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Operational bounds and diagnostics for coherence in energy transfer
Excitation energy transfer in light-harvesting aggregates is highly efficient, yet whether quantum coherence plays an operational role in transport remains debated. A central challenge is that coherence is usually inferred from spectroscopic signatures, whereas transport performance is assessed through specific observables and depends on both the open system dynamics and the initial state preparation. Here, we develop a resource theoretic approach that quantifies the maximum change that initial site-basis coherence can induce in a chosen readout under fixed reduced dynamics. The central quantity is the resource impact functional, which yields state independent, readout specific bounds on coherence-induced changes in signals and transport figures of merit. We apply the framework to two models. For a donor–acceptor dimer, we analyze coherence sensitivity across coupling and bath-timescale regimes and bound trapping efficiency and average transfer time in terms of the impact functional. For a multi-site chain with terminal trapping, we derive rigorous criteria that distinguish population placement from sensitivity to initial state site-basis coherence. These include upper bounds on the largest advantage over incoherent preparations, necessary delocalization requirements for achieving a prescribed improvement, and a simple pairwise sufficient condition that can be checked from local information. For quasi-local reduced dynamics, we further obtain a Lieb–Robinson-type bound that constrains when coherence prepared in a distant region can influence a localized readout at finite times. Together, these results provide operational diagnostics and rigorous bounds for benchmarking coherence effects and for identifying regimes in which they are necessarily negligible or potentially relevant in excitonic transport models.
Simulation of homogeneous electrochemical proton-coupled electron transfer using the hybrid-bath hierarchical equations of motion
The dynamics of homogeneous electrochemical proton-coupled electron transfer (PCET) are governed by the complex interactions among the continuous electronic states of the electrode, molecular vibrational modes, and the solvent environment. Here, we study this process within a Newns–Anderson model using the hierarchical equations of motion (HEOM) method combined with matrix product states (MPS) for hybrid fermionic and bosonic baths. The simulations reveal how the reaction dynamics depend on a variety of parameters, including the proton-transfer distance, electrode chemical potential, molecule–electrode coupling strength, and solvent reorganization energy. Comparison with Fermi’s Golden Rule shows that the perturbative rate theory is reliable in the weak-coupling regime, but may become inaccurate at strong molecule–electrode coupling. Rates extracted from population dynamics yield Tafel plots whose shapes depend on both solvent and electrode couplings. The calculations also reproduce a primary kinetic isotope effect, with hydrogen transfer faster than deuterium transfer and with a larger effective transfer coefficient. These results highlight the capability of the hybrid-bath MPS-HEOM method to provide a unified description of electrochemical PCET in a wide range of parameter regimes.
How to improve the accuracy of semiclassical and quasiclassical dynamics with and without generalized quantum master equations
Semi- and quasi-classical (SC) theories can handle anharmonic interactions and are thus well-suited to predict atomistic quantum dynamics in condensed phases that encode energy and charge transport, spectroscopic responses, and chemical reactivity. However, SC theories can be computationally expensive and inaccurate. When combined with generalized quantum master equations (GQMEs), the resulting SC-GQMEs can enhance the efficiency and accuracy of SC dynamics. Yet, while the origin of improved efficiency is clear, the mechanism that improves accuracy remains elusive. Even worse, SC-GQMEs can yield unphysical dynamics in challenging parameter regimes—a shortcoming that might be avoided if the mechanism of accuracy improvement were understood. Here, we uncover this mechanism. We leverage short-time analyses to prove that exact, “left-handed” time-derivatives delay the onset of SC inaccuracy, even without the GQME. However, these derivatives are a double-edged sword: while offering greater short-time accuracy, they become unphysical in challenging parameter regimes. Because short-lived SC-GQME kernels combine short-time accuracy with long-time stability, we develop a protocol to unambiguously determine the memory kernel cutoff, even in challenging cases where previous treatments had failed. Our protocol employs only SC calculations and combines self-consistency with mixed-accuracy auxiliary kernels to triangulate a propitious kernel cutoff, yielding SC-GQMEs with greater accuracy than SC theory alone, while remaining physical and accurate over arbitrary times. Our insights into accuracy improvement, identification of when the SC-GQME is advantageous, and kernel cutoff protocol are general and can be expected to apply to complex systems that go beyond simple models.
Determination of zero-field splitting in magnetically diluted cobalt(II)-based single molecule magnets using circular dichroism Fourier-transform IR spectroscopy
Single-molecule magnets (SMMs) with total electron spin S = 3/2 are promising platforms for optical magnetization control. Their study in such a context is relevant in both magnetically concentrated and diluted samples and assumes the excitation of magnetic dipole transitions by resonant radiation. Such experiments require precise determination of the energy splitting between Kramers doublets (EZFS), since this value determines the resonant radiation frequency. The direct spectroscopic method available for such measurements is frequency-domain Fourier transform terahertz electron paramagnetic resonance (FD-FT THz-EPR) spectroscopy. It usually requires a setup that includes an FTIR-spectrometer and a superconducting magnet to create a magnetic field in the sample area. In this work, we propose a method for the rapid determination of EZFS of SMMs without using a superconducting magnet. The method is based on circular dichroism of an SMM placed in a static external magnetic field. It was implemented using a standard FTIR spectrometer with a sample holder modified by inserting a permanent magnet. Circular polarization was created using a grid polarizer and a quarter-wave plate. Model Co(II)-based SMMs with a varying degree of magnetic dilution were investigated by the proposed method. The results were confirmed by FD-FT THz-EPR. The obtained EZFS values of 43.4–43.6 cm−1 demonstrate a slight downward trend with a decrease in the paramagnetic center content. Such preliminary measurements of EZFS in magnetically diluted SMMs pave the way for the resonant excitation of magnetic dipole transitions using narrowband sources and even for coherent control of magnetic quantum states.
Molecular dynamics insights into water confined in zeolite-templated carbon nanomaterials
Water confined in zeolite-templated carbons (ZTCs) exhibits properties fundamentally different from those of bulk liquid, with profound implications for energy storage, separation technologies, and catalysis. Despite the technological importance of water behavior in ZTC nanopores, molecular-level understanding remains limited. This work presents comprehensive molecular dynamics (MD) simulations investigating the structure, dynamics, and hydrogen bonding characteristics of water confined within faujasite-derived ZTC. Classical MD simulations were developed with validated force fields to characterize radial and spatial distribution functions, hydrogen bond networks and lifetimes, cluster size distributions, domain formation, translational and rotational dynamics, and velocity autocorrelation functions. Systematic comparison with bulk liquid water reveals confinement-induced modifications to tetrahedral hydrogen bonding networks, spatial organization into discrete domains, hydrogen bond dynamics, and transport properties. The three-dimensional hierarchical pore topology of ZTC creates unique confinement environments distinct from one-dimensional nanotubes or two-dimensional slit pores. These findings provide molecular-level insights essential for the rational design of ZTC-based materials for electrochemical energy storage, water desalination membranes, proton exchange systems, and aqueous-phase catalysis, thereby advancing fundamental understanding of water confinement in complex carbon nanostructures.
Computational hole mobilities in (pseudo-)amorphous organic semiconductors
The development of novel organic semiconductors with enhanced conducting properties is often hindered by the challenge of accurately describing and modeling charge transport within the (pseudo-)amorphous films typically found in optoelectronic devices. In this study, we present a multiscale computational protocol to predict hole mobilities of non-crystalline hole-transporting materials with order-of-magnitude accuracy. Our approach, which integrates density functional theory, molecular dynamics, docking, and kinetic Monte Carlo simulations, reveals the impact of modeling different film morphologies—amorphous and pseudo-amorphous films as well as docking aggregates—on the charge transport properties of these materials. In particular, we demonstrate that experimentally observed mobility trends across a family of ten hole-transporting molecules, including the enhancement associated with increased aromatic core planarity and extended π-conjugation, can only be reproduced when both amorphous disorder and locally ordered molecular aggregates are explicitly considered. This work establishes a robust, morphology-aware framework for the rational, in silico design and optimization of next-generation organic semiconductors.
Brownian dynamics with soft constraints in soft matter systems
Stiff forces, which bind objects together or otherwise confine motion, are found widely in soft-matter systems—e.g., colloids with short-range attractions, ligand–receptor contacts, particles in optical traps, and fibers that resist stretching. To assess the long-term effect of these stiff forces on dynamics and structure, it is useful to consider the limit where they are treated as constraints, so the system evolves strictly within allowed configurations. Efforts to derive equations involving both constraints, and the stochastic motion appropriate at the scales of soft matter, began around 50 years ago, yet we are still lacking a straightforward way to extract the projected equations and apply them in modern formulations of mesoscale dynamics. Here, we address this gap with two key contributions: (1) a practical summary of the constrained Brownian dynamics equations with “soft” constraints, i.e., constraints imposed by stiff forces, which is illustrated through several representative examples, taking care to highlight the nontrivial effects of the constraints, and (2) a derivation using singular perturbation theory, establishing the validity of these equations over timescales exceeding the relaxation of stiffly constrained degrees of freedom. We further extend our approach to “soft–soft” constraints, where mobility varies on lengthscales comparable with the restraining forces—a scenario typical for particles in fluids experiencing hydrodynamic interactions. We hope our results will be useful for soft matter research, as a robust toolkit for studying tethered or confined systems.
One nitrogen atom as electron source is enough for efficient intermolecular charge transfer in organic cocrystals toward NIR-photothermal conversion
In organic donor–acceptor (D-A) materials, a nitrogen atom can serve as a skeleton electron source to tune the inter-/intra-molecular charge transfer (CT) nature and photophysical/photochemical properties. Here, we employ the model molecule stilbene modified with non-/one-/two-nitrogen atoms in the benzene ring skeleton (TSB/TSP/DPE) as a donor and F4TCNQ as an acceptor to synthesize three cocrystals by a one-step mechanochemical method toward NIR photothermal conversion (NIR-PTC). The results show that “One Nitrogen Atom Is Good, Two Are Too Many.” That is, one nitrogen atom in the donor (TSP) is enough to induce optimal performance of the CT effect with the degree of charge transfer of ∼1.16, redshift absorption of ∼2500 nm, and NIR-PTC efficiency of ∼89.4% @ 808 nm. Femtosecond transient absorption spectra exhibit that superior NIR-PTC of TSP-F4TCNQ cocrystal can be attributed to the first ultrafast internal conversion (IC) with a lifetime of 1.7 ± 0.4 ps and subsequent nonradiative decay (NR) via rotation/twisting of cyano-groups out of the plane of central ring of F4TCNQ with a lifetime of 17.1 ± 3.4 ps, followed by the third vibrational relaxation (VR) with a lifetime of 754 ± 220 ps. The individual partition contribution factor of IC/NR/VR channels is resolved to be about 0.33:1.51:1.12 based on a simple linear approximation treatment for the first time. This work provides a simple and potential approach for regulating photophysical properties of D-A cocrystals by introducing a skeleton electron source.
Two-dimensional fluorescence spectroscopy with quantum entangled photons: Idler-referenced timing without pump detection
Entangled photons have attracted increasing interest as resources for developing time-resolved spectroscopic techniques. Theoretical studies suggest that their non-classical correlations enable time-resolved spectroscopy with monochromatic pumping and can selectively isolate specific Liouville pathways in nonlinear optical signals. In an earlier study, we proposed a fluorescence detection scheme that could, in principle, be implemented using existing single-photon detectors [Y. Fujihashi et al., Sci. Adv. 12, eaed7026 (2026)]. In that design, the time origin was defined by detecting the arrival of the pulsed laser used to pump the nonlinear crystal for spontaneous parametric down-conversion, a requirement that made the overall experiment cumbersome. This study theoretically examines an alternative protocol that defines the reference time based on the arrival of idler photons. We demonstrate that this idler-referenced scheme functions effectively when the entangled photons exhibit either negative or negligible frequency correlations. Eliminating the pump-timing channel simplifies the optical layout and lowers the experimental barrier to realizing time-resolved two-dimensional fluorescence spectroscopy with entangled photons. Although the photons may exhibit frequency correlations in isolation, their frequency-time degrees of freedom can behave as effectively uncorrelated when considered over the full measurement timescale. Therefore, fully exploiting non-classical correlations requires an entangled photon source whose temporal characteristics are carefully matched to the overall timescale of the experiment.
Velocity gauge for oscillator strength in ΔSCF theory
Delta self-consistent-field (ΔSCF) theory is widely used for electronic excitation energy calculations. However, calculating the corresponding oscillator strengths is challenging. The corresponding many-electron wavefunctions are not directly accessible. Both the ground-state and the excited-state wave functions from ΔSCF are described by reference Kohn–Sham (KS) single-determinant wavefunctions for the fictitious non-interacting systems. The non-orthogonality between the ground and excited Kohn–Sham determinants from two different SCF calculations leads to unphysically origin-dependent transition properties, such as transition dipole moment and length-gauge oscillator strength. Including nuclei contribution to the perturbation is theoretically rigorous, but its effectiveness is limited only to neutral systems, as we show theoretically and numerically. While several other practical approaches have been proposed to tackle the non-orthogonality problem and yield reasonable results, inevitably, the determinant of the ground state or the excited state is changed, as well as the density matrix. In this work, we explore the use of the velocity gauge to compute oscillator strength within ΔSCF theory. We demonstrate that the velocity gauge is capable of naturally accounting for the non-orthogonality of ΔSCF KS wavefunctions and offering origin-independent predictions without any additional correction schemes to the KS wavefunctions. Compared to the length-gauge results obtained via symmetric orthogonalization, the velocity gauge can offer comparable results. Furthermore, the adoption of spin-purified singlet excitation energy in the velocity-gauge transition dipole moment significantly enhances the overall performance of the velocity gauge for ΔSCF oscillator strength predictions of conjugated chromophores.
R-matrix benchmark study of SO2 photoionization dynamics
Sulfur dioxide is a molecule of broad atmospheric and astronomical relevance, playing a central role in greenhouse warming and ozone chemistry. It is widely detected in planetary and interstellar environments and further participates in sulfur plasma and shock-driven processes. For this purpose, the ab initio R-matrix method within the close-coupling approximation is employed to investigate the photoionization dynamics of sulfur dioxide. Total and state-resolved cross sections for the three lowest ionic states, arising from ionization of the valence orbitals, are calculated, revealing rich autoionizing resonances in the near-threshold region. The high-resolution computed cross sections are benchmarked against available experimental datasets, including both direct measurements and reconstructed data, with the reported partial-channel cross sections representing the first direct state-resolved theoretical results for the dominant photoionization channels. In the absence of fully state-resolved experimental measurements for the cationic states of SO2, the results are interpreted through comparison with fragment-resolved data, enabling a direct correspondence between the computed ionic states and dominant molecular ion production channels, where the lowest three ionic states, X2A1(8a1−1), A2B2(5b2−1), and B2A2(1a2−1), contribute solely to the formation of the parent molecular ion SO2+. To assess the reliability of the results, a series of systematic benchmarks with respect to active space size, basis set, target-state expansion, and R-matrix radius confirms the convergence and robustness of the computed cross sections. The present results provide reliable reference data for modeling photochemical and radiative processes in planetary atmospheres and the interstellar medium and establish SO2 as a benchmark system for molecular photoionization studies.
Development of a recombinant single-cycle influenza viral vector as an intranasal vaccine against SARS-CoV-2
Abstract The COVID-19 pandemic has demonstrated the detrimental potential of zoonotic coronavirus transmission to human populations. Effective vaccines capable of eliciting immunity to SARS-CoV-2 have been pivotal in mitigating the spread of the virus. In this study, we describe the generation of a non-replicating pseudotyped influenza A virus (S-FLU), where the native haemagglutinin (HA) sequence is replaced with the coding sequence of either a membrane-anchored form (TM) or secretory form (Sec) of the receptor-binding domain (RBD) of the ancestral SARS-CoV-2 Wuhan (S-RBD Wuhan). We showed that both S-RBD-TM and S-RBD-Sec viruses can be generated via reverse genetics and grown to high titre. Intranasal immunisation in mice with S-RBD-TM elicits robust serum binding and neutralisation activity against SARS-CoV-2, superior to S-RBD-Sec. Furthermore, we demonstrate that a heterologous prime-boost immunisation regimen in mice with S-RBD-TM Wuhan and S-RBD-TM BM48-31 (a distant Clade 3 SARS-like betacoronavirus (sarbecovirus)) increases antibody binding breadth against mismatched sarbecoviruses compared to homologous prime-boost with S-RBD-TM Wuhan, although this did not translate into significantly enhanced cross-neutralisation across the tested virus panel. These results demonstrate that S-RBD delivery via the intranasal route induces both systemic and mucosal antibody responses and provide a foundation for further optimisation of S-RBD sarbecovirus vaccine strategies.
Impact of Gaussian feathering on diagnostic metrics in tile-based micro-CT sinogram infilling
Abstract Tile-based sinogram infilling methods for micro-CT require merging overlapping output tiles to reconstruct full images. Gaussian feathering, the standard blending approach, produces visually seamless results but its effect on diagnostic image quality metrics has not been characterized. This study quantifies how Gaussian feathering affects noise power spectrum (NPS), modulation transfer function (MTF), noise equivalent quanta (NEQ), structural similarity index (SSIM), and peak signal-to-noise ratio (PSNR) compared to nearest priority blending, also known as Voronoi partition blending. We mathematically derived the variance reduction mechanism in Gaussian blending and experimentally compared both methods using sinograms infilled by DeepFill v2 as a representative generative inpainting model, applied to a micro-CT quality assurance phantom reconstructed from 50% undersampled data. Gaussian feathering reduced variance by up to 19.6% at overlap centers, causing NPS reduction of up to 13.8% at low spatial frequencies and NEQ inflation of up to 38.5%. MTF showed mixed effects with improvements at low frequencies but reductions at high frequencies. SSIM and PSNR showed statistically significant differences: sinogram PSNR differed by 0.05 dB ( $$p = 0.003$$ ) and reconstruction SSIM by 0.009 ( $$p = 0.036$$ ), both with small effect sizes. In this experimental configuration, Gaussian feathering distorted diagnostic metrics through a variance reduction mechanism, while standard fidelity metrics detected only subtle changes. Nearest priority blending may be preferred when diagnostic metrics are used to validate infilling methods, pending broader empirical validation.
Health promotion and options for digital health interventions on board merchant vessels
Superior synergistic corrosion inhibition of brass in NaCl solution by 2-mercaptobenzothiazole and TiO2 nanoparticles compared with SiO2
Abstract 2-Mercaptobenzothiazole (MBT) combined with nanoparticles exhibits a synergistic corrosion inhibition effect for brass in 3.5% NaCl solution. The corrosion behavior was evaluated using open circuit potential (OCP), electrochemical impedance spectroscopy (EIS), and potentiodynamic polarization techniques. The inhibition efficiency increased with MBT concentration (0–20 ppm), reaching 97.4% at 20 ppm. The addition of 10 ppm nanoparticles further enhanced the inhibition performance. In particular, TiO 2 nanoparticles improved the efficiency to 98.2%, showing superior performance compared with SiO 2 nanoparticles (94%). The adsorption studies showed that the Langmuir isotherm model (R² = 0.9941) was adopted by MBT, with ΔG° ads = (− 12.66 kJ mol −1 ) and K ads = 2.98 L mol −1 , indicating spontaneous adsorption dominated by physical with weak chemical interaction. Density Functional Theory (DFT) calculations at the B3LYP/LANL2DZ level were performed to study the electronic properties and adsorption behavior of MBT and its nanoparticle-modified systems. The results show that nanoparticle incorporation enhances the reactivity and adsorption characteristics of MBT. The MBT–TiO 2 system exhibits the most negative adsorption energy, smaller energy gap, and higher charge transfer ability (ΔN max ), indicating strong interaction with partial chemisorption character, while the MBT–SiO 2 system shows weaker adsorption despite higher electrophilicity. This improvement is attributed to the synergistic interaction between MBT and the incorporated nanoparticles, which enhanced the adsorption strength of inhibitor molecules onto the brass surface and promoted the formation of a highly compact protective layer through effective filling of surface pores and structural imperfections. The originality of this work is demonstrated by the fact that the electronic nature of the nanoparticles, rather than the physical barrier effect, dominates the compactness, interfacial stability and electrochemical performance of the MBT-based protective films.