相关论文: Improved neighbor list algorithm in molecular simu…

In this paper we propose a novel algorithm to combine two or more cellular complexes, providing a minimal fragmentation of the cells of the resulting complex. We introduce here the idea of arrangement generated by a collection of cellular…

The CUR decomposition is a technique for low-rank approximation that selects small subsets of the columns and rows of a given matrix to use as bases for its column and rowspaces. It has recently attracted much interest, as it has several…

This paper studies the nucleus decomposition problem, which has been shown to be useful in finding dense substructures in graphs. We present a novel parallel algorithm that is efficient both in theory and in practice. Our algorithm achieves…

Spectral clustering approaches have led to well-accepted algorithms for finding accurate clusters in a given dataset. However, their application to large-scale datasets has been hindered by computational complexity of eigenvalue…

In this article the most fundamental decomposition-based optimization method - block coordinate search, based on the sequential decomposition of problems in subproblems - and building performance simulation programs are used to reason about…

The combination of Markov state modeling (MSM) and molecular dynamics (MD) simulations has been shown in recent years to be a valuable approach to unravel the slow processes of molecular systems with increasing complexity. While the…

This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…

In evolutionary multi-objective optimization, the indicator-based subset selection problem involves finding a subset of points that maximizes a given quality indicator. Local search is an effective approach for obtaining a high-quality…

Dense femtocells are the ultimate goal of the femtocellular network deployment. Among three types of handovers: femtocell-to-macrocell, macrocell-to-femtocell, and femtocell-to-femtocell, the latter two are the main concern for the dense…

We propose a novel application of coded computing to the problem of the nearest neighbor estimation using MatDot Codes [Fahim. et.al. 2017], that are known to be optimal for matrix multiplication in terms of recovery threshold under storage…

In this letter, we investigate the resource allocation for downlink multi-cell coordinated OFDMA wireless networks, in which power allocation and subcarrier scheduling are jointly optimized. Aiming at maximizing the weighted sum of the…

We present a new molecular-dynamics algorithm for integrating the equations of motion for a system of particles interacting with mixed continuous/impulsive forces. This method, which we call Impulsive Verlet, is constructed using operator…

The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by…

A simple method for improving cache efficiency of serial and parallel explicit finite procedure with application to casting solidification simulation over three-dimensional complex geometries is presented. The method is based on division of…

We develop methods for accelerating metric similarity search that are effective on modern hardware. Our algorithms factor into easily parallelizable components, making them simple to deploy and efficient on multicore CPUs and GPUs. Despite…

We present a quantum algorithm for data classification based on the nearest-neighbor learning algorithm. The classification algorithm is divided into two steps: Firstly, data in the same class is divided into smaller groups with sublabels…

Grouping elements into families to analyse them separately is a standard analysis procedure in many areas of sciences. We propose herein a new algorithm based on the simple idea that members from a family look like each other, and don't…

A new maximum approximate likelihood (ML) estimation algorithm for the mixture of Kent distribution is proposed. The new algorithm is constructed via the BSLM (block successive lower-bound maximization) framework and incorporates manifold…

This study addresses the challenge of simulating realistic particle systems by proposing a novel particle decomposition scheme that improves the parallel performance of surface resolved particle simulations. Realistic particle systems often…

This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…