Related papers: Accelerating scientific codes by performance and a…
Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be…
We report new statistical time-series analysis tools providing significant improvements in the rapid, precision extraction of discrete state dynamics from large databases of experimental observations of molecular machines. By building…
In parametric design, the geometric model is edited by changing relevant parameters in the parametric model, which is commonly done sequentially on multiple parameters. Without guidance on allowable parameter ranges that can guarantee the…
The paper investigates the techniques of quantum computation in metrological predictions, with a particular emphasis on enhancing prediction potential through variational parameter estimation. The applicability of quantum simulations and…
In this study we address existing deficiencies in the literature on applications of Particle Swarm Optimization to generate optimal designs. We present the results of a large computer study in which we bench-mark both efficiency and…
Data movement between memory and processors is a major bottleneck in modern computing systems. The processing-in-memory (PIM) paradigm aims to alleviate this bottleneck by performing computation inside memory chips. Real PIM hardware (e.g.,…
We examine the issue of assessing the efficiency of components of a parallel program at the example of the MD package LAMMPS. In particular, we look at how LAMMPS deals with the issue and explain why the approach adopted might lead to…
Large scale atomistic simulations with suitable interatomic potentials are widely employed by scientists or engineers of different areas. Quick generation of high-quality interatomic potentials is of urgent need under present circumstances,…
In a software product line (SPL), a collection of software products is defined by their commonalities in terms of features rather than explicitly specifying all products one-by-one. Several verification techniques were adapted to establish…
Meshfree simulation methods are emerging as compelling alternatives to conventional mesh-based approaches, particularly in the fields of Computational Fluid Dynamics (CFD) and continuum mechanics. In this publication, we provide a…
Based on the particle-in-cell (PIC) plasma simulation method, the speed-limited PIC (SLPIC) method delivers faster kinetic plasma simulation in cases where the particle distributions evolve slowly compared with the maximum stable PIC…
Computational models of human language often involve combinatorial problems. For instance, a probabilistic parser may marginalize over exponentially many trees to make predictions. Algorithms for such problems often employ dynamic…
The identification of performance-optimizing parameter settings is an important part of the development and application of algorithms. We describe an automatic framework for this algorithm configuration problem. More formally, we provide…
Simulating physical systems is a core component of scientific computing, encompassing a wide range of physical domains and applications. Recently, there has been a surge in data-driven methods to complement traditional numerical simulations…
A promising research direction in enabling LLMs to generate consistently correct code involves addressing their inability to properly estimate program execution, particularly for code they generate. In this work, we demonstrate that Code…
Despite the numerous uses of semidefinite programming (SDP) and its universal solvability via interior point methods (IPMs), it is rarely applied to practical large-scale problems. This mainly owes to the computational cost of IPMs that…
Particle swarm optimisation is a metaheuristic algorithm which finds reasonable solutions in a wide range of applied problems if suitable parameters are used. We study the properties of the algorithm in the framework of random dynamical…
We present a Quality by Design (QbD) styled approach for optimizing lipid nanoparticle (LNP) formulations, aiming to offer scientists an accessible workflow. The inherent restriction in these studies, where the molar ratios of ionizable,…
Scientific applications are often irregular and characterized by large computationally-intensive parallel loops. Dynamic loop scheduling (DLS) techniques improve the performance of computationally-intensive scientific applications via load…
Parameter identification for electrochemical battery models has always been challenging due to the multitude of parameters involved, most of which cannot be directly measured. This paper evaluates the efficiency and optimality of three…