Atomic imaging of complex molecular
One of the significant challenges of modern science is to track and image chemical reactions as they occur. The molecular movies, the precise spatiotemporal tracking of changes in their molecular dynamics, will provide a wealth of actionable insights into how nature works. Experimental techniques ne...
| Autor: | |
|---|---|
| Tipo de recurso: | tesis doctoral |
| Fecha de publicación: | 2022 |
| País: | España |
| Institución: | Universitat Politècnica de Catalunya (UPC) |
| Repositorio: | UPCommons. Portal del coneixement obert de la UPC |
| Idioma: | inglés |
| OAI Identifier: | oai:upcommons.upc.edu:2117/374424 |
| Acceso en línea: | https://hdl.handle.net/2117/374424 https://dx.doi.org/10.5821/dissertation-2117-374424 |
| Access Level: | acceso abierto |
| Palabra clave: | Àrees temàtiques de la UPC::Física |
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Atomic imaging of complex molecular |
| title |
Atomic imaging of complex molecular |
| spellingShingle |
Atomic imaging of complex molecular Liu, Xinyao Àrees temàtiques de la UPC::Física |
| title_short |
Atomic imaging of complex molecular |
| title_full |
Atomic imaging of complex molecular |
| title_fullStr |
Atomic imaging of complex molecular |
| title_full_unstemmed |
Atomic imaging of complex molecular |
| title_sort |
Atomic imaging of complex molecular |
| dc.creator.none.fl_str_mv |
Liu, Xinyao |
| author |
Liu, Xinyao |
| author_facet |
Liu, Xinyao |
| author_role |
author |
| dc.contributor.none.fl_str_mv |
Biegert, Jens |
| dc.subject.none.fl_str_mv |
Àrees temàtiques de la UPC::Física |
| topic |
Àrees temàtiques de la UPC::Física |
| description |
One of the significant challenges of modern science is to track and image chemical reactions as they occur. The molecular movies, the precise spatiotemporal tracking of changes in their molecular dynamics, will provide a wealth of actionable insights into how nature works. Experimental techniques need to resolve the relevant molecular motions in atomic resolution, which includes (10^(-10) m) spatial dimensions and few- to hundreds of femtoseconds (10^(-15) s) temporal resolution. Laser-induced electron diffraction (LIED), a laser-based electron diffraction technique, images even singular molecular structures with combined sub-atomic picometre and femto-to attosecond spatiotemporal resolution. Here, a laser-driven attosecond electron wave packet scatters the parent’s ion after photoionization. The measured diffraction pattern of the electrons provides a unique fingerprint of molecular structure. Taking snapshots of molecular dynamics via the LIED technique is proved to be a potent tool to understand the intertwining of molecules and how they react, change, break, bend, etc. This thesis is especially interested in exploiting advanced LIED imaging techniques to retrieve large complex molecular structures. So far, LIED has successfully retrieved molecular information from small gas-phase molecules like oxygen (O2), nitrogen (N2), acetylene (C2H2), carbon disulfide (CS2), ammonia (NH3) and carbonyl sulfide (OCS). Nevertheless, most biology interesting organic molecules typically exist as liquid or solid at room temperature. In order to accomplish the final goal to extract these larger complex molecular structural information, we need to overcome two main challenges: delivering the liquid or solid samples as a gas-phase jet with sufficient gas density in the experiment and developing a new retrieval algorithm to extract the geometrical information from the diffraction pattern. We tested one of the most simple liquid molecules - water H2O in the reaction chamber as a primary step. We traced the variation of H2O+ cation structure under the different electric fields. To solve the problem of unsatisfactory gas density, we present a novel delivery system utilizing Tesla valves that generates more than an order-of-magnitude denser gaseous beam. Machine learning is well qualified to solve difficulties with manifold degrees of freedom. We use convolutional neural networks (CNNs) combined with LIED techniques to enable atomic-resolution imaging of the complex chiral molecule Fenchone (C10H16O). |
| publishDate |
2022 |
| dc.date.none.fl_str_mv |
2022 2022-07-27 2022 2022-10-13 |
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doctoral thesis http://purl.org/coar/resource_type/c_db06 VoR http://purl.org/coar/version/c_970fb48d4fbd8a85 |
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info:eu-repo/semantics/doctoralThesis |
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doctoralThesis |
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https://hdl.handle.net/2117/374424 https://dx.doi.org/10.5821/dissertation-2117-374424 |
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https://hdl.handle.net/2117/374424 https://dx.doi.org/10.5821/dissertation-2117-374424 |
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Inglés eng |
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Inglés |
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eng |
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open access http://purl.org/coar/access_right/c_abf2 |
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info:eu-repo/semantics/openAccess |
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open access http://purl.org/coar/access_right/c_abf2 |
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openAccess |
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application/pdf |
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Universitat Politècnica de Catalunya |
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Universitat Politècnica de Catalunya |
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reponame:UPCommons. Portal del coneixement obert de la UPC instname:Universitat Politècnica de Catalunya (UPC) |
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Universitat Politècnica de Catalunya (UPC) |
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1869418011721465856 |
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Atomic imaging of complex molecularLiu, XinyaoÀrees temàtiques de la UPC::FísicaOne of the significant challenges of modern science is to track and image chemical reactions as they occur. The molecular movies, the precise spatiotemporal tracking of changes in their molecular dynamics, will provide a wealth of actionable insights into how nature works. Experimental techniques need to resolve the relevant molecular motions in atomic resolution, which includes (10^(-10) m) spatial dimensions and few- to hundreds of femtoseconds (10^(-15) s) temporal resolution. Laser-induced electron diffraction (LIED), a laser-based electron diffraction technique, images even singular molecular structures with combined sub-atomic picometre and femto-to attosecond spatiotemporal resolution. Here, a laser-driven attosecond electron wave packet scatters the parent’s ion after photoionization. The measured diffraction pattern of the electrons provides a unique fingerprint of molecular structure. Taking snapshots of molecular dynamics via the LIED technique is proved to be a potent tool to understand the intertwining of molecules and how they react, change, break, bend, etc. This thesis is especially interested in exploiting advanced LIED imaging techniques to retrieve large complex molecular structures. So far, LIED has successfully retrieved molecular information from small gas-phase molecules like oxygen (O2), nitrogen (N2), acetylene (C2H2), carbon disulfide (CS2), ammonia (NH3) and carbonyl sulfide (OCS). Nevertheless, most biology interesting organic molecules typically exist as liquid or solid at room temperature. In order to accomplish the final goal to extract these larger complex molecular structural information, we need to overcome two main challenges: delivering the liquid or solid samples as a gas-phase jet with sufficient gas density in the experiment and developing a new retrieval algorithm to extract the geometrical information from the diffraction pattern. We tested one of the most simple liquid molecules - water H2O in the reaction chamber as a primary step. We traced the variation of H2O+ cation structure under the different electric fields. To solve the problem of unsatisfactory gas density, we present a novel delivery system utilizing Tesla valves that generates more than an order-of-magnitude denser gaseous beam. Machine learning is well qualified to solve difficulties with manifold degrees of freedom. We use convolutional neural networks (CNNs) combined with LIED techniques to enable atomic-resolution imaging of the complex chiral molecule Fenchone (C10H16O).Uno de los desafíos importantes de la ciencia moderna es rastrear y obtener imágenes de las reacciones químicas a medida que ocurren. Las películas moleculares, el seguimiento espaciotemporal preciso de los cambios en su dinámica molecular, proporcionarán una gran cantidad de conocimientos prácticos sobre cómo funciona la naturaleza. Las técnicas experimentales necesitan resolver los movimientos moleculares relevantes en resolución atómica, que incluye ($10^{-10}$ m) dimensional espacial y resolución temporal de pocos a cientos de femtosegundos ($10^{-15}$ s). La difracción de electrones inducida por láser (LIED-Laser-induced electron diffraction), una técnica de difracción de electrones basada en láser, crea imágenes incluso de estructuras moleculares singulares con una resolución espaciotemporal subatómica combinada de picómetro y femto a attosegundo. Aquí, un paquete de ondas de electrones de attosegundos impulsado por láser dispersa el ion del padre después de la fotoionización. El patrón de difracción medido de los electrones proporciona una huella única de la estructura molecular. Se ha demostrado que tomar instantáneas de la dinámica molecular a través de la técnica LIED es una herramienta potente para comprender el entrelazamiento de las moléculas y cómo reaccionan, cambian, se rompen, se doblan, etc. Esta tesis está especialmente interesada en explotar técnicas avanzadas de imagen LIED para recuperar estructuras moleculares grandes y complejas. Hasta ahora, LIED ha recuperado con éxito información molecular de pequeñas moléculas en fase gaseosa como oxígeno (O2), nitrógeno (N2), acetileno (C2H2), disulfuro de carbono (CS2), amoníaco (NH3) y sulfuro de carbonilo (OCS). Sin embargo, la mayoría de las moléculas orgánicas interesantes para la biología suelen existir como líquidas o sólidas a temperatura ambiente. Para lograr el objetivo final de extraer esta información estructural molecular compleja más grande, debemos superar dos desafíos principales: entregar las muestras líquidas o sólidas como un chorro de fase gaseosa con suficiente densidad de gas en el experimento y desarrollar un nuevo algoritmo de recuperación para extraer la información geométrica del patrón de difracción. Probamos una de las moléculas líquidas más simples: agua H2O en la cámara de reacción como primer paso. Trazamos la variación de la estructura del catión H2O+ bajo los diferentes campos eléctricos. Para resolver el problema de la densidad de gas insatisfactoria, presentamos un novedoso sistema de suministro que utiliza válvulas Tesla que genera más de un haz gaseoso más denso en un orden de magnitud. El aprendizaje automático está bien calificado para resolver dificultades con múltiples grados de libertad. Utilizamos redes neuronales convolucionales (CNN-convolutional neural networks) combinadas con técnicas LIED para permitir imágenes de resolución atómica de la molécula quiral compleja Fenchone (C10H16OUniversitat Politècnica de CatalunyaBiegert, Jens20222022-07-2720222022-10-13doctoral thesishttp://purl.org/coar/resource_type/c_db06VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/doctoralThesisapplication/pdfhttps://hdl.handle.net/2117/374424https://dx.doi.org/10.5821/dissertation-2117-374424reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/3744242026-05-27T15:37:01Z |
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15,301629 |