamine (P) bonds, leading to ultrafast nonradiative relaxation via S1(1ππ*)/S0 internal conversion. This internal conversion process is facilitated by multiple S1/S0 conical intersections with dominant imidazolinone (ΦI) dihedral rotations. Our results provide insight into the effect of the amino group on the dynamics of fluorescent probes. Therefore, these observations contribute to a valuable understanding of photoinduced switching phenomena and find a relation between structure and dynamics.

Metabolic dynamics of human external urethral sphincter myoblast differentiation and the effects of tricarboxylic acid cycle inhibition

Abstract Stress urinary incontinence commonly arises with aging or following prostatectomy, yet its underlying mechanisms remain unclear. To address this, we investigated the role of metabolic pathways—particularly the tricarboxylic acid (TCA) cycle—in the differentiation of human external urethral sphincter myoblasts. Immortalized sphincter cells (US2-KD) were induced to differentiate over 192 h. Metabolomic profiling using gas chromatography–mass spectrometry, along with pathway enrichment analysis, identified key metabolic changes. Inhibition of mitochondrial pyruvate transport with UK5099 markedly suppressed TCA cycle metabolites, including citrate, α-ketoglutarate, fumarate, and malate. This inhibition also significantly reduced MYH7 expression and intracellular adenosine triphosphate levels throughout the differentiation period. These results demonstrate that the TCA cycle plays a critical role in both energy metabolism and the differentiation of urethral sphincter myoblasts. This study is the first to suggest that impaired TCA cycle activity may contribute to the pathogenesis of Stress urinary incontinence and represents a potential therapeutic target. Our findings offer new insight into age-related metabolic decline associated with Stress urinary incontinence and support the development of therapies that combine metabolic modulation with regenerative approaches.

Extension of the Fermi–Amaldi functional to fractional electron number

The Fermi–Amaldi correction is a conceptually significant density-functional approximation with explicit dependence on the electron number N. This dependence raises the question of whether N should be treated as the integral of the total electron density for systems with noninteger (fractional) N. We answer this question negatively by observing that the Fermi–Amaldi functional is identical with the exact exchange functional for any number of fermions or bosons occupying the same spatial orbital and in systems where occupied orbitals have zero differential overlap. This conclusion is consistent with previous reports that the preservation of certain properties of N-dependent functionals requires treating N as a parameter. Our analysis also suggests that the Fermi–Amaldi functional is discontinuous within a given spin-channel of the total electron density and continuous on the boundaries between different spin-channels at N = 1. This implies that the jump discontinuity of the exact exchange–correlation potential observed at N = 1 is a correlation effect. The last conclusion is illustrated with numerical calculations.

Exploring the relationship between circadian syndrome, serum uric acid levels, and hyperuricemia: evidence from NHANES 2005–2018

Classical dynamics in a quantum spirit: Refining semi-classical corrections for the scattering of H2 on W(100)

The collision dynamics of hydrogen on tungsten is studied using a combination of classical and quantum molecular dynamics approaches, making use of a multidimensional potential energy surface interpolated from density functional theory energies based on the vdW-DF2 functional. Corrections inspired by a semi-classical model are then introduced to improve the predictions of the classical description. In particular, a refined version of the adiabaticity correction (AC) is developed. This study demonstrates that, for H2 on W(100) in its ground state and in various rotationally excited states, applying both Gaussian binning and this refined AC to classical trajectories yields unparalleled agreement with time-dependent quantum wave packet results.

Epitaxial growth of monolayer white phosphorus on Cd(0001)

As a promising two-dimensional (2D) material, phosphorene has attracted tremendous research interest in both fundamental research and potential applications. Up to now, black phosphorene, blue phosphorene, violet phosphorene, and ultrathin nanosheets of red phosphorus have been successfully synthesized by mechanical exfoliation or epitaxial growth, while the synthesis of 2D white phosphorus (WP) has not been achieved. Here, we report the epitaxial growth of monolayer WP on Cd(0001) by means of low temperature (90 K) deposition. Scanning tunneling microscopy observation and first-principles calculations demonstrate that the monolayer WP is comprised of parallel dimer rows of P4 molecules, resembling the a–c plane of γ-phase WP. The monolayer WP is semiconducting with a bandgap of 1.5 eV. Increasing the substrate temperature to 120 K leads to the formation of a quasi-3 × 3 superstructure with building blocks of P4 nonamers. Voltage pulses from STM tip result in the structural transition from the quasi-3 × 3 superstructure to a 3 × 1 superstructure, of which the latter consists of alternating dimer rows and polymerized monomer rows. These observations demonstrate the essential role of dimerization, trimerization, and polymerization of P4 molecules in the formation of 2D white phosphorus.

Ancient DNA reveals the prehistory of the Uralic and Yeniseian peoples

Thermodynamic analysis of heterogeneous nucleation on refractory nanoparticles

The present study investigates the influence of size effects and wettability on the process of heterogeneous nucleation of crystalline phase on refractory nanoparticles of different shapes. This work is based on the classical theory of nucleation. Formulas for the nucleation energy, incorporating linear tension as well as the influence of the nucleation surface curvature on surface tension, were employed for two distinct scenarios: the nucleation being formed on a convex (spherical) nanosubstrate or on a flat nanosubstrate. From the equilibrium condition of a spherical-cap nucleus on a convex surface, an equation defining the wetting contact angle by the standard angle of a large nucleus on a flat surface was obtained, and from the condition of the extremum of the nucleus energy, an equation for its critical radius was obtained. The method of successive approximations by the small parameter was utilized to solve these equations. A similar approach was adopted for the case of spherical-cap nucleation on a flat surface. This approach enabled the derivation of explicit expressions for the wetting function on both convex and flat substrates. The analysis of the obtained dependencies demonstrated that incorporating the linear tension and the Tolman effect resulted in a reduction of the energy required for heterogeneous nucleation. This effect is most significant on well-wetted convex nanosubstrates.

Molecular processes as quantum information resources

In this contribution to Abraham Nitzan’s Festschrift, we present a perspective of theoretical research over the years that has pointed to the potential of molecular processes to act as quantum information resources. Under appropriate control, homonuclear dimer (diatom) dissociation (half-collision) and the inverse process of atom-pair collisions are shown to reveal translational (EPR-like) entanglement that enables molecular wave packet teleportation. When such processes involve electronic-state excitation of the diatom, the fluorescence following dissociation can serve as an entanglement witness that unravels the molecular-state characteristics and evolution. Such entangling processes can also exhibit anomalous quantum thermodynamic features, particularly temperature enhancement of a cavity field that interacts with dissociated entangled diatoms.

Algorithms and software for open quantum system dynamics

Evaluate the clinical performance of Bio-HPP and Vitallium frameworks in free-end removable partial dentures

Epigenetic evolution and clinicopathological implications of distinct DNA methylation profiles in pancreatic ductal adenocarcinoma

Chiral Metallic DM-EDT-TTF Radical Cation Salts: Anion Size-Dependent Structural and Electronic Transitions, Charge Ordering, and Chirality-Induced Spin Selectivity

Microgrid anti islanding protection scheme based on deep neural network algorithm and unscented Kalman filtering

Strain-Distinct α-Synuclein and Tau Cross-Seeding Uncovered by Correlative Approach with Optical Photothermal Infrared Sub-Micron Imaging

Design of a novel shunt active harmonic compensator with AUV-PQ-SRF reference current extraction, OSV-MPC and SMC techniques

An increase in Fusobacterium is associated with the severity of oral mucositis after radiotherapy

Abstract Radiotherapy is a common treatment for head and neck cancer but often causes oral mucositis, which reduces quality of life. Recent studies suggest that radiotherapy affects the oral microbiota, but whether it contributes to the severity of mucositis has been unclear. This study investigated the association between radiotherapy-induced changes in the oral microbiota and the severity of mucositis using 16 S rRNA gene sequencing. Oral samples were collected before, during, and after radiotherapy and were analyzed for changes in bacterial composition and diversity using the Shannon index and Chao1 index. Severity of mucositis was assessed, and its association with changes in bacterial groups was investigated. In total, 43 patients participated in the study. Fusobacterium was significantly increased in the group with severe mucositis (p = 0.020), with an occupancy rate of more than 7% after radiotherapy and a positive correlation with severity of mucositis (p = 0.042). There was a significant increase in the Chao1 index after radiotherapy (p = 0.001) but not in the Shannon index. Changes in oral microbiota may determine the severity of radiotherapy-induced mucositis. An increase in Fusobacterium was found to be closely associated with the severity of mucositis and should be controlled to prevent radiotherapy-induced mucositis in head and neck cancer patients.

Photocurrent Experiments as Probes and Prods in Large-Area Molecular Electronic Junctions

Trait emotion regulation similarity and well-being

Abstract The ways people manage their emotions (emotion regulation; ER) have been found to affect their own well-being and the well-being of others. In the present research, we extended prior work by examining whether similarity between people’s ER habits is also associated with well-being. The study consisted of 254 American romantic couples (N = 508) who completed self-report measures of habitual, or trait-level, use of a wide range of ER strategies (when regulating positive emotions and negative emotions), as well as psychological well-being and relational well-being indices. Contrary to our hypothesis, similarity in trait ER was not associated with any well-being index. This was the case across all ER strategies and the results converged across analyses that used three different metrics of similarity (difference scores, profile correlations, actor x partner interaction). The results suggest that although one’s own ER, and their romantic partner’s ER, may be tied to well-being, similarity between romantic partners’ ER habits may not matter as much.

Chemostructurally Stable Polyionomer Coatings Regulate Proton-Intermediate Landscape in Acidic CO₂ Electrolysis