QC 20100628

Doctor of Philosophy / Department of Physics / Igor V. Litvinyuk / The goal of this dissertation project was to study the dynamics of nuclear motion in diatomic (H[subscript]2, N[subscript]2, O[subscript]2, CO) and triatomic (CO[subscript]2) molecules initiated by the ionization and/or excitation of these molecules with near-IR few-cycle laser pulses. This dynamics includes vibrational and rotational motion on the electronic potential surfaces of the molecules and their molecular ions. The experimental techniques used included the pump-probe approach, laser Coulomb explosion imaging and the COLTRIMS technique. The results are presented in four chapters. A study of rotational and vibrational nuclear dynamics in H[subscript]2 and D[subscript]2 molecules and ions initiated by 8 fs near-IR pulses is presented in Chapter 4. Transient alignment of the neutral molecules was observed and simulated; rotational frequency components contributing to the rotational wavepacket dynamics were recovered. Chapter 5 is dedicated to revealing the contribution of excited dissociative states of D[subscript]2[superscript]+ ions to the process of fragmentation by electron recollision. It was shown that it is possible to isolate the process of resonant excitation and estimate the individual contributions of the [superscript]2sigma[subscript]u[superscript]+ and [superscript]2pi[subscript]u states. In Chapter 6 the subject of investigation is the nuclear dynamics of N[subscript]2, O[subscript]2 and CO molecules initiated by ionization of a neutral molecule by a short intense laser pulse. It was shown that the kinetic energy release of the Coulomb explosion fragments, measured as a function of the delay time between pump and probe pulses, reveals the behavior of nuclear wave packet evolution on electronic states of the molecular ions. It was shown that information on the dissociation and excitation pathways can be extracted from the experimental spectra and the relative contributions of particular electronic states can be estimated. Chapter 7 is focused on studying the fragmentation of CO[subscript]2 following the interaction of this molecule with the laser field. The most important result of this study was that it presented direct experimental evidence of charge-resonant enhanced ionization (CREI), a phenomenon well-studied for diatomic molecules and predicted theoretically for triatomic molecules. The critical internuclear distance, the relevant ionic charge state and a pair of charge-resonant states responsible for the CREI were also found.

This thesis presents theoretical studies of several x-ray spectroscopies - x-ray absorption, x-ray photoelectron emission, radiative and non-radiative resonant Raman scattering spectroscopy. The main focus point is investigating the influence of nuclear dynamics on these spectra for a variety of small molecules - naphthalene, biphenyl, ethylene, the water dimer, HCl, CO. The theoretical tools used consist of the basic equations of the relevant x-ray spectroscopy. Wave packet methods are also used. The molecular parameters needed for our simulations are obtained through suitable quantum chemical calculations, based on either wave function or density functional methods. Our simulations are compared to experimental data, where available. Simulations of x-ray absorption and x-ray photoionization spectra for naphthalene and biphenyl show that the spectral shapes are heavily influenced by the joint effect of two factors -- chemical shifts and excitations of vibrational progression. Comparison between the two molecules and also comparison to a reference case -- benzene, provides useful insight into the molecular behavior under core excitation. In a further step, we consider the O1s x-ray photoelectron spectrum of the water dimer. A substantial broadening of the two bands originating from the donor and the acceptor oxygen is found. It is caused by excitations of soft intermolecular vibrational modes, associated with the hydrogen bond. Another strong influence of the nuclear dynamics is clearly seen in the resonant x-ray Raman scattering of HCl. Vibrational collapse is observed experimentally and confirmed theoretically for distinctive situations. This effect allows to eliminate completely the vibrational broadening, and hence, considerably increase the spectral resolution. We considered also the vibrational dynamics in resonant soft x-ray Raman scattering from ethylene. The importance of vibronic coupling and symmetry effects is discussed and emphasized. We obtained excellent agreement with the experimental data. We predict an interference effect in the resonant Auger scattering from fixed-in-space molecules. By exciting a molecule to a dissociative state and measuring the angular distribution of the Auger electrons in coincidence with the molecular ion, one can observe this effect. The interference pattern can be used after Fourier transformation for extracting structural data about the studied system. We have found that two-center interference leads to an enhancement of the recoil effect. Finally, it is shown that core excitation to doubly-excited dissociative Pi state is accompanied by Doppler splitting of the atomic peak in resonant Auger scattering from carbon monoxide. / QC 20100910

In this thesis Langevin approach is applied to analyze the nuclear dissipative dynamics in fission and fusion reactions. In these investigations, the nuclear elongation coordinate and the corresponding momentum are chosen as collective variables. By considering changes in these variables the decay rate of fission and the formation probability of fusion for heavy ion reactions are calculated. These calculations are performed using simulation techniques and the results thus obtained are compared with the corresponding results of analytic solutions.

<p>In this thesis we have performed core-electron spectroscopy studies of gas phase molecular systems starting with smaller diatomic, continuing with triatomic and extending our research to more complex polyatomic ones. We can subdivide the results presented here into two categories: the first one focusing on electronic fine structure and effect of the chemical bonds on molecular core-levels and the other one dealing with nuclear dynamics induced by creation of a core hole. In our research we have mostly used synchrotron radiation based techniques such as X-ray Photoelectron (XPS), X-ray Absorption (XAS), normal and Resonant Auger (AES and RAS, respectively) and Energy-Selected Auger Electron PhotoIon COincidence (ES-AEPICO) spectroscopies.</p><p>We have demonstrated that resonant Auger spectroscopy can be used to aid interpretation of the features observed in XAS for Rydberg structures in the case of Cl₂ and C1s⁻¹π*¹ states of allene molecules. The combined use of high-resolution spectroscopy with <i>ab initio</i> calculations can help the interpretation of strongly overlapped spectral features and disentangle their complex profiles. This approach enabled us to determine the differences in the lifetimes for core-hole 2p sublevels of Cl₂ which are caused by the presence of the chemical bond. We have shown that contribution in terms of the Mulliken population of valence molecular orbitals is a determining factor for resonant enhancement of different final states and fragmentation patterns reached after resonant Auger decays in N₂O.</p><p>We have also performed a systematic study of the dependence of the C1s resonant Auger kinetic energies on the presence of different substituents in CH₃X compounds. For the first time we have studied possible isomerization reaction induced by core excitation of acetylacetone. We could observe a new spectral feature in the resonant Auger decay spectra which we interpreted as a signature of core-excitation-induced keto-enol tautomerism.</p>

In this thesis we have performed core-electron spectroscopy studies of gas phase molecular systems starting with smaller diatomic, continuing with triatomic and extending our research to more complex polyatomic ones. We can subdivide the results presented here into two categories: the first one focusing on electronic fine structure and effect of the chemical bonds on molecular core-levels and the other one dealing with nuclear dynamics induced by creation of a core hole. In our research we have mostly used synchrotron radiation based techniques such as X-ray Photoelectron (XPS), X-ray Absorption (XAS), normal and Resonant Auger (AES and RAS, respectively) and Energy-Selected Auger Electron PhotoIon COincidence (ES-AEPICO) spectroscopies. We have demonstrated that resonant Auger spectroscopy can be used to aid interpretation of the features observed in XAS for Rydberg structures in the case of Cl2 and C1s−1π*1 states of allene molecules. The combined use of high-resolution spectroscopy with ab initio calculations can help the interpretation of strongly overlapped spectral features and disentangle their complex profiles. This approach enabled us to determine the differences in the lifetimes for core-hole 2p sublevels of Cl2 which are caused by the presence of the chemical bond. We have shown that contribution in terms of the Mulliken population of valence molecular orbitals is a determining factor for resonant enhancement of different final states and fragmentation patterns reached after resonant Auger decays in N2O. We have also performed a systematic study of the dependence of the C1s resonant Auger kinetic energies on the presence of different substituents in CH3X compounds. For the first time we have studied possible isomerization reaction induced by core excitation of acetylacetone. We could observe a new spectral feature in the resonant Auger decay spectra which we interpreted as a signature of core-excitation-induced keto-enol tautomerism.

PolyHistidine repeats and DYRK1A: from the localization to the functionEl principal objectiu d'aquesta tesi ha estat el d'esbrinar noves funcions de la proteína quinasa DYRK1A en el nucli cel.lular. Donat que el domini de repetició d'histidines de DYRK1A dirigeix la proteína al compartiment d'speckles nuclears, aquesta propietat ha estat utilitzada per adreçar aquesta pregunta. Els resultats obtinguts en aquesta tesi han permès proposar els homopolímers d'histidina com una nova i general senyal de localització a speckles nuclears. Proteïnes amb segments de polihistidines, la majoria d'elles factors de transcripció, mostren un comportament intranuclear dinàmic, compatible amb un model en el quèl diferents dominis d'interacció competeixen entre ells pel reclutament de la proteína a diferents subcompartiments nuclears. El mecanisme molecular que media l'acumulació a speckles de les proteïnes amb polihistines s'ha estudiat utilitzant DYRK1A com a model. Els resultats obtinguts exclouen la unió a l'RNA com a mecanisme de reclutament i concloure que, aquest, ocorre mitjançant la interacció amb proteïnes residents. S'han identificat dues noves proteïnes interactores per a DYRK1A, l'RNA polimerasa II i el factor de transcripció Brn-3b. La fosforilació de DYRK1A sobre el domini C-terminal o CTD de l'RNA polimerasa II suggereix una funció directa de la quinasa en el procés de transcripció o del seu acoblament al processament d'RNAs missatgers. La fosforilació de DYRK1A sobre el domini d'activació de Brn-3b sembla regular positivament l'activitat transcripcional d'aquest factor. Aquests resultats indiquen una funció activa de DYRK1A en la regulació de la transcripció gènica, tant directament sobre la maquinària transcripcional com indirectament, modulant l'activitat de factors de transcripció. PolyHistidine repeats and DYRK1A: from the localization to the functionThe main objective of this thesis work has been to identify new roles for the protein kinase DYRK1A in the cell nucleus. Given that a histidine repeat in DYRK1A targets the protein to the nuclear speckle compartment, this property has been used as a tool to approach the question. The results obtained in this thesis work have allowed proposing homopolymeric histidine runs as a novel and general nuclear speckle-directing signal. Proteins with polyHistidine segments, mostly transcription factors, present a dynamic intranuclear behaviour compatible with a model in which distinct interacting domains compete for recruiting elements within the nucleus. The molecular mechanisms that mediate speckle accumulation have been studied in DYRK1A as a model system. The results allow excluding RNA binding as the recruiting mechanism and concluding that targeting is mediated by interaction with speckle-resident proteins. Two novel DYRK1A interactors have been identified during the study, the RNA polymerase II and the transcription factor Brn-3b. DYRK1A phosphorylation of the C-terminal domain or CTD of the RNA polymerase II suggests a direct role of DYRK1A on transcription or coupling of transcription with RNA processing. DYRK1A phosphorylation of Brn-3b within its activation domain seems to positively regulate Brn-3b transcriptional activity. These results confirm an active role for DYRK1A in gene transcription regulation both direct on the transcriptional machinery and indirect by modulating the activity of transcription factors.