Metabolic channelling occurs when two enzymes that act on a common substrate pass that intermediate directly from one active site to the next without allowing it to diffuse into the surrounding aqueous medium. In this study, properties of channelling are investigated through the use of computational models and cell simulation tools. The effects of enzyme kinetics and thermodynamics on channelling are explored with the emphasis on validating the hypothesized roles of metabolic channelling in living cells. These simulations identify situations in which channelling can induce acceleration of reaction velocities and reduction in the free concentration of intermediate metabolites. Databases of biological information, including metabolic, thermodynamic, toxicity, inhibitory, gene fusion and physical protein interaction data are used to predict examples of potentially channelled enzyme pairs. The predictions are used both to support the hypothesized evolutionary motivations for channelling, and to propose potential enzyme interactions that may be worthy of future investigation.

Metabolic channelling occurs when two enzymes that act on a common substrate pass that intermediate directly from one active site to the next without allowing it to diffuse into the surrounding aqueous medium. In this study, properties of channelling are investigated through the use of computational models and cell simulation tools. The effects of enzyme kinetics and thermodynamics on channelling are explored with the emphasis on validating the hypothesized roles of metabolic channelling in living cells. These simulations identify situations in which channelling can induce acceleration of reaction velocities and reduction in the free concentration of intermediate metabolites. Databases of biological information, including metabolic, thermodynamic, toxicity, inhibitory, gene fusion and physical protein interaction data are used to predict examples of potentially channelled enzyme pairs. The predictions are used both to support the hypothesized evolutionary motivations for channelling, and to propose potential enzyme interactions that may be worthy of future investigation.

It has been seen in physical experiments as early as the 1960’s that when a positively charged particle is injected into a crystal in certain directions and with sufficiently high energy, the particle can penetrate into the crystalline structure to a depth which is unexpectedly long. Such motions in the crystal are referred to as channelling trajectories. Herein, we consider a Hamiltonian model for particle motion in a crystal. We then proceed to show that the results of KAM theory are applicable to the model, and moreover that these result predict the existence of trajectories for the fired particle which do indeed penetrate the crystal deeply. Finally, we present the results of two series of numerical simulations which strongly suggest that this behaviour is observable in our model. / text

In this thesis the following problems are studied: 1-Relativistic self-focusing and channelling of intense laser pulses have been studied in underdense plasma using 2D PIC simulations, for different laser powers and plasma densities. Analytical solutions for the stationary evacuated channels have been recovered in PIC simulations. It is shown that otherwise stable channels can accelerate electrons due to surface waves on the walls of the channels. Relativistic filaments with finite electron density are unstable to transverse modulations which lead in the nonlinear stage to the break-up of laser pulses into independent filaments. 2-Although 3D simulations are limited, they are more realistic. Azimuthal stability of the laser pulses in interaction with underdense plasma can only be studied in 3D geometry. Relativistic self-focusing and channelling of intense laser pulses have been studied in underdense plasma using 3D PIC simulations, for different laser powers and plasma densities. Analytical solutions for the stationary evacuated channels and ring structure have been recovered in PIC simulations. The stability of ring structure due to azimuthal perturbations has been studied both in theory and in simulations. The gain length of such instability is smaller at higher densities $(>0.1n_{cr})$. It is shown that the azimuthal perturbation can break up the azimuthal symmetry of the laser pulse. 3-Working with circularly polarized laser pulses, gave us a motivation to study Inverse Faraday Effect in interaction of circularly polarized laser pulses with plasma. Axial magnetic field generation by intense circularly polarized laser beams in underdense plasmas has been studied with 3D particle-in-cell (PIC) simulations and by means of theoretical analysis. The source of azimuthal nonlinear currents and of the axial magnetic field depends on the transverse inhomogeneities of the electron density and laser intensity. The fields reach maximum strength of several tens of MG for laser pulses undergoing relativistic self-focusing and channelling in moderately relativistic regime. 4-Electron wakefield acceleration was studied in support of the experiment which was carried on using 7 TW laser beam at Canadian Advanced Laser Light source facility. 2D simulations were performed to study this problem. The energy the electrons gained in the process was peaked at 20-30 Mev close to the experimental results.

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At the Tandem accelerator in the Ångström laboratory, Uppsala, Rutherford backscattering spectrometry (RBS) is one of the methods used for thin film analysis, providing information on thickness and composition. The films are commonly grown on silicon substrates, whose crystal structure gives rise to channelling effects (a strong angular dependence in the intensity of the signal), which can cause faulty results. For other samples, channelling may also be used to get information on crystal structure and quality. This work demonstrates new functions to the existing software, aiming at minimizing these effects. The new methods have been tested by measurements both in channelling directions and in directions determined by the old method. In comparison with the earlier method the worst-case error is of order 80 %,commonly around 20 %, but it is possible to achieve an error which is not detectable. It is worth to note that the stated errors appear in tests oriented for maximum channelling, where effects without the new methods give an error corresponding to an apparent thin-film thickness almost 18 times that of the actual thickness. / Vid Tandemlabbet i Ångströmlaboratoriet, Uppsala, används bland annat Rutherford backscattering spectrometry (RBS) för att undersöka egenskaper, t.ex tjocklek och sammansättning, hos tunnfilmer som ofta är odlade på kiselsubstrat. Kiselkristallernas struktur ger upphov till kanaliseringseffekter, d.v.s starkt vinkelberoende intensitet, som i detta sammanhang kan ge felaktiga resultat. För andra prover kan kanaliseringseffekter användas för att få information om kristallstruktur och kvalitet. I det här arbetet demonstreras nyskrivna funktioner till befintlig mjukvara med syfte att minimera dessa effekter. De nya funktionerna har testats genom provtagningar i orienteringar som är gynnsamma och icke gynnsamma för kanalisering. Vid jämförelse med tidigare metoder ger de nya metoderna ett fel på i värsta fall ca. 80%, med bättre parametrar sjunker felet till ca 20 % och med rätt val av parametrar försvinner felet jämfört med tidigare metod. Värt att notera är att ovanstående maximala fel uppstår vid test orienterat för maximal kanalisering, där effekterna utan de nya metoderna ger ett fel på uppemot en faktor 18.

The tricarboxylic acid (TCA) cycle is one of the central pathways in respiration and also plays an important role in a variety of metabolic processes including the synthesis of secondary metabolites and the provision of carbon skeletons for ammonium assimilation and amino acid biosynthesis. Effective regulation of these multiple demands on the TCA cycle is likely to be very important for plant fitness. One way that this regulation could be achieved is through metabolite channelling. This occurs when metabolites are transferred between enzyme active sites without diffusing into the bulk aqueous phase of the cell, and is known to be important in regulating demands in metabolic pathways. Although there is evidence that metabolite channelling exists in animals, there have been no attempts to investigate it in plant. The first aim of this thesis was therefore to investigate whether metabolite channelling exists in the plant TCA cycle. Isotope dilution experiments were developed to investigate metabolite channelling, and were able to show that metabolite channelling was present between certain enzymes of the TCA cycle in both S. tuberosum and A. thaliana mitochondria. The second aim of the thesis was investigate whether metabolite channelling is important in regulating the TCA cycle in plant mitochondria. The pattern of metabolite channelling did not change in mitochondria isolated from the light and the dark, or from mitochondria with increased or decreased TCA cycle rates, but it was not possible to say whether the metabolite channelling altered in a quantitative fashion. Overall the thesis provides the first direct evidence of channelling in the TCA cycle in plants, and further work should help to elucidate what role, if any, it plays.

The discovery of carbon nanotubes by Iijima in 1991 has created a torrent of new research activities. Research on carbon nanotubes ranges from studying their fundamental properties, such as their electron band structure and plasma frequencies, to developing new applications, such as self-assembled nano-circuits and field emission displays. Robust models are now needed to enable a better understanding of the electronic response of carbon nanotubes. We use time-dependent density functional theory to derive a two-fluid two-dimensional (2D) hydrodynamic model describing the collective response of a multiwalled carbon nanotube with dielectric media embedded inside or surrounding the nanotube. We study plasmon hybridization of the nanotube system in the UV range, the stopping force for ion channelling, the dynamical image potential for fast ions, channelled diclusters and point dipoles, and the energy loss for ions with oblique trajectories. Comparisons are made of results obtained from the 2D hydrodynamic model with those obtained from an extension of the 3D Kitagawa model to cylindrical geometries.

Cette thèse est consacrée à l'étude de la déstabilisation structurale du dioxyded' uranium monocristallin. L'irradiation avec des ions Xe de 470 keV, Ce de 500 keV et La de 500 keV (correspondant à un parcours projeté Rp 85 nm et à l'écart type delta Rp 40 nm selon le code de calcul SRIM) ont été réalisées pour étudier la déstabilisation du monocristal induit, d'une part, par la création de défauts dû au processus de ralentissement nucléaire des fragments de fission à la fin de leur parcours (contribution balistique),et, d'autre part, par l'incorporation de produits de fission à forte concentration (contribution chimique). L'énergie cinétique des éléments incorporés a été choisie de sorte que leurs parcours dans le solide soient identiques afin de comparer directement les effets induits par des espèces solubles (La et Ce) et insolubles (Xe) dans le dioxyde d'uranium.La Spectrométrie de Rétrodiffusion Rutherford en canalisation (RBS/C) a été appliquée pour caractériser et quantifier les défauts générés par l'irradiation. Les données ont été analysées par simulation Monte-Carlo en considérant un modèle original comportant de deux-type de défauts (i) des atomes aléatoirement déplacés dans le cristal (RDA) et (ii) des distorsions des ranges atomiques (BC). L'accumulation de la fraction d'atomes déplacés RDA avec l'augmentation de la fluence conduit à une forte augmentation du nombre dedéfauts observé entre 4 et 7 dpa, indépendamment de la nature des ions. Une seconde augmentation spectaculaire est observée à partir de 300 dpa (correspondant à une concentration excédant 5 % atomique d'ions implantes) pour le cas spécifique des cristaux irradiés avec des ions Xe. Un comportement différentié est clairement observé pour les espèces solubles par rapport à leurs homologues insolubles. Cette différence se traduit d'une part par l'augmentation spectaculaire de RDA lorsque le cristal est implanté à très haute concentration dans le cas d'espèce insolubles, et, d'autre part, par un endommagement plus prononcé entre 7 et 300 dpa. Ce phénomène est notamment la conséquence des différences de taille entre les rayons atomiques de La et de Ce, très inférieure à celles du Xe. A contrario, l'accumulation de défauts de type distorsion des rangées atomiques BC avec l'augmentation de la fluence conduit à une évolution très similaire quelle que soit la nature de l'élément incorpore. Cette augmentation se produit principalement entre 10 et 100 dpa - correspondant à un plateau pour l'évolution des défauts de type RDA – et traduit une importante évolution structurale du dioxyde d'uranium irradie, explorée pour la première fois dans ce travail de thèse. / This thesis is dedicated to the investigation of the structural destabilisation of UO2 single crystal. Irradiations with 470-keV Xe, 500-keV Ce and 500-keV La ions (with corresponding ion range of Rp 85 nm and range straggling of Delta Rp _ 40 nm according to SRIM calculation) have been performed to investigate the destabilisation of UO2 single crystals induce by (i) the radiation damage effects due to the nuclear stopping process of a fission fragment at the end of their trajectories (ballistic contribution) and by (ii) the incorporation of a fission product at high concentration (chemical contribution). The energies and masses of bombarding ions were deliberately chosen so that they would have very similar projected range in UO2 in order to compare the effects induced by solubles (La and Ce) versus non soluble Xe species in UO2. Rutherford Backscattering Spectrometry in channelling geometry (RBS/C) was applied to study the defects induced. Channelling data were analysed afterwards by Monte-Carlo simulation with McChasy code assuming a two-class model of defects comprising (i) the randomly displaced atoms (RDA) and the bent channels (BC) defects. The accumulation of RDA with increasing ion fluence leads to a steep increase (build-up of defects) observed from 4 to 7 dpa regardless of nature of ions and a dramatic increase observed from 300 dpa (corresponding to _ 5 at. % of implanted ions) only for Xe irradiated crystal. The difference due to the soluble versus insoluble species was clearly observed. Such a difference was observed via the dramatic increase of RDA when the crystal is implanted at very high concentration only for crystal implanted with insoluble species. Moreover, the difference is also observed via the higher fraction of RDA created in the crystal irradiated with insoluble element. This phenomenon is mostly due to the size of implanted species in the matrix. Insoluble Xe atoms have the atomic radius which is larger than twice the atomic radius of U sub-lattice while soluble La and Ce atoms have the atomic radii of similar size as compared to U atom. Xe creates a much stronger stress field in UO2 crystal in comparison to La or Ce; a higher fraction of RDA is thus created. Conversely, the accumulation of BC with increasing ion fluence leads to very similar evolution versus ion fluence in all crystals implanted with the three elements .

The discovery of carbon nanotubes by Iijima in 1991 has created a torrent of new research activities. Research on carbon nanotubes ranges from studying their fundamental properties, such as their electron band structure and plasma frequencies, to developing new applications, such as self-assembled nano-circuits and field emission displays. Robust models are now needed to enable a better understanding of the electronic response of carbon nanotubes. We use time-dependent density functional theory to derive a two-fluid two-dimensional (2D) hydrodynamic model describing the collective response of a multiwalled carbon nanotube with dielectric media embedded inside or surrounding the nanotube. We study plasmon hybridization of the nanotube system in the UV range, the stopping force for ion channelling, the dynamical image potential for fast ions, channelled diclusters and point dipoles, and the energy loss for ions with oblique trajectories. Comparisons are made of results obtained from the 2D hydrodynamic model with those obtained from an extension of the 3D Kitagawa model to cylindrical geometries.