Browse Articles

Impact of land use change on the long-term economic value of carbon sequestration in Central Alborz, Iran

Identifying hot-spot pathways in fishery science and technology innovation through temporal heterogeneous graph neural networks

Early prediction of severe Omicron pneumonia using a multimodal a.i. model integrating delta CT radiomics and laboratory indicators

Clinical pathways matter for multimodal deep learning in early Alzheimer’s disease detection

Abstract Identifying individuals at risk of Alzheimer’s disease (AD), particularly in the preclinical and early stages, remains challenging. Although deep learning approaches based on structural MRI show promise as a non-invasive biomarker, existing multimodal models require task-specific training and depend on biomarkers that are not routinely available in clinical practice. Here, we propose a zero-shot multimodal feature extraction framework based on SigLIP that combines structural MRI embeddings with text embeddings of routinely collected clinical variables for early AD risk stratification in individuals at preclinical or mild cognitive impairment (MCI) stages. We evaluated the approach in 416 individuals from the ADNI cohort (age: 72.73 ± 6.7). SigLIP was used without fine-tuning to extract MRI and clinical text embeddings, which were combined into multimodal representations for individual-level AD risk prediction within 4 years. We further compared the model performance in a single-visit and two-visit settings to assess the value of longitudinal information and framework scalability. In the 1-visit setting, combining MRI embeddings with MMSE, age, and sex achieved an AUC of 0.91 ± 0.02, showing higher performance than the CSF Aβ42-based model (AUC 0.73 ± 0.08) and MMSE-based model (AUC 0.85 ± 0.22). In the 2-visit setting, performance was maintained or improved, supporting the scalability of the approach to longitudinal data. These findings suggest that multimodal fusion of SigLIP-derived MRI features and routinely collected clinical variables may provide a practical and scalable strategy for early AD risk progression prediction without task-specific training.

Study on the multi-dimensional paths of ecological ethics influencing the realisation of the value of herders’ grassland ecological products

Multi-objective optimization of EDM machining of Waspaloy employing composite electrode

Deletion of activating transcription factor 3 (Atf3) promotes cardiomyocyte differentiation from embryonic stem cells

Application of the aperiodic defect model to a negatively charged monovacancy in phosphorene

We apply the recently introduced aperiodic defect model (ADM) to a negatively charged monovacancy in a phosphorene monolayer. In contrast to conventional supercell approaches, the ADM treats a single defect embedded in the true non-defective crystalline mean field, thereby avoiding spurious defect–defect interactions and the need for charge corrections. At the same time, it effectively reduces the calculation to a fragment, enabling the use of high-level molecular electronic-structure methods. Converging the Hartree–Fock and correlation contributions to the thermodynamic limit yields a benchmark CCSD(T)/POB-TZVP-rev2 formation energy of 0.81 eV for the negatively charged monovacancy in the (5|9) configuration. The excitation energy to the lowest singlet excited state of this defect at the EOM-CCSD/POB-TZVP-rev2 level is found to be 1.95 eV. Overall, the ADM provides a highly promising route toward quantitatively accurate and systematically improvable descriptions of defects in solids and on surfaces, bridging the gap between solid-state physics and molecular quantum chemistry.

Stochastic process description of lipid flip-flop

Since lipid bilayers are self-assembled macroscopic aggregates, their constituent lipid molecules can spontaneously transition between the two leaflets. This so-called “flip-flop” is almost universally described via first-order chemical kinetics: the net “flux” leaving a given leaflet is proportional to the number of lipids it contains. However, this model ignores interactions, such as those arising from packing or non-ideal mixing, and restricting the analysis to macroscopic rate equations misses fluctuations. Here, we employ tools from the field of stochastic processes to examine the impact of stress and non-ideal mixing on lipid flip-flop, and we discuss several methods for quantifying the associated fluctuations—ranging from stochastic trajectories to evolution equations for probability densities. We show that differential stress strongly enhances the rate at which lipid abundance asymmetry decays, while compositional relaxation in mixed systems can be closer to ideal under suitable conditions. For the case of binary systems in the presence of packing constraints, we employ a linear noise approximation to the system’s master equation and show that it leads to an easily manageable Ornstein–Uhlenbeck process for the fluctuations of (and correlations between) compositions. We also show how to include non-ideal mixing, which leads to large and very slow compositional fluctuations as we approach the critical point.

TiDES: A time-dependent electronic structure code for real-time electron and spin dynamics

In this work, we present the TiDES (Time-Dependent Electronic Structure) code, an open-source real-time electronic structure theory package. The software is written in Python and interfaces with the Python-based Simulations of Chemistry Framework (PySCF), an open-source quantum chemistry library. The philosophy of the TiDES software package is to provide an incredibly modular real-time software package to allow for easy development and implementation of new methodology. The package allows for explicit time propagation of chemical systems within the spin-restricted, unrestricted, and generalized frameworks of both real-time time-dependent Hartree–Fock and real-time time-dependent density functional theory. Additional features include the ab initio Ehrenfest dynamics method for the simulation of coupled electronic and nuclear motion and the incorporation of a complex absorbing potential that enables the simulation of ionization events. To illustrate both the value of real-time dynamics and the intuitive nature of TiDES, we simulate spectroscopic properties and non-equilibrium electron and spin dynamics in several example systems. We also show how general external potentials can be defined and easily applied during time propagation. Lastly, the features within PySCF, such as spin–orbit coupling, interface readily with the real-time calculations, providing a powerful tool for simulating electron and spin dynamics with the capacity for extensive customization.

Double helix crookedness regulates the twist–stretch coupling: A quantitative molecular dynamics analysis

DNA conformation and twist–stretch coupling play a fundamental role in multiple biological processes. The contrasting elongation of DNA and shortening of RNA upon overwinding hint at a helix-related twist–stretch coupling, yet elucidating the underlying relationship between conformation and twist–stretch coupling is still a challenge. Here, our molecular dynamics simulations reveal that DNA sequence-dependent variation in helical structure can significantly regulate its twist–stretch coupling, even inducing shortening upon overwinding. In particular, our simulations reveal a non-monotonic relationship between the twist–stretch coupling parameter dL/dN and DNA conformation quantified by DNA crookedness β: dL/dN first increases and then decreases as β increases. Empirically, the variation in dL/dN arises from the evolution of helical radius with the stretching force. Further analysis, at the base-pair level, quantitatively reveals that this relationship is primarily driven by the variation of base-pair center distance Lbp upon overwinding, which arises mainly from slide and rise base-pair parameters. These results establish a structure–elasticity framework for the twist–stretch coupling of dsDNA.

On the single-Hessian Gaussian wavepacket dynamics

Single-Hessian Gaussian wavepacket dynamics (GWD) significantly reduces the computational burden of Heller’s local harmonic GWD while maintaining comparable accuracy in approximating vibronic spectra. Here, we provide a new, symplectic derivation of the equations of motion of single-Hessian GWD and show that, unlike the local harmonic version, this method conserves the non-canonical symplectic structure on the manifold of Gaussian wavepackets and—for bounded dynamics in smooth potentials—avoids the drift of energy. Our numerical results suggest that, despite being much more efficient than the local harmonic variant, the single-Hessian GWD exhibits the same O(ℏ) asymptotic error in averages of observables. To further accelerate numerical simulations, we implement high-order time-stepping geometric integrators that are time-reversible and conserve the norm and symplectic structure exactly, regardless of the time step. In addition, we present explicit expressions for the exact evolution of the width of a single-Hessian Gaussian wavepacket in a general potential, as well as for the exact evolution of the whole wavepacket in a global harmonic potential. Using on-the-fly ab initio Gaussian wavepacket dynamics on the first excited-state surface of ammonia, we numerically confirm the conservation of geometric properties by these integrators and demonstrate that high-order integrators can enhance both accuracy and computational efficiency. We also compute the photoelectron spectrum of the difluorocarbene anion and the absorption spectrum of methylamine and find that, in comparison with experiment, single-Hessian GWD outperforms global harmonic models and matches the accuracy of local harmonic GWD. Finally, we identify which spectral features are sensitive to the choice of reference Hessian.

Predicting the hydrogen bond strength from water reorientation dynamics at short timescales

Path-integral molecular dynamics simulations and electronic structure-based energy decomposition analysis (EDA) are employed to connect hydrogen bond (H-bond) strength, its asymmetry, and the total delocalization energy at the water/air interface to experimentally measurable observables, such as the reorientation dynamics and the sum-frequency generation (SFG) spectrum. Using SFG spectra for distinct layers at the water/air interface, we validate the accuracy of our simulations and report a red-shift from the interface to the bulk and a strongly bonded water peak at around 3250 cm−1 in the layer closest to the bulk. The reorientation dynamics of water molecules slow down from the interface to the bulk, which correlates with the SFG results. From our EDA based on absolutely localized molecular orbitals, we observe a strong decline in total delocalization energy from bulk to the interface, as well as a decline in the strength of the strongest donor and acceptor interactions. The asymmetry between the two strongest interactions similarly rises toward the interface, while the importance of interactions from the outer solvation shells is greatly diminished and is lower than previously reported. Finally, we find that the strength of the strongest H-bond donor/acceptor is best correlated with the local minimum of the autocorrelation function resembling the L2 band librational motions. Following that, we propose a simple yet quantitative relationship between H-bond strength and the short-time reorientation dynamics at the water/air interface, which could potentially be extended to predict H-bond strength in other hydrophobic systems from experimentally obtainable observables.

Development and application of external electric fields for advanced polarizable force fields

External electric fields can dramatically alter the structure and dynamics of molecules and materials. The electric field response involves both the direct electrostatics and the polarization of the molecule. The polarization term is not included in non-polarizable force fields, yet it is essential for correctly describing the response. Here, we implement static and oscillating external electric fields in the Tinker molecular dynamics software for use with polarizable force fields. We demonstrate the implementation through dielectric spectra of water, dielectric spectra of an aqueous glucose solution, and trajectory analysis of an amyloid beta protein.

Coupling between phase separation and geometry on a closed elastic curve: Free energy minimization and dynamics

We study the free energy and dynamics of a closed elastic filament (a one-dimensional curve in two dimensions) coupled to a scalar concentration field representing, for example, an adsorbed species. The density variable has a tendency to phase-separate whereas the local spontaneous curvature is concentration-dependent. We address analytically and by simulation both the free energy landscape and the dynamics (the latter comprising a coupled Willmore flow and Cahn–Hilliard gradient flow on the full differential geometry of a closed filament), addressing issues that previous work typically sidestepped by restricting to the Monge gauge. Specifically, we find that the closure constraint for a deformable filament qualitatively changes the free energy landscape compared with either a rigid closed filament or an open elastic one, admitting metastable and stable states with more than one domain of each type. By numerical global free energy minimization, we explore equilibrium morphologies across a wide range of model parameters. For selected parameter values, we present fully dynamical results, tracking the time evolution of the various contributions to the free energy and confirming the emergence of both metastable and equilibrium multi-domain morphologies.

Configuration interaction extension of AGP for incorporating inter-geminal correlations

In this paper, we develop a class of antisymmetrized geminal power configuration interaction (AGP-CI) wave functions that extend the AGP framework by incorporating inter-geminal correlations through a CI expansion. To make these wavefunctions computationally tractable, we evaluate them by rewriting the AGP-CI ansatz as a linear combination of AGPs (LC-AGP), for which overlaps and Hamiltonian matrix elements can be computed with standard AGP machinery. Motivated by border-rank decompositions, we further reorganize this ansatz into a compact linear combination of AGPs depending on a small deformation parameter τ, which controls how closely the truncated expansion approximates the full AGP-CI state. Benchmark applications to the Hubbard model and to the small molecules H2O and N2 demonstrate that the proposed wavefunctions achieve consistently high accuracy and outperform the LC-AGP, particularly for systems with more electrons and in strongly correlated regimes.

Molecular dynamics simulation of high slip flow of water confined between graphene nanochannels at experimentally accessible shear rates

The transient time correlation function (TTCF) method has emerged as a powerful methodology for accurately probing systems at low shear rates. In the present study, TTCF was used to evaluate the shear rate dependence of the slip length in a high-slip system consisting of water confined between graphene walls at experimentally accessible shear rates, for which classical nonequilibrium molecular dynamics (NEMD) is unfeasible. The corresponding Navier friction coefficient was computed for all shear rates spanning six orders of magnitude and compared with the equilibrium limit. We report for the first time NEMD results obtained at experimentally accessible shear rates using the TTCF approach for a system that has attracted significant interest over the past decades. The slip length calculated with TTCF is in good agreement with previous equilibrium molecular dynamics simulations and experiments. Our aim here is to highlight the extraordinary power of TTCF, particularly for high-slip (low effective shear rate) systems, and to verify that equilibrium methods directly match NEMD measurements at experimentally accessible shear rates.

Two-dimensional IR–Raman spectroscopy of vibrational polaritons: Role of dipole surfaces

Nonlinear spectroscopy provides a unique perspective to understand time-resolved molecular dynamics under vibrational strong coupling (VSC). Herein, equilibrium–nonequilibrium cavity molecular dynamics simulations are performed to compute the two-dimensional (2D) infrared–infrared–Raman (IIR) spectroscopy of liquid water under VSC. In conventional computational chemistry practices, accurate molecular spectra are often constructed by using an advanced molecular dipole or polarizability model to post-process molecular dynamics trajectories evolved under a computationally efficient potential. By contrast, this work highlights the necessity of employing a consistent dipole surface model in both cavity molecular dynamics (CavMD) simulations and spectroscopic post-processing. While utilizing inconsistent dipole models only mildly influences the linear polariton spectrum, it severely distorts 2D spectra in wide frequency regions. With a consistent dipole–induced-dipole model, compared to the outside-cavity molecular 2D-IIR spectrum, the cavity 2D-IIR spectrum splits the OH stretch band to a pair of polariton branches only along the IR (not Raman) axis, while fading molecular signals at other frequency regions. This work provides the foundation for employing direct CavMD simulations to construct 2D spectra of realistic molecules under VSC.

Generalized Einstein relations between absorption and emission spectra in the electric-dipole approximation

Recently, Ryu et al. showed that two broadened bands connected by a set of four Einstein-coefficient spectra for stimulated and spontaneous single-photon transitions will obey detailed balance at equilibrium if the spectra satisfy generalized Einstein relations. Here, quantum mechanical expressions for Einstein-coefficient spectra are obtained in the electric-dipole approximation using an intramolecular Boltzmann distribution and the quantized field operators in isotropic, dispersive media of Nienhuis and Alkemade [Physica B+C 81, 181–188 (1976)]. These expressions suggest relationships between Einstein-coefficient spectra and dipole-strength spectra. The electrodynamic relationship between the spectral density for electromagnetic energy and the spectral density for the square of the electric field is developed and used to define dipole-strength spectra in terms of conditional transition probabilities per unit time. These rigorously relate dipole-strength spectra to Einstein-coefficient spectra, thus establishing quantum formulas for dipole-strength spectra and new generalized Einstein relations between dipole-strength spectra. For transitions between two bands, the dipole-strength spectra depend on a single total dipole strength but replace Einstein’s degeneracy ratio and transition frequency with a change in standard chemical potential and a single underlying lineshape that is manifested differently in the four spectra. At equilibrium, the relations specify the Stokes’ shift between forward and reverse transitions. The relationships between dipole-strength spectra, spontaneous emission spectral densities, and stimulated transition cross sections depend on the refractive index, the dielectric constant, and the local field, but not on the derivative of the refractive index. The broadband relationships reduce to known relationships for narrow spectra inside materials and for line spectra in vacuum.

A new Fe(IV) superoxide: The perferrate isomerization re-examined

The perferrate anion [FeVIIO4]−, the elusive iron analog of permanganate, has been extensively investigated, yet key questions remain unresolved concerning its stability with respect to isomerization. A previous computational work had been unable to reproduce the stability trend between the peroxide and perferrate: [FeVO2(η2-O2)]− > [FeVIIO4]−. Herein, the manifold of possible structures is revisited, for the first time, using an MRCISD+Q/x2c-TZVP//CASPT2(25,17)/ANO-RCC-VDZP level of theory. Computationally, we not only reproduce the correct stability trend but also find that the most stable species is a cyclometalated superoxide [FeIVO2(η2-O2)]− (6B1 ground state), perferrate being less stable by +29.2 kcal mol−1. In parallel, gas-phase ions of [FeO4]− stoichiometry were generated via an alternative electrospray ionization-based approach and probed by collision-induced dissociation mass spectrometry, providing complementary evidence for the presence of O–O motifs in the experimentally generated ions, in agreement with the computational results.