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Coupling streaming AI and HPC ensembles to achieve 100-1000x faster biomolecular simulations [article]

Alexander Brace, Igor Yakushin, Heng Ma, Anda Trifan, Todd Munson, Ian Foster, Arvind Ramanathan, Hyungro Lee, Matteo Turilli, Shantenu Jha
2022 arXiv   pre-print
We demonstrate that DeepDriveMD can achieve between 100-1000x acceleration for protein folding simulations relative to other methods, as measured by the amount of simulated time performed, while covering  ...  We present DeepDriveMD, a framework for ML-driven steering of scientific simulations that we have used to achieve orders-of-magnitude improvements in molecular dynamics (MD) performance via effective coupling  ...  Compared to the Anton simulations, the ML + RMSD strategy (for which uncertainty from 10 trials is shown in light red) reaches 80% sampling more than 1000× faster.  ... 
arXiv:2104.04797v5 fatcat:vd6l3vyx2ngjtjv7wbdorqcgyu

Expanding the boundaries of ligand–target modeling by exascale calculations

Viacheslav Bolnykh, Giulia Rossetti, Ursula Rothlisberger, Paolo Carloni
2021 Wiley Interdisciplinary Reviews. Computational Molecular Science  
Molecular simulations and molecular docking are widely used tools to investigate ligand/target interactions and in drug design.  ...  This review discusses how innovative HPC algorithms and hardware are being exploited in current simulations and docking codes, pointing also at some of the limitations of these approaches.  ...  For small system sizes (10-100 QM atoms) the scaling limit is around 1000-10,000 cores, whereas, for larger systems, it can be in the area of millions. 97 Recently, CPMD was also coupled with ML in order  ... 
doi:10.1002/wcms.1535 fatcat:wwu4ixhvhngivkz4olvzm3c6r4

ETP4HPC's Strategic Research Agenda for High-Performance Computing in Europe 4 [article]

Michael Malms, Marcin Ostasz, Maike Gilliot, Pascale Bernier-Bruna, Laurent Cargemel, Estela Suarez, Herbert Cornelius, Marc Duranton, Benny Koren, Pascale Rosse-Laurent, María S. Pérez-Hernández, Manolis Marazakis (+11 others)
2020 Zenodo  
The main objective of this SRA is to identify the European technology research priorities in the area of HPC and High-Performance Data Analytics (HPDA), which should be used by EuroHPC to build its 2021  ...  HPC form what we have come to call "The Digital Continuum".  ...  Such systems will enable the coupling (the Digital Continuum, from Edge-level, embedded HPC to HPC of simulation, databases and data streams, data analytics and clouds and Exascale computing and  ... 
doi:10.5281/zenodo.4605343 fatcat:lcsgbea5dzgdfmj5dkw6pr7vni

CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations

Thomas D. Kühne, Marcella Iannuzzi, Mauro Del Ben, Vladimir V. Rybkin, Patrick Seewald, Frederick Stein, Teodoro Laino, Rustam Z. Khaliullin, Ole Schütt, Florian Schiffmann, Dorothea Golze, Jan Wilhelm (+27 others)
2020 Journal of Chemical Physics  
This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations.  ...  CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems.  ...  (CPU) cores, allowing for MP2-based structure relaxation and even AIMD simulations on HPC facilities.  ... 
doi:10.1063/5.0007045 pmid:33687235 fatcat:a5o4bngmcrcslmfj3dcsr5blxi

CP2K: An electronic structure and molecular dynamics software package

Gloria Tabacchi
2020 Figshare  
CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculationsThomas D.  ...  (CPU) cores, allowing for MP2-based structure relaxation and even AIMD simulations on HPC facilities.  ...  However, the linear scaling version can be coupled with subsystem DFT to achieve true linear scaling behavior.  ... 
doi:10.6084/m9.figshare.12520709 fatcat:geqacrvi5jbwndgg33wu6nl3hq

第56回年会予稿集

2018 Seibutsu Butsuri  
Biophysical Society of Japan (BSJ) grants "Early Career Award in Biophysics" and "Early Career Presentation Award" to young BSJ members for their excellent presentations that show great potential to contribute  ...  Up to five awardees of the Early Career Award in Biophysics will be selected and announced at the banquet 3SEA-5 光遺伝子操作による単一の糸球体の活性により誘因される恐怖行動の探索 Immobility responses are induced by photoactivation of  ...  ensemble, and string method.  ... 
doi:10.2142/biophys.58.s1 fatcat:6slkwnu64fen7cjixehxrcmdzm

CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations

Thomas D Kühne, Marcella Iannuzzi, Mauro Del Ben, Vladimir V Rybkin, Patrick Seewald, Frederick Stein, Teodoro Laino, Rustam Z Khaliullin, Ole Schütt, Florian Schiffmann, Dorothea Golze, Jan Wilhelm (+18 others)
2020
CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid,molecular, and biological systems.  ...  This review revisits the main capabilities of CP2K to perform efficient andaccurate electronic structure simulations.  ...  (CPU) cores, allowing for MP2-based structure relaxation and even AIMD simulations on HPC facilities.  ... 
doi:10.5167/uzh-192979 fatcat:whml3d55jzh25nl5kwjcqolgme

Dagstuhl Reports, Volume 4, Issue 11, November 2014, Complete Issue [article]

2015
Between 10 and 100 Mb/s, with data budgets of at least 100 GB, streaming video-on-demand becomes plausible, while, longer term, a full TV replacement at 4K quality is likely to push the monthly data volume  ...  raises the need for faster simulation algorithms.  ...  Standard formats such as SBML and CellML have allowed the exchange of models of biochemical reaction networks between users and simulation software, enhanced reproducibility of models and enables the creation  ... 
doi:10.4230/dagrep.4.11 fatcat:zzps76cx7rfldla5z5dikvsqbe