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Traditional pairwise sequence alignment is based on matching individual samples from two sequences, under time monotonicity constraints. However, in many application settings matching subsequences (segments) instead of individual samples…
We have developed a parallel Particle-Particle, Particle-Mesh (P^3M) simulation code for the T3E well suited to studying the time evolution of systems of particles interacting via gravity and gas forces in cosmological contexts. The…
Metamaterials and metasurfaces have given possibilities for manipulating electromagnetic (EM) waves that in the past would have seemed impossible. The majority of metasurface designs are suitable for a particular frequency and angle of…
Adaptive representations are increasingly indispensable for reducing the in-memory and on-disk footprints of large-scale data. Usual solutions are designed broadly along two themes: reducing data precision, e.g., through compression, or…
It is well known that domain-decomposition-based multiscale mixed methods rely on interface spaces, defined on the skeleton of the decomposition, to connect the solution among the non-overlapping subdomains. Usual spaces, such as…
In this paper, we propose an adaptive proximal inexact gradient (APIG) framework for solving a class of nonsmooth composite optimization problems involving function and gradient errors. Unlike existing inexact proximal gradient methods, the…
An alternating direction method of multipliers (ADMM) solver is described for optimal resource allocation problems with separable convex quadratic costs and constraints and linear coupling constraints. We describe a parallel implementation…
We have developed a parallel Particle-Particle, Particle-Mesh (P3M) simulation code for the Cray T3E parallel supercomputer that is well suited to studying the time evolution of systems of particles interacting via gravity and gas forces in…
We theoretically investigate the optical properties of parity-time (PT)-symmetric three dimensional metamaterials composed of strongly-coupled planar plasmonic waveguides. By tuning the loss-gain balance, we show how the initially isotropic…
In recent years graphical processing units (GPUs) have become a powerful tool in scientific computing. Their potential to speed up highly parallel applications brings the power of high performance computing to a wider range of users.…
We present a method to match three dimensional shapes under non-isometric deformations, topology changes and partiality. We formulate the problem as matching between a set of pair-wise and point-wise descriptors, imposing a continuity prior…
We describe and implement an adaptive particle-mesh algorithm to solve the Poisson equation for grid-based hydrodynamics codes with nested grids. The algorithm is implemented and extensively tested within the astrophysical code Enzo against…
The Particle-in-Cell (PIC) simulation has been a widely used method for studying plasma physics. However, fully three-dimensional PIC simulations always require huge computational resources. For problems with near azimuthal symmetry, recent…
In this paper we present the Python framework pySDC for solving collocation problems with spectral deferred correction methods (SDC) and their time-parallel variant PFASST, the parallel full approximation scheme in space and time. pySDC…
This is the first part of a threefold article, aimed at solving numerically the Poisson problem in three-dimensional prismatic or axisymmetric domains. In this first part, the Fourier Singular Complement Method is introduced and analysed,…
In this paper, we present resolvent4py, a parallel Python package for the analysis, model reduction and control of large-scale linear systems with millions or billions of degrees of freedom. This package provides the user with a friendly…
The Poisson-Boltzmann equation is a widely used model to study the electrostatics in molecular solvation. Its numerical solution using a boundary integral formulation requires a mesh on the molecular surface only, yielding accurate…
A fast Poisson solver software package PoisFFT is presented. It is available as a free software licensed under the GNU GPL license version 3. The package uses the fast Fourier transform to directly solve the Poisson equation on a uniform…
This work introduces a novel, fully robust and highly-scalable, $h$-adaptive aggregated unfitted finite element method for large-scale interface elliptic problems. The new method is based on a recent distributed-memory implementation of the…
Embedding models are a cornerstone of modern AI. Driven by Multimodal Large Language Models (MLLMs), they have made great progress in architecture and data curation, while the holistic paradigm is still limited to SSC, i.e., single input,…