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In the fusion community, the use of high performance computing (HPC) has been mostly dominated by heavy-duty plasma simulations, such as those based on particle-in-cell and gyrokinetic codes. However, there has been a growing interest in…

We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, arXiv:1308.5587). Our approach is inspired by a traditional CPU-based…

CPU-GPU heterogeneous systems are now commonly used in HPC (High-Performance Computing). However, improving the utilization and energy-efficiency of such systems is still one of the most critical issues. As one single program typically…

Training large language models requires extensive processing, made possible by many high-performance computing resources. This study compares multi-node and multi-GPU environments for training large language models of electrocardiograms. It…

The complex regulatory dynamics of a biological network can be succinctly captured using discrete logic models. Given even sparse time-course data from the system of interest, previous work has shown that global optimization schemes are…

Complex workflows play a critical role in accelerating scientific discovery. In many scientific domains, efficient workflow management can lead to faster scientific output and broader user groups. Workflows that can leverage resources…

Using a realistic molecular catalyst system, we conduct scaling studies of ab initio molecular dynamics simulations using the CP2K code on both Intel Xeon CPU and NVIDIA V100 GPU architectures. We explore using process placement and…

Public cloud computing environments, such as Amazon AWS, Microsoft Azure, and the Google Cloud Platform, have achieved remarkable improvements in computational performance in recent years, and are also expected to be able to perform…

Database-search algorithms, that deduce peptides from Mass Spectrometry (MS) data, have tried to improve the computational efficiency to accomplish larger, and more complex systems biology studies. Existing serial, and high-performance…

Technological advances in the past decade, hardware and software alike, have made access to high-performance computing (HPC) easier than ever. We review these advances from a statistical computing perspective. Cloud computing makes access…

Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…

The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to…

High-Performance Computing (HPC) platforms enable scientific software to achieve breakthroughs in many research fields such as physics, biology, and chemistry, by employing Research Software Engineering (RSE) techniques. These include 1)…

Molecular docking is a critical computational strategy in drug design and discovery, but the complex diversity of biomolecular structures and flexible binding conformations create an enormous search space that challenges conventional…

We identify hardware that is optimal to produce molecular dynamics trajectories on Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we benchmark the GROMACS performance on a diverse set of compute nodes and relate…

Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this…

Hybrid computational architectures based on the joint power of Central Processing Units and Graphic Processing Units (GPUs) are becoming popular and powerful hardware tools for a wide range of simulations in biology, chemistry, engineering,…

Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…

High-performance computing (HPC) is reshaping computational drug discovery by enabling large-scale, time-efficient molecular simulations. In this work, we explore HPC-driven pipelines for Alzheimer's disease drug discovery, focusing on…

Realistic simulations of detailed, biophysics-based, multi-scale models require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are designed to allow…