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1. WelQrate: Defining the Gold Standard in Small Molecule Drug Discovery Benchmarking

Author

Yunchao, Liu, Dong, Ha, Wang, Xin, Moretti, Rocco, Wang, Yu, Su, Zhaoqian, Gu, Jiawei, Bodenheimer, Bobby, Weaver, Charles David, Meiler, Jens, and Derr, Tyler

Subjects
Computer Science - Machine Learning, Computer Science - Artificial Intelligence, Quantitative Biology - Biomolecules
Abstract

While deep learning has revolutionized computer-aided drug discovery, the AI community has predominantly focused on model innovation and placed less emphasis on establishing best benchmarking practices. We posit that without a sound model evaluation framework, the AI community's efforts cannot reach their full potential, thereby slowing the progress and transfer of innovation into real-world drug discovery. Thus, in this paper, we seek to establish a new gold standard for small molecule drug discovery benchmarking, WelQrate. Specifically, our contributions are threefold: WelQrate Dataset Collection - we introduce a meticulously curated collection of 9 datasets spanning 5 therapeutic target classes. Our hierarchical curation pipelines, designed by drug discovery experts, go beyond the primary high-throughput screen by leveraging additional confirmatory and counter screens along with rigorous domain-driven preprocessing, such as Pan-Assay Interference Compounds (PAINS) filtering, to ensure the high-quality data in the datasets; WelQrate Evaluation Framework - we propose a standardized model evaluation framework considering high-quality datasets, featurization, 3D conformation generation, evaluation metrics, and data splits, which provides a reliable benchmarking for drug discovery experts conducting real-world virtual screening; Benchmarking - we evaluate model performance through various research questions using the WelQrate dataset collection, exploring the effects of different models, dataset quality, featurization methods, and data splitting strategies on the results. In summary, we recommend adopting our proposed WelQrate as the gold standard in small molecule drug discovery benchmarking. The WelQrate dataset collection, along with the curation codes, and experimental scripts are all publicly available at WelQrate.org., Comment: * denotes equal contribution

Published
2024

2. REvoLd: Ultra-Large Library Screening with an Evolutionary Algorithm in Rosetta

Author

Eisenhuth, Paul, Liessmann, Fabian, Moretti, Rocco, and Meiler, Jens

Subjects
Quantitative Biology - Quantitative Methods
Abstract

Ultra-large make-on-demand compound libraries now contain billions of readily available compounds. This represents a golden opportunity for in-silico drug discovery. One challenge, however, is the time and computational cost of an exhaustive screen of such large libraries when receptor flexibility is taken into account. We propose an evolutionary algorithm to search combinatorial make-on-demand chemical space efficiently without enumerating all molecules. We exploit the feature of make-on-demand compound libraries, namely that they are constructed from lists of substrates and chemical reactions. Our novel algorithm RosettaEvolutionaryLigand (REvoLd) explores the vast search space of combinatorial libraries for protein-ligand docking with full ligand and receptor flexibility through RosettaLigand. A benchmark of REvoLd on five drug targets showed improvements in hit rates by factors between 869 and 1,622 compared to random selections. REvoLd is available as an application within the Rosetta software suite., Comment: 29 pages, 9 figures

Published
2024

3. Posttranslationally modified self-peptides promote hypertension in mouse models

Author

Bloodworth, Nathaniel, Chen, Wei, Hunter, Kuniko, Patrick, David, Palubinsky, Amy, Phillips, Elizabeth, Roeth, Daniel, Kalkum, Markus, Mallal, Simon, Davies, Sean, Ao, Mingfang, Moretti, Rocco, Meiler, Jens, and Harrison, David G.

Subjects
Major histocompatibility complex -- Health aspects, Peptides -- Health aspects, Hypertension -- Diagnosis -- Care and treatment
Abstract

Posttranslational modifications can enhance immunogenicity of self-proteins. In several conditions, including hypertension, systemic lupus erythematosus, and heart failure, isolevuglandins (IsoLGs) are formed by lipid peroxidation and covalently bond with protein lysine residues. Here, we show that the murine class I major histocompatibility complex (MHC-I) variant [H-2D.sup.b] uniquely presents isoLG-modified peptides and developed a computational pipeline that identifies structural features for MHC-I accommodation of such peptides. We identified isoLG-adducted peptides from renal proteins, including sodium glucose transporter 2, cadherin 16, Kelch domain-containing protein 7A, and solute carrier family 23, that are recognized by [CD8.sup.+] T cells in tissues of hypertensive mice, induce T cell proliferation in vitro, and prime hypertension after adoptive transfer. Finally, we find patterns of isoLG-adducted antigen restriction in class I human leukocyte antigens that are similar to those in murine analogs. Thus, we have used a combined computational and experimental approach to define likely antigenic peptides in hypertension., Introduction Accumulating evidence from the last several decades implicates inflammation and immune activation in the genesis of hypertension and its sequelae (1). Both the innate and adaptive immune systems contribute [...]

Published
2024
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4. Deep Learning for Virtual Screening: Five Reasons to Use ROC Cost Functions

Author

Golkov, Vladimir, Becker, Alexander, Plop, Daniel T., Čuturilo, Daniel, Davoudi, Neda, Mendenhall, Jeffrey, Moretti, Rocco, Meiler, Jens, and Cremers, Daniel

Subjects
Quantitative Biology - Biomolecules, Computer Science - Machine Learning, Quantitative Biology - Quantitative Methods, Statistics - Machine Learning, 68T07 (Primary) 62H30, 92E99, 68T10, 62F07 (Secondary), G.3, I.2.1, I.2.6, I.5.1, J.3
Abstract

Computer-aided drug discovery is an essential component of modern drug development. Therein, deep learning has become an important tool for rapid screening of billions of molecules in silico for potential hits containing desired chemical features. Despite its importance, substantial challenges persist in training these models, such as severe class imbalance, high decision thresholds, and lack of ground truth labels in some datasets. In this work we argue in favor of directly optimizing the receiver operating characteristic (ROC) in such cases, due to its robustness to class imbalance, its ability to compromise over different decision thresholds, certain freedom to influence the relative weights in this compromise, fidelity to typical benchmarking measures, and equivalence to positive/unlabeled learning. We also propose new training schemes (coherent mini-batch arrangement, and usage of out-of-batch samples) for cost functions based on the ROC, as well as a cost function based on the logAUC metric that facilitates early enrichment (i.e. improves performance at high decision thresholds, as often desired when synthesizing predicted hit compounds). We demonstrate that these approaches outperform standard deep learning approaches on a series of PubChem high-throughput screening datasets that represent realistic and diverse drug discovery campaigns on major drug target families., Comment: 10 pages

Published
2020

5. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

Author

Koehler Leman, Julia, Lyskov, Sergey, Lewis, Steven M, Adolf-Bryfogle, Jared, Alford, Rebecca F, Barlow, Kyle, Ben-Aharon, Ziv, Farrell, Daniel, Fell, Jason, Hansen, William A, Harmalkar, Ameya, Jeliazkov, Jeliazko, Kuenze, Georg, Krys, Justyna D, Ljubetič, Ajasja, Loshbaugh, Amanda L, Maguire, Jack, Moretti, Rocco, Mulligan, Vikram Khipple, Nance, Morgan L, Nguyen, Phuong T, Ó Conchúir, Shane, Roy Burman, Shourya S, Samanta, Rituparna, Smith, Shannon T, Teets, Frank, Tiemann, Johanna KS, Watkins, Andrew, Woods, Hope, Yachnin, Brahm J, Bahl, Christopher D, Bailey-Kellogg, Chris, Baker, David, Das, Rhiju, DiMaio, Frank, Khare, Sagar D, Kortemme, Tanja, Labonte, Jason W, Lindorff-Larsen, Kresten, Meiler, Jens, Schief, William, Schueler-Furman, Ora, Siegel, Justin B, Stein, Amelie, Yarov-Yarovoy, Vladimir, Kuhlman, Brian, Leaver-Fay, Andrew, Gront, Dominik, Gray, Jeffrey J, and Bonneau, Richard

Subjects
Information and Computing Sciences, Software Engineering, Bioengineering, Networking and Information Technology R&D (NITRD), Benchmarking, Binding Sites, Humans, Ligands, Macromolecular Substances, Molecular Docking Simulation, Protein Binding, Proteins, Reproducibility of Results, Software
Abstract

Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and computational environments. Here we show how scientific software applications can be created in a reproducible manner when simple design goals for reproducibility are met. We describe the implementation of a test server framework and 40 scientific benchmarks, covering numerous applications in Rosetta bio-macromolecular modeling. High performance computing cluster integration allows these benchmarks to run continuously and automatically. Detailed protocol captures are useful for developers and users of Rosetta and other macromolecular modeling tools. The framework and design concepts presented here are valuable for developers and users of any type of scientific software and for the scientific community to create reproducible methods. Specific examples highlight the utility of this framework, and the comprehensive documentation illustrates the ease of adding new tests in a matter of hours.

Published
2021

6. Macromolecular modeling and design in Rosetta: recent methods and frameworks

Author

Leman, Julia Koehler, Weitzner, Brian D, Lewis, Steven M, Adolf-Bryfogle, Jared, Alam, Nawsad, Alford, Rebecca F, Aprahamian, Melanie, Baker, David, Barlow, Kyle A, Barth, Patrick, Basanta, Benjamin, Bender, Brian J, Blacklock, Kristin, Bonet, Jaume, Boyken, Scott E, Bradley, Phil, Bystroff, Chris, Conway, Patrick, Cooper, Seth, Correia, Bruno E, Coventry, Brian, Das, Rhiju, De Jong, René M, DiMaio, Frank, Dsilva, Lorna, Dunbrack, Roland, Ford, Alexander S, Frenz, Brandon, Fu, Darwin Y, Geniesse, Caleb, Goldschmidt, Lukasz, Gowthaman, Ragul, Gray, Jeffrey J, Gront, Dominik, Guffy, Sharon, Horowitz, Scott, Huang, Po-Ssu, Huber, Thomas, Jacobs, Tim M, Jeliazkov, Jeliazko R, Johnson, David K, Kappel, Kalli, Karanicolas, John, Khakzad, Hamed, Khar, Karen R, Khare, Sagar D, Khatib, Firas, Khramushin, Alisa, King, Indigo C, Kleffner, Robert, Koepnick, Brian, Kortemme, Tanja, Kuenze, Georg, Kuhlman, Brian, Kuroda, Daisuke, Labonte, Jason W, Lai, Jason K, Lapidoth, Gideon, Leaver-Fay, Andrew, Lindert, Steffen, Linsky, Thomas, London, Nir, Lubin, Joseph H, Lyskov, Sergey, Maguire, Jack, Malmström, Lars, Marcos, Enrique, Marcu, Orly, Marze, Nicholas A, Meiler, Jens, Moretti, Rocco, Mulligan, Vikram Khipple, Nerli, Santrupti, Norn, Christoffer, Ó’Conchúir, Shane, Ollikainen, Noah, Ovchinnikov, Sergey, Pacella, Michael S, Pan, Xingjie, Park, Hahnbeom, Pavlovicz, Ryan E, Pethe, Manasi, Pierce, Brian G, Pilla, Kala Bharath, Raveh, Barak, Renfrew, P Douglas, Burman, Shourya S Roy, Rubenstein, Aliza, Sauer, Marion F, Scheck, Andreas, Schief, William, Schueler-Furman, Ora, Sedan, Yuval, Sevy, Alexander M, Sgourakis, Nikolaos G, Shi, Lei, Siegel, Justin B, Silva, Daniel-Adriano, Smith, Shannon, and Song, Yifan

Subjects
Biological Sciences, Networking and Information Technology R&D (NITRD), Bioengineering, Macromolecular Substances, Models, Molecular, Molecular Docking Simulation, Peptidomimetics, Protein Conformation, Proteins, Software, Technology, Medical and Health Sciences, Developmental Biology, Biological sciences
Abstract

The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and extended. Its advantages are its performance and interoperability between broad modeling capabilities. Here we review tools developed in the last 5 years, including over 80 methods. We discuss improvements to the score function, user interfaces and usability. Rosetta is available at http://www.rosettacommons.org.

Published
2020

12. Engineering an allosteric transcription factor to respond to new ligands.

Author

Taylor, Noah, Garruss, Alexander, Moretti, Rocco, Chan, Sum, Arbing, Mark, Cascio, Duilio, Rogers, Jameson, Isaacs, Farren, Baker, David, Fields, Stanley, Church, George, Raman, Srivatsan, and Kosuri, Sriram

Subjects
Allosteric Regulation, DNA, Bacterial, Disaccharides, Escherichia coli, Escherichia coli Proteins, Fucose, Gene Expression Regulation, Bacterial, Genetic Engineering, Lac Repressors, Models, Molecular, Mutation, Protein Binding, Protein Conformation, Sucrose, Sugar Alcohols
Abstract

Genetic regulatory proteins inducible by small molecules are useful synthetic biology tools as sensors and switches. Bacterial allosteric transcription factors (aTFs) are a major class of regulatory proteins, but few aTFs have been redesigned to respond to new effectors beyond natural aTF-inducer pairs. Altering inducer specificity in these proteins is difficult because substitutions that affect inducer binding may also disrupt allostery. We engineered an aTF, the Escherichia coli lac repressor, LacI, to respond to one of four new inducer molecules: fucose, gentiobiose, lactitol and sucralose. Using computational protein design, single-residue saturation mutagenesis or random mutagenesis, along with multiplex assembly, we identified new variants comparable in specificity and induction to wild-type LacI with its inducer, isopropyl β-D-1-thiogalactopyranoside (IPTG). The ability to create designer aTFs will enable applications including dynamic control of cell metabolism, cell biology and synthetic gene circuits.

Published
2016

18. Discovery of post-translationally modified self-peptides that promote hypertension

Author

Bloodworth, Nathaniel, primary, Chen, Wei, additional, Patrick, David, additional, Palubinsky, Amy, additional, Phillips, Elizabeth, additional, Roeth, Daniel, additional, Kalkum, Markus, additional, Mallal, Simon, additional, Davies, Sean S, additional, Ao, Mingfang, additional, Moretti, Rocco, additional, Meiler, Jens, additional, and Harrison, David G, additional

Published
2023
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19. Drugit: Crowd-sourcing molecular design of non-peptidic VHL binders

Author

Scott, Thomas, primary, Smethurst, Christian Alan Paul, additional, Westermaier, Yvonne, additional, Mayer, Moriz, additional, Greb, Peter, additional, Kousek, Roland, additional, Biberger, Tobias, additional, Bader, Gerd, additional, Jandova, Zuzana, additional, Schmalhorst, Philipp S., additional, Fuchs, Julian E., additional, Magarkar, Aniket, additional, Hoenke, Christoph, additional, Gerstberger, Thomas, additional, Combs, Steven A., additional, Pape, Richard, additional, Phul, Saksham, additional, Kothiwale, Sandeepkumar, additional, Bergner, Andreas, additional, Waterson, Alex G., additional, Players, Foldit, additional, Weinstabl, Harald, additional, McConnell, Darryl B., additional, Böttcher, Jark, additional, Meiler, Jens, additional, and Moretti, Rocco, additional

Published
2023
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24. Abstract 019: T Cell Recognition Of Isolevuglandin-adducted Proteins In Hypertension Is Mhc Class 1-restricted

Author

Bloodworth, Nathaniel C, primary, Chen, Wei, additional, Ruggeri Barbaro, Natalia R, additional, Ao, Mingfang, additional, Palubinsky, Amy M, additional, O'Niel, Richard T, additional, Phillips, Elizabeth J, additional, Moretti, Rocco, additional, Davies, Sean S, additional, Mallal, Simon A, additional, Meiler, Jens, additional, and Harrison, David G, additional

Published
2022
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26. Business Process Modeling for Organizational Knowledge Management

Author

Abeti, Luca, Ciancarini, Paolo, Moretti, Rocco, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Degano, Pierpaolo, editor, De Nicola, Rocco, editor, and Meseguer, José, editor

Published
2008
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28. On the Education of Future Software Engineers

Author

Bolognesi, Andrea, Ciancarini, Paolo, Moretti, Rocco, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Inverardi, Paola, editor, and Jazayeri, Mehdi, editor

Published
2006
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29. Towards a Language for a Satisfaction-Based Selection of Grid Services

Author

Andreozzi, Sergio, Ciancarini, Paolo, Montesi, Danilo, Moretti, Rocco, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Dough, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Wyrzykowski, Roman, editor, Dongarra, Jack, editor, Meyer, Norbert, editor, and Waśniewski, Jerzy, editor

Published
2006
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31. Towards a Metamodeling Based Method for Representing and Selecting Grid Services

Author

Andreozzi, Sergio, Ciancarini, Paolo, Montesi, Danilo, Moretti, Rocco, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Jeckle, Mario, editor, Kowalczyk, Ryszard, editor, and Braun, Peter, editor

Published
2004
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33. Développement d'une Technique de Simulation Aérodynamique fondée sur la Vortex Particle Method

Author

Valentin, Johan, Moretti, Rocco, Bernardos, Luis, and André, Cécile

Subjects
VORTEX, [SPI] Engineering Sciences [physics], PARTICULE, Aerodynamic Simulation, Fast Multipole Method, METHODE PARTICULAIRE, VPM, [PHYS] Physics [physics], Vortex Ring, MÉTHODE POTENTIELLE, AILE ELLIPTIQUE, Lifting Line, SIMULATION AERODYNAMIQUE, Vortex Particle
Abstract

The study detailed in this paper aims to provide a solver able to simulate of a complex flows with multiple unsteady interactions. The numerical application of vortex methods has been studied intensively during the second half of the 20 th century. In particular, the Vortex Particle Method (VPM), aims to represent an incompressible flow through singular particles. However, its computational cost curtailed its use until recently. Since each particle influences one another, the VPM cost is O(N 2 p), with N p the number of particles. Fortunately enough, recent methods can be used to accelerate such problems to make it a O(N) problem. After introducing the VPM, its implementation and acceleration are detailed. A validation of the algorithm is conducted on several test cases. In addition, a comparison with other similar studies is carried out to validate its robustness and accuracy. Eventually a lifting line is added to study the reaction of the VPM when confronted with a wing., L'étude détaillée dans ce papier a pour but de fournir un simulateur capable de simuler un écoulement complexe avec de multiples interactions instationnaires. L'application numérique des méthodes vortex a été étudiée en profondeur pendant la seconde moitié du 20e siècle. En particulier, la Vortex Particle Method (VPM), cherche à représenter un écoulement incompressible au moyen de particules singulières. Cependant son coût de calcul empêchait son utilisation jusqu'à récemment. Comme toutes les particules s'influencent entre elles, la VPM a un coût de o(Np^2), avec Np le nombre de particules. Fort heureusement des méthodes récentes peuvent être utilisées pour accélérer de telles problèmes afin d'en faire des problèmes de coût o(Np). Après avoir présenté la VPM; son implémentation et son accélération son détaillées. La validation de l'algorithme est faite sur plusieurs cas test. De plus, une comparaison avec d'autres études similaires est faite pour valider sa robustesse et sa précision. Enfin une Ligne Portante est ajoutée afin d'étudier le comportement de la VPM lorsqu'une aile est ajoutée.

Published
2022

35. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

Author

Koehler Leman, Julia, primary, Lyskov, Sergey, additional, Lewis, Steven, additional, Adolf-Bryfogle, Jared, additional, Alford, Rebecca F., additional, Barlow, Kyle, additional, Ben-Aharon, Ziv, additional, Farrell, Daniel, additional, Fell, Jason, additional, Hansen, William A., additional, Harmalkar, Ameya, additional, Jeliazkov, Jeliazko, additional, Kuenze, Georg, additional, Krys, Justyna D., additional, Ljubetič, Ajasja, additional, Loshbaugh, Amanda L., additional, Maguire, Jack, additional, Moretti, Rocco, additional, Mulligan, Vikram Khipple, additional, Nguyen, Phuong T., additional, Ó Conchúir, Shane, additional, Roy Burman, Shourya S., additional, Smith, Shannon T., additional, Teets, Frank, additional, Tiemann, Johanna KS, additional, Watkins, Andrew, additional, Woods, Hope, additional, Yachnin, Brahm J., additional, Bahl, Christopher D., additional, Bailey-Kellogg, Chris, additional, Baker, David, additional, Das, Rhiju, additional, DiMaio, Frank, additional, Khare, Sagar D., additional, Kortemme, Tanja, additional, Labonte, Jason W., additional, Lindorff-Larsen, Kresten, additional, Meiler, Jens, additional, Schief, William, additional, Schueler-Furman, Ora, additional, Siegel, Justin, additional, Stein, Amelie, additional, Yarov-Yarovoy, Vladimir, additional, Kuhlman, Brian, additional, Leaver-Fay, Andrew, additional, Gront, Dominik, additional, Gray, Jeffrey J., additional, and Bonneau, Richard, additional

Published
2021
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36. Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

Author

Schoeder, Clara T., primary, Schmitz, Samuel, additional, Adolf-Bryfogle, Jared, additional, Sevy, Alexander M., additional, Finn, Jessica A., additional, Sauer, Marion F., additional, Bozhanova, Nina G., additional, Mueller, Benjamin K., additional, Sangha, Amandeep K., additional, Bonet, Jaume, additional, Sheehan, Jonathan H., additional, Kuenze, Georg, additional, Marlow, Brennica, additional, Smith, Shannon T., additional, Woods, Hope, additional, Bender, Brian J., additional, Martina, Cristina E., additional, del Alamo, Diego, additional, Kodali, Pranav, additional, Gulsevin, Alican, additional, Schief, William R., additional, Correia, Bruno E., additional, Crowe, James E., additional, Meiler, Jens, additional, and Moretti, Rocco, additional

Published
2021
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37. Étude et amélioration des méthodologies de couplage aérothermique fluide-structure

Author

Moretti, Rocco, DAAA, ONERA, Université Paris-Saclay (COmUE) [Châtillon], ONERA-Université Paris Saclay (COmUE), UNIVERSITE PSL PARIS, Frédéric FEYEL, Centre des Matériaux (MAT), MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres, Frédéric Feyel, and Marc-Paul Errera

Subjects
[PHYS]Physics [physics], CONDITIONS AUX LIMITES, TURBOMACHINE, STABILITY, INTERACTION FLUIDE-STRUCTURE, Turbomachines, BOUNDARY CONDITIONS, Précision, AEROTHERMAL COUPLING (CHT), Stabilité, [SPI.MAT]Engineering Sciences [physics]/Materials, STABILITE, FLUID-STRUCTURE INTERACTION, TURBOMACHINERY, PRECISION, [SPI]Engineering Sciences [physics], COUPLAGE AEROTHERMIQUE, Couplage aérothermique
Abstract

This work deals with the solution of coupled aerothermal problems. The aim of the work is to improve the accuracy and robustness of the coupling techniques. The stability of the aerothermal coupling for steady state problems is first studied (weak coupling). A numerical Biot number is defined, which allows to evaluate the intensity of the fluid-structure thermal interaction. Several methods (Dirichlet-Robin, Neumann-Robin and Robin-Robin) are studied and their ranges of validity are defined. The Dirichlet-Robin method with a safety coefficient, which presents the easiest implementation, proves to be the most robust. Taking radiation into account implies a major destabilization of the aerothermal problem. Thus, the stabilization method is modified in order to be able to stabilize this type of calculation. In the second part, the solution of coupled aerothermal problems in the transient regime is studied using the quasidynamic partitioned algorithm. This is an iterative procedure (strong coupling) between the thermal problem in the solid solved in the transient regime and the flow field at the steady state, thus ensuring equal heat flux and temperature at each coupling time. The accuracy of this algorithm is analysed and improved. Finally, the quasi-dynamic algorithm is analysed on quasi-industrial aerothermal problems of aeronautical compressor and turbine discs.; Ces travaux s’inscrivent dans la résolution de problèmes couplés aérothermiques. Il s’agit notamment d’améliorer les méthodes de couplage en termes de précision et de robustesse. La stabilité du couplage aérothermique en régime permanent a été d’abord étudiée (couplage faible). Un nombre de Biot numérique a été défini ce qui permet d’évaluer l’intensité de l’interaction thermique fluide-structure. Plusieurs méthodes (Dirichlet-Robin, Neumann-Robin et Robin-Robin) ont été étudiées et leur domaine de validité a été défini. La méthode Dirichlet-Robin avec un coefficient de sécurité s’est avérée la plus robuste et simple à mettre en œuvre. La prise en compte du rayonnement implique une déstabilisation majeure du problème aérothermique. La méthode de stabilisation a donc été modifiée afin de pouvoir stabiliser ce type de calcul. Dans un deuxième temps, la résolution de problèmes couplés aérothermiques en régime transitoire a été étudiée via l’algorithme partitionné quasi-instationnaire. Il s’agit d’une procédure itérative (couplage fort) entre le solide en régime transitoire et des états fluides en régime stationnaire, assurant ainsi l’égalité des flux de chaleur et de la température à chaque instant de couplage. La précision de cet algorithme a été analysée et améliorée. Enfin, l’algorithme quasi-instationnaire a été analysé sur des problèmes aérothermiques quasi-industriels de disques de turbine et compresseur aéronautiques.

Published
2019

47. Accuracy of Heat Load Transfer in a Quasi-Dynamic Fluid-Structure Interaction

Author

Moretti, Rocco, Lazareff, Marc, Errera, Marc, Feyel, Frédéric, Soubrié, Tristan, Benyoucef, Farid, DAAA, ONERA, Université Paris-Saclay (COmUE) [Châtillon], Université Paris Saclay (COmUE)-ONERA, Centre des Matériaux (MAT), MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Safran tech, Andheo, and Safran Aircraft Engines

Subjects
METHODE DIRICHLET-ROBIN, [PHYS]Physics [physics], TRANSIENT CHT, METHODES D'INTERPOLATION, INTERPOLATION METHODS, PRECISION DE LA SOLUTION, INTERACTION THERMIQUE, QUADRATURE DE GAUSS, DIRICHLET-ROBIN METHOD, [SPI]Engineering Sciences [physics], THERMAL INTERACTION, GAUSS QUADRATURE, SYSTEME COUPLE FLUIDE-STRUCTURE, SOLUTION ACCURACY
Abstract

This paper is devoted to investigate the temporal and spatial accuracy in transient conjugate heat transfer problems where the influence of unsteadi-ness in the fluid is supposed to be negligible. The numerical method is based on an iterative procedure with interpolated boundary conditions on the solid side. Emphasis is put on these interpolation procedures. First it is shown that a temporal interpolation is by no means the most appropriate way of estimating the flow boundary conditions prescribed on the coupled solid surfaces. In contrast, when these conditions are based on the heat flux/temperature linearity, significantly better results are obtained. Indeed, they compare very well against a reference solution provided by a non-iterative and non-interpolated coupled computation. Moreover, important improvements were made by adequately defining the integral contribution of the boundary condition using the Gauss points in the finite element solid code. Finally, it was also revealed that a relevant approximation of the heat transfer requires a sufficiently fine solid mesh at the interface.; Cet article est consacré à l'étude de la précision temporelle et spatiale dans les problèmes aérothermiques en régime transitoire où l'influence des effets instationnaires dans le fluide est supposée être négligeable. La méthode numérique est basée sur une procédure itérative avec des conditions aux limites interpolées sur l'interface solide. L'accent est mis sur ces procédures d'interpolation. Tout d'abord, il est montré qu'une interpolation temporelle n'est en aucun cas le moyen le plus approprié d'estimer les conditions limites de l'écoulement prescrites sur les surfaces solides couplées. En revanche, lorsque ces conditions sont basées sur la linéarité flux de chaleur/température, les résultats obtenus sont nettement meilleurs. En effet, la comparaison avec une solution de référence obtenue par un calcul couplé non itératif et non interpolé est satisfaisante. De plus, d'importantes améliorations ont été apportées en définissant adéquatement la contribution intégrale de la condition limite à l'aide des points de Gauss situés sur l'interfaces du solide. Enfin, il a également été révélé qu'une approximation pertinente du transfert de chaleur nécessite un maillage solide suffisamment fin à l'interface fluide-structure.

Published
2019

48. Précision du calcul de la charge thermique dans des problèmes d'interaction fluide-structure quasi-instationnaire

Author

Moretti, Rocco, Lazareff, Marc, Errera, Marc, Feyel, Frédéric, Soubrié, Tristan, Benyoucef, Farid, DAAA, ONERA, Université Paris-Saclay (COmUE) [Châtillon], Université Paris Saclay (COmUE)-ONERA, Centre des Matériaux (MAT), MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Safran tech, Andheo, and Safran Aircraft Engines

Subjects
METHODE DIRICHLET-ROBIN, [PHYS]Physics [physics], TRANSIENT CHT, METHODES D'INTERPOLATION, INTERPOLATION METHODS, PRECISION DE LA SOLUTION, INTERACTION THERMIQUE, QUADRATURE DE GAUSS, DIRICHLET-ROBIN METHOD, [SPI]Engineering Sciences [physics], THERMAL INTERACTION, GAUSS QUADRATURE, SYSTEME COUPLE FLUIDE-STRUCTURE, SOLUTION ACCURACY
Abstract

This paper is devoted to investigate the temporal and spatial accuracy in transient conjugate heat transfer problems where the influence of unsteadi-ness in the fluid is supposed to be negligible. The numerical method is based on an iterative procedure with interpolated boundary conditions on the solid side. Emphasis is put on these interpolation procedures. First it is shown that a temporal interpolation is by no means the most appropriate way of estimating the flow boundary conditions prescribed on the coupled solid surfaces. In contrast, when these conditions are based on the heat flux/temperature linearity, significantly better results are obtained. Indeed, they compare very well against a reference solution provided by a non-iterative and non-interpolated coupled computation. Moreover, important improvements were made by adequately defining the integral contribution of the boundary condition using the Gauss points in the finite element solid code. Finally, it was also revealed that a relevant approximation of the heat transfer requires a sufficiently fine solid mesh at the interface.; Cet article est consacré à l'étude de la précision temporelle et spatiale dans les problèmes aérothermiques en régime transitoire où l'influence des effets instationnaires dans le fluide est supposée être négligeable. La méthode numérique est basée sur une procédure itérative avec des conditions aux limites interpolées sur l'interface solide. L'accent est mis sur ces procédures d'interpolation. Tout d'abord, il est montré qu'une interpolation temporelle n'est en aucun cas le moyen le plus approprié d'estimer les conditions limites de l'écoulement prescrites sur les surfaces solides couplées. En revanche, lorsque ces conditions sont basées sur la linéarité flux de chaleur/température, les résultats obtenus sont nettement meilleurs. En effet, la comparaison avec une solution de référence obtenue par un calcul couplé non itératif et non interpolé est satisfaisante. De plus, d'importantes améliorations ont été apportées en définissant adéquatement la contribution intégrale de la condition limite à l'aide des points de Gauss situés sur l'interfaces du solide. Enfin, il a également été révélé qu'une approximation pertinente du transfert de chaleur nécessite un maillage solide suffisamment fin à l'interface fluide-structure.

Published
2019

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