Measurements are made on data collected at a centre-of-mass energy of 7 TeV using the ATLAS detector at the LHC. Jets from non-collision sources for the inclusive jet cross-section are evaluated for jet transverse momentum values from 20 GeV to 1.5 TeV and for rapidity values up to |y| < 4.4. Measurements are made using anti-kT jets with the distance parameters R = 0.4 and R = 0.6, corresponding to 37 pb−1 of data. Analysis of the sub-structure of QCD jets at high transverse momentum is performed using anti-kT R = 1.0 and Cambridge-Aachen R = 1.2, using 35 pb−1 of data. The first measurement of jet mass is presented.

Mars is a planet that has lacked a global magnetic field for most of its history, around 3.5 billion years, leaving the upper atmosphere unprotected from the scavenging by the solar wind. This is thought to have played a significant role in the evolution of the Martian atmosphere and consequently on the loss of water which once flowed over the surface and made possible the conditions for life to exist. This is unlike the Earth that has a large enough magnetic field to offer protection from the solar wind and radiation. As such, it is important to understand the nature of the space plasma around Mars. In 1998, Mars Global Surveyor discovered magnetisations from the crust of Mars, which altered the view of how the solar wind behaves as it travels past the planet. The importance of these remanent magnetic fields over time and in the different plasma regions around Mars is not completely resolved. This thesis contributes to the understanding of the interaction of Mars with the solar wind and presents the analysis of data from the Analyser of Space Plasmas and Energetic Atoms (ASPERA-3) Electron Spectrometer (ELS) on the Mars Express (MEX) spacecraft, for the investigation of how remanent fields from Mars affect the local space plasma. We have found that the crustal magnetisations have a considerable influence up to the altitudes of 1300 km and possibly enhance the escape of atmosphere beyond. The signature of the crustal fields focusing electrons, called intensifications, occurred with the greatest rates on the dayside below 500 km, due to the intrusion of the solar wind plasma along the crustal fields and from the forcing of the ionopause below its average position. Effects of the crustal fields are most identifiable in the dusk sector and possibly connect regions of large plasma density at higher altitudes (»2000 km) with the atmosphere at low altitudes, and to the magnetic pile-up region, where reconnection with draped IMF could occur. This would allow transport of electrons and ambi-polar extraction of ions over a large distance in altitude and so enhance the escape of the atmosphere. Observations in the regions at night show closed magnetic fields from the crust coincide with voids in the electron flux, a sign of the crustal fields protecting the neutral atmosphere. There was little evidence to connect the distribution of the voids to a Venus-type plasma channel, which limits the amount of atmospheric loss that could occur through ionospheric holes. The voids dominate events on the night side below 500 km, where the rate of intensifications is low. The reverse is true for regions on the nightside above 500 km, where the greatest proportion of intensifications is from the crustal fields, which could occur through aurora and perhaps even tail reconnection.

Positronium, Ps, is the atom-like bound state of an electron and its antimatter counterpart, the positron. This work encompasses the experimental techniques required to produce a collimated beam of Ps atoms and recent investigations of Ps collisions on a variety of atomic and molecular targets to determine Ps total and fragmentation cross-sections. For the former experiment, the present work is compared to theory - for which there is now very good agreement for low energy Ps–He collisions - and to other projectiles where the present data shows that total cross-sections for equivelocity Ps and electrons are nearly identical for a wide range of targets and velocities. The Ps fragmentation measurements proceed via the detection of ejected electrons or positrons for Ps collisions on Xe at 18 and 30 eV. Detection of ejected positrons is a unique signature of Ps fragmentation and the recent integrated measurements for this process agree well with theory, as do the shapes of the differential cross-sections with respect to the longitudinal energy of the ejected positrons. Concerning these, the energy dependence of the positron distributions appear similar for the present measurements on Xe and those previously measured for a He target. When detecting ejected electrons, the experiment is sensitive to reactions in which the projectile and/or target are ionised, and the integrated cross-sections indicate that target-ionisation is significant at only ∼3 eV above threshold in Xe.

The requirements for the proposed Electron Analyser System (EAS) for the ESA Solar Orbiter spacecraft pose significant challenges that cannot be addressed with existing electrostatic analyser technology. The thesis covers three core issues that are required to be addressed for this instrument. The first is the design of an electrostatic analyser head to meet the stringent requirements of the Solar Orbiter mission that could not be met with an existing geometry. A systematic series of computer simulations were undertaken, starting with an existing flight-proven geometry (Cluster II PEACE-LEEA), and covering the entire parameter space of a number of possible solutions. The final proposed geometry provides the required 10% energy resolution whilst minimizing the reduction in instrument sensitivity. In addition to this, a deflection system now provides the proposed instrument with a at analyser-constant, energy resolution and geometric factor response over the required +_45 field of view. The second issue addressed is the generalized desire for an electrostatic variable sensitivity system in Top-Hat electrostatic Analysers. Three potential solutions were studied in detail. A method was identified which permitted an order of magnitude reduction in sensitivity, whilst improving all other instrument parameters. The final study was the first to examine the effectiveness of existing secondary electron rejection mechanisms. This is particularly important for EAS, since secondary electrons have an energy distribution that overlaps significantly with the low energy Solar Wind that the instrument will be required to measure. Several improvements to rejection mechanisms have been suggested that potentially increases secondary electron rejection by a factor of four.

This thesis describes the construction and characterisation of a unique cold argon atom source for sympathetic cooling of molecules. Argon atoms were laser cooled from their lowest lying metastable state using the 4s[3/2]2 → 4p[5/2]3 transition at 811.5 nm. A magneto-optical trap (MOT) was used to cool the metastable argon (Ar*) atoms to 73.2 ± 0.4 μK and trap them at a density of 3.93 × 10^9 cm-3. Cooling was facilitated using an external-cavity diode laser which was frequency-stabilised to the cooling transition using a magnetic dichroism technique. This was the first application of this technique to a plasma operated at our pressures where the applied magnetic field affected the gas behaviour. The Ar* atoms in the MOT were used to demonstrate chirped optical Stark acceleration for the first time. Atoms were accelerated up to velocities of 191 ± 1 ms-1 while maintaining narrow energy spreads in the accelerated ensemble (30-100 mK). The acceleration occurred over tens of nanoseconds and on micrometre length scales. Control over the number of particles accelerated was achieved by tailoring the depth of the optical lattice potential. Monte Carlo numerical simulations of acceleration were used to fit experimental results and study the dynamics of particles over the acceleration duration. Trapping of Ar* atoms in a quasi-electrostatic trap (QUEST) has also been demonstrated. The QUEST was formed at the focus of a 100 W laser beam with a wavelength of 10.6 μm. A trap lifetime of 18.3 ± 0.3 ms was measured.

Antibiotic resistance is a rapidly emerging global health problem as year on year more drugs are rendered ineffective and fewer new antibiotics developed to meet the demand. This is exemplified by Vancomycin, the `antibiotic of last resort' for decades, now facing growing resistance among bacteria. Interest around modifying existing drugs to improve their antibiotic action and stabilise them against resistance is raising the need for detailed understanding of the modes of action of antibiotics. Nanocantilevers provide a complementary method for exploring both the binding process and the mechanical mode of action by which Vancomycin and its derivatives weaken and destroy bacterial cell wall. When functionalised with monolayers of peptides analogous to cell wall precursors the cantilevers measure the build up of surface stresses in-plane, on a surface, representative of the antibacterial interactions in-situ. This thesis reports the first steps towards a comprehensive theoretical model of stress induction on a nanocantilever, focusing on elucidating the chemical and geometric nature of experimentally observed responses to Vancomycin. The chemical origins of stress generation are explored within, using a monolayer of decanethiol as a model system and looking at contributions from both adsorbate-adsorbate and adsorbate-substrate interactions. How those individual molecular contributions combine across the cantilever to produce the eventual deflection is investigated by varying the coverage of Vancomycin binding events across an appropriately functionalised cantilever, using an interaction potential extrapolated from molecular dynamics simulations and a lattice model developed in this thesis to return the corresponding stress and deflection. The elastic response of the beam itself is also examined in some detail, as is the effect of the operating medium on the cantilever's action. All findings provide the first steps to a truly representative, and quantitatively predictive, model of nanocantilever operation and insight into the technology's unique merit in the race to discover a new generation of antibiotics.

In live tissues, alterations in metabolism induce changes in the fluorescence decay of the spectrally identical redox carriers NADH and NADPH. The biochemical pathways and photophysical mechanisms that contribute to these changes are largely unknown. This work combined ultrafast laser spectroscopy and live-cell imaging to investigate these phenomena. Time-resolved spectroscopy of NADH and NADPH was performed using single-photon and two-photon excitation. In solution, the fluorescence lifetimes of the two cofactors were identical. The anisotropy decay dynamics of both molecules indicated that distinct molecular configurations caused the presence of two emitting states, perhaps involving alternate cis/trans geometries of the amide group. Using a range of water/glycerol mixtures as solvents, the viscosity dependence of the non-radiative decay of NAD(P)H was shown to be well described by Kramers and Kramers-Hubbard models of activated barrier crossing. This suggested that variations in the fluorescence lifetimes of the cofactors when bound to different enzymes result from differing levels of conformational restriction of the nicotinamide ring in the binding site. Despite identical fluorescence lifetimes in solution, studies on genetically modified cell lines in which NAD kinase was overexpressed or knocked down indicated that intracellular NADPH was associated with a significantly larger fluorescence lifetime when bound to enzymes (~4.4 ns) than enzyme-bound NADH (~1.5 ns). This suggested that variations in the NAD(P)H fluorescence decay upon metabolic perturbation by pharmacological or pathological means, reported both in this work and in the literature, result from changes in the relative concentrations of NADH and NADPH. NAD(P)H FLIM was used to observe elevated NADPH concentrations in the support cells of the mammalian cochlea, highlighting the potential of the technique as a label-free method for monitoring the metabolic state of complex tissue preparations.

In this thesis, optical properties of phytoplankton assemblages are investigated to identify the relationship between Chlorophyll-a spectral signatures and the assemblage abundance. A new algorithm is developed to determine Chlorophyll-a concentrations from three types of waters, including eukaryote dominant waters, cyanobacteria dominant waters and waters that have a mixture of eukaryotes and cyanobacteria; with a flag being proposed for mapping of spatial distributions of surface scums. The result of the algorithm calibration indicates that 79% of the variance within the near concurrent in situ data is explained by the new algorithm, with the MAPE of 16.9%. The validation result shows that the RMSE and MAPE are 0.24 and 16.5%, respectively, with R2=0.69. Regional and global application examples are given to demonstrate the general applicability. This algorithm is applied to a decade of MERIS observations to retrieve phytoplankton bloom dynamics from the Baltic Sea between 2002 and 2011, which are then used for the investigation of ecological responses to the environmental change. The result indicates that phytoplankton blooms have seasonal cycles, alongside high the interannual variability. In addition, a significant increasing spring bloom trend is detected in the Baltic and Bothnian Sea, whereas a decreasing trend is observed in the Baltic Sea during summers. Regarding the ecological responses, the Baltic Proper spring bloom intensities are positively correlated with February Nitrate and Nitrate+Phosphate concentrations, and the correlation with surface layer water temperatures are evident. The summer bloom intensities show strong positive correlations with both spring excess Phosphate and June Phosphate concentrations. Additionally, the summer bloom intensities are correlated with July-August water temperatures, Photosynthetic Active Radiation and wind stress in the Baltic Proper and Gulf of Finland, but the relationship is not detected in the Bothnian Sea. These findings enabled the models to be developed to predict summer bloom intensities.

One of the most important physics targets for any future electron positron linear collider will be the precision measurements of the top quark properties, and especially the top quark mass. Top-antitop production at threshold provides the ideal environment for making such measurements but is complicated by the machine’s luminosity spectrum and thus needs to be carefully studied to understand the constraints involved and the potential precision reach. This thesis presents developments in both the understanding of the luminosity spectrum and the top quark production threshold by the means of new simulation tools and simulation results of systematic and statistical uncertainties in the measurements of the luminosity spectrum and the top quark parameters by the use of a threshold scan. The luminosity spectrum is studied by employing a new parametrization method that takes into account the beam energy spread in the fit parameters, and detailed simulation studies of the measurement of the luminosity spectrum by the use of Bhabha scattering events. A detailed account is given of the possible systematic uncertainties arising due to beam-beam and detector induced effects influencing the luminosity measurement, by looking at the different luminosity spectra of the International Linear Collider (ILC) Reference Design Report (RDR) accelerator parameter plane. A new simulation tool for the top quark production threshold is presented, in the form of a new fully differential Monte Carlo event generator using a state-of-the-art next-to-next-to leading order (NNLO) QCD calculation of the top quark production threshold in order to describe the total and differential distributions that can be used in the top threshold measurements, by including a full description of the luminosity spectrum. Finally, a study of how the uncertainties of the luminosity spectrum measurement can affect the top quark threshold measurements is presented, by examining simulated threshold scan measurements for the different luminosity spectra of the ILC RDR accelerator parameter plane.

Multi-wavelength observations from various solar missions have revealed the dynamic nature of the solar corona. The work presented in this thesis represents a contribution towards understanding some of the physical mechanisms that drive the activity observed in the corona and out into the heliosphere. In particular, the role of reconnection in active region (AR) outflows and AR-coronal hole (CH) interactions using observations of the associated plasma flow signatures and their relationship to the underlying magnetic field topology is examined. Persistent outflows discovered by Hinode EUV Imaging Spectrometer (EIS) occur at the boundary of all ARs over monopolar magnetic regions. It is demonstrated that the outflows originate from specific locations of the magnetic topology where field lines display strong gradients of magnetic connectivity, namely quasi-separatrix layers (QSLs). Magnetic reconnection at QSLs is shown to be a viable mechanism for driving AR outflows which are likely sources of the slow solar wind. Observational signatures and consequences of interchange reconnection (IR) are identified and analyzed in a number of solar configurations. Jet light curves of several emission lines show a post-jet enhancement in cooler coronal lines which has not been previously observed. In the case of emerging flux near a CH, it is shown that closed loops forming between the AR and CH leads to the retreat of the CH and a dimming of the corona in the vicinity of the like-polarity region. A filament eruption and coronal mass ejection (CME) from an AR inside a CH are observed from the solar disk into the heliosphere. An anemone structure of the erupting AR and the passage in-situ of an interplanetary CME (ICME) with open magnetic topology are interpreted to be a direct result of IR. Plasma flows resulting from the interaction between an AR embedded in a CH observed by Hinode EIS are investigated. Velocity profiles of hotter coronal lines reveal intensification in outflow velocities prior to a CME. The AR’s plasma flows are compared with 3D magnetohydrodynamic (MHD) numerical simulations which show that expansion of AR loops drives outflows along the neighboring CH field. The intensification of outflows observed prior to the CME is likely to result from the expansion of a flux rope containing a filament further compressing the neighboring CH field.