Zobrazeno 1 - 10 of 13 pro vyhledávání: '"Fabio Affinito"'
1
D8.2: Interim Progress Report – Staff and Established Project Structure
Autor: Fabio Affinito, Joost VandeVondele
This document gives a brief overview of the eight projects funded in PRACE-6IP Work Package (WP) 8. The previous deliverable, D8.1, described the selection process. Therefore, in this deliverable we give an overview of how the project teams are start
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6b17236d876cef75207d84d5889e01cd
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2
Prediction of Time-to-Solution in Material Science Simulations Using Deep Learning
Autor: Fabio Affinito, Federico Pittino, Pietro Bonfà, Andrea Bartolini, Luca Benini, Carlo Cavazzoni
Publikováno v: PASC
PASC '19 Proceedings of the Platform for Advanced Scientific Computing Conference
Proceedings of the Platform for Advanced Scientific Computing Conference
Proceedings of the Platform for Advanced Scientific Computing Conference on -PASC '19
Proceedings of the Platform for Advanced Scientific Computing Conference on-PASC 19
Predicting the time to solution for massively parallel scientific codes is a complex task. The reason for this is the presence of multiple, strongly interconnected algorithms that possibly react differently to the changes in compute power, vectorizat
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ab292ac47e4b89740c155022d8f15dee
http://hdl.handle.net/11585/718393
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3
FFT data distribution in plane-waves DFT codes. A case study from Quantum ESPRESSO
Autor: Carlo Cavazzoni, Fabio Affinito
Publikováno v: EuroMPI
Density Functional Theory calculations with plane waves and pseudopotentials represent one of the most important simulation techniques in high performance computing. Together with parallel linear algebra (ZGEMM and matrix diagonalization), the most i
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::e3bfa7d6cc10985f53a63434d3035350
https://doi.org/10.1145/2966884.2966892
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4
Biased Molecular Simulations for Free-Energy Mapping: A Comparison on the KcsA Channel as a Test Case
Autor: Fabio Affinito, Carlo Jacoboni, Enrico Piccinini, Rossella Brunetti, Matteo Ceccarelli
Publikováno v: Journal of chemical theory and computation 4 (2008): 173–183.
info:cnr-pdr/source/autori:Piccinini, E; Ceccarelli, M; Affinito, F; Brunetti, R; Jacoboni, C/titolo:Biased molecular simulations for free-energy mapping: A comparison on the KcsA channel as a test case/doi:/rivista:Journal of chemical theory and computation/anno:2008/pagina_da:173/pagina_a:183/intervallo_pagine:173–183/volume:4
The calculation of free-energy landscapes in proteins is a challenge for modern numerical simulations. As to the case of potassium ion channels is concerned, it is particularly interesting because of the nanometric dimensions of the selectivity filte
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ac6028236cd3dc7518fc77febd691899
https://pubmed.ncbi.nlm.nih.gov/26619991
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5
Enabling a Quantum Monte Carlo application for the DEEP architecture
Autor: Fabio Affinito, Andrew Emerson
Publikováno v: HPCS
In the DEEP project a prototype Exascale system consisting of a standard Intel Xeon cluster linked to a “Booster” part containing Intel Xeon Phi nodes connected in a high-speed network, is being designed and constructed. In order to evaluate this
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::b2e7c71d9db735c4a9c06e3baa1e1b3d
https://doi.org/10.1109/hpcsim.2015.7237075
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6
Computational Analysis of Current and Noise Properties of a Single Open Ion Channel
Autor: Enrico Piccinini, Fabio Affinito, Rossella Brunetti, Massimo Rudan, Carlo Jacoboni
Publikováno v: Journal of chemical theory and computation 3 (2007): 248–255.
info:cnr-pdr/source/autori:Piccinini, E; Affinito, F; Brunetti, R; Jacoboni, C; Rudan, M/titolo:Computational analysis of current and noise properties of a single open ion channel/doi:/rivista:Journal of chemical theory and computation/anno:2007/pagina_da:248/pagina_a:255/intervallo_pagine:248–255/volume:3
This paper presents a computational analysis of the noise associated with the ion current in single open ion channels. The study is performed by means of a coupled molecular dynamics/Monte Carlo approach able to simulate the onduction process on the
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::36884b38f6a6dc6a522b317e9001ae99
https://doi.org/10.1021/ct6002077
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8
Performance Analysis And Petascaling Enabling Of Gromacs
Autor: Fabio Affinito
The work aims at evaluating the performance of GROMACS on different platforms and and determine the optimal set of conditions for given architectures for petascaling molecular dynamics simulations. The activities have been organized into three tasks
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9
Multidimensional View of Amyloid Fibril Nucleation in Atomistic Detail
Autor: Fabio Pietrucci, Alessandro Laio, Fahimeh Baftizadeh, Xevi Biarnés, Fabio Affinito
Starting from a disordered aggregate, we have simulated the formation of ordered amyloid-like beta structures in a system formed by 18 polyvaline chains in explicit solvent, employing molecular dynamics accelerated by bias-exchange metadynamics. We e
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d00e1bb3d4121876c0297c7e46b22808
http://hdl.handle.net/20.500.11767/14094
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10
Physical Mechanisms for ion-current levelling off in the KcsA channel through combined Monte Carlo/Molecular Dynamics simulations
Autor: Fabio Affinito, Massimo Rudan, Enrico Piccinini, Rossella Brunetti, Carlo Jacoboni
Publikováno v: Nonequilibrium Carrier Dynamics in Semiconductors ISBN: 9783540365877
Conduction and noise properties of potassium ions in the KcsA membrane channel are analysed by means of a combined Molecular Dynamics-Monte Carlo numerical approach. The high-voltage part of the experimental I(V) characteristics shows a tendency to l
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f3440009d014f5ae9deca2cf3c508589
https://hdl.handle.net/11380/464176
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