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Effective human-robot teaming is crucial for the practical deployment of robots in human workspaces. However, optimizing joint human-robot plans remains a challenge due to the difficulty of modeling individualized human capabilities and…
We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…
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…
Exascale computing holds great opportunities for molecular dynamics (MD) simulations. However, to take full advantage of the new possibilities, we must learn how to focus computational power on the discovery of complex molecular mechanisms,…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…
Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail. However, the inherent scalability problem of particle-particle…
Large-scale HPC simulations of plasma dynamics in fusion devices require efficient parallel I/O to avoid slowing down the simulation and to enable the post-processing of critical information. Such complex simulations lacking parallel I/O…
There is a large body of recent work applying machine learning (ML) techniques to query optimization and query performance prediction in relational database management systems (RDBMSs). However, these works typically ignore the effect of…
We study the dynamics of parallel tempering simulations, also known as the replica exchange technique, which has become the method of choice for simulation of proteins and other complex systems. Recent results for the optimal choice of the…
Simulations of physical phenomena are essential to the expedient design of precision components in aerospace and other high-tech industries. These phenomena are often described by mathematical models involving partial differential equations…
The implicit 2D3V particle-in-cell (PIC) code developed to study the interaction of ultrashort pulse lasers with matter [G. M. Petrov and J. Davis, Computer Phys. Comm. 179, 868 (2008); Phys. Plasmas 18, 073102 (2011)] has been parallelized…
In recent years, various means of efficiently detecting changepoints in the univariate setting have been proposed, with one popular approach involving minimising a penalised cost function using dynamic programming. In some situations, these…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Furthering our understanding of many of today's interesting problems in plasma physics---including plasma based acceleration and magnetic reconnection with pair production due to quantum electrodynamic effects---requires large-scale kinetic…
The physical processes at the interface of a low-temperature plasma and a solid are extremely complex. They involve a huge number of elementary processes in the plasma, in the solid as well as charge, momentum and energy transfer across the…
Calculating interactions or correlations between pairs of particles is typically the most time-consuming task in particle simulation or correlation analysis. Straightforward implementations using a double loop over particle pairs have…
In this paper, we describe the algorithms we implemented in FDPS to make efficient use of accelerator hardware such as GPGPUs. We have developed FDPS to make it possible for many researchers to develop their own high-performance parallel…
The decay process of the schematic one-dimensional three-body system is considered. A time-dependent approach is used in combination with a one-dimensional three-body model, which is composed of a heavier core nucleus and two nucleons, with…
Macroscopic simulations of dense plasmas rely on detailed microscopic information that can be computationally expensive and is difficult to verify experimentally. In this work, we delineate the accuracy boundary between microscale…
Molecular dynamics (MD) simulations are powerful tools for elucidating the macroscopic physical properties of materials from microscopic atomic behaviors. However, the massive, high-dimensional datasets generated by MD simulations pose a…