Browse Articles

Finite element analysis for pullout resistance and progressive failure of strip anchors in strain softening marine soils

Decoherence dynamics in molecular qubits: Exponential, Gaussian and beyond

In this work, we examine how the structure of system–bath interactions can determine commonly encountered temporal decoherence patterns, such as Gaussian and exponential decay, in molecular and other qubits coupled to a thermal bosonic bath. The analysis, based on a pure dephasing picture that admits analytical treatment, shows that decoherence, in general, is neither purely Gaussian nor exponential but rather the exponential of oscillatory functions, with periods determined by the bath’s frequencies. For initially unentangled qubit-bath states, Gaussian decay is always present at early times. It becomes increasingly dominant with increasing temperature, qubit–bath interaction strength, and bath correlation time. Initial system–bath entanglement that arises due to displacement in the position of the bath states preserves the Gaussian decay. By contrast, strict exponential decay arises only in very specific models that we isolate. However, it becomes dominant for times longer than the bath correlation time or for early times when there is initial entanglement due to momentum displacement of the bath states. For molecular electronic decoherence, the long-time exponential regime plays a limited role as it emerges after most coherence is lost. Thus, the Gaussian decay provides a more suitable (albeit imperfect) model of such decoherence. Furthermore, we discuss the connection between electronic decoherence dynamics and electronic spectroscopic line shape theory, where Gaussian spectral peaks correspond to Gaussian coherence decay and Lorentzian peaks correspond to exponential coherence decay. We find that Gaussian spectral peaks, usually associated with inhomogeneous broadening, can emerge from the entangling unitary system–bath dynamics even when there is no inhomogeneity in the initial conditions.

Changes in long-term life expectancy and years of life lost following the Great East Japan Earthquake in Fukushima Prefecture

Abstract Prolonged evacuation after disasters increases the risks of diseases and challenges in healthcare access. This study aimed to analyze changes in life expectancy (LE) and years of life lost (YLL) in Fukushima Prefecture after the Great East Japan Earthquake. LE and YLL were calculated based on a dataset of 276,314 deaths in Fukushima Prefecture from January 2006 to December 2018 and were aggregated and compared in three time periods: 2006–2010, 2012–2015, and 2016–2018. LE and YLL were obtained using a life table method, focusing on four major causes of death: heart diseases, cerebrovascular diseases, pneumonia, and cancers. The overall LE for both males and females in Fukushima prefecture showed an increasing trend in all three periods. Notably, in 2012–2015, the increase in LE and YLL due to cancer was greater in areas with evacuation zones compared to those without evacuation zones. In contrast, in 2016–2018, a notable decrease in YLL due to cerebrovascular diseases for both males and females and due to heart diseases for males was observed in areas with evacuation zones compared to areas without. LE continued to rise in Fukushima Prefecture despite the significant long-term impact of the disaster on the population. Post-disaster changes in LE and YLL differed between areas with and without evacuation zones, suggesting that implementation of effective measures and policies in the region contributed to a successful recovery. This study may be crucial for evaluating future health measures and conditions in Fukushima Prefecture.

Photoelectron–remnant interaction effect on remnant wavefunction in low-kinetic energy electron detachment events

Low-kinetic energy photoelectron detachment experiments have revealed the unexpected dependence of transition intensities on photon energy, which is hypothesized to result from time-dependent coupling between low-kinetic energy photoelectrons and the remnant molecule. This study explores how the kinetic energy and detachment axis of the photoelectron influence the interaction and modify the final remnant electronic structure. Using real-time simulations on several model systems (H2, NO, N2, and C2 hydrocarbons), this study demonstrates that electron–remnant interactions are strongly dependent on the detachment orientation, electron kinetic energy, and remnant electronic structure. The results reveal that higher kinetic energies lead to significant nonadiabatic transitions, while lower kinetic energies yield more adiabatic behavior. While generally lower kinetic energies show prolonged electron–remnant interactions, the extent of temporal and spatial interactions does not necessarily vary linearly with the kinetic energy, and the final remnant electronic structure is found to be very sensitive to the exact nature of the photoelectron–remnant interactions. In addition, the point charge model employed for the photoelectron provides a useful approach for the deconvolution of more complete simulations to provide deeper insights into the specific photoelectron–remnant interactions that determine the eventual remnant wavefunction. The findings underscore the importance of considering both temporal and spatial electron dynamics in understanding low-kinetic energy photodetachment processes and provide a foundation for a further exploration of electron–molecule interactions in the low-energy regime.

Fairness identification of large language models in recommendation

Erratum: “Modeling of collision-induced excitation and quenching of atomic nitrogen” [J. Chem. Phys. 161, 014104 (2024)]

The superoxide dismutase mimetic TEMPOL modulates nicotine-induced hyperlocomotor activity and nicotine-taking behavior in male rats

On the entanglement of chromophore and solvent orbitals

Among various types of chromophore–solvent interactions, the entanglement of chromophore and solvent orbitals, when significant, can cause the chromophore frontier orbitals to spread over to nearby solvent molecules, introducing partial charge-transfer character to the lowest excitations of the chromophore and lowering the excitation energies. While highly intuitive, the physical details of such orbital entanglement effects on the excitation energies of chromophores have yet to be fully explored. Here, using two well-known biochromophores (oxyluciferin and p-hydroxybenzyledene imidazolinone) as examples, we show that the chromophore–solvent orbital entanglements can be elucidated using two quantum mechanical embedding schemes: density matrix embedding theory and absolutely localized molecular orbitals. However, there remains a great challenge to incorporate the orbital entanglement effect in combined quantum mechanical molecular mechanical (QM/MM) calculations, and we hope that our findings will stimulate the development of new methods in that direction.

Goos–Hänchen shift of inelastically scattered spin-wave beams and cascade nonlinear magnon processes

Abstract We study, using micromagnetic simulations, the inelastic scattering of spin-wave beams on edge-localized spin-wave modes in a thin ferromagnetic film. In the splitting and confluence processes, the new spin-wave beams are generated with frequencies shifted by the edge-mode frequency. We report that inelastically scattered spin-wave beams in both processes not only change their direction of propagation but also undergo lateral shifts along the interface, analogous to the Goos–Hänchen effect known in optics. These shifts of inelastically scattered beams, for a few special cases described in the paper, can be in the range of several wavelengths, which is larger than the Goos–Hänchen shift of elastically reflected beam. Unexpectedly, at selected frequencies, we found a significant increase in the value of the lateral shifts of the scattered spin-wave beams formed in the confluence process. We show that this effect is associated with the cascading nonlinear processes taking place at the edge of the film and involving the primary edge spin wave. Our results make an important contribution to the understanding of the nonlinear nature of spin waves and provide a way to exploit it in signal processing with magnons.

The vibrational wavepackage dynamics and phase modulation via the resonant Rydberg states in molecules

The observation of vibrational coherence has become significant because it reflects the spatial and temporal localization of a nucleus in a specific mode and characterizes energy flow and multiple kinetic relaxations in chemical dynamics. Vibrational coherence in the S1 state of 2,4-difluoroanisole has been investigated in real time by femtosecond time-resolved photoelectron spectroscopy and time-of-flight mass spectroscopy. Quantum beats of superpositions exhibit temporal oscillations with a frequency of 78 cm−1. Combining the structure computations, oscillations derive from the structure change from planar to nonplanar geometry, which correspond the coherence wavepackets moving from the Franck–Condon region toward the minimum point of the potential energy surface, elucidating the energy flows following the excitation of 2,4-difluoroanisole in the S1 state. The phases of the quantum beat via the resonant Rydberg states exhibit a shift of π rad. The vibrational coherent phase modulation via the resonant Rydberg states will facilitate the chemical coherence control in complex molecular systems.

RENEB interlaboratory comparison for biological dosimetry based on dicentric chromosome analysis and cobalt-60 exposures higher than 2.5 Gy

Abstract In previous RENEB interlaboratory comparisons based on the manual scoring of dicentric chromosomes, a tendency for systematic overestimation for doses > 2.5 Gy was found. However, these exercises included only very few doses in the high dose range, and they were heterogeneous in terms of radiation quality and evaluation mode, and comparable only to a limited extent. Here, this presumed deviation was explored by investigating three doses > 2.5 Gy. Blood samples were irradiated (2.56, 3.41 and 4.54 Gy) using a 60Co source and sent to 14 member laboratories of the RENEB network, which performed the dicentric chromosome assay (manual and/or semi-automatic scoring) and reported dose estimates. Most participants provided estimates that agreed very well with the physical reference doses and all provided dose estimates were in the correct clinical category (> 2 Gy). The previously observed tendency for a systematic bias across all laboratories was not confirmed. However, tendencies for systematic underestimation were detected for dose estimations for reference doses given in terms of absorbed dose to blood and for some participants, a laboratory-specific trend of systematic under- or overestimation was observed. The importance of regularly performed quality checks for a broad dose range became obvious to avoid misinterpretation of results.

The role of functionalization in the translocation of peptides through multilayer graphene nanopores

The rapid translocation speed of peptides through graphene nanopores poses a challenge, hindering the accurate sensing of the biomarkers. Employing the functionalized graphene nanopores is at the forefront of reducing the translocation speed. The current work details the translocation of a negatively charged peptide endothelin-1 through a bare multilayer graphene nanopore, a hydrogen-functionalized graphene nanopore, and a hydroxyl-functionalized graphene nanopore by applying electric fields. The hydroxyl-functionalized graphene nanopore significantly reduces the peptide’s translocation speed. The time required for the peptide to translocate through the hydroxyl-functionalized graphene nanopore is 2.25 times longer than in the non-functionalized graphene nanopore and 1.25 times longer than in the hydrogen-functionalized graphene nanopore. We critically analyze the factors influencing the reduced translocation speed, including the interactions between the pore and the peptide, the conformational changes of the peptide within the pore, the solvent velocity inside the pore, and the solvent’s viscosity near the peptide. The altered solvent velocities within functionalized pores have a minimal role in the speed reduction of peptides. When a constant force is applied to the peptide without any electric field, the hydroxyl-functionalized graphene nanopore delivers the lowest diffusion rate. The persistence time, which serves as a measure of the solvent viscosity near the peptide, is the highest within the hydroxyl-functionalized pore. Finally, we conclude that the Coulombic interactions between the peptide and the pore play a major role in its speed reduction inside the hydroxyl-functionalized graphene nanopore.

Pan-serological antibodies and liver cancer risk: a nested case-control analysis

Abstract Recently, studies have reported that pan-viral serology signatures may be predictive for liver cancer development. However, whether these same findings are observed for prospective studies has not been previously investigated. The nested case-control analysis included 191 persons who developed liver cancer and 382 controls from the PLCO prospective cohort. The presence of circulating antibodies, measured by VirScan, was determined in serum samples obtained at study recruitment. The presence of antibodies was compared between cases and controls using multivariable conditional logistic regressions, and prediction models were used to estimate whether exposures predicted liver cancer development. No significant associations were found between antibodies to viruses, bacteria or allergens and liver cancer risk after adjustment for multiple testing. The agent most significantly associated with risk was hepatitis C virus (HCV), but it was only detected among 23 participants (odds ratio (OR): 3.98; 95% confidence intervals (CI):1.59–9.99; p = 0.0032, False Discovery Rate (FDR) = 0.35). In prediction models based on 109 antibody features, no associations with liver cancer risk were observed (area under the curve [AUC]: 0.52–0.54). In analyses restricted to the most common type of liver cancer, hepatocellular carcinoma, the association with HCV was stronger (OR: 23.16, 95% CI: 4.55-117.68; FDR p-value = 0.0016), although prediction models based on all detected antibodies were similar (AUC = 0.55; 95% CI:0.43–0.68). Antibodies to no infectious agents, other than HCV, were found to be prospectively associated with liver cancer risk. The utility of using an antibody exposure signature prospectively for liver cancer development needs to be further explored.

Unveiling nucleosome dynamics: A comparative study using all-atom and coarse-grained simulations enhanced by principal component analysis

The conformational dynamics of the DNA in the nucleosome may play a role in governing gene regulation and accessibility and impact higher-order chromatin structure. This study investigates nucleosome dynamics using both all-atom and coarse-grained (CG) molecular dynamics simulations, focusing on the SIRAH force field. Simulations are performed for two nucleosomal DNA sequences—alpha satellite palindromic and Widom-601—over 6 μs at physiological salt concentrations. A comparative analysis of structural parameters, such as groove widths and base pair geometries, reveals good agreement between atomistic and CG models, although CG simulations exhibit broader conformational sampling and greater breathing motion of DNA ends. Principal component analysis is applied to DNA structural parameters, revealing multiple free energy minima, especially in CG simulations. These findings highlight the potential of the SIRAH CG force field for studying large-scale nucleosome dynamics, offering insights into DNA repositioning and sequence-dependent behavior.

Nitrogen addition restricts key soil ecological enzymes and nutrients by reducing microbial abundance and diversity

Electron-propagator methods versus experimental ionization energies

Select electron-propagator (EP) methods agree as closely with experimental standards for molecular vertical ionization energies as they do with computational data of nearly full-configuration-interaction quality. Several EP methods consistently attain higher accuracy than alternatives with equal arithmetic bottlenecks expressed in terms of occupied (O) and virtual (V) orbital dimensions. The cubically scaling methods realize a mean absolute error (MAE) below 0.2 eV and are feasible whenever conventional self-consistent-field calculations are performed. O2V3-scaling EP self-energies achieve an MAE slightly above 0.1 eV and are as feasible as conventional second-order perturbative calculations of total energies. OV4 methods are more accurate (MAEs ∼0.075 eV) than ΔCCSD(T) and are more efficient than third-order total-energy calculations. An equally accurate generalization with full self-energy matrices and non-iterative O2V4 contractions produces Dyson orbitals in their most general form. Composite EP models that accurately estimate the effects of basis-set saturation drastically improve efficiency without sacrificing accuracy. No adjustable parameters are employed in the self-energy formulas or in the generation of reference-state orbitals. When Dyson-orbital probability factors indicate that Koopmans’s theorem is qualitatively valid, simple perturbative corrections suffice to approach chemical accuracy.

Characterizing variability in passive myocardial stiffness in healthy human left ventricles using personalized MRI and finite element modeling

An efficient approach to estimate electronic couplings in molecular pairs using molecular orbital grids

The estimation of electronic couplings between diabatic states is crucial for the comprehension of electron transfer phenomena between molecular systems. Therefore, the development of efficient approximations that enable a very fast, yet accurate, estimation of electronic couplings is an important research goal in the context of organic semiconductors. The most popular methods (diabatization schemes, projection approximations, or methods using fragment molecular orbitals) usually involve the use of electronic structure calculations and can be computationally prohibitive if a large number of electronic coupling estimations is required. In this paper, we propose a novel strategy (CubeMap) to evaluate electronic couplings between molecular pairs in an extremely efficient manner. CubeMap employs the well-established linear relationship between the electronic coupling and the overlap integral between the corresponding molecular orbitals localized on the interacting molecules. In particular, CubeMap is based on the efficient calculation of the overlap integral in real space using molecular orbital grids of moderate size. The CubeMap efficiency partly comes from the fact that only a single electronic structure calculation of an individual molecule (reference geometry) is enough for the subsequent evaluation of overlap integrals and electronic couplings in multiple dimer dispositions. We show that CubeMap is particularly appealing to rapidly estimate the electronic coupling distributions in molecular crystals due to thermal fluctuations (dynamic disorder), which is an important effect for the accurate description of charge transport in organic semiconductors. Compared with the methods usually employed to evaluate electronic couplings, the CubeMap approach drastically reduces the computational cost by several orders of magnitude.

Dual observers based sliding mode control for QUAVs with unknown disturbances and time varying delays

Abstract This paper presents a dual-observers-based nonsingular fast terminal sliding mode control scheme for quadrotor unmanned aerial vehicles (QUAVs) with unknown disturbances and time-varying delays. Firstly, to facilitate the controller design, the QUAVs model is decoupled into two subsystems: position subsystem and attitude subsystem. Secondly, for the position subsystem, a sliding mode controller is presented to control the position of the QUAVs. For the attitude subsystem, by introducing an exponential term, a nonsingular fast terminal sliding mode controller is obtained to ensure the fast convergence of the attitude angles. Moreover, based on the exponential term, the singularity problem of the conventional terminal sliding mode is solved. Thirdly, the disturbance and time-varying delay observers are presented by considering the time-varying delayed signals and unknown disturbances. Finally, the effectiveness and feasibility of the proposed control scheme are demonstrated by some computer simulations.

CUT-E as a 1/<i>N</i> expansion for multiscale molecular polariton dynamics

Molecular polaritons arise when the collective coupling between an ensemble of N molecules and an optical mode exceeds individual photon and molecular linewidths. The complexity of their description stems from their multiscale nature, where the local dynamics of each molecule can, in principle, be influenced by the collective behavior of the entire ensemble. To address this, we previously introduced a formalism called collective dynamics using truncated equations (CUT-E). CUT-E approaches the problem in two stages. First, it exploits permutational symmetries to obtain a substantial simplification of the problem. However, this is often insufficient for parameter regimes relevant to most experiments. Second, it takes the exact solution of the problem in the N → ∞ limit as a reference and derives systematic finite-N corrections. Here, we provide a novel derivation of CUT-E based on recently developed bosonization techniques. We lay down its connections with 1/N expansions that are ubiquitous in other fields of physics and present previously unexplored key aspects of this formalism, including various types of approximations and extensions to high-excitation manifolds.