Related papers: Fast Kinetic Scheme : efficient MPI parallelizatio…

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 apply the collision-based hybrid introduced in \cite{hauck} to the Boltzmann equation with the BGK operator and a hyperbolic scaling. An implicit treatment of the source term is used to handle stiffness associated with the BGK operator.…

The Lattice Boltzmann method (LBM) for solving fluid flow is naturally well suited to an efficient implementation for massively parallel computing, due to the prevalence of local operations in the algorithm. This paper presents and analyses…

We describe a parallel algorithm for solving the time-independent 3d Schrodinger equation using the finite difference time domain (FDTD) method. We introduce an optimized parallelization scheme that reduces communication overhead between…

We present a parallel hierarchical solver for general sparse linear systems on distributed-memory machines. For large-scale problems, this fully algebraic algorithm is faster and more memory-efficient than sparse direct solvers because it…

Kinetic or Boltzmann schemes are interesting alternatives to the macroscopic numerical methods for solving the hyperbolic conservation laws of gas dynamics. They utilize the particle-based description instead of the wave propagation models.…

In this paper we genealize the fast semi-Lagrangian scheme developed in [J. Comput. Phys., Vol. 255, 2013, pp 680-698] to the case of high order reconstructions of the distribution function. The original first order accurate semi-Lagrangian…

The recently developed semi-Lagrangian discontinuous Galerkin approach is used to discretize hyperbolic partial differential equations (usually first order equations). Since these methods are conservative, local in space, and able to limit…

Spectral methods, thanks to their high accuracy and the possibility to use fast algorithms, represent an effective way to approximate the collisional kinetic equations of Boltzmann type, such as the Boltzmann-Nordheim equation. This…

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…

In this paper, we propose a fast multipole method (FMM) for 3-D linearized Poisson-Boltzmann (PB) equation in layered media. The main framework of the algorithm is analogous to the FMM for Helmholtz and Laplace equation in layered media…

Immersed boundary-lattice Boltzmann method (IB-LBM) has been widely used for simulation of particle-laden flows recently. However, it was limited to small-scale simulations with no more than O(103) particles. Here, we expand IB-LBM for…

The term `Convected Scheme' (CS) refers to a family of algorithms, most usually applied to the solution of Boltzmann's equation, which uses a method of characteristics in an integral form to project an initial cell forward to a group of…

The standard kinetic Monte Carlo algorithm is an extremely efficient method to carry out serial simulations of dynamical processes such as thin-film growth. However, in some cases it is necessary to study systems over extended time and…

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…

In this paper, we present a GPU-accelerated direct-sum 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…

The gyro-kinetic model is an approximation of the Vlasov-Maxwell system in a strongly magnetized magnetic field. We propose a new algorithm for solving it combining the Semi-Lagrangian (SL) method and the Arakawa (AKW) scheme with a…

The lattice Boltzmann equation (LBE), rooted in kinetic theory, provides a powerful framework for capturing complex flow behaviour by describing the evolution of single-particle distribution functions (PDFs). Despite its success, solving…

In recent years, leveraging parallel and distributed computational resources has become essential to solve problems of high computational cost. Bayesian optimization (BO) has shown attractive results in those expensive-to-evaluate problems…

Bayesian networks (BNs) are attractive, because they are graphical and interpretable machine learning models. However, exact inference on BNs is time-consuming, especially for complex problems. To improve the efficiency, we propose a fast…