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Abstract An invariant domain preserving arbitrary Lagrangian-Eulerian method for solving non-linear hyperbolic systems is developed. The numerical scheme is explicit in time and the approximation in space is done with continuous finite elements. The method is made invariant domain preserving for the Euler equations using convex limiting and is tested on various benchmarks.
In this paper, we develop high-order nodal discontinuous Galerkin (DG) methods for hyperbolic conservation laws that satisfy invariant domain preserving properties using subcell flux corrections and convex limiting. These methods are based on a subcell flux corrected transport (FCT) methodology that involves blending a high-order target scheme with a robust, low-order invariant domain preserving method that is obtained using a graph viscosity technique. Furthermore, the new low-order discretizations are based on sparse stencils which do not increase with the polynomial degree of the high-order DG method. As a result, the accuracy of the low-order method does not degrade when used with high-order target methods. The method is applied to both scalar conservation laws, for which the discrete maximum principle is naturally enforced, and to systems of conservation laws such as the Euler equations, for which positivity of density and a minimum principle for specific entropy are enforced. Numerical results are presented on a number of benchmark test cases.
Here, we present a fully discrete approximation technique for the compressible Navier–Stokes equations that is second-order accurate in time and space, semi-implicit, and guaranteed to be invariant domain preserving. The restriction on the time step is the standard hyperbolic CFL condition, i.e. τ ≲ O ( h ) / V where V is some reference velocity scale and h the typical meshsize.
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Here, we present a general family of subcell limiting strategies to construct robust high-order accurate nodal discontinuous Galerkin (DG) schemes. The main strategy is to construct compatible low order finite volume (FV) type discretizations that allow for convex blending with the high-order variant with the goal of guaranteeing additional properties, such as bounds on physical quantities and/or guaranteed entropy dissipation. For an implementation of this main strategy, four main ingredients are identified that may be combined in a flexible manner: (i) a nodal high-order DG method on Legendre–Gauss–Lobatto nodes, (ii) a compatible robust subcell FV scheme, (iii) a convex combination strategy for the two schemes, which can be element-wise or subcell-wise, and (iv) a strategy to compute the convex blending factors, which can be either based on heuristic troubled-cell indicators, or using ideas from flux-corrected transport methods. By carefully designing the metric terms of the subcell FV method, the resulting methods can be used on unstructured curvilinear meshes, are locally conservative, can handle strong shocks efficiently while directly guaranteeing physical bounds on quantities such as density, pressure or entropy. We further show that it is possible to choose the four ingredients to recover existing methods such as a provably entropy dissipative subcell shock-capturing approach or a sparse invariant domain preserving approach. We test the versatility of the presented strategies and mix and match the four ingredients to solve challenging simulation setups, such as the KPP problem (a hyperbolic conservation law with non-convex flux function), turbulent and hypersonic Euler simulations, and MHD problems featuring shocks and turbulence.
Here, we introduce a high-order space–time approximation of the Shallow Water Equations with sources that is invariant-domain preserving (IDP), well-balanced with respect to rest states, and employs a novel explicit Runge–Kutta (ERK) introduced in Ern and Guermond (SIAM J. Sci. Comput. 44(5), A3366–A3392, 2022) for systems of non-linear conservation equations. The resulting method is then numerically illustrated through verification and validation.
Here, this paper is concerned with the approximation of the compressible Euler equations supplemented with an arbitrary or tabulated equation of state. The proposed approximation technique is robust, formally second-order accurate in space, invariant-domain preserving, and works for every equation of state, tabulated or analytic, provided the pressure is nonnegative. An entropy surrogate functional that grows across shocks is proposed. The numerical method is verified with novel analytical solutions and then validated with several computational benchmarks seen in the literature including problems with composite waves.
In this article, we introduce a numerical method for approximating the dispersive Serre–Green–Naghdi equations with topography using continuous finite elements. The method is an extension of the hyperbolic relaxation technique introduced in Guermond et al. (J Comput Phys 450:110809, 2022). It is explicit, second-order accurate in space, third-order accurate in time, and is invariant-domain preserving. It is also well balanced and parameter free. Special attention is given to the convex limiting technique when physical source terms are added in the equations. The method is verified with academic benchmarks and validated by comparison with laboratory experimental data.
Protein homology search is foundational to bioinformatics: it supports annotation transfer, structure/function inference, and evolutionary analysis over rapidly expanding sequence repositories (e.g., UniProtKB). Profile hidden Markov models (pHMMs), as implemented in HMMER, remain the most widely trusted approach because they provide statistically calibrated E-values; however, their gap behavior is fixed once a profile is trained, despite biological evidence that insertion/deletion tolerance varies across flexible loops and intrinsically disordered regions. We present CAHS (Context-Aware Homology Search), a lightweight query-time adapter for pHMM search that incorporates learned and biologically motivated signals without changing HMMER's downstream search pipeline or its calibrated E-value reporting. Given a query sequence, CAHS computes per-residue representations from a protein language model and a disorder predictor, maps these to profile coordinates, and modulates only match-state transition rows (gap-open and gap-extension probabilities) while preserving Plan7 constraints. We comprehensively evaluate CAHS across six structurally diverse protein families and multi-domain architectures against a 570k-sequence target corpus. CAHS expands detection capability, retrieving thousands of additional remote homologs at relaxed thresholds by maintaining alignment quality through flexible regions. For multi-domain proteins, context-aware modulation resolves 94% of fragmented alignments. Crucially, CAHS preserves hit-set invariance at stringent operating points (E<10-10), demonstrating increased statistical confidence without inflating false positives. Furthermore, sharper statistical distinction between homologs and background noise during early filter stages yields up to a 3.87× acceleration in end-to-end wall-clock time on high-performance computing clusters. Overall, CAHS illustrates a practical AI-for-science design pattern: augmenting a trusted probabilistic model with query-specific learned signals to improve interpretable, reproducible inference in data-rich biology.
The research described here was performed as part of the DOE SciDAC project Coupling Approaches for Next Generation Architectures (CANGA). A framework was developed for the derivation of novel algorithms for the multirate time integration of two-component systems coupled across an interface between spatial domains. The multirate aspect means that different time steps are allowed by each component integrator. The framework provides a way to construct multirate integrators with desirable properties related to stability, accuracy and preservation of system invariants. This report describes the framework and summarizes the major results, examples and research products.
This code implements a Fully Homomorphic Encryption (FHE) system, enabling secure computation on encrypted data without requiring decryption. It supports encryption, decryption, and homomorphic operations like matrix multiplication and addition. This code is adaptable for integrating FHE into linear-time invariant (LTI) systems, including digital control and filtering. With proper configuration from subject matter expertise, encrypted system parameters and signals can be manipulated to perform tasks like state updates, output calculations, and convolution in the encrypted domain. By preserving the structure of LTI systems while ensuring privacy, the framework facilitates secure applications in areas such as autonomous systems, signal processing, and industrial automation. The code initializes the encryption system using parameters provided in the env dictionary. These parameters include the ciphertext modulus, key dimension, plaintext fixed-point scaling factor, and noise bound. During initialization, a secret key is generated, which is essential for encrypting and decrypting data securely. The modular design allows users to tailor these parameters to specific use cases or security requirements. The code implements multiple cryptographic schemes. The learning with errors (LWE) encryption method encodes cleartext message to their plaintext fixed-point representation then encrypted into ciphertext space with additive noise. This noise ensures the security of the scheme, relying on the computational hardness of the LWE problem. The code also includes the Gentry-Sahai-Waters (GSW) scheme based off the LWE problem. Homomorphic matrix multiplication is performed between the LWE and GSW to encrypted data. This is achieved using a decomposition function on the LWE ciphertext during the multiplication operation. For higher-dimensional data, the code includes a method to encrypt entire matrices (GSWMat) using GSW encryption. These encrypted matrices can then be used for homomorphic matrix multiplications (MatMult). The decryption function uses the secret key to recover the original plaintext, removing the added noise and scaling that was originally applied during encryption.
Here, we propose a consistent and conservative model for multiphase and multicomponent incompressible flows, where there can be arbitrary numbers of phases and components. Each phase has a background fluid called the pure phase, each pair of phases is immiscible, and components are dissolvable in some specific phases. The model is developed based on the multiphase Phase-Field model including the contact angle boundary condition, the diffuse domain approach, and the analyses on the proposed consistency conditions for multiphase and multicomponent flows. The model conserves the mass of individual pure phases, the amount of each component in its dissolvable region, and thus the mass of the fluid mixture, and the momentum of the flow. It ensures that no fictitious phases or components can be generated and that the summation of the volume fractions from the Phase-Field model is unity everywhere so that there is no local void or overfilling. It satisfies a physical energy law and it is Galilean invariant. A corresponding numerical scheme is developed for the proposed model, whose formal accuracy is 2nd-order in both time and space. It is shown to be consistent and conservative and its solution is demonstrated to preserve the Galilean invariance and energy law. Numerical tests indicate that the proposed model and scheme are effective and robust to study various challenging multiphase and multicomponent flows.
We study the phase ordering dynamics of the classical antiferromagnetic 𝐽 1 −𝐽 2 (nearest-neighbor and next-nearest-neighbor couplings) Heisenberg model on the square lattice in the strong frustration regime (𝐽 2 /𝐽 1 > 1/2). While thermal fluctuations preclude any long-range magnetic order at finite temperatures, the system exhibits a long-range spin-driven nematic phase at low temperatures. The transition into the nematic phase is further shown to belong to the two-dimensional Ising universality class based on the critical exponents near the phase transition. Our large-scale stochastic Landau-Lifshitz-Gilbert simulations find a two-stage phase ordering when the system is quenched from a high-temperature paramagnetic state into the nematic phase. In the early stage, collinear alignments of spins lead to a locally saturated Ising-nematic order. Once domains of well-defined Ising order are developed, the late-stage relaxation is dominated by curvature-driven domain coarsening, as described by the Allen-Cahn equation. The characteristic size of Ising-nematic domains scales as the square root of time, similar to the kinetic Ising model described by the time-dependent Ginzburg-Landau theory. Our results confirm that the late-stage ordering kinetics of the spin-driven nematic, which is a vestigial order of the frustrated Heisenberg model, belongs to the dynamical universality class of a nonconserved Ising order. Interestingly, the system shows no violation of the superuniversality hypothesis under weak bond disorder. The dynamic scaling invariance is preserved in the presence of weak bond disorder. Here, we also discuss possible applications of our results to materials for which vestigial Ising-nematic order is realized.