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Structure: Internal structure identifier : 555012

Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution

Miki Nakano , Osamu Miyashita , Slavica Jonic , Atsushi Tokuhisa , Florence Tama et al.
Journal of Synchrotron Radiation, 2018, 25 (4), pp.1010-1021. ⟨10.1107/S1600577518005568⟩
Journal articles hal-02324599v1

Editorial: Hybrid Biomolecular Modeling

Slavica Jonic , Osamu Miyashita , Isabelle Callebaut
Frontiers in Molecular Biosciences, 2018, 5, ⟨10.3389/fmolb.2018.00098⟩
Journal articles hal-02324595v1
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Toward an integrated NWP-DA-AI system for 30-second-update precipitation prediction

Shigenori Otsuka , Yasumitsu Maejima , Pierre Tandeo , Takemasa Miyoshi
ECMWF-ESA Workshop on Machine Learning for Earth System Observation and Prediction, Oct 2020, Virtual Conference, United Kingdom
Conference poster hal-02967547v1

A Case Study of the Reproducibility Issues in EigenExa

Roman Iakymchuk , Imamura Toshiyuki , Stef Graillat , Stefano Markidis , Erwin Laure et al.
EASC2016, Exascale Applications and Software Conference, Apr 2016, Stockholm, Sweden
Conference papers hal-01539365v1
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Conjugate Gradient Solvers with High Accuracy and Bit-wise Reproducibility between CPU and GPU using Ozaki Scheme

Daichi Mukunoki , Katsuhisa Ozaki , Takeshi Ogita , Roman Iakymchuk
Preprints, Working Papers, ... hal-02986873v1
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Remedies for Reproducibility Issue in Conjugate Gradient Solvers

Daichi Mukunoki , Roman Iakymchuk , Fabienne Jézéquel , Katsuhisa Ozaki , Takeshi Ogita et al.
Sparse Days conference, Jun 2022, Saint-Girons, France
Conference poster hal-03783027v1
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Neutron star mergers as the astrophysical site of the r-process in the Milky Way and its satellite galaxies

Shinya Wanajo , Yutaka Hirai , Nikos Prantzos
Monthly Notices of the Royal Astronomical Society, 2021, 505 (4), pp.5862-5883. ⟨10.1093/mnras/stab1655⟩
Journal articles hal-03422626v1
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Comparing the performance of rigid, moldable and grid-shaped applications on failure-prone HPC platforms

Valentin Le Fèvre , Thomas Herault , Yves Robert , Aurelien Bouteiller , Atsushi Hori et al.
Parallel Computing, 2019, 85, pp.1-12. ⟨10.1016/j.parco.2019.02.002⟩
Journal articles hal-03360189v1
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An International Survey on MPI Users

Atsushi Hori , Emmanuel Jeannot , George Bosilca , Takahiro Ogura , Balazs Gerofi et al.
Parallel Computing, 2021, 108, pp.102853. ⟨10.1016/j.parco.2021.102853⟩
Journal articles hal-03347652v1

3rd IEEE International Workshop on Extreme-Scale Storage and Analysis (ESSA 2022)

Osamu Tatebe , Gabriel Antoniu , Kento Sato , Murali Emani
2022 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), IEEE, pp.1098-1099, 2022, ⟨10.1109/IPDPSW55747.2022.00178⟩
Proceedings hal-03933407v1

Protein - ligand interactions from a quantum fragmentation perspective : the case of the SARS-CoV-2 main protease interacting with α−ketoamide inhibitors

Luigi Genovese , William Dawson , Takahito Nakajima , Viviana Cristiglio , Valérie Vallet et al.
Preprints, Working Papers, ... hal-02933298v1
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Macromolecular Dynamics by Hybrid Electron Microscopy Normal Mode Analysis

Qiyu Jin , Carlos Oscar S. Sorzano , Jose Miguel de La Rosa-Trevín , Florence Tama , Slavica Jonić et al.
Microscopy and Microanalysis, Aug 2014, Hartford, United States. pp.1218 - 1219, ⟨10.1017/S143192761400782X⟩
Conference papers hal-01431467v1

Hybrid approach for structural modeling of biological systems from X-ray free electron laser diffraction patterns

Atsushi Tokuhisa , Slavica Jonic , Florence Tama , Osamu Miyashita
Journal of Structural Biology, 2016, 194, pp.325 - 336. ⟨10.1016/j.jsb.2016.03.009⟩
Journal articles hal-01430528v1
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Iterative Elastic 3D-to-2D Alignment Method Using Normal Modes for Studying Structural Dynamics of Large Macromolecular Complexes

Qiyu Jin , Carlos Oscar S. Sorzano , José Miguel de La Rosa-Trevín , José Román Bilbao-Castro , Rafael Nunez-Ramirez et al.
Structure, 2014, 22 (3), pp.496-506. ⟨10.1016/j.str.2014.01.004⟩
Journal articles hal-01430531v1
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NMMD: Efficient cryo-EM flexible fitting based on simultaneous Normal Mode and Molecular Dynamics atomic displacements

Rémi Vuillemot , Osamu Miyashita , Florence Tama , Isabelle Rouiller , Slavica Jonic et al.
Journal of Molecular Biology, 2022, 434 (7), pp.167483. ⟨10.1016/j.jmb.2022.167483⟩
Journal articles hal-03577246v1
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Joint Estimation of Model and Observation Error Covariance Matrices in Data Assimilation: a Review

Pierre Tandeo , Pierre Ailliot , Marc Bocquet , Alberto Carrassi , Takemasa Miyoshi et al.
Preprints, Working Papers, ... hal-01867958v1
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Blind test of density-functional-based methods on intermolecular interaction energies

Decarlos Taylor , János Ángyán , Giulia Galli , Cui Zhang , Francois Gygi et al.
Journal of Chemical Physics, 2016, 145 (12), pp.124105. ⟨10.1063/1.4961095⟩
Journal articles hal-03958068v1
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Global structure and sodium ion dynamics in Mercury's magnetosphere with the offset dipole

Manabu Yagi , Kanako Seki , Y. Matsumoto , Dominique C. Delcourt , François Leblanc et al.
Journal of Geophysical Research Space Physics, 2017, 122 (11), pp.10,990-11,002. ⟨10.1002/2017JA024082⟩
Journal articles insu-01585106v1
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Can we avoid rounding-error estimation in HPC codes and still get trustful results?

Fabienne Jézéquel , Stef Graillat , Daichi Mukunoki , Toshiyuki Imamura , Roman Iakymchuk et al.
Preprints, Working Papers, ... hal-02486753v1

Minimal-Precision Computing for High-Performance, Energy-Efficient, and Reliable Computations

Taisuke Boku , Norihisa Fujita , Stef Graillat , Jens Huthmann , Roman Iakymchuk et al.
2nd R-CCS international symposium, K to Fugaku: Simulation, Big Data and AI supporting Society 5.0, Feb 2020, Kobe, Japan
Conference poster hal-02486850v1

Minimal-Precision Computing for High-Performance, Energy-Efficient, and Reliable Computations

Taisuke Boku , Norihisa Fujita , Stef Graillat , Jens Huthmann , Roman Iakymchuk et al.
International Conference on High Performance Computing, Networking, Storage and Analysis (SC19), Nov 2019, Denver, United States
Conference poster hal-02401757v1
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Is Japanese HPC another Galapagos? - Interim Report of MPI International Survey

Atsushi Hori , George Bosilca , Emmanuel Jeannot , Takahiro Ogura , Yutaka Ishikawa et al.
Summer United Workshops on Parallel, Distributed and Cooperative Processing, Jul 2019, Kitami, Japan
Conference papers hal-02193264v1
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Do moldable applications perform better on failure-prone HPC platforms?

Valentin Le Fèvre , George Bosilca , Aurelien Bouteiller , Thomas Herault , Atsushi Hori et al.
[Research Report] RR-9174, Inria Grenoble Rhône-Alpes. 2018, pp.1-24
Reports hal-01799498v1

Seamless Simulations of Earthquake Disasters and Economy at 1:1 scale Utilizing Big-data

Amit Gill , Maddegedara Lalith , Yoshiki Ogawa , Hideyuki O-Tani , Tsuyoshi Ichimura et al.
WI-IAT '21: IEEE/WIC/ACM International Conference on Web Intelligence, Dec 2021, Melbourne VIC, Australia. pp.101-108, ⟨10.1145/3498851.3498937⟩
Conference papers hal-03677307v1

MYX: Runtime Correctness Analysis for Multi-Level Parallel Programming Paradigms

Joachim Protze , Miwako Tsuji , Christian Terboven , Thomas Dufaud , Hitoshi Murai et al.
Software for Exascale Computing - SPPEXA 2016-2019, 136, Springer International Publishing, pp.545-567, 2020, Lecture Notes in Computational Science and Engineering, ⟨10.1007/978-3-030-47956-5_18⟩
Book sections hal-03429330v1
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Multi-SPMD Programming Model with YML and XcalableMP

Miwako Tsuji , Hitoshi Murai , Taisuke Boku , Mitsuhisa Sato , Serge Petiton et al.
XcalableMP PGAS Programming Language, Springer Singapore, pp.219-243, 2021, ⟨10.1007/978-981-15-7683-6_9⟩
Book sections hal-03429306v1

A comprehensive workflow for general-purpose neural modeling with highly configurable neuromorphic hardware systems.

Daniel Brüderle , Mihai A Petrovici , Bernhard Vogginger , Matthias Ehrlich , Thomas Pfeil et al.
Biological Cybernetics (Modeling), 2011, 104 (4-5), pp.263-96. ⟨10.1007/s00422-011-0435-9⟩
Journal articles hal-00635967v1
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A Review of Innovation-Based Methods to Jointly Estimate Model and Observation Error Covariance Matrices in Ensemble Data Assimilation

Pierre Tandeo , Pierre Ailliot , Marc Bocquet , Alberto Carrassi , Takemasa Miyoshi et al.
Monthly Weather Review, 2020, 148 (10), pp.3973-3994. ⟨10.1175/MWR-D-19-0240.1⟩
Journal articles hal-02922301v1

Prefetching on storage servers through mining access patterns on blocks

Jianwei Liao , François Trahay , Balazs Gerofi , Yutaka Ishikawa
IEEE Transactions on Parallel and Distributed Systems, 2016, 27 (9), pp.2698 - 2710. ⟨10.1109/TPDS.2015.2496595⟩
Journal articles hal-01354329v1

Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol

Carlos Oscar S. Sorzano , José Miguel de La Rosa-Trevín , Florence Tama , Slavica Jonić
Journal of Structural Biology, 2014, 188 (2), pp.134-141. ⟨10.1016/j.jsb.2014.09.005⟩
Journal articles hal-01148382v1