Related papers: Optimized Parallelization of Boundary Integral Poi…
In this paper we have derived explicitly computable bounds on the error in energy norms for the fully nonlinear Poisson-Boltzmann equation. Together with the computable bounds, we have also obtained efficient error indicators which can…
Efficiently solving Poisson equations on complex, irregular domains remains a fundamental challenge in scientific computing, as classical iterative solvers often suffer from prohibitive runtime due to ill-conditioned systems. While neural…
This work further improves the pseudo-transient approach for the Poisson Boltzmann equation (PBE) in the electrostatic analysis of solvated biomolecules. The numerical solution of the nonlinear PBE is known to involve many difficulties,…
Sustaining a large fraction of single GPU performance in parallel computations is considered to be the major problem of GPU-based clusters. In this article, this topic is addressed in the context of a lattice Boltzmann flow solver that is…
We develop an algorithm for bosonic path integral molecular dynamics (PIMD) simulations with periodic boundary conditions (PBC) that scales quadratically with the number of particles. Path integral methods are a powerful tool to simulate…
Heterogeneous computing environments combining CPU and GPU resources provide a great boost to large-scale scientific computing applications. Code generation utilities that partition the work into CPU and GPU tasks while considering data…
The parallelism afforded by GPUs presents significant advantages in training controllers through reinforcement learning (RL). However, integrating model-based optimization into this process remains challenging due to the complexity of…
We present a numerical framework for the simulation of collisional plasma dynamics, based on a coupling between Direct Simulation Monte Carlo (DSMC) and Particle-in-Cell (PIC) methods for the Vlasov-Maxwell-Landau system. The approach…
Correlation Plenoptic Imaging (CPI) is a novel technological imaging modality enabling to overcome drawbacks of standard plenoptic devices, while preserving their advantages. However, a major challenge in view of real-time application of…
We present an MPI + OpenACC implementation of the kernel-independent barycentric Lagrange treecode (BLTC) for fast summation of particle interactions on GPUs. The distributed memory parallelization uses recursive coordinate bisection for…
Strongly coupled immersed boundary (IB) methods solve the nonlinear fluid and structural equations of motion simultaneously for strongly enforcing the no-slip constraint on the body. Handling this constraint requires solving several large…
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…
It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…
In this paper we present a parallelization strategy on distributed memory systems for the Fast Kinetic Scheme --- a semi-Lagrangian scheme developed in [J. Comput. Phys., Vol. 255, 2013, pp 680-698] for solving kinetic equations. The…
A promising route towards fault-tolerant quantum error correction is the concatenation of a Gottesman-Kitaev-Preskill (GKP) code with a qubit code. Development of such concatenated codes requires simulation tools which realistically model…
To obtain a better understanding of the trade-offs between various objectives, Bi-Objective Integer Programming (BOIP) algorithms calculate the set of all non-dominated vectors and present these as the solution to a BOIP problem.…
We study parallel particle-in-cell (PIC) methods for low-temperature plasmas (LTPs), which discretize kinetic formulations that capture the time evolution of the probability density function of particles as a function of position and…
Under the most common experimental conditions, the adsorption of proteins to solid surfaces is an spontaneous process that leads to a rather compact layer of randomly oriented molecules. Due to the importance of this process for the…
Solving exactly Combinatorial Optimization Problems (COPs) using a Branch-and-Bound (B&B) algorithm requires a huge amount of computational resources. Therefore, we recently investigated designing B&B algorithms on top of graphics…
The nonlinear Poisson-Boltzmann equation (NPBE) is an elliptic partial differential equation used in applications such as protein interactions and biophysical chemistry (among many others). It describes the nonlinear electrostatic potential…