Parallel solution of the obstacle problem in Grid environments

2011 ◽  
Vol 25 (4) ◽  
pp. 488-495 ◽  
Author(s):  
M. Chau ◽  
R. Couturier ◽  
J. Bahi ◽  
P. Spiteri
Keyword(s):  
Iterative Algorithm ◽  
Obstacle Problem ◽  
General Framework ◽  
Large Scale ◽  
Three Dimensional ◽  
Computational Experiments ◽  
Parallel Solution ◽  
Asynchronous Algorithms ◽  
Grid Environments ◽  
Dimensional Domain

The present study deals with the solution of the obstacle problem defined in a three-dimensional domain. In order to solve a large-scale obstacle problem, the use of parallelism is necessary. In this work we present a parallel synchronous iterative algorithm to solve this problem and its asynchronous version. For the considered problem, the convergence of parallel synchronous and asynchronous algorithms is analysed in a general framework. Finally, computational experiments on GRID’5000, the French national grid, are presented and analysed. They allow us to compare both synchronous and asynchronous versions with local and distributed clusters.

scholarly journals The Stability Principle and global weak solutions of the free surface semi-geostrophic equations in geostrophic coordinates

2019 ◽  
Vol 475 (2229) ◽  
pp. 20180787
Author(s):  
M. J. P. Cullen ◽  
T. Kuna ◽  
B. Pelloni ◽  
M. Wilkinson
Keyword(s):  
Weak Solutions ◽  
Large Scale ◽  
Optimal Transport ◽  
Three Dimensional ◽  
Mathematical Framework ◽  
Atmospheric Flows ◽  
Stability Principle ◽  
The Stability ◽  
Dimensional Domain ◽  
Upper Boundary

The semi-geostrophic equations are used widely in the modelling of large-scale atmospheric flows. In this note, we prove the global existence of weak solutions of the incompressible semi-geostrophic equations, in geostrophic coordinates, in a three-dimensional domain with a free upper boundary. The proof, based on an energy minimization argument originally inspired by the Stability Principle as studied by Cullen, Purser and others, uses optimal transport techniques as well as the analysis of Hamiltonian ODEs in spaces of probability measures as studied by Ambrosio and Gangbo. We also give a general formulation of the Stability Principle in a rigorous mathematical framework.

Virtual Demonstration Tests of Large-Scale and Complex Artifacts Using an Open Source Parallel CAE System, ADVENTURE

2006 ◽  
Vol 110 ◽  
pp. 133-142 ◽  
Author(s):  
Shinobu Yoshimura
Keyword(s):  
Open Source ◽  
Large Scale ◽  
Three Dimensional ◽  
Element Model ◽  
General Purpose ◽  
Full Scale ◽  
Grid Environments ◽  
Dimensional Finite Element ◽  
Three Dimensional Finite Element ◽  
Cae System

The ADVENTURE project started as one of the research projects in the "Computational Science & Engineering" field selected for the "Research for the Future" Program sponsored by the Japan Society for the Promotion of Science during 1997-2002. Since March 2002, the project has continued as an independent project. In the project we have been developing an advanced general-purpose computational mechanics system, named ADVENTURE, running in various kinds of parallel and ditributed environments. The system is designed to be able to analyze a three-dimensional finite element model of arbitrary shape with 10-100 million DOFs mesh, and additionally to enable parametric and non-parametric shape optimization. The first version of the system has been released from the project website as open source software since March, 2002. 2,049 registered users in academia and industries have downloaded 12,827 modules and been using them, while one company has developed and released its commercial version named ADVENTUREcluster. The ADVENTURE system has been successfully implemented in various types of parallel and distributed environments including PC clusters, massively parallel processers such as Hitachi SR8000/MPP and the Earth Simulator, and Grid environments such as ITBL (IT-based Laboratory). The system has been successfully applied to solve various real world problems such as response of a full scale nuclear pressure vessel model and thermoelastic deformation of full scale electric mounting board of a mobile PC.

Target-Templated de novo Design of Macrocyclic D-/L-Peptides: Inhibitors of the PD-1/PD-L1 Interaction

2020 ◽  
Author(s):  
Salvador Guardiola ◽  
Monica Varese ◽  
Xavier Roig ◽  
Jesús Garcia ◽  
Ernest Giralt
Keyword(s):  
Protein Interactions ◽  
Cyclic Peptides ◽  
General Framework ◽  
Large Scale ◽  
De Novo ◽  
Inhibitory Effect ◽  
Original Text ◽  
Protein Protein Interactions ◽  
Retraction Notice ◽  
Pharmaceutical Properties

<p>NOTE: This preprint has been retracted by consensus from all authors. See the retraction notice in place above; the original text can be found under "Version 1", accessible from the version selector above.</p><p><br></p><p>------------------------------------------------------------------------</p><p><br></p><p>Peptides, together with antibodies, are among the most potent biochemical tools to modulate challenging protein-protein interactions. However, current structure-based methods are largely limited to natural peptides and are not suitable for designing target-specific binders with improved pharmaceutical properties, such as macrocyclic peptides. Here we report a general framework that leverages the computational power of Rosetta for large-scale backbone sampling and energy scoring, followed by side-chain composition, to design heterochiral cyclic peptides that bind to a protein surface of interest. To showcase the applicability of our approach, we identified two peptides (PD-<i>i</i>3 and PD-<i>i</i>6) that target PD-1, a key immune checkpoint, and work as protein ligand decoys. A comprehensive biophysical evaluation confirmed their binding mechanism to PD-1 and their inhibitory effect on the PD-1/PD-L1 interaction. Finally, elucidation of their solution structures by NMR served as validation of our <i>de novo </i>design approach. We anticipate that our results will provide a general framework for designing target-specific drug-like peptides.<i></i></p>

A Target-Based Method for Designing Heterochiral Cyclic Peptide Binders: De Novo Inhibitors of the PD-1/PD-L1 Interaction

2020 ◽  
Author(s):  
Salvador Guardiola ◽  
Monica Varese ◽  
Xavier Roig ◽  
Jesús Garcia ◽  
Ernest Giralt
Keyword(s):  
Protein Interactions ◽  
Cyclic Peptides ◽  
General Framework ◽  
Large Scale ◽  
Cyclic Peptide ◽  
De Novo ◽  
Inhibitory Effect ◽  
Original Text ◽  
Retraction Notice ◽  
Pharmaceutical Properties

<p>NOTE: This preprint has been retracted by consensus from all authors. See the retraction notice in place above; the original text can be found under "Version 1", accessible from the version selector above.</p><p><br></p><p>------------------------------------------------------------------------</p><p><br></p><p>Peptides, together with antibodies, are among the most potent biochemical tools to modulate challenging protein-protein interactions. However, current structure-based methods are largely limited to natural peptides and are not suitable for designing target-specific binders with improved pharmaceutical properties, such as macrocyclic peptides. Here we report a general framework that leverages the computational power of Rosetta for large-scale backbone sampling and energy scoring, followed by side-chain composition, to design heterochiral cyclic peptides that bind to a protein surface of interest. To showcase the applicability of our approach, we identified two peptides (PD-<i>i</i>3 and PD-<i>i</i>6) that target PD-1, a key immune checkpoint, and work as protein ligand decoys. A comprehensive biophysical evaluation confirmed their binding mechanism to PD-1 and their inhibitory effect on the PD-1/PD-L1 interaction. Finally, elucidation of their solution structures by NMR served as validation of our <i>de novo </i>design approach. We anticipate that our results will provide a general framework for designing target-specific drug-like peptides.<i></i></p>

Target-Templated de novo Design of Macrocyclic D-/L-Peptides: Inhibitors of the PD-1/PD-L1 Interaction

2020 ◽  
Author(s):  
Salvador Guardiola ◽  
Monica Varese ◽  
Xavier Roig ◽  
Jesús Garcia ◽  
Ernest Giralt
Keyword(s):  
Protein Interactions ◽  
Cyclic Peptides ◽  
General Framework ◽  
Large Scale ◽  
De Novo ◽  
Inhibitory Effect ◽  
Original Text ◽  
Protein Protein Interactions ◽  
Retraction Notice ◽  
Pharmaceutical Properties

<p>NOTE: This preprint has been retracted by consensus from all authors. See the retraction notice in place above; the original text can be found under "Version 1", accessible from the version selector above.</p><p><br></p><p>------------------------------------------------------------------------</p><p><br></p><p>Peptides, together with antibodies, are among the most potent biochemical tools to modulate challenging protein-protein interactions. However, current structure-based methods are largely limited to natural peptides and are not suitable for designing target-specific binders with improved pharmaceutical properties, such as macrocyclic peptides. Here we report a general framework that leverages the computational power of Rosetta for large-scale backbone sampling and energy scoring, followed by side-chain composition, to design heterochiral cyclic peptides that bind to a protein surface of interest. To showcase the applicability of our approach, we identified two peptides (PD-<i>i</i>3 and PD-<i>i</i>6) that target PD-1, a key immune checkpoint, and work as protein ligand decoys. A comprehensive biophysical evaluation confirmed their binding mechanism to PD-1 and their inhibitory effect on the PD-1/PD-L1 interaction. Finally, elucidation of their solution structures by NMR served as validation of our <i>de novo </i>design approach. We anticipate that our results will provide a general framework for designing target-specific drug-like peptides.<i></i></p>

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