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Cellular migration is essential for an assortment of developmental processes ranging from embryogenesis to neurodevelopment. Oftentimes, cellular migration through narrow spaces is limited by nuclear migration,such as is the case for cancer metastasis and in immune response (i.e. white blood cells rushing to the site of injury). Nuclear migration through small constrictions has been studied in vitro but not in vivo. Here, we look at nuclear migration in the context of the developing vulval and neural precursors of Caenorhabditis elegans. During the mid-L1 larval stage, six pairs of P-cell nuclei migrate from the lateral half of the worm to the ventral cord, where they will divide and progress into the vulval and neural precursor cells. These nuclei must migrate through a constriction between the cuticle and the muscle of the developing animal that is about 5% of the diameter of nucleus in the early L1 stage. We explore the mechanisms which allow them to stably migrate in this normal developmental process. Typically, this process has been facilitated by the microtubule-based SUN-KASH pathway, which serve as the tracks for the migrating nuclei. Previous studies have shown that in the absence of the SUN-KASH pathway, these nuclei still migrate at 15°C. We found that there is an actin-based pathway which aids the migration process at 15°C in parallel and in absence of the SUN-KASH pathway. We hypothesized that FLN-2, a filamin, crosslinks branched actin networks and organized actin bundles to support stable nuclear migration through narrow spaces. We found that in the absence of unc-84 (a SUN protein) and/or fln-2, that nuclear rupture events were more prevalent in the migrating P cells, while the absence of unc-84 resulted in the formation of micronuclei in the early and mid-migration stages. We propose future work to determine how FLN-2 may be facilitating P-cell nuclear migration, along with its relationship to UNC-84, LMN-1 (lamin), and CGEF-1 (Cdc42 guanine exchang

Cellular migration is essential for an assortment of developmental processes ranging from embryogenesis to neurodevelopment. Oftentimes, cellular migration through narrow spaces is limited by nuclear migration,such as is the case for cancer metastasis and in immune response (i.e. white blood cells rushing to the site of injury). Nuclear migration through small constrictions has been studied in vitro but not in vivo. Here, we look at nuclear migration in the context of the developing vulval and neural precursors of Caenorhabditis elegans. During the mid-L1 larval stage, six pairs of P-cell nuclei migrate from the lateral half of the worm to the ventral cord, where they will divide and progress into the vulval and neural precursor cells. These nuclei must migrate through a constriction between the cuticle and the muscle of the developing animal that is about 5% of the diameter of nucleus in the early L1 stage. We explore the mechanisms which allow them to stably migrate in this normal developmental process. Typically, this process has been facilitated by the microtubule-based SUN-KASH pathway, which serve as the tracks for the migrating nuclei. Previous studies have shown that in the absence of the SUN-KASH pathway, these nuclei still migrate at 15°C. We found that there is an actin-based pathway which aids the migration process at 15°C in parallel and in absence of the SUN-KASH pathway. We hypothesized that FLN-2, a filamin, crosslinks branched actin networks and organized actin bundles to support stable nuclear migration through narrow spaces. We found that in the absence of unc-84 (a SUN protein) and/or fln-2, that nuclear rupture events were more prevalent in the migrating P cells, while the absence of unc-84 resulted in the formation of micronuclei in the early and mid-migration stages. We propose future work to determine how FLN-2 may be facilitating P-cell nuclear migration, along with its relationship to UNC-84, LMN-1 (lamin), and CGEF-1 (Cdc42 guanine exchang

In this thesis the electronic structure and dynamics of iodine, krypton and bromine atoms in isolated and molecular forms are investigated through K-shell photoexcitation and subsequent Auger decay. The experimental studies are carried out using hard x-ray photoelectron spectroscopic techniques and the theoretical work by applying relativistic ab initio quantum mechanical models. The reported photoelectron spectra from iodine compounds CH3I and CF3I have the highest binding energy, 33.2 keV, recorded from any molecule in the gas phase up to date. From the spectra it is shown that chemical shifts are observable even at such deep core orbitals. From krypton a detailed analysis of Auger decay and Fluorescence cascade following K and L-shell ionization up to quadruple ionized states is presented. The work concerning bromine provides an analysis of photoionization, excitation, lifetime, Auger decay and nuclear dynamics around the K-edge of HBr molecule.

Molten salt reactors (MSRs) are a class of nuclear reactor which uses a molten ionic liquidas either the coolant or also as the fuel. While a 8 MWth MSR was successfully operatedin the 1960s it was not until the early 2000s that MSRs gained widespread attention. Sincethen MSRs have enjoyed plentiful research support. Despite such support only one generalMSR fuel cycle analysis tool is available for use by the research community and even thisthis tool lacks features necessary for modelling a MSR, and so possibly providing answers ofa lower quality.In this work a method is proposed and implemented within the SERPENT 2 reactorphysics Monte-Carlo code. This method, named ADER - the Advanced Depletion Extensionfor Reprocessing - is a seamlessly incorporated source code modification to the SERPENT2 base code which allows the user to define arbitrary collections of elements, isotopes, andchemicals as well as relationships among them.Furthermore ADER allows the user to specify a variety of mass flows subject to theconstraints as defined through the collections of elements, isotopes, and chemicals the userhas structured. Along with support for constraints involving both corrosion and nuclearcontrol concerns, ADER allows the user to optimize the solution against a quantity of interest- e.g, total uranium fed into the system.Through these structures much of the complex chemistry, corrosion modelling, and nuclear concerns of operating a MSR can be linearized and solved against an optimizationtarget, which is necessary given the large number of constraints and variables in such aproblem space. Linearization reduces the problem complexity and eliminates concerns overlocal versus global optimization targets. Within the typically narrow operating parametersof MSRs linearization is an appropriate approximation to the higher dimensional equationsrepresenting the phenomenon involved.2This linear system and optimization target may then be passed to a linear optimizationsolver, in this

Molten salt reactors (MSRs) are a class of nuclear reactor which uses a molten ionic liquidas either the coolant or also as the fuel. While a 8 MWth MSR was successfully operatedin the 1960s it was not until the early 2000s that MSRs gained widespread attention. Sincethen MSRs have enjoyed plentiful research support. Despite such support only one generalMSR fuel cycle analysis tool is available for use by the research community and even thisthis tool lacks features necessary for modelling a MSR, and so possibly providing answers ofa lower quality.In this work a method is proposed and implemented within the SERPENT 2 reactorphysics Monte-Carlo code. This method, named ADER - the Advanced Depletion Extensionfor Reprocessing - is a seamlessly incorporated source code modification to the SERPENT2 base code which allows the user to define arbitrary collections of elements, isotopes, andchemicals as well as relationships among them.Furthermore ADER allows the user to specify a variety of mass flows subject to theconstraints as defined through the collections of elements, isotopes, and chemicals the userhas structured. Along with support for constraints involving both corrosion and nuclearcontrol concerns, ADER allows the user to optimize the solution against a quantity of interest- e.g, total uranium fed into the system.Through these structures much of the complex chemistry, corrosion modelling, and nuclear concerns of operating a MSR can be linearized and solved against an optimizationtarget, which is necessary given the large number of constraints and variables in such aproblem space. Linearization reduces the problem complexity and eliminates concerns overlocal versus global optimization targets. Within the typically narrow operating parametersof MSRs linearization is an appropriate approximation to the higher dimensional equationsrepresenting the phenomenon involved.2This linear system and optimization target may then be passed to a linear optimizationsolver, in this

This thesis presents studies on dissociation of two model molecules: Butadiene and Cyclopropane. Tunable synchrotron radiation was used to ionize or excite the molecules in the gas phase, and the momentum correlation of the resulting fragment ions were measured using a 3D momenta coincident ion spectroscopy. The experimental results were interpreted with the aid of ab-initio quantum calculation. This allows us to gain insight into the fundamental processes behind the molecular dissociation, that how correlated electronic and nuclear dynamics drive molecular dissociation.Tunable XUV-radiation was used to doubly ionize molecules to different states.By Comparing experimental and theoretical values for appearance energy and kinetic energy released of the dissociation channels, electronic gateway state of each dissociation channels were identified. By analysing the momentum vector of ion pairs as a function of photon energy and internal energy sharing in the dissociative double ionization channels, mechanisms of double ionization (direct or indirect) processes were investigated. The studies shed light on the electron-electron and electron-nuclear correlation effects in the molecules.Tunable X-rays were used to selectively excite a localized core electron to different valence orbitals, and the subsequent autoionization and dissociation processes were studied by analysing the correlated momentum of ionic fragments. In butadiene, the dependence of molecular dissociation on the initial site of core-hole was studied for the chemically shifted terminal and central carbon core-electrons excitation.In cyclopropane the dependence of molecular dissociation on the changing of the molecular bonding character was studied for different core-to-valence excitation.The studies indicated the importance of the ultra-fast nuclear dynamics initiatedwithin a few femtosecond core-hole lifetime changing the picture of electron-electron correlation in autoionization processes and leading to spec

Dissociation, a simple unimolecular reaction, can be obscure, especially in complex molecules with inuirnerous degrees of freedom. Here we suggest an ultrafast dissociation mechanism involving multimode dynamics evolving on the barrierless potential energy surface. The mechanism is elaborated from the analysis of the nuclear dynamics in X-ray excited molecules. It implies that in large molecules dissociation may yield to heavy fragments on very short timescales owing to the internal motion of light linkages. In particular, the rotation of the C2H4-moiety in 1-bromo-2-chloroethane leads to the dissociation of C-C1 or C-Br bonds in C12p or Br3d core-excited states in similar to 7 is., QC 20161017

A detailed study of inelastic x-ray scattering from the ground state to the Σg3(3σg-13sg1) state of the O2 molecule is presented. The observed angular anisotropy shows that the vibrational excitations within this final state are strongly dependent on the polarization of the incident radiation. The analysis demonstrates that this is a manifestation of interference between resonant and direct nonresonant inelastic x-ray scattering. This interference provides a new tool to monitor nuclear dynamics by relative rotation of the polarization vectors of the incident and scattered photons., QC 20131106

This study focuses on the two C1s-to-LUMO (lowest unoccupied molecular orbital) excitations of the iso-dichloroethylene (H2C=CCl2) and the subsequent Auger decay. We investigate the effect of the two different carbon core excitations on the population of the cation produced after electronic relaxation. The resonant Auger spectra are interpreted by comparison to the valence shells photoionization spectrum and with the help of theoretical calculations. Several consequences of the core-hole localization on the electronic decay are observed. In particular, the resonant excitation of the C1s(CH2) to the LUMO leads to a large intensity increase in the region of the first satellite state, whereas no dramatic changes are observed for the C1s(CCl2) excitation.

The nonadiabatic nuclear dynamics of low-energy Na + H collisions is studied by the branching classical trajectory approach. The calculated inelastic cross sections are in good agreement with the results of full quantum calculations.

The photoinduced nonadiabatic nuclear dynamics of the ammonia cation is studied by the branching classical trajectory approach. The time-dependent populations of different electronic states of the ammonia cation are calculated and are in good agreement with the results of full quantum calculations.

We report calculations on high-order harmonic generation in water molecules. Spectra are determined for various initial vibrational states of H2O and its isotope D2O. It is demonstrated that the ratio of the spectra for D2O and H2O is close to unity when the initial state is the vibronic ground state, indicating that nuclear dynamics is of minor importance. For vibrationally excited initial states, the high-harmonic intensities show a clear dependence on both the initial-state quantum number and the isotopic species. © 2010 The American Physical Society.

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.

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.

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 excelle, QC 20100910

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 excelle, QC 20100910

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 excelle, QC 20100910

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 excelle, QC 20100910

BRCA1 coordinates cellular responses to DNA damage. It functions as a co-repressor of GADD45atranscription through interactions with a DNA-binding protein termed ZBRK1. Our goal is to develop a biosensor system to visualize transcription control by ZBRK1 and BRCA1 in single living and/or fixed cells. The rationale is to use integrated DNA binding sites to obtain real time, multiplex-based data. The reportable outcomes for the period are: 1) UAS and ZREarray-bearing plasmids have been constructed; 2) Transient and stable reporter expression have been demonstrated; 3) Stable cell lines with G20, G40 and Z32 are on line for studies;4) Construction of fluorescent GAL4-DBD and ZBRK1 fusion protein has been achieved, and BRCA1 derivatives are in progress. When operational, this system will document real time nuclear dynamics of ZBRK1/BRCA1-dependent chromatin modification systems, as cells mount transcriptional responses to genotoxins., The original document contains color images.

QC 20100628

QC 20100628

QC 20100628

QC 20100628