Coupling of quantum chemistry models and high-performance algorithms for the global exploration of the energy landscape of atomic and molecular systems ; Couplage de modèles de chimie quantique et d'algorithmes haute performance pour l'exploration globale du paysage énergétique de systèmes atomiques et moléculaires
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| Názov: | Coupling of quantum chemistry models and high-performance algorithms for the global exploration of the energy landscape of atomic and molecular systems ; Couplage de modèles de chimie quantique et d'algorithmes haute performance pour l'exploration globale du paysage énergétique de systèmes atomiques et moléculaires |
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| Autori: | Milia, Valentin |
| Prispievatelia: | Équipe Robotique et InteractionS (LAAS-RIS), Laboratoire d'analyse et d'architecture des systèmes (LAAS), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT), Université de Toulouse, Juan Cortés, Mathias Rapacioli |
| Zdroj: | https://theses.hal.science/tel-04771034 ; Data Structures and Algorithms [cs.DS]. Université de Toulouse, 2024. English. ⟨NNT : 2024TLSEP095⟩. |
| Informácie o vydavateľovi: | CCSD |
| Rok vydania: | 2024 |
| Zbierka: | Université Toulouse III - Paul Sabatier: HAL-UPS |
| Predmety: | Global optimization, Atomic and molecular modeling, Potential energy surfaces, Conformational exploration, Robotics-inspired algorithms, Transition path identification, Identification de chemins de transition, Optimisation globale, Algorithmes inspirés de la robotique, Exploration du paysage conformationnel, Surfaces d'énergie potentielle, Modélisation atomique et moléculaire, [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS], [INFO]Computer Science [cs] |
| Popis: | National audience ; The primary aim of this thesis is to develop efficient methods for characterizing molecular conformations at a quantum level. Various methods devoted to the computation of molecular potential energy are reviewed, as well as the most popular potential energy surfaces (PES) global exploration schemes. In this context, a key contribution of this thesis is the coupling of the robotics-inspired Iterative Global exploration and LOcal Optimization (IGLOO) method, implemented in the MoMA software, with the quantum Density-Functional based Tight-Binding (DFTB) potential, implemented in the deMonNano software. The IGLOO algorithm integrates the motion planning Rapidly-exploring Random Trees (RRT) algorithm with local optimization and structural filtering. A proof of concept has been done through the identification of low-energy conformations of the alanine dipeptide.The IGLOO/DFTB coupling has been applied to the mapping of the PES of three close-sized molecules of the phthalate family (dibutyl phthalate DBP, benzyl butyl phthalate BBP and di-2-ethylhexyl phthalate DEHP), providing detailed insights into their different conformational landscapes. Various geometrical descriptors have been used to analyze their structure-energy relationships. Coulomb interactions, steric hindrance, and dispersive interactions have been found to drive the geometric properties and a strong correlation has been evidenced between the two dihedral angles describing the side-chains orientation of the phthalate molecules. The results demonstrate the method's capability to identify low-energy minima without prior knowledge of the PES.Furthermore, an innovative algorithm for the large-scale generation of molecular structures, including a conformational variety, is presented. It combines molecular graph generation with atom or fragment addition techniques. It is applied to provide an extensive database of 3D structures of hydrogenated amorphous carbon (a-CH) molecules. The analysis of the database generated in this study provides ... |
| Druh dokumentu: | doctoral or postdoctoral thesis |
| Jazyk: | English |
| Relation: | NNT: 2024TLSEP095 |
| Dostupnosť: | https://theses.hal.science/tel-04771034 https://theses.hal.science/tel-04771034v1/document https://theses.hal.science/tel-04771034v1/file/137555_MILIA_2024_archivage.pdf |
| Rights: | info:eu-repo/semantics/OpenAccess |
| Prístupové číslo: | edsbas.32913FCE |
| Databáza: | BASE |
Nájsť tento článok vo Web of Science | Abstrakt: | National audience ; The primary aim of this thesis is to develop efficient methods for characterizing molecular conformations at a quantum level. Various methods devoted to the computation of molecular potential energy are reviewed, as well as the most popular potential energy surfaces (PES) global exploration schemes. In this context, a key contribution of this thesis is the coupling of the robotics-inspired Iterative Global exploration and LOcal Optimization (IGLOO) method, implemented in the MoMA software, with the quantum Density-Functional based Tight-Binding (DFTB) potential, implemented in the deMonNano software. The IGLOO algorithm integrates the motion planning Rapidly-exploring Random Trees (RRT) algorithm with local optimization and structural filtering. A proof of concept has been done through the identification of low-energy conformations of the alanine dipeptide.The IGLOO/DFTB coupling has been applied to the mapping of the PES of three close-sized molecules of the phthalate family (dibutyl phthalate DBP, benzyl butyl phthalate BBP and di-2-ethylhexyl phthalate DEHP), providing detailed insights into their different conformational landscapes. Various geometrical descriptors have been used to analyze their structure-energy relationships. Coulomb interactions, steric hindrance, and dispersive interactions have been found to drive the geometric properties and a strong correlation has been evidenced between the two dihedral angles describing the side-chains orientation of the phthalate molecules. The results demonstrate the method's capability to identify low-energy minima without prior knowledge of the PES.Furthermore, an innovative algorithm for the large-scale generation of molecular structures, including a conformational variety, is presented. It combines molecular graph generation with atom or fragment addition techniques. It is applied to provide an extensive database of 3D structures of hydrogenated amorphous carbon (a-CH) molecules. The analysis of the database generated in this study provides ... |
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