Computational methods, numerical algorithms for physics problems.
Solidification governs the microstructure and, therefore, the mechanical response of metal components, yet the atomistic details of nucleation and defect formation are often difficult to determine experimentally. Molecular dynamics can bridge this gap, but only if the interatomic model is both accurate and computationally efficient. Here, we develop a Machine Learning Potential (MLP) for aluminum and demonstrate its near ab initio fidelity when trained with the sequential-refinement workflow that fine-tunes the model on low-energy structures. The favorable scaling of the model enables nanosecond simulations involving millions of atoms, thereby overcoming finite-size effects in simulations of polycrystalline solidification and subsequent mechanical testing. Comparison with classical potentials and recent MLP models, including a general-purpose model, shows that inaccuracies in stacking-fault energetics and diffusion can lead to qualitatively incorrect solidified grain structures and post-solidification mechanical behavior. Since our framework is based on an equivariant graph neural network, it allows for straightforward extensions to multi-component systems, providing valuable guidance for the future design and fine-tuning of both specialized and universal MLPs in computational mechanics simulations.
2603.24061We derive the conserved energy-like quantity and ensemble measure for Martyna--Tobias--Klein (MTK) barostats in which only a restricted subset of the cell degrees of freedom are active. In the standard fully anisotropic MTK formulation, the number of barostat degrees of freedom is $d^{2}$, where $d$ is the spatial dimension. When only $n_c$ axes of the cell matrix are allowed to fluctuate, the conserved energy-like quantity retains the same functional form but with $d^{2}$ replaced by $n_c$ in every term that counts barostat degrees of freedom. The derivation builds on the generalized Liouville framework for non-Hamiltonian systems and the existing MTK integration machinery. We verify that this quantity is exactly conserved, show that the resulting dynamics samples the isothermal--isobaric ensemble restricted to the submanifold of cell shapes in which inactive components are held fixed, and provide a complete Liouville-operator-based integration scheme for the masked MTK variant.
Finite-difference time-domain (FDTD) simulations often involve physical quantities spanning multiple orders of magnitude, such as the speed of light or electromagnetic field amplitudes. The standard practice for maintaining numerical accuracy in many FDTD implementations is to use 32-bit or 64-bit floating-point values to represent the electric and magnetic fields. However, this approach is not always optimal when recording field values, particularly during time-reversible gradient computation where electric and magnetic field values need to be saved at the boundary of the simulation domain. Since this memory bottleneck is often the limiting factor in time-reversible inverse design for nanophotonics, we present two field optimizations for enhancing memory efficiency in FDTD simulations. Using a smaller bit-width representation of field values as well as interpolation, we achieve similar accuracy at lower memory cost. This approach is particularly beneficial for GPU-accelerated computing, where reduced-precision data types are increasingly preferred due to their computational efficiency and prevalence in machine learning frameworks. We integrate our approach into FDTDX, an open-source, differentiable FDTD solver that natively supports time-reversible gradient computation. Our approach is especially important for future developments towards large-scale open-source simulations, which are critical for advancing computational nanophotonic applications.
2603.23283We derive an exact reduction of the screened second-order exchange (SOSEX) energy in the uniform electron gas to a triple integral for a specific class of single-pole screened interaction. The reduction proceeds by rescaling the frequency variable to factorize the propagator denominators, applying a Fourier decomposition to separate the two particle-hole blocks, and finally performing a change of integration variables that brings the geometric structure into a tractable form. The reduction to a one-variable integral kernel is possible if and only if the screened interaction belongs to a one-pole class characterized by a single momentum-independent frequency scale~$μ$, which we call the reduction-compatible single-pole (RC-SP) model. The RC-SP model does not approximate plasmon dispersions in real materials, but provides an exactly reducible reference model for analyzing dynamically screened exchange, and gives natural basis elements for approximating more general one-pole screening. We analyze the $μ$-dependence of the SOSEX energy asymptotically at both small and large~$μ$ and establish the leading behaviors at the theorem level. Under a power-law mapping from~$μ$ to the density parameter~$r_s$, this asymptotic structure constrains the analytic form of the screened-exchange correction in $r_s$-space, providing a diagrammatically justified basis for beyond-RPA functional construction. Direct numerical integration of the reduced representation confirms the asymptotic behaviors quantitatively.
Wafer-to-wafer (WxW) bonding is a key enabler for three-dimensional integration, including hybrid bonding for fine-pitch Cu-Cu interconnects. During bonding, wafer deformation and the air entrapped between the wafers interact through a strongly coupled, time-dependent fluid-structure interaction (FSI) that can produce non-intuitive bonding dynamics and process sensitivities. This paper develops a mathematically consistent reduced-order model for WxW bonding by deriving a Kirchhoff-Love plate equation for wafer bending from three-dimensional linear elasticity and coupling it to a Reynolds lubrication equation for the inter-wafer air film. The resulting nonlinear plate-Reynolds system is discretized and solved monolithically in the high-performance FEniCSx framework using a $C^0$ interior-penalty formulation for the fourth-order plate operator, standard continuous Galerkin discretization for the pressure field, implicit time integration, and a Newton solver with automatic differentiation. Simulations reproduce experimentally reported probe-displacement histories for multiple initial gaps and verify force equilibrium at the bond front, where the Reynolds pressure acts as an effective contact reaction. Parametric studies reveal nonlinear, and in some cases non-monotonic, sensitivities of bonding-front kinetics to the initial gap, air viscosity, and interfacial energy, providing actionable trends for process optimization.
In complex engineering systems such as electro-thermal-fluid coupling, rapid and accurate prediction of multi-physics fields is essential for advanced applications like digital twins and real-time condition monitoring. Traditional numerical methods often suffer from high computational latency, whereas standard Physics-Informed Neural Networks (PINNs) frequently fail to capture critical local features, such as irregular interfaces, localized high-gradient regions, and multi-peak transport structures. To address these limitations and provide high-fidelity intelligent predictions for engineering decision-making, this paper proposes a Residual-Attention Physics-Informed Neural Network (RA-PINN) as a powerful surrogate modeling engine. The proposed method incorporates residual learning and attention enhancement into the network backbone to improve the representation of oblique transition structures, narrow charge layers, and distributed hotspots while strictly preserving global field consistency. To evaluate its effectiveness as an intelligent prediction framework, three representative benchmark cases are constructed, including an oblique asymmetric interface, a bipolar high-gradient charge layer, and a multi-peak Gaussian charge migration field. Under unified training settings, the proposed RA-PINN is systematically compared with a standard pure PINN and an LSTM-PINN in terms of average error, local maximum error, structural similarity, and convergence behavior. The results show that RA-PINN consistently achieves the best overall performance across all benchmark cases, demonstrating its tremendous potential as a highly reliable core inference engine for the condition monitoring and digital twin modeling of complex multi-physics engineering systems.
Absolute binding free energy (ABFE) calculations offer a theoretically rigorous approach for predicting protein--ligand binding affinities without the scaffold constraints of relative binding free energy (RBFE) perturbations. However, broad adoption of ABFE in high-throughput hit discovery campaigns has been hindered by high computational costs and a lack of large-scale validation. Here, we present Felis, an open-source, automated, and scalable toolkit designed for high-throughput ABFE calculations. Paired with ByteFF, a previously developed data-driven molecular mechanics force field for drug-like molecules, Felis achieves ranking performance comparable to state-of-the-art RBFE methods on a diverse dataset comprising 43 protein targets and 859 ligands. Furthermore, we demonstrate robust convergence and ranking performance of Felis on a more challenging KRAS(G12D) dataset, where some ligands and the cofactor are highly charged. Crucially, all Felis predictions in this study were generated in a strict zero-shot manner, eschewing custom force-field modifications and alchemical schedule fine-tuning. This demonstrates the viability of Felis as an effective, ready-to-use tool for computational structure-based drug design.
We introduce a low-cost every-$K$-step correction for one-dimensional Euler computations. The correction uses differentiated Riemann variables (DRVs) -- characteristic derivatives that isolate the left acoustic wave, the contact, and the right acoustic wave -- to locate the current wave packet, sample the surrounding constant states, perform a short Newton update for the intermediate pressure and contact speed, and conservatively remap a sharpened profile back onto the grid. The ingredients are elementary -- filtered centered differences, local state sampling, a single Newton step, and conservative cell averaging -- yet the effect on accuracy is disproportionate. On a long-time severe-expansion benchmark ($N=900$, $t=0.4$), intermittent correction drives the intermediate-state errors from $O(10^{-2})$ to $O(10^{-13})$, i.e. to machine precision. On a long-time LeBlanc benchmark ($N=800$, $t=1$), the method crosses a qualitative threshold: one-shot final-time reconstruction fails entirely (shock location error $2.7\times 10^{-1}$), whereas correction every three steps recovers an almost exact sharp solution with contact and shock positions accurate to machine precision. The same detector-and-Newton mechanism handles two-shock and two-rarefaction packets without case-specific logic, with plateau improvements of four to sixteen orders of magnitude. In an unoptimized Python prototype the wall-clock overhead is below a factor of two even on the most aggressively corrected benchmark. To our knowledge, no comparably lightweight fixed-grid add-on has been shown to recover this level of coarse-grid accuracy on the long-time LeBlanc and related near-vacuum problems.
2603.21947Matrix elements of spherical tensor operators are fundamental to the analysis of lanthanide spectra in both amorphous and crystalline host materials. In the intermediate coupling scheme, the eigenvectors of the Hamiltonian define the electronic structure, while the eigenvalues determine the energy levels of the $f^N$ configuration. By utilizing these eigenvectors to evaluate electric and magnetic dipole operators, one can identify the radiative line strengths for all transitions in both absorption and emission. This work presents a comprehensive framework for the direct calculation of angular matrix elements using a Slater determinant basis and their subsequent transformation to the traditional $LS$-coupling scheme. Unlike conventional indirect methods, this approach is more universally applicable, though it is computationally more intensive. A concise set of general rules is prepared to enable the calculation of angular matrix elements for virtually any spherical tensor operator within an $f^N$ configuration. The computational overhead of this direct approach is well within the capabilities of modern desktop computing. Furthermore, since these configuration-specific angular matrices are mathematical constants independent of the host environment, they need only be calculated once. The Python package AMELI is introduced, which employs exact arithmetic to generate the matrix elements with absolute mathematical precision. Both the underlying algorithms and the calculated matrices for all lanthanide ions are provided in open-access repositories. This removes a significant barrier for experimentalists, providing the necessary operator matrices without requiring them to navigate the intricate theory and algorithmic implementation.
We study the use of a learned forward operator in the inverse problem of photoacoustic tomography. The Fourier neural operator to approximate the photoacoustic wave propagation is used. Further, the inverse problem is solved using a gradient-based approach with automatic differentiation. The methodology is evaluated using numerical simulations, and the results are compared to a conventional approach, where the forward operator is approximated using the pseudospectral $k$-space method. The results show that the learned forward operator can be used to approximate the photoacoustic wave propagation with good accuracy, and that it can be utilised as a computationally efficient forward operator in solving the inverse problem of photoacoustic tomography.
Coupled partial differential equations underpin a wide range of multiphysics systems, yet existing neural PDE solvers still struggle to resolve localized high-risk regions and often fail to preserve structural admissibility across coupled fields. To address these limitations, we propose the Partition-of-unity Information-geometric Certified Solver (PICS), a closed-loop framework that strictly enforces structural admissibility at the level of representation rather than relying on an additional soft penalty. By constructing a gate-structured admissible manifold coupled with a restricted jet prolongation, PICS ensures that geometry-sensitive approximations and closure-essential differential coordinates enter the solver as a strongly enforced, structure-preserving ansatz. Furthermore, the framework integrates entropic tail-risk control and \textit{a posteriori} certificate-driven empirical measure transport, dynamically reallocating training efforts toward uncertified, error-prone transition zones. Evaluated against standard baseline methods across three two-dimensional coupled benchmarks, PICS achieves more consistently accurate and balanced cross-field recovery while retaining practical computational efficiency, thereby providing a rigorous route toward highly reliable multiphysics simulation.
Accurately resolving steady electrohydrodynamic (EHD) flows presents a formidable computational challenge due to the strong nonlinear coupling between charged-particle density, velocity fields, and electric potential. These interactions frequently induce sharp transition layers, crossing fronts, and multiscale spatial structures, which notoriously degrade the predictive accuracy of standard mesh-free solvers like Physics-Informed Neural Networks (PINNs). To systematically address this bottleneck, we formulate a unified four-variable operator framework and develop a comprehensive benchmark suite for two-dimensional steady EHD shock-like problems. The benchmark comprises eight rigorously designed cases featuring diverse front geometries, such as oblique, curved, and intersecting layers, alongside complex multiscale patterns. Under strictly identical configurations, including governing equations, source terms, sampling strategies, and loss formulations, we evaluate a Standard MLP-based PINN, a Residual Attention PINN (ResAtt-PINN), and an LSTM-PINN that leverages pseudo-sequential spatial encoding. Extensive numerical experiments demonstrate that the LSTM-PINN consistently achieves the highest predictive accuracy across all eight cases. It successfully reconstructs sharp gradients and intricate multiscale structures where other architectures fail or over-smooth. Furthermore, the LSTM backbone efficiently captures long-range spatial correlations while maintaining an exceptionally low computational overhead and GPU memory footprint. These findings not only establish the LSTM-PINN as a robust and efficient solver for strongly coupled PDEs with shock-like features, but also provide the computational physics community with a standardized, reproducible benchmark for future algorithmic evaluations.
This work presents a variational physics-informed deep learning framework for phase-field modelling of brittle crack propagation in anisotropic media. Previous Deep Ritz Method (DRM) approaches have focused on second-order, isotropic phase-field fracture formulations. In contrast, the present work introduces, for the first time within a variational deep learning setting, a family of higher-order anisotropic phase-field models through a generalised crack density functional. The resulting fracture problem is solved by minimising the total energy using the DRM. The trial space is enriched with higher-order B-spline basis functions to represent higher-order gradients accurately and stably, thereby eliminating the need for conventional automatic differentiation. The methodology is assessed for isotropic, cubic, and orthotropic fracture surface energy densities. Numerical examples demonstrate direction-dependent crack growth in anisotropic cases, highlighting the capability of the method to accurately capture this behaviour.
Accurately calculating time delays between signals is pivotal in many modern physics applications. One approach to estimating these delays is computing the cross-spectrum in the time-frequency domain. Linear time-frequency representations, such as the continuous wavelet transform (CWT), are widely used to construct these cross-spectra. However, it is well known that the frequency resolution is inherently limited by the localized nature of the convolving wavelet. Moreover, the functional form of the CWT cross-spectrum is not a proper correlation measure and typically requires post-processing smoothing. Conversely, quadratic representations achieve joint time-frequency resolution approaching the Gabor-Heisenberg limit while also providing an adequate measure of similarity between the signals. Motivated by these advantages, we propose a time-delay estimation method based on the Wigner-Ville Distribution (WVD). Considering nonstationary signals arising from two typical wave-physics scenarios, we show that the WVD yields more accurate time-delay estimates with lower uncertainty, particularly in the most energetic frequency bands.
Machine-learning electronic Hamiltonians achieve orders-of-magnitude speedups over density-functional theory, yet current models omit long-range Coulomb interactions that govern physics in polar crystals and heterostructures. We derive closed-form long-range Hamiltonian matrix elements in a nonorthogonal atomic-orbital basis through variational decomposition of the electrostatic energy, deriving a variationally consistent mapping from the electron density matrix to effective atomic charges. We implement this framework in HamGNN-LR, a dual-channel architecture combining E(3)-equivariant message passing with reciprocal-space Ewald summation. Benchmarks demonstrate that physics-based long-range corrections are essential: purely data-driven attention mechanisms fail to capture macroscopic electrostatic potentials. Benchmarks on polar ZnO slabs, CdSe/ZnS heterostructures, and GaN/AlN superlattices show two- to threefold error reductions and robust transferability to systems far beyond training sizes, eliminating the characteristic staircase artifacts that plague short-range models in the presence of built-in electric fields.
Quantitative high-resolution transmission electron microscopy (HRTEM) provides an indispensable means to understand the structure-property relationships of a material in atomic dimensions. Successful quantification requires reliable retrieval of essential atomic structural information despite artifacts arising from unwanted but practically unavoidable imaging imperfections. Experimental observation carried out in tandem with model-based iterative image simulation shows vast applications in quantitative structural and chemical determination of objects spanning zero to three dimensions [Prog. Mater. Sci. 133, 101037, 2023]. However, the large number of parameters involved in the simulations make the current multi-step, user-guided iterative approach highly time consuming, thereby restricting its application primarily to small sample areas and to experienced users. In this work, we implement and apply a physics-informed Bayesian optimization (BO) framework to advance HRTEM quantification towards full automation and large-field-of-view analysis. Unlike conventional optimization approaches, our method adopts a stepwise strategy that fully leverages the strength of BO in handling high-dimensional parameters, while its probabilistic engine rigorously and efficiently refines the parameter space to enable rapid quantification. Using a BaTiO3 single crystal that contains heavy, medium and light elements as a model system, we demonstrate that the three-dimensional crystal structure can be determined from a single HRTEM image with a three to four order-of-magnitude improvement in time efficiency. This approach thus opens new avenues for fast and automated image quantification over larger sample volumes and, potentially, in the time domain.
We introduce a distribution-free lattice Boltzmann formulation for general compartmental reaction--diffusion systems arising in mathematical epidemiology. The proposed scheme, termed a single-step simplified lattice Boltzmann method (SSLBM), evolves directly macroscopic compartment densities, eliminating the need for particle distribution functions and explicit streaming operations. This yields a compact and computationally efficient framework while retaining the kinetic consistency of lattice Boltzmann methodologies. The approach is applied to a SEIRD (Susceptible-Exposed-Infected-Recovered-Deceased) reaction-diffusion model as a representative case. The resulting discrete evolution equations are derived and shown to recover the target macroscopic dynamics. The method is systematically validated against a fourth-order finite difference reference solution and compared with a standard BGK lattice Boltzmann formulation. Numerical results demonstrate that the SSLBM consistently improves accuracy across all compartments and norms. The error reduction is robust with respect to both the basic reproduction number and diffusion strength, typically ranging between factors of approximately two and five depending on the regime. In particular, the method shows enhanced control of localised errors in regimes characterised by strong nonlinear coupling and steep spatial gradients. Our findings indicate that the proposed formulation provides an accurate and efficient alternative to classical lattice Boltzmann approaches for reaction-diffusion systems, with particular advantages in stiff and nonlinear epidemic dynamics.
Applications ranging from nuclear safeguards to dark matter detection require accurate predictions of neutron fields produced by ($α$,n) reactions. Legacy tools like SOURCES-4C remain widely used but suffer from significant limitations, including outdated nuclear data, missing target nuclides, and restricted accessibility. Here, we present ALPHANSO, an open-source Python package for calculating ($α$,n) neutron source terms. ALPHANSO incorporates modern nuclear data libraries and formats covering all naturally occurring target nuclides and provides a transparent, modular framework for updating or extending the data as new evaluations are released. Comparison with SOURCES-4C and experimental measurements across a range of elements and materials shows that ALPHANSO reproduces neutron yields and spectra that typically match or exceed the accuracy of existing codes. These results demonstrate that ALPHANSO is a reliable, accessible, modern replacement for legacy ($α$,n) source term codes. Its open-source design and modular data handling make it readily extensible to future evaluated nuclear data and low-background applications.
OpenMC can be used to computationally model depletion and produce estimates of decay heat. As an input to depletion simulations, OpenMC requires a depletion chain that details nuclide transmutation pathways. The simplified CASL depletion chain was designed to track relatively few nuclides while still accurately modeling the effective neutron multiplication factor and nuclide number densities. However, the CASL chain dramatically underestimates decay heat due to the many nuclides it does not contain. In this work, we modify the CASL depletion chain to improve its accuracy while maintaining its computational efficiency. We demonstrate the effectiveness of adding pseudo-nuclides to the CASL chain, with each pseudo-nuclide capturing the behavior of a large group of nuclides. We further introduce "delay nuclides," which dramatically improve the accuracy of decay heat estimates.
We introduce a postprocessing procedure that recovers sub-cell wave geometry from a standard one-dimensional Euler shock-capturing computation using differentiated Riemann variables (DRVs) -- characteristic derivatives that separate the three wave families into distinct localized spikes. Filtered DRV surrogates detect the waves, plateau sampling extracts the local states, and a pressure-wave-function Newton closure completes the geometry. The entire pipeline adds less than $0.25\%$ to the cost of a baseline WENO--5/HLLC solve. For Sod, a severe-expansion problem, and the LeBlanc shock tube, wave locations are recovered to within roundoff or $O(10^{-4})$ and the contact is sharpened to one cell width; a pattern-agnostic extension handles all four Riemann configurations with errors at the $10^{-6}$--$10^{-8}$ level. Direct comparison with MUSCL--THINC--BVD and WENO-Z--THINC--BVD shows that neither reproduces the combination of sharp contacts, small contact-window internal-energy error, and elimination of the LeBlanc positive overshoot achieved by the DRV reconstruction.