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1	Charge migration and one-electron oxidation at adenine and thymidine containing DNA strands and role of guanine N1 imino proton in long range charge migration through DNA Ghosh, Avik Kumar 16 May 2007 (has links) DNA is the carrier of biological information and damage to DNA has been believed to be responsible for many diseases including aging and cancer. One electron oxidation by charge migration through DNA is one of the processes that lead to DNA damage. It is known that the guanine N1 imino proton can be transferred to the N3 of cytidine that is hydrogen bonded to it. Some reports have implication that this proton transfer and radical cation migration are coupled to each other. We have incorporated 5-fluoro-2 -deoxycytidine (F5dC) in place of normal dC in DNA duplexes. Although, the lower pKa of F5dC should perturb the proton transfer process from the guanine to it, we do not see any change in the charge migration ability compared to the strands having normal cytidines. However, there is a considerable decrease in the guanine damage, when there is F5dC opposite to it. These results indicate that the charge migration is not coupled with proton transfer process, but the change in basicity affects the reactivity of the guanine radical cation. We have also reported a systematic study on the charge migration through adenine (A) and thymidine (T) containing DNA strands. The damage has predominantly seen in thymidine, although from oxidation potentials reaction at adenine was expected. The thymidine reaction has been analyzed thoroughly. It has similar distance dependence property as the well known guanine damage. Study of thymidine damage in presence of radical scavengers, replacement of thymidines by Uracil and HPLC-MS study point toward reactions involving tandem lesion. On the basis of these information and molecular modeling study we have proposed a possible pathway leading to one-electron oxidation at the thymidines. DNA Charge migration Oxidative damage
2	Charge Migration through Duplex DNA: A Study of the Mechanism for Charge Migration and Oxidative Damage Schlientz, Nathan William 19 May 2006 (has links) DNA sequences containing contiguous AA or TT mismatches, as well as sequences containing a 3-deazacytidine analogue were synthesized. Irradiation of anthraquinone abstracts an electron from the DNA. The loss of an electron from double-stranded DNA results in the formation of a radical cation that migrates through the DNA where it reacts irreversibly with H2O or O2 at GG steps. Subsequent treatment with piperidine or Fpg enzyme cleaves the backbone of the DNA at the site of reaction. DNA oligomers were designed to contain contiguous AA, TT, or G3-deazacytidine mismatches. It was revealed that the mismatches destabilize the duplex DNA; however, there is no measurable effect on the overall secondary structure of the DNA. The contiguous (AA)n mismatch, where n lt 7, was shown to have no effect on charge migration efficiency. In contrast, the contiguous (TT)n mismatch, where n gt 2, was shown to have near complete inhibition of charge migration through the mismatch region. Charge migration through the G3-deazacytidine mismatch was shown to have no effect on charge migration efficiency as well. Interestingly, reaction at the (G3-deazacytidine)2 base pairs revealed a change in the ratio of oxidative damage at the Gs. In (GC)2 base pairs, the ratio of damage at the two Gs is 10:1 with the majority of damage occurring at the 5-G. However, the (G3-deazacytidine)2 base pairs had an equal distribution of damage at the 5 and 3-Gs, with the amount of total reactivity equaling the (GC)2 base pairs. These findings indicate that the base composition in mismatched DNA determines the effect on charge migration efficiency and trapping reactivity. Radical cation Charge transfer Deazacytidine DNA Oxidative damage Charge migration DNA Cations Charge transfer
3	Dynamique électronique à l'échelle attoseconde et femtoseconde en physique moléculaire : une approche ab-initio / Electron dynamics at attosecond and femtosecond time scale in molecular physics : an ab-initio approach Despré, Victor 25 September 2015 (has links) L'avènement de la physique attoseconde a amené de nouveaux challenges tant expérimentaux que théoriques. En effet, l'observation de processus dynamiques, intervenant aux échelles de temps intrinsèques des mouvements des charges aux échelles atomiques, permet d'envisager des nouveaux processus pour lesquels le rôle des corrélations et des couplages non-adiabatiques deviennent primordiaux. Les travaux présentés dans ce manuscrit s'inscrivent dans le cadre de l'étude des molécules complexes, en particulier carbonées, soumises à une impulsion lumineuse courte. Pour de telles échelles de temps (femtoseconde / attoseconde) et d'énergie (IR / UVX), les principales approximations permettant l'étude des systèmes électroniques ne sont plus valides. Cette thèse présente les simulations théoriques réalisées permettant l'étude théorique de molécules dans de telles conditions. L'étude des dynamiques de migration de charges corrélées au sein des molécules de benzène, de différents hydrocarbures aromatiques polycycliques ainsi qu'au sein de molécules d'intérêt biologique telles que la phénylalanine, a été réalisée. Ce type de dynamiques n'a jamais pu être observé expérimentalement. Une attention particulière a donc été portée à la faisabilité d'une expérience dans le cas de la molécule de benzène. Les relaxations non-adiabatiques de la molécule de naphtalène soumise à une impulsion UVX ont été étudiées. Enfin, les dynamiques à l'échelle du cycle optique, rencontrées par un groupe de molécules de taille intermédiaire soumis à une impulsion IR, ont été abordées. Ces simulations ont permis d'interpréter des expériences pompe-sonde réalisées par des membres de notre équipe / The advent of attosecond physics has brought new experimental and theoretical challenges. Indeed, the observation of dynamic processes occurring at the intrinsic time scale of charge motion at atomic scale, allows to consider new processes for which the role of correlations and non-adiabatic couplings become primordial. The work presented in this manuscript falls in the context of the study of complex molecules subject to a short light pulse. For such time (femtosecond / attosecond) and energy scales (IR / XUV), the main approximations that permit the study of electronic systems are no longer appropriate. In this thesis, we present the simulations realized for the theoretical study of molecules in such conditions. We studied the correlated charge migration dynamics in several molecules like the benzene, different polycyclic aromatic hydrocarbons and molecules of biological interest such as phenylalanine. This kind of dynamics has never been observed experimentally. Hence, a particular attention was paid to the feasibility of an experiment in the case of the benzene molecule. The non-adiabatic relaxations of the naphthalene molecule subjected to a XUV pulse were also studied. Finally, dynamics occurring at the optical cycle time scale experienced by a group of medium-sized molecules subject to an IR pulse, were discussed. These simulations were used to interpret pump-probe experiments made by members of our team Dynamique électronique Attoseconde Femtoseconde Corrélation électronique Couplage vibronique Migration de charge Ab-initio Photoionisation Dynamic electronic Attoseconde Femtoseconde Electronic correlation Vibronic coupling Charge migration Ab-initio Photoionization 537.5
4	Étude de la dynamique électronique ultra-rapide suivant l’ionisation de la molécule de Caféine par la méthode TD-DFTB / Study of the ultrafast electronic dynamics following ionization of Caffeine molecule with the TD-DFTB method Meziane, Mehdi 24 July 2019 (has links) Depuis la fin des années 80 et l'avènement de la femto-chimie nous pouvons sonder la dynamique nucléaire à l’œuvre au cours de réactions chimiques à l'échelle de la femtoseconde. Plus récemment, la production d'impulsions lasers attosecondes isolées permet d'atteindre une résolution temporelle plus grande encore. Par elle, il devient possible de sonder la dynamique d'origine purement électronique induite par photo-excitation, et notamment photo-ionisation. Dans ce contexte, avec le développement des techniques de spectroscopie résolue en temps, il est important de disposer d'approches théoriques fiables aidant à l'appréhension de résultats toujours plus nombreux dans ce domaine. La tâche et néanmoins rendue difficile par le caractère profondément multi-électronique des processus en jeu. Traiter de tels effets précisément requiert une grande puissance de calcul, ce qui a limité les études disponibles aujourd'hui à de petits systèmes. Au cours de cette thèse, j'ai tenté d'expliquer les résultats d'une expérience de type "pompe-sonde" (UVX-IR) sur molécule de Caféine menée par une équipe de collaborateurs à l'Institut lumière matière. J'ai utilisé pour cela une méthode basée sur la théorie de la fonctionnelle de la densité dépendante du temps, la TD-DFTB dont le coût numérique réduit par rapport à cette dernière permet des calculs sur de gros systèmes en temps raisonnable. J'y présente une étude du paysage énergétique de la Caféine ainsi que le résultat de 2 approches distinctes pour simuler l'ionisation de ce composé. La première, l'approximation de l'ionisation soudaine cosiste à retirer "à la main" un électron à l'une des orbitales Kohn-Sham occupées du système neutre et ne tient pas compte du champ laser. La seconde à recours à un potentiel imaginaire (ou CAP - Complex Absorbing Potential) pour simuler la perte d'electrons, et tiens explicitement compte du champ laser / Since the advent of femtochemistry, at the end of 1980's, we are able to probe the nuclear dynamics underlying chemical reactions down to the scale of a femtosecond. More recently, the production of isolated attosecond pulses allows to reach an even bigger temporal resolution. It is now possible to probe the ultrafast electronic dynamics following a photo-excitation. In this context, with the developpement of time-resolved spectroscopy techniques, it is important to have reliable theorectical approaches in order to apprehend the increasing number of results in this field. This task is made difficult by the intrinsic multi-electronic nature processes at play. The precise treatment of such effects requires a considerable computing power, and have thus limited the availables studies to relatively small systems. In this thesis, I tried to explain the outcome of a "pump-probe" (XUV-IR) experiment on Caffeine molecule realized by our collaborators at the Insitut Lumière Matière. To do so, I used a method based on density functional theory, the TD-DFTB, which lower numerical cost with respect to TD-DFT allows calculation on bigger compounds. I present in the document a study of the energetical landscape of Caffeine, and 2 approaches to simulate ionization. The first one, the so called sudden-ionization approximation consist to retrieve "by hand" an electron from the occupied Kohn-Sham orbitals of the neutral system without taking the laser field into account. The other one is based on the introduction of a complex absorbing potential (CAP) to account for electron loss and take explicitely the laser field into account. DFT Real-time TD-DFT TD-DFTB Migration de charge Physique attoseconde Photoionisation Ionisation soudaine Potentiels absorbants complexes DFT Real-time TDDFT TD-DFTB Charge migration Photoionization Attosecond Science Sudden Ionization Complex absorbing Potential 530
5	Untersuchung photorefraktiver Materialien mittels optischer Ptychographie / Investigation of photorefractive materials using optical ptychography Bernert, Constantin 05 January 2017 (has links) (PDF) In der vorliegenden Arbeit wird die neuartige Mikroskopiemethode der Ptychographie für die Untersuchung photorefraktiver Materialien genutzt. Photorefraktive Materialien zeichnen sich durch die Generation lichtinduzierter Brechungsindexänderungen aus. Die Ptychographie bietet die Möglichkeit, neben der generierten Brechungsindexänderung im photorefraktiven Material auch die für die Generation genutzte Intensitätsverteilung des Laserstrahls zu bestimmen. Es wird sowohl die Abhängigkeit der Brechungsindexänderung von der Zeit der Generation als auch die Abhängigkeit von der Polarisation des Lasers gemessen. Durch den Vergleich der gewonnenen Werte mit einer numerischen Simulation des photorefraktiven Effekts werden mikroskopische Parameter der lichtinduzierten Ladungswanderung ermittelt. Zudem wird aus der polarisationsabhängigen ptychographischen Messung das Raumladungsfeld und die korrespondierende Ladungsdichte im Material berechnet. Die Ptychographie liefert damit einen neuen Zugang zum quantitativen Verständnis der Photorefraktivität. / In the present thesis the novel microscopy technique of ptychography is applied to the investigation of photorefractive materials. Photorefractive materials exhibit a change of the refractive index due to the exposure to light. The method of ptychography determines the refractive index change of the material together with the intensity distribution of the laser beam that was used for its generation. In one part of the experiment the time dependence of the refractive index change versus the generation time is investigated, in the other part of the experiment the dependence of the refractive index change to the polarisation of the laser beam is examined. Microscopic parameters of the photorefractive charge migration are determined with the utilisation of a numerical simulation of the photorefractive effect and its comparison with the measurement. Finally, the whole space charge field with the corresponding space charge density is calculated from a set of ptychographic measurements of one refractive index change with different polarisation directions of the laser. The presented experiments and their evaluation show, that the method of ptychography opens a new possibility for a quantitative understanding of the photorefractive effect. Photorefraktivität photorefraktiv Photorefraktiver Effekt photorefraktives photorefraktiver photorefraktive lichtinduziert lichtinduzierte lichtinduzierter lichtinduziertes Lithiumniobat LiNbO3 LiNbO3:Fe linbo3 linbo3:fe Ladungstransport Brechungsindexänderung Brechungsindexänderungen Raumladungsfeld elektrooptischer Effekt Pockels Effekt photovoltaischer Effekt photovoltaische Stromdichte photovoltaische photovoltaischer Photovoltaik photovoltaissches Ptychographie ptychographisch ptychographische ptychographisches Interferometrie interferometrisch interferometrische interferometrische Untersuchung interferometrisches Holographie holographisches holographische holographische Untersuchung digitale Holographie photorefractive effect photorefractive photo refractive light-induced lightinduced light induced Lithium niobate Lithiumniobate LiNbO3 LiNbO3:Fe linbo3 linbo3:fe charge transport chargetransport refractive index change refractive index changes space charge field electrooptic effect electrooptic Pockels effect photovoltaic effect photovoltaic current photovoltaic ptychography ptychographic interferometry interferometric holography holographic digital holography ddc:530 rvk:VG 8600 Photorefraktivität Photorefraktiver Effekt Lithiumniobat Ladungstransport Brechungsindexänderung elektrooptischer Effekt Pockels Effekt photovoltaischer Effekt photovoltaische Stromdichte Photovoltaik Ptychographie Interferometrie Holographie digitale Holographie Photorefractive Effect Lithium niobate charge transport charge migration refractive index change electrooptic effect Pockels effect photovoltaic effect photovoltaic current ptychography interferometry holography digital holography
6	Untersuchung photorefraktiver Materialien mittels optischer Ptychographie Bernert, Constantin 04 October 2016 (has links) In der vorliegenden Arbeit wird die neuartige Mikroskopiemethode der Ptychographie für die Untersuchung photorefraktiver Materialien genutzt. Photorefraktive Materialien zeichnen sich durch die Generation lichtinduzierter Brechungsindexänderungen aus. Die Ptychographie bietet die Möglichkeit, neben der generierten Brechungsindexänderung im photorefraktiven Material auch die für die Generation genutzte Intensitätsverteilung des Laserstrahls zu bestimmen. Es wird sowohl die Abhängigkeit der Brechungsindexänderung von der Zeit der Generation als auch die Abhängigkeit von der Polarisation des Lasers gemessen. Durch den Vergleich der gewonnenen Werte mit einer numerischen Simulation des photorefraktiven Effekts werden mikroskopische Parameter der lichtinduzierten Ladungswanderung ermittelt. Zudem wird aus der polarisationsabhängigen ptychographischen Messung das Raumladungsfeld und die korrespondierende Ladungsdichte im Material berechnet. Die Ptychographie liefert damit einen neuen Zugang zum quantitativen Verständnis der Photorefraktivität.:1 Einleitung 2 Theoretische Vorbetrachtungen 2.1 Ptychographie 2.1.1 Messung 2.1.2 Modell und Rekonstruktion 2.1.3 Ortsauflösung 2.2 Photorefraktiver Efekt 2.2.1 Lithiumniobat - Musterbeispiel für die Photorefraktivität 2.2.2 Ein-Zentrum-Modell 2.2.3 Brechungsindexänderung 2.2.4 Hohe Intensitäten 2.3 Raumladungsfeld 2.3.1 Ableitung des Feldes aus den Messgrößen 2.3.2 Raumladungsverteilung 2.3.3 Oberflächendeformation 2.3.4 Dynamik der Ladungen und des Feldes 3 Messungen 3.1 Proben 3.1.1 Ptychographische Teststruktur 3.1.2 LiNbO3:Fe 3.2 Versuchsanordnung 3.2.1 Experimenteller Aufbau 3.2.2 Grenze der Ortsauflösung 3.2.3 Charakterisierung des Laserstrahls 3.2.4 Experimentelle Überprüfung der Näherungen 3.3 Dynamik der Brechungsindexänderung 3.4 Polarisationsabhängigkeit der Brechungsindexänderung 4 Auswertung 4.1 Dynamik des Raumladungsfeldes und der Ladungen 4.1.1 Simulation 4.1.2 Vergleich zwischen Messung und Simulation 4.1.3 Dynamik der Ladungsverteilung 4.1.4 Fazit 4.2 Berechnung des Raumladungsfeldes 4.2.1 Raumladungsfeld und Ladungsverteilung 4.2.2 Simulation 4.2.3 Asymmetrie der Ladungsverteilung 4.2.4 Fazit 5 Zusammenfassung Appendizes A Physikalische Konstanten B Tensoren für LiNbO3 C Ungenäherte Herleitung der Brechungsindexänderung D Implementierung eines iterativen Verfahrens zur Bestimmung der Dynamik des Ein-Zentrum-Modells E Quelltext der Implementierung des iterativen Verfahrens Literaturverzeichnis / In the present thesis the novel microscopy technique of ptychography is applied to the investigation of photorefractive materials. Photorefractive materials exhibit a change of the refractive index due to the exposure to light. The method of ptychography determines the refractive index change of the material together with the intensity distribution of the laser beam that was used for its generation. In one part of the experiment the time dependence of the refractive index change versus the generation time is investigated, in the other part of the experiment the dependence of the refractive index change to the polarisation of the laser beam is examined. Microscopic parameters of the photorefractive charge migration are determined with the utilisation of a numerical simulation of the photorefractive effect and its comparison with the measurement. Finally, the whole space charge field with the corresponding space charge density is calculated from a set of ptychographic measurements of one refractive index change with different polarisation directions of the laser. The presented experiments and their evaluation show, that the method of ptychography opens a new possibility for a quantitative understanding of the photorefractive effect.:1 Einleitung 2 Theoretische Vorbetrachtungen 2.1 Ptychographie 2.1.1 Messung 2.1.2 Modell und Rekonstruktion 2.1.3 Ortsauflösung 2.2 Photorefraktiver Efekt 2.2.1 Lithiumniobat - Musterbeispiel für die Photorefraktivität 2.2.2 Ein-Zentrum-Modell 2.2.3 Brechungsindexänderung 2.2.4 Hohe Intensitäten 2.3 Raumladungsfeld 2.3.1 Ableitung des Feldes aus den Messgrößen 2.3.2 Raumladungsverteilung 2.3.3 Oberflächendeformation 2.3.4 Dynamik der Ladungen und des Feldes 3 Messungen 3.1 Proben 3.1.1 Ptychographische Teststruktur 3.1.2 LiNbO3:Fe 3.2 Versuchsanordnung 3.2.1 Experimenteller Aufbau 3.2.2 Grenze der Ortsauflösung 3.2.3 Charakterisierung des Laserstrahls 3.2.4 Experimentelle Überprüfung der Näherungen 3.3 Dynamik der Brechungsindexänderung 3.4 Polarisationsabhängigkeit der Brechungsindexänderung 4 Auswertung 4.1 Dynamik des Raumladungsfeldes und der Ladungen 4.1.1 Simulation 4.1.2 Vergleich zwischen Messung und Simulation 4.1.3 Dynamik der Ladungsverteilung 4.1.4 Fazit 4.2 Berechnung des Raumladungsfeldes 4.2.1 Raumladungsfeld und Ladungsverteilung 4.2.2 Simulation 4.2.3 Asymmetrie der Ladungsverteilung 4.2.4 Fazit 5 Zusammenfassung Appendizes A Physikalische Konstanten B Tensoren für LiNbO3 C Ungenäherte Herleitung der Brechungsindexänderung D Implementierung eines iterativen Verfahrens zur Bestimmung der Dynamik des Ein-Zentrum-Modells E Quelltext der Implementierung des iterativen Verfahrens Literaturverzeichnis info:eu-repo/classification/ddc/530 ddc:530

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