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The Poisson-Boltzmann model is an effective and popular approach for modeling solvated biomolecules in continuum solvent with dissolved electrolytes. In this paper, we report our recent work in developing a Galerkin boundary integral method…

Machine learning methods have been lately used to solve partial differential equations (PDEs) and dynamical systems. These approaches have been developed into a novel research field known as scientific machine learning in which techniques…

A novel approach is presented for fast generation of synthetic seismograms due to microseismic events, using heterogeneous marine velocity models. The partial differential equations (PDEs) for the 3D elastic wave equation have been…

Study of general purpose computation by GPU (Graphics Processing Unit) can improve the image processing capability of micro-computer system. This paper studies the parallelism of the different stages of decimation in time radix 2 FFT…

The Poisson-Boltzmann (PB) model governs the electrostatics of solvated biomolecules, i.e., potential, field, energy, and force. These quantities can provide useful information about protein properties, functions, and dynamics. By…

We present the design and optimization of a linear solver on General Purpose GPUs for the efficient and high-throughput evaluation of the marginalized graph kernel between pairs of labeled graphs. The solver implements a preconditioned…

This paper proposes some efficient and accurate adaptive two-grid (ATG) finite element algorithms for linear and nonlinear partial differential equations (PDEs). The main idea of these algorithms is to utilize the solutions on the $k$-th…

We describe a method for parallelizing the lexicographic enumeration algorithm for the factorization set of an element in a numerical semigroup via bounds. This enables the use of GPU and distributed computing methods. We provide a CUDA…

We present a general method for accelerating by more than an order of magnitude the convolution of pixelated functions on the sphere with a radially-symmetric kernel. Our method splits the kernel into a compact real-space component and a…

This paper introduces a novel meshfree methodology based on Radial Basis Function-Finite Difference (RBF-FD) approximations for the numerical solution of partial differential equations (PDEs) on surfaces of codimension 1 embedded in…

The implicit boundary integral method (IBIM) provides a framework to construct quadrature rules on regular lattices for integrals over irregular domain boundaries. This work provides a systematic error analysis for IBIMs on uniform…

The past decade has witnessed a dramatic acceleration of lattice quantum chromodynamics calculations in nuclear and particle physics. This has been due to both significant progress in accelerating the iterative linear solvers using…

Time-independent Partial Differential Equations (PDEs) on large meshes pose significant challenges for data-driven neural PDE solvers. We introduce a novel graph rewiring technique to tackle some of these challenges, such as aggregating…

This article proposes an efficient numerical method for solving nonlinear partial differential equations (PDEs) based on sparse Gaussian processes (SGPs). Gaussian processes (GPs) have been extensively studied for solving PDEs by…

The finite element method (FEM) is a cornerstone numerical technique for solving partial differential equations (PDEs). Here, we present $\textbf{Qu-FEM}$, a fault-tolerant era quantum algorithm for the finite element method. In contrast to…

Multigrid methods have proven to be an invaluable tool to efficiently solve large sparse linear systems arising in the discretization of partial differential equations (PDEs). Algebraic multigrid methods and in particular adaptive algebraic…

In this paper, we present a parallel higher-order boundary integral method to solve the linear Poisson-Boltzmann (PB) equation. In our method, a well-posed boundary integral formulation is used to ensure the fast convergence of Krylov…

We develop an algorithm to solve tridiagonal systems of linear equations, which appear in implicit finite-difference schemes of partial differential equations (PDEs), being the time-dependent Schr\"{o}dinger equation (TDSE) an ideal…

We present a Pseudo-Transient Topology Optimization (PeTTO) approach that can leverage graphics processing units (GPUs) to efficiently solve single-material and multi-material topology optimization problems. By integrating PeTTO with phase…

For the parallel computation of partial differential equations, one key is the grid partitioning. It requires that each process owns the same amount of computations, and also, the partitioning quality should be proper to reduce the…