<p>Scanning transmission x-ray microscopes (STXM) focus monochromatic x-rays into an intense sub-30 nm diameter spot. Samples are then positioned at the focal plane and raster scanned through the spot while the transmitted x-rays are acquired to build up images at x-ray photon energies. In addition, x-ray absorption spectroscopy (XAS) can be performed by recording image sequences over a photon energy range of interest. STXMs excel at characterizing thin sections of inhomogeneous soft matter with their combination of high spatial (<30 nm) and photon energy (<0.1 eV) resolution. However, the overarching theme of this thesis is to apply the intense, tightly focused spot of x-rays to induce spatially resolved chemical and physical changes, and directly pattern materials, primarily thin polymer films. The irradiated areas are then investigated using several types of microscopy (scanning transmission x-ray, atomic force, scanning electron) and XAS. The experiments cover three broad areas: i) Nanofabrication; realization of the smallest possible feature sizes, and fabrication schemes unique to focused x-rays with applications including nanofluidics. ii) Radiation chemistry and physics; investigating the mechanisms of radiation-induced processes such as bond formation/loss, morphological change, carbon contamination, and temperature increase. iii) X-ray optics; the spatial distribution of x-rays at a focal plane can be recorded in a thin polymer film and later read out using an atomic force microscope. Applications include feedback for optics fabrication and enhanced image processing, the ultimate goal being increased spatial resolution.</p> / Doctor of Philosophy (PhD)

Designing materials for fusion applications is a very challenging problem, requiring detailed understanding of the behaviour of materials under the kinds of extreme conditions expected in a fusion environment. During the lifetime of fusion-reactor components, materials will be subjected to high levels of neutron irradiation, but must still perform effectively at high operating temperatures and under significant loading conditions. Body-centred cubic (bcc) transition metals are some of the most promising candidates for structural materials in fusion because of their relatively high density, which allows for effective neutron-shielding with the minimum volume and mass of material. In this work we perform atomistic simulations on two of the most important of these, Fe and W. In this thesis we describe atomic-scale simulations of defects found in bcc systems. In part I we consider the vacancy and interstitial loop defects that are produced and accumulated as a result of irradiation-induced displacement cascades. We show that vacancy dislocation loops have a critical size below which they are highly unstable relative to planar void defects, and thus offer an explanation as to why they are so rarely seen in TEM observations of irradiated bcc metals. Additionally, we compare the diffusion rates of these vacancy loops to their interstitial counterparts and find that, while interstitial loops are more mobile, the difference in mobility is not as significant as might have been expected. In part II we study screw dislocations, which, as the rate limiting carriers of plastic deformation, are significantly responsible for the strength of materials. We present results from large-scale finite temperature molecular dynamics simulations of screw dislocations under stress and observe the thermally-activated kink-pair formation regime at low stress, which appears to be superseded by a frictional regime at higher stresses. The mobility functions fitted to the results are vital components in simulations of dislocation networks and other large-scale phenomena. Lastly, we develop a multi-string Frenkel-Kontorova model that allows us to study the core structure of screw dislocations. Subtle changes in the form of the interaction laws used in this model demonstrate the difference between the non-degenerate and degenerate core structures. We provide simple criteria to guarantee the correct structure when developing interatomic potentials for bcc metals.

Inert gases in metals can occur due to ion implantation, from a plasma in a magnetron device or as a result of being by-products of nuclear reactions. Mainly because of the nuclear applications, the properties of the inert gases, helium, argon and xenon in the body centred cubic (bcc) iron crystal are examined theoretically using a combination of molecular dynamics, static energy minimisation and long time scale techniques using empirical potential functions. The same techniques are also used to investigate argon and xenon in aluminium. The primary interest of the work occurred because of He produced in nuclear fission and its effect on the structural materials of a fission reactor. This structure is modelled with perfectly crystalline bcc Fe. In bcc iron, helium is shown to diffuse rapidly forming small bubbles over picosecond time scales, which reach a certain optimum size. In the initial phase of He accumulation, Fe interstitials are ejected. This occurs instantaneously for bubbles containing 5 He atoms and as the more He accumulates, more Fe interstitials are ejected. The most energetically favourable He to vacancy ratios at 0 K, vary from 1 : 1 for 5 vacancies up to about 4 : 1 for larger numbers of vacancies. An existing He bubble can be enlarged by a nearby collision cascade through the ejection of Fe interstitials, allowing more He to be trapped. Ar and Xe in bcc Fe prefer to be substitutional rather than interstitial and there are large barriers to be overcome for the inert gas atoms to diffuse from a substitutional site. Bubbles that form can again be enlarged by the presence of a nearby collision cascade or at very high temperatures. In this case the most energetically favourable vacancy ratios in the bubbles is 1: 1 for Ar and from 0.6: 1 to 0.8: 1 for Xe. For Ar and Xe, bubble formation is more likely as a direct result of radiation or radiation enhanced diffusion rather than diffusion from a substitutional site. Ar in aluminium is also studied. Ar atoms in fcc Al prefer to be substitutional rather than interstitial and evolution into substitutional occurs over picosecond time scales at room temperature. Bubble formation can occur more easily than in bcc iron, mainly because the barriers for vacancy diffusion are much lower but the time scales for bubble accumulation are much longer than those for He. A vacancy assisted mechanism is found which allows Ar to diffuse through the lattice. Finally some preliminary results on the energetics of different geometrical structures of larger Xe bubbles in Al are investigated since experiment has indicated that these can become facetted.

<p>This thesis presents two measurements of the top quark pair production cross section at sqrt{s} = 1.96 TeV using data from the DØ experiment. Both measurements are performed in the dilepton final state and make use of secondary vertex b-tagging. With 158 pb^-1 of data in the electron-muon final state, the measured cross section is:</p><p>σ(top-antitop) = 11.1 +5.8 -4.3 (stat) +- 1.4 (syst) +- 0.7 (lumi) pb.</p><p>With 425 pb^-1 of data in the electron+track and muon+track final states, the measured cross section is:</p><p>sigma(top-antitop) = 6.3 +2.1 -1.8 (stat) +- 1.1 (syst) +- 0.4 (lumi) pb.</p><p>Both measurements are in agreement with the prediction from perturbative QCD calculations. In addition, an estimate of the DØ silicon detector lifetime is presented. The radiation damage is determined by studying the depletion voltage of the silicon sensors as a function of time. Based on this data the silicon detector is estimated to remain operational up to delivered luminosities of 6-8 fb^-1.</p>

<p>Radiation damage limits the resolution in imaging experiments. Damage is caused by energy deposited into the sample during exposure. Ultrashort and extremely bright X-ray pulses from free-electron lasers (FELs) offer the possibility to outrun key damage processes, and temporarily improve radiation tolerance. Theoretical models indicate that high detail-resolutions could be realized on non-crystalline samples with very short pulses, before plasma expansion.</p><p>Studies presented here describe the interaction of a very intense and ultrashort X-ray pulse with material, and investigate boundary conditions for flash diffractive imaging both theoretically and experimentally. In the hard X-ray regime, predictions are based on particle simulations with a continuum formulation that accounts for screening from free electrons.</p><p>First experimental results from the first soft X-ray free-electron laser, the FLASH facility in Hamburg, confirm the principle of flash imaging, and provide the first validation of our theoretical models. Specifically, experiments on nano-fabricated test objects show that an interpretable image can be obtained to high resolution before the sample is vaporized. Radiation intensity in these experiments reached 10^14 W/cm^2, and the temperature of the sample rose to 60000 Kelvin after the 25 femtosecond pulse left the sample. Further experiments with time-delay X-ray holography follow the explosion dynamics over some picoseconds after illumination.</p><p>Finally, this thesis presents results from biological flash-imaging studies on living cells. The model is based on plasma calculations and fluid-like motions of the sample, supported by the time-delay measurements. This study provides an estimate for the achievable resolutions as function of wavelength and pulse length. The technique was demonstrated by our team in an experiment where living cells were exposed to a single shot from the FLASH soft X-ray laser.</p>

This thesis presents two measurements of the top quark pair production cross section at sqrt{s} = 1.96 TeV using data from the DØ experiment. Both measurements are performed in the dilepton final state and make use of secondary vertex b-tagging. With 158 pb-1 of data in the electron-muon final state, the measured cross section is: σ(top-antitop) = 11.1 +5.8 -4.3 (stat) +- 1.4 (syst) +- 0.7 (lumi) pb. With 425 pb-1 of data in the electron+track and muon+track final states, the measured cross section is: sigma(top-antitop) = 6.3 +2.1 -1.8 (stat) +- 1.1 (syst) +- 0.4 (lumi) pb. Both measurements are in agreement with the prediction from perturbative QCD calculations. In addition, an estimate of the DØ silicon detector lifetime is presented. The radiation damage is determined by studying the depletion voltage of the silicon sensors as a function of time. Based on this data the silicon detector is estimated to remain operational up to delivered luminosities of 6-8 fb-1.

Radiation damage limits the resolution in imaging experiments. Damage is caused by energy deposited into the sample during exposure. Ultrashort and extremely bright X-ray pulses from free-electron lasers (FELs) offer the possibility to outrun key damage processes, and temporarily improve radiation tolerance. Theoretical models indicate that high detail-resolutions could be realized on non-crystalline samples with very short pulses, before plasma expansion. Studies presented here describe the interaction of a very intense and ultrashort X-ray pulse with material, and investigate boundary conditions for flash diffractive imaging both theoretically and experimentally. In the hard X-ray regime, predictions are based on particle simulations with a continuum formulation that accounts for screening from free electrons. First experimental results from the first soft X-ray free-electron laser, the FLASH facility in Hamburg, confirm the principle of flash imaging, and provide the first validation of our theoretical models. Specifically, experiments on nano-fabricated test objects show that an interpretable image can be obtained to high resolution before the sample is vaporized. Radiation intensity in these experiments reached 10^14 W/cm^2, and the temperature of the sample rose to 60000 Kelvin after the 25 femtosecond pulse left the sample. Further experiments with time-delay X-ray holography follow the explosion dynamics over some picoseconds after illumination. Finally, this thesis presents results from biological flash-imaging studies on living cells. The model is based on plasma calculations and fluid-like motions of the sample, supported by the time-delay measurements. This study provides an estimate for the achievable resolutions as function of wavelength and pulse length. The technique was demonstrated by our team in an experiment where living cells were exposed to a single shot from the FLASH soft X-ray laser.

Single particle electron cryomicroscopy (cryo-EM) is a method of structure determination that uses many randomly oriented images of the specimen to construct a three-dimensional density map. In this thesis, single particle cryo-EM has been used to determine the structure of intact adenosine triphosphate (ATP) synthase from bovine heart mitochondria, an approximately 550 kDa membrane protein complex. In respiring organisms, ATP synthase is responsible for synthesizing the majority of ATP, a molecule that serves as an energy source for many cellular reactions. In order to understand the mechanism of ATP synthase, knowledge of the arrangement of subunits in the intact complex is necessary. To obtain maps of intact ATP synthase showing internal density distributions by single particle cryo-EM, methodological improvements to image acquisition, map refinement, and data selection were developed. Further, a novel segmentation algorithm was developed to aid in interpretation of maps. The use of these tools allowed for construction and interpretation of two maps of ATP synthase, solubilized in different membrane mimetics, in which the arrangement of subunits could be identified. These maps revealed interactions within the complex important for its function. In addition, evidence was obtained for curvature of membrane mimetics around ATP synthase, suggesting a role for the complex in maintenance of mitochondrial membrane morphology.

Single particle electron cryomicroscopy (cryo-EM) is a method of structure determination that uses many randomly oriented images of the specimen to construct a three-dimensional density map. In this thesis, single particle cryo-EM has been used to determine the structure of intact adenosine triphosphate (ATP) synthase from bovine heart mitochondria, an approximately 550 kDa membrane protein complex. In respiring organisms, ATP synthase is responsible for synthesizing the majority of ATP, a molecule that serves as an energy source for many cellular reactions. In order to understand the mechanism of ATP synthase, knowledge of the arrangement of subunits in the intact complex is necessary. To obtain maps of intact ATP synthase showing internal density distributions by single particle cryo-EM, methodological improvements to image acquisition, map refinement, and data selection were developed. Further, a novel segmentation algorithm was developed to aid in interpretation of maps. The use of these tools allowed for construction and interpretation of two maps of ATP synthase, solubilized in different membrane mimetics, in which the arrangement of subunits could be identified. These maps revealed interactions within the complex important for its function. In addition, evidence was obtained for curvature of membrane mimetics around ATP synthase, suggesting a role for the complex in maintenance of mitochondrial membrane morphology.

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