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From low dimensions to full configuration space: Generalising models for nonadiabatic molecular dynamics
Get PDFThis thesis aims to bridge the development of nonadiabatic dynamics methods and their application for studies of real molecular systems.
First, this work explores fundamental concepts of photochemistry by investigating two different pictures, arising from the Born-Oppenheimer and the exact factorisation representation. Based on a simplistic model, a photochemical experiment from the excitation up to the formation of photoproducts is simulated. This study then compares the Born-Oppenheimer and exact factorisation representations of the processes. Subsequently, the influence of the Born-Oppenheimer picture for approximate nonadiabatic dynamics is investigated on two-dimensional model systems around conical intersections. The effects of neglected couplings and geometric phase are evaluated for ab initio multiple spawning (AIMS), a method for nonadiabatic molecular dynamics based on classically moving Gaussians.
Afterwards, this work introduces a standardised test set of molecules to connect between tests of newly developed nonadiabatic dynamics methods on one-dimensional model systems and their intended application to full-dimensional molecules. Inspired by the widely used one-dimensional Tully models, three molecules are selected to form the molecular Tully models, which undergo similar photophysical processes, but in a high-dimensional space. In addition, the recently proposed stochastic-selection AIMS framework is also tested on two molecules undergoing ring-opening reactions to explore the strengths and limitations of the method.
Finally, a direct comparison between experimental and computational results is presented. The photochemistry of 2(5H)-thiophenone is probed during and after the initial ring opening using time-resolved photoelectron spectroscopy. Static and dynamic calculations unravel the photoprocesses and identify a variety of photoproducts. Using the computational results, the experimental signal can be translated to insights into the ongoing photochemistry.
Overall, this thesis aims to bring models in nonadiabatic dynamics in a real-world context. This work contributes to facilitating the transfer of new nonadiabatic dynamics methods towards the study of molecules in their full dimensionality
Computational study of the temporal evolution of the excited state character in the photoexcited adenine oligonucleotide
No full textDas Ziel dieser Arbeit besteht darin, die langlebigen Zustände zu identifizieren, welche experimentell spezifisch in einsträngiger DNS mit einer Sequenz von 20 Adeninbasen, (dA )20 , beobachtet worden sind. Da es äußerst umstritten ist, ob diese langlebigen Zustände durch starken Landungstransfer verursacht oder als Exzitone klassifizierbar sind, wurde nicht adiabatische Potentialflächensprungdynamik kombiniert mit gleichzeitiger Wellenfunktionsanalyse angewandt, um diese langlebigen Zustände charakterisieren zu können.
Durch vielfältige methodische Untersuchungen ist festgestellt worden, dass das Absorptionsspektrum ausreichend gut reproduziert werden kann, wenn vier Adeninbasen quantenmechanisch mit TD-CAM-B3LYP/def2-SV(P) behandelt werden, während der Rest des Systems klassisch mit molekularer Mechanik beschrieben wird. Die nicht adiabatische Potentialflächensprungdynamik wurde 500 fs lang simuliert. Dabei wurde beobachtet, dass durch die ursprüngliche Anregung Exzitone und monomerartige Zustände gebildet werden. Die Exzitone wurden innerhalb der ersten 100 fs vollständig zu monomerartigen Zuständen (80 %) oder Exziplexen (20 %) umgewandelt. Drei Viertel der Monomere bildeten Exziplexe, wobei sie übergangsweise Exzimerzustand annahmen, während das übrige Viertel der Monomere in den Grundzustand übergingen. Die gesamte Zeitkonstante für die Entstehung von Exziplexen wurde mit circa 700 fs bestimmt, was höher liegt als der experimentell gemessene Wert (∼ 400 fs), allerdings noch immer in derselben Größenordnung. Für den Übergang zum Grundzustand wurde eine Zeitkonstante von circa 3 ps simuliert, was ausreichend gut mit dem Experiment (∼2 ps) übereinstimmt.
Der Abstand der Nucleobasen verringerte sich während der Bildung von Exziplexen, was darauf hindeutet, dass Basenstapelung eine wichtige Rolle im dynamischen Verhalten von (dA)20 spielt.
Diese Studie bietet mittels angeregter Zustandsdynamik die ersten computergestützten Anzeichen, dass langlebige Ladungsübertragungszustände (Exziplexe) in (dA)20 gebildet werden.The goal of this work is to investigate the nature of the long-lived excited states observed experimentally in single stranded DNA, specifically poly-adenosine phosphate ( (dA)20, in the following also called polyadenine), after UV irradiadtion. Since there was some controversy about whether these long-lived states are charge-transfer states or excitons, non-adiabatic surface hopping dynamics have been employed in combination with an on the fly wavefunction analysis to characterise
involved the long-lived excited states.
After several methodical investigations, it was found that the absorption spectrum is well described with four adenines treated at the TD-CAM-B3LYP/def2-SV(P) level of theory, while the other parts of the single strand as well as the surrounding water are described with molecular mechanics. The non-adiabatic surface hopping dynamics were simulated for 500 fs. It was observed that initially excitons and monomer-like states are formed. Excitons decayed completely within the first 100 fs either to monomer-like states (80 %) or forming exciplexes (20 %). 75 % of the monomer-like states formed exciplexes through an intermediate excimeric state, while the other 25 % of the monomers are expected to decay to the ground state. The overall time constant for the formation of exciplexes equals around 700 fs, which is higher than the experimentally observed value (∼400 fs) but still in the same order of magnitude. The decay to the ground state was simulated to occur with a time constant of around 3 ps which agrees with the experimental result of ∼2 ps.
The separation between the nucleobases was observed to decrease during the formation of exciplexes which indicates that base stacking is an important factor for the dynamical behaviour of (dA) 20.
This study provides the first computational evidence that long-lived charge transfer states are formed in (dA)20 through excited state dynamics simulations
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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