28 papers · ranked by Valyu relevance
Claude Tadonki
High Performance Computing (HPC) aims at providing reasonably fast computing solutions to scientific and real life problems. Many efforts have been made on the way to powerful supercomputers, including generic and customized configurations. The advent of multicore architectures is noticeable in the HPC history, because…
Lansaol Yang, Michael E. Bryan, Eduardo Veiga, Ian Lowenhoff + 41 more
Artificial intelligence (AI) has rapidly become the focal point of global governmental attention and investment. Nations are launching AI for science strategies on a scale comparable to historic endeavors such as Apollo and the Manhattan Project. These coordinated programs carry profound promise for people living with…
Pablo García‐Risueño, Pablo Ibáñez
The increase of existing computational capabilities has made simulation emerge as a third discipline of Science, lying midway between experimental and purely theoretical branches [1, 2]. Simulation enables the evaluation of quantities which otherwise would not be accessible, helps to improve experiments and provides…
Cristian Di Pietrantonio, Christopher Harris, Maciej Cytowski
—In this paper we present a new accounting model for heterogeneous supercomputers. An increasing number of supercomputing centres adopt heterogeneous architectures consisting of CPUs and hardware accelerators for their systems. Accounting models using the core hour as unit of measure are redefined to provide an…
Authors not listed
The era of exascale computing presents both exciting opportunities and unique challenges for quantum mechanical simulations. While the transition from petaflops to exascale computing has been marked by a steady increase in computational power, the shift towards heterogeneous architectures, particularly the dominant…
Derek Groen, Simon Portegies Zwart
—We describe the political and technical complications encountered during the astronomical CosmoGrid project. CosmoGrid is a numerical study on the formation of large scale structure in the universe. The simulations are challenging due to the enormous dynamic range in spatial and temporal coordinates, as well as the…
Quanyong Xu, Hu Ren, Hanfeng Gu, Jie Wu + 5 more
'Zhifeng Xie' 'Guangwen Yang' 'Xinlong Feng' 'Hui Xu'] Computational fluid dynamics- (CFD-) based component-level numerical simulation technology has been widely used in the design of aeroengines. However, due to the strong coupling effects between components, the numerical simulation of the whole engine considering…
János Végh
Supercomputer building is a many sceene, many authors game, comprising a lot of different technologies, manufacturers and ideas. Checking data available in the public database in a systematic way, some general tendencies and limitations can be concluded, both for the past and the future. The feasibility of building…
C. Richard A. Catlow, Nora H. De Leeuw, Angelos Michaelides, Scott M. Woodley
The development and optimization of materials is critical to several contemporary scientific and technological challenges, including renewable energy technologies, novel catalytic routes to sustainable fuels and chemicals and electronic technologies. Computational modelling now plays an essential role in materials…
Matthias Möller, C. Vuik
Quantum computing technologies have become a hot topic in academia and industry receiving much attention and financial support from all sides. Building a quantum computer that can be used practically is in itself an outstanding challenge that has become the 'new race to the moon'. Next to researchers and vendors of…
Fan Yang, Andrew A. Chien
—Power consumption (supply, heat, cost) and associated carbon emissions (environmental impact) are increasingly critical challenges in scaling supercomputing to Exascale and beyond. We proposes to exploit stranded power, renewable energy that has no value to the power grid, for scaling supercomputers, Zero-Carbon Cloud…
Lin Chen, Yuhan Chen, Ziqi Cheng, Jing Guo + 20 more
MHPC512 is a massively parallel, special-purpose supercomputer designed primarily for atomic-level molecular dynamics (MD) simulations of biomolecular systems. It comprises 512 processor units interconnected by a high-speed three-dimensional torus network and employs a custom chip architecture that uses 35-bit…
Hyungwook Shim
The exponential growth of artificial intelligence and data-intensive applications has led to a significant surge in demand for supercomputing resources. However, limited infrastructure capacity and rising construction costs have made traditional supply-side expansion strategies increasingly unsustainable. In response…
Pau Andrio, Adam Hospital, Cristian Ramon-Cortes, Javier Conejero + 4 more
The usage of workflows has led to progress in many fields of science, where the need to process large amounts of data is coupled with difficulty in accessing and efficiently using High Performance Computing platforms. On the one hand, scientists are focused on their problem and concerned with how to process their data.…
Patrick McKeever, Varun Mittal, Bryce Fukuda, Ka Yee Yeung + 1 more
The exponential growth of omics data requires novel strategies for storage, transfer, and processing of said data. We present a scheduler based on the Temporal.io workflow framework which enables two key optimizations of bioinformatics workflows. Firstly, we enable users to transparently map workflow steps to diverse…
Skirmantas Janušonis, Ralf Metzler, Thomas Vojta
Serotonergic axons (fibers) are a universal feature of all vertebrate brains. They form meshworks, typically quantified with regional density measurements, and appear to support neuroplasticity. The self-organization of this system remains poorly understood, partly because of the strong stochasticity of individual…
Yuri Matsuzaki, Nobuyuki Uchikoga, Masahito Ohue, Takehiro Shimoda + 3 more
'Toshiyuki Sato' 'Takashi Ishida' 'Yutaka Akiyama'] Background Protein-protein interaction (PPI) plays a core role in cellular functions. Massively parallel supercomputing systems have been actively developed over the past few years, which enable large-scale biological problems to be solved, such as PPI network…
George B. Stefano
Quantum computing and supercomputing are two distinct approaches that can be used to solve complex computational problems. Supercomputers first became available for general use in the mid-1990s and are currently employed routinely to solve calculation-intensive problems, for example, weather forecasting and molecular…
Xiaoyong Tang, Xiaoyi Liao, Yong Wang
Recently, computational Grids have proven to be a good solution for processing large-scale, computation intensive problems. However, the heterogeneity, dynamics of resources and diversity of applications requirements have always been important factors affecting their performance. In response to these challenges, this…
Yann Garniron, Thomas Applencourt, Kevin Gasperich, Anouar Benali + 15 more
Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2). The determinant-driven…
Yann Garniron, Thomas Applencourt, Kevin Gasperich, Anouar Benali + 15 more
Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2). The determinant-driven…
Anda Trifan, Defne Gorgun, Zongyi Li, Alexander Brace + 30 more
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication transcription complex (RTC) is a multi-domain protein responsible for replicating and transcribing the viral mRNA inside a human cell. Attacking RTC function with pharmaceutical compounds is a pathway to treating COVID-19. Conventional tools…
Viacheslav Bolnykh, Jógvan Magnus Haugaard Olsen, Simone Meloni, Martin P. Bircher + 3 more
We present a highly scalable DFT-based QM/MM implementation developed within MiMiC, a recently introduced multiscale modeling framework that uses a loose-coupling strategy in conjunction with a multiple-program multiple-data (MPMD) approach. The computation of electrostatic QM/MM interactions is parallelized exploiting…
Oliver Lee, Malte Gather, Eli Zysman-Colman
We describe a new tool for the efficient management of computational chemistry. Digichem is a program that automates and simplifies nearly the entire computational pipeline, including large-scale batch submission of calculations, analysis and results parsing, the generation of 3D density plots and 2D graphs of…
Samarth Sandeep, Sona Aramyan, Armen H. Poghosyan, Vaibhav Gupta
Determining an optimal protein configuration for the employment of protein binding analysis as completed by Temperature based Replica Exchange Molecular Dynamics (T-REMD) is an important process in the accurate depiction of a protein’s behavior in different solvent environments, especially when determining a protein’s…
Alexander J. Bryer, Juan R. Perilla
Dimensionality reduction via coarse grain modeling has positioned itself as an indispensable tool for decades, particularly for biomolecular simulations where atomic systems encompass hundreds of millions of atoms. While distinct flavors of coarse grain modeling exist, those occupying the coarse end of the spectrum are…
Authors not listed
Computational chemistry has entered a new era where machine learning (ML) models—particularly graph neural networks and machine learning force fields—routinely deliver quantum mechanical accuracy at classical speeds, scaling to millions of atoms and reshaping workflows in drug discovery, catalysis, and materials…
Authors not listed
High-level quantum mechanical (QM) simulations provide accurate electronic information of chemical systems but scale unfavourably with system size, making calculations of applied systems challenging. Hierarchical quantum mechanics in quantum mechanics embedding (QM/QM) addresses this issue by localising the highly…