Related papers: Optimized Parallelization of Boundary Integral Poi…
Porous electrodes are widely used in electrochemical systems, where accurately determining electric potentials, particularly overpotentials, is essential for understanding electrode behavior. At the macroscopic scale, porous electrodes are…
Memory-bound algorithms show complex performance and energy consumption behavior on multicore processors. We choose the lattice-Boltzmann method (LBM) on an Intel Sandy Bridge cluster as a prototype scenario to investigate if and how…
Partially Observable Markov Decision Processes (POMDPs) are fundamental to decision-making under uncertainty. We introduce a novel scalable approach to accelerate upper bound estimation in Point-Based Value Iteration (PBVI) algorithms, the…
The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…
Traditional electrostatic simulation are meshed-based methods which convert partial differential equations into an algebraic system of equations and their solutions are approximated through numerical methods. These methods are time…
Progress in the atomic-scale modelling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic…
Bayesian global optimization (BGO) is an efficient surrogate-assisted technique for problems involving expensive evaluations. A parallel technique can be used to parallelly evaluate the true-expensive objective functions in one iteration to…
We show how to accelerate the direct solution of the Boltzmann equation using Graphics Processing Units (GPUs). In order to fully exploit the computational power of the GPU, we choose a method of solution which combines a finite difference…
In this article, we describe an algorithm for solving Quadratic Unconstrained Binary Optimization problems on the Intel Loihi 2 neuromorphic processor. The solver is based on a hardware-aware fine-grained parallel simulated annealing…
A nonlinear Poisson--Boltzmann equation with transmission boundary conditions at the interface between two materials is investigated. The model describes the electrostatic potential generated by a vector of ion concentrations in a periodic…
Most machine learning and deep neural network algorithms rely on certain iterative algorithms to optimise their utility/cost functions, e.g. Stochastic Gradient Descent. In distributed learning, the networked nodes have to work…
An efficient parallelization approach to simulate optical properties of ensembles of quantum emitters in realistic electromagnetic environments is considered. It relies on balancing computing load of utilized processors and is built into…
Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. The computational studies of membrane proteins…
Elliptic equations play a crucial role in turbulence models for magnetic confinement fusion. Regardless of the chosen modeling approach - whether gyrokinetic, gyrofluid, or drift-fluid - the Poisson equation and Amp\`{e}re's law lead to…
This article presents the principles, software architecture, and performance analysis of the GPU port of the lattice Boltzmann software library Palabos (J. Latt et al., "Palabos: Parallel lattice Boltzmann solver", Comput. Math. Appl. 81,…
The non-linear Poisson-Boltzmann equation for a circular, uniformly charged platelet, confined together with co- and counter-ions to a cylindrical cell, is solved semi-analytically by transforming it into an integral equation and solving…
Two algorithms that combine Brownian dynamics (BD) simulations with mean-field partial differential equations (PDEs) are presented. This PDE-assisted Brownian dynamics (PBD) methodology provides exact particle tracking data in parts of the…
A widely used electrostatics model in the biomolecular modeling community, the nonlinear Poisson-Boltzmann equation, along with its finite element approximation, are analyzed in this paper. A regularized Poisson-Boltzmann equation is…
In this paper, we consider an approach to the parallelizing of the algorithms realizing the modified probability changigng method with adaptation and partial rollback procedure for constrained pseudo-Boolean optimization problems. Existing…
We present a new adaptive parallel algorithm for the challenging problem of multi-dimensional numerical integration on massively parallel architectures. Adaptive algorithms have demonstrated the best performance, but efficient many-core…