1,721,013 research outputs found
Auger Spectrum of a Water Molecule after Single and Double Core-Ionization by Intense X-Ray Radiation
No full textThe Low Barrier Hydrogen Bond in the Photoactive Yellow Protein: A Vacuum Artifact Absent in the Crystal and Solution
Full text linkThere has been considerable debate on the existence of a low-barrier hydrogen bond (LBHB) in the photoactive yellow protein (PYP). The debate was initially triggered by the neutron diffraction study of Yamaguchi et al. ( Proc. Natl. Acad. Sci., U. S. A., 2009, 106, 440−444) who suggested a model in which a neutral Arg52 residue triggers the formation of the LBHB in PYP. Here, we present an alternative model that is consistent within the error margins of the Yamaguchi structure factors. The model explains an increased hydrogen bond length without nuclear quantum effects and for a protonated Arg52. We tested both models by calculations under crystal, solution, and vacuum conditions. Contrary to the common assumption in the field, we found that a single PYP in vacuum does not provide an accurate description of the crystal conditions but instead introduces strong artifacts, which favor a LBHB and a large 1H NMR chemical shift. Our model of the crystal environment was found to stabilize the two Arg52 hydrogen bonds and crystal water positions for the protonated Arg52 residue in free MD simulations and predicted an Arg52 pKa upshift with respect to PYP in solution. The crystal and solution environments resulted in almost identical 1H chemical shifts that agree with NMR solution data. We also calculated the effect of the Arg52 protonation state on the LBHB in 3D nuclear equilibrium density calculations. Only the charged crystal structure in vacuum supports a LBHB if Arg52 is neutral in PYP at the previously reported level of theory ( J. Am. Chem. Soc., 2014, 136, 3542−3552). We attribute the anomalies in the interpretation of the neutron data to a shift of the potential minimum, which does not involve nuclear quantum effects and is transferable beyond the Yamaguchi structure
Ultrafast Quantum-Classical Dynamics: Applications in X-ray Spectroscopy and Method Development
No full textRecent advances in laser technologies such as x-ray free-electron lasers and high harmonic generation have led to ever-shorter light pulses that enable us to probe ultrafast nuclear and electronic dynamics in atoms and molecules. Theoretical quantum dynamics simulations are indispensable in gaining deeper insights into these ultrafast processes. However, treating both electrons and nuclei fully quantum mechanically is computationally not feasible for large systems. Hence, due to their computational efficiency, mixed quantum-classical dynamics methods such as Tully’s fewest switches surface hopping (FSSH) have become popular, in spite of their limitations. In this thesis, I demonstrate how FSSH dynamics, combined with advanced statistical analysis techniques, can be used to understand ultrafast phenomena traced in experimental spectra such as time-resolved x-ray absorption spectra (TRXAS). Furthermore, I introduce a new method developed to improve FSSH to provide a better description of electronic coherences relevant in attosecond science.
With the aim of understanding the first steps of radiation damage in biomolecules, the first part of this thesis focuses on ab initio FSSH dynamics simulations of valence ionized urea monomer and dimer in vacuum as a prototypical example. Investigating the carbon, nitrogen, and oxygen K-edges in the simulated TRXAS reveals rich insights into the ultrafast processes. Further information is gained by applying machine learning techniques for statistical analysis which unravel uncorrelated collective motions that most influence the spectra. Extending these simulations to urea in aqueous solution, I show in the second part of this thesis how the effect of proton transfer between two hydrogen-bonded ureas and the subsequent electronic structure changes leave two distinct marks on the carbon K-edge of the TRXAS. This enables us to separate the effect of nuclear and electronic motion on the spectra. These liquid phase results are in good agreement with recent pump-probe experiments on aqueous urea.
In the last part, I present a new method, named ring polymer surface hopping - density matrix approach (RPSH-DM), developed to alleviate one of the shortcomings of FSSH, namely the so-called overcoherence problem, which manifests as a poor description of electronic coherence and decoherence phenomena. RPSH-DM combines FSSH with ring polymer molecular dynamics to incorporate decoherence effects by utilizing the spatial extent of the ring polymer, mimicking the width of the nuclear wave packet. By applying this method to a one-dimensional model system, I show how RPSH-DM can capture crucial decoherence mechanisms that are not present in FSSH. In future studies, employing RPSH-DM to investigate polyatomic systems can provide vital insights into ultrafast electronic processes occurring in attosecond experiments
Coulomb explosion as a high-dimensional probe of single molecules
No full textThe past decades saw the development of X-ray induced Coulomb explosion imaging as one of several methods to perform single-particle molecular imaging on a femtosecond timescale. It has been enabled by the advent of x-ray free electron lasers. It works by firing intense ultrashort x-ray pulses on a gas jet of molecules. A single pulse rapidly and strongly ionizes a single molecule, resulting in its ultrafast dissociation, after which the momenta of the atomic fragments are measured in coincidence. This method has been successfully applied to molecules composed of few atoms, but its extension to larger systems remains a challenge. In this thesis, we use simulation and advanced analysis techniques to explore the potential of Coulomb explosion imaging and its applicability to larger molecules, focusing on the 2-iodopyridine molecule (C5H4NI), which has been measured experimentally. We show that, despite detecting only few fragments in coincidence, Coulomb explosion imaging provides meaningful images of the molecule. Analyzing our simulations in detail, we establish that collisions between atoms during the explosion induce measurable correlations between the momenta of the measured fragments, indicating that a large amount of information is hidden in the high dimensionality of the data. We then include the vibrational ground-state fluctuations of the molecule in our simulations, and show that they also leave a fingerprint in the ion-ion correlations, demonstrating that Coulomb explosion can be used to image the complex collective features of a distribution of molecular structures. To apply those analyses to the experiment, we develop an algorithm to systematically find the correlations in the experimental data. Our method succeeds despite the random orientation of the molecule in the lab frame and the limited efficiency of the detectors, thereby opening new ways to interpret Coulomb explosion data, and allowing to exploit some of its untapped potential.In den vergangenen Jahrzehnten wurden zahlreiche Methoden zur Untersuchung einzelner Moleküle auf der Femtosekunden-Zeitskala entwickelt. Eine dieser Methoden ist die Röntgenstrahlen-induzierte Coulomb-Explosion, die durch der Einsatz von Röntgen-Freie-Elek-tronen-Lasern ermöglicht wurde. Hierbei werden intensive, ultrakurze Röntgenpulse auf einen Gasstrahl aus Molekülen geschossen. Die Wechselwirkung eines Röntgenpulses mit einem einzelnen Molekülen verursacht dessen schnelle und starke Ionisation und führt dadurch zu einer ultraschnellen Dissoziation in seine atomaren Fragmente. Danach werden die Impulse der Atomfragmente gleichzeitig gemessen. Diese Methode wurde bereits erfolgreich auf Moleküle, die aus nur wenigen Atomen bestehen, angewandt, die Ausweitung auf größere Systeme bleibt jedoch eine Herausforderung. In dieser Arbeit nutzen wir Simulationen und fortgeschrittene Analysemethoden, um das Potenzial der Coulomb-Explosion und die Anwendbarkeit auf größere Moleküle zu untersuchen. Dabei konzentrieren wir uns auf das 2-Iodpyridin-Molekül (C5H4NI), das experimentell untersucht wurde. Wir zeigen, dass die gleichzeitige Messung von nur wenigen Fragmenten genügt, um mittels Coulomb-Explosions-Bildgebung aussagekräftige Bilder des untersuchten Moleküls zu erhalten. Durch eine detaillierte Analyse unserer Simulationen stellen wir fest, dass Kollisionen zwischen Atomen während der Explosion messbare Korrelationen zwischen den Impulsen der gemessenen Fragmente hervorrufen. Dies verdeutlicht den großen, in der hohen Dimensionalität der Daten verborgenen Informationsanteil. Die Berücksichtigung von Grundzustandsfluktuationen des Moleküls in den Simulationen zeigt, dass diese einen Fingerabdruck in den Ionen-Ionen-Korrelationen hinterlässt. Dies weist darauf hin, dass die Coulomb-Explosion genutzt werden kann, um die die komplexen kollektiven Merkmale einer Verteilung von Molekülstrukturen abzubilden. Um diese Analysen auf Experimente anzuwenden, entwickeln wir einen Algorithmus zum systematischen Auffinden der Korrelationen in experimentellen Daten. Die entwickelte Methode ist trotz der zufälligen Orientierung des Moleküls im Laborsystem und der begrenzten Detektoreffizienz erfolgreich und eröffnet somit neue Wege, Coulomb-Explosionsdaten zu interpretieren und einen Teil ihres bisher ungenutzten Potenzials auszuschöpfen
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Full text link“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
Full text linkWe 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
Auger decay in double core ionized molecules
Full text linkRöntgen Freie Elektronen Laser ermöglichen es Doppel-K-Schalen Löchern in Molekülen in aufeinanderfolgenden mehrfachen Ionisationsschritten in bedeutender Anzahl zu erzeugen. Die Eigenschaften dieser zweifach ionisierten Zustände ist insbesondere relevant für die Strahlungsschäden bei Beugungsexperimenten mit kohärenter Röntgenstrahlung zur Bildgebung einzelner Moleküle. In dieser Arbeit wird der Auger Zerfall doppelt K-Schalen ionisierter Moleküle mittels quantenchemischer ab-initio Methoden untersucht. Zur Beschreibung des emittierten Auger Elektrons im kontinuierlichen Energiespektrum wird dabei die Ein-Zentrums Methode verwendet, in der die elektronische Wellenfunktion auf einem radialen Gitter beschrieben wird unter Verwendung von sphärischen Harmonischen. Wie anhand desWassermoleküls gezeigt wird, ergeben sich durch die Doppel-K-Loch induzierte Protonendynamik in dem Auger Spektrum ausgeprägte Flanken im höherenergetischen Teil jeder Spektralspitze. Die Lebensdauer von Doppel-K-Schalen Löchern in Molekülen ist deutlich verringert im Vergleich zu einfachen K-Löchern durch die K-Loch induzierten Abschirmeffekte der Valenzelektronen. Dieser Mechanismus wird durch ein einfaches Modell erklärt aus dem eine Beziehung zwischen Zerfallsrate und Valenzelektronenpopulation abgeleitet. Mögliche Konsequenzen dieser Ergebnisse für Röntgenbeugungsexperimente sind: Erstens, auch für Röntgenpulse kürzer als 10fs wird das Beugungsbild durch die K-Loch induzierten Umstrukturierungen der Valenzelektronen beeinflußt. Zweitens, die Gesamt-Ionisationsrate ist erhöht aufgrund der schnelleren Neubesetzung der K-Löcher.X-ray free electron lasers allow to create and probe double core holes in molecules via successive ionization in considerable amount. The properties of these double core ionized states are in particular relevant for the radiation damage in X-ray coherent diffractive imaging (CDI) experiments with single molecules. In this thesis the Auger decay of double core ionized states in small molecules is investigated via quantum chemical ab-initio methods. To model the emitted Auger electrons at continuous energy levels the single center method is used, in which the electronic wave function is described on a radial grid using spherical harmonics. As shown for the example of a water molecule, the proton dynamics induced by the double core ionization is reflected in the Auger spectrum by marked tails on the high-energy part of each spectral peak. The life time of double
core holes in molecules is significantly reduced compared to that of single core holes due to the core hole induced screening effects of the valence electrons. This mechanism is explained by a simple model from which a relation for the decay rate and valence electron population is derived. Possible consequences of these results for X-ray diffraction experiments are: First, even for pulses shorter than 10fs the diffraction patterns is biased by the core hole induced rearrangement of the electronic valence structure. Second, the overall ionization rate is enhanced because of the faster refilling of double core holes
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe 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
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