Physics Theses

The work presented in this thesis is primarily concerned with the radiation and ions emitted by laser produced plasmas (LPPs) containing tin. If the semiconductor manufacturing industry is to meet Moore’s law (a doubling in the number of transistors per square inch on integrated circuits every two years), new lithographic techniques are required. EUV lithography (EUVL) shows the most promise, requiring a bright source of radiation in the 2% band centered at 13.5 nm, known as in-band radiation. This is due to the high reflectivity of molybdenum/silicon multilayer mirrors at these wavelengths. Tin-based LPPs have been shown to emit strongly in the in-band region. Chapter 2 presents a unique optical system with the ability to present a range of observing angles to a fixed detector, while maintaining normal incidence for the laser onto a planar solid target. This allows the system to be rotated, with respect to a fixed detector, while maintaining spatially stable plasma formation. Chapter 3 presents absolute intensity measurements of in-band radiation, emitted from pure tin laser produced plasmas, for a range of angles. Also measured is the angular distribution of intensities from 10 to 18 nm. Light, from outside the 2% band at 13.5 nm in this region, will result in flare at the resist in extreme ultraviolet lithography, thus limiting the feature resolution attainable. Two of the main problems facing next generation lithography are thermal and debris mitigation. Sn-based LPPs are highly emissive in the region of 100 to 3000 nm, where the multilayer optics can be highly reflective. This out-of-band (OOB) radiation can cause flare, heat the wafer and create overlay issues. It is necessary to quantify the levels of OOB radiation, over a range of wavelength regions, to facilitate the development of suitable optical components that will reduce the OOB radiation at the wafer plane to acceptable levels. Chapter 4 presents the angular distributions of OOB radiation for a range of wavelength regions between 200 and 1000 nm. Also, ions that are emitted from these LPPs may cause significant damage to the components in a real world projection lithography system. Fast ions, impinging on multilayer optics, can lead to the sputtering of mirror layers and debris deposited on multilayer optics and can degrade in-band reflectivity. In order to effectively mitigate this damage it is necessary to know the speed and direction of the emitted ions. The angular distribution of the total number of ions, from Sn1+ to Sn9+, emitted from a Snbased LPP, is investigated in Chapter 5. The charge state, energy and relative number of these ions have also been determined. In order to facilitate comparison between EUV, OOB and ion data in chapters 3, 4 and 5, the measurements in these chapters were performed at approximately equal plasma conditions. This comparison is explored and detailed in Chapter 6.

The wide range of applications of extreme ultraviolet (EUV) and softX-ray sources including for next generation photolithography around 13.5 nm and 6.7 nm as well as for broadband EUV sources lead to the investigations of various methods to generate the radiation. In this thesis, spectral emission from laser-produced plasmas (LPPs) of several target materials such as tin, tin-gold alloy, tin-lead alloy, galinstan and gadolinium for EUV sources has been theoretically and experimentally characterized. LPPs of pure tin targets show very bright EUV emission around 13.5 nm whereas LPPs of Gd targets show unresolved transition arrays (UTAs) near 6.7 nm. Alloy targets such asSn-Au, Sn-Pb and galinstan give rise to a broadband EUV emission in the 10 - 18 nm regions, though the most intense radiation remains observed around 13.5 nm. The temporal behavior of Sn, Sn-Au and Sn-Pb alloys as well as Gd closely matches the temporal profile of the Nd:YAG laser used in the experiments.This thesis is divided into 9 Chapters. The theoretical background andmotivations of this PhD work are presented in Chapter 1, whereas theexperimental apparatus is described in Chapter 2. Chapter 3 discusses the theoretical calculations of the EUV and soft X-ray emission from several atomic elements including tin (Sn), gold (Au), lead (Pb), gallium (Ga), indium (In) as well as gadolinium (Gd) using the Cowan codes. Various steady state plasma calculations performed using the Colombant and Tonon model are also presented in Chapter 3. Spectral analysis of EUV emission from laser produced plasmas (LPPs) of Sn, Au and Sn-Au along with their conversion efficiencies (CEs) are compared in Chapter 4, whereas a galinstan LPP is highlighted in Chapter 5 as a promising EUV source around 13.5 nm based on its spectral behaviour at different laser fluxes and spot sizes. In the lastthree results and discussion chapters (Chapters 6-8), the temporal evolution of several material targets including Sn, Sn-Au, Sn-Pb and gadolinium is presented. Eventually Chapter 9 concludes the whole work.

The work presented in this thesis is primarily concerned with the optimisation of extreme ultraviolet (EUV) photoemission around 13.5 nm, from laser produced tin (Sn) plasmas. EUV lithography has been identified as the leading next generation technology to take over from the current optical lithography systems, due to its potential of printing smaller feature sizes on integrated circuits. Many of the problems hindering the implementation of EUV lithography for high volume manufacturing have been overcome during the past 20 years of development. However, the lack of source power is a major concern for realising EUV lithography and remains a major roadblock that must be overcome. Therefore in order to optimise and improve the EUV emission from Sn laser plasma sources, many parameters contributing to the make-up of an EUV source are investigated.Chapter 3 presents the results of varying several different experimental parameters on the EUV emission from Sn laser plasmas. Several of the laser parameters including the energy, gas mixture, focusing lens position and angle of incidence are changed, while their effect on the EUV emission is studied. Double laser pulse experiments are also carried out by creating plasma targets for the main laser pulse to interact with. The resulting emission is compared to that of a single laser pulse on solid Sn.Chapter 4 investigates tailoring the CO2 laser pulse duration to improve the efficiency of an EUV source set-up. In doing so a new technique for shortening the time duration of the pulse is described. The direct effects of shortening the CO2 laser pulse duration on the EUV emission from Sn are then studied and shown to improve the efficiency of the source.In Chapter 5 a new plasma target type is studied and compared to the previous dual laser experiments. Laser produced colliding plasma jet targets form a new plasma layer, with densities that can be optimised for re-heating with the main CO2 laser pulse.Chapter 6 will present some experiments carried out on laser produced gadolinium plasmas, with its photoemission around 6.7 nm seen as a potential beyond EUV source. Three different laser pulse durations and a range of laser intensities are utilised in experiments to try to optimise the in-band emission, while also observing the effect on ion emission from the plasma. Finally, the experiments presented in thesis and their results are summarised in Chapter 7, along with presenting possible future work.

We perform Restrained hybrid Monte Carlo simulations to compute the equilibrium constant of the dissociation reaction of HF in HF(H₂O)₇. We find that, like in the bulk, hydrofluoric acid, is a weak acid also in the cubic HF(H₂O)₇ cluster, and that its acidity is higher at lower T. This latter phenomenon has a (vibrational) entropic origin, namely it is due to the reduction of the (negative) T∆S contribution to the variation of free energy between the reactant and product. We found also a temperature dependence of the reactions mechanism. At low T (≤225 K) the dissociation reaction follows a concerted path, with the H atoms belonging to the relevant hydrogen bond chain moving synchronously. At higher T (300 K), first two hydrogen atoms move together, forming an intermediate metastable state having the structure of an Eigen ion H₉O₄+, then the third hydrogen migrates completing the reaction. We also compute the dissociation rate constant, k_rp. We find that at very low T (≤75 K), k_rp depends strongly on the temperature, while it is almost constant at higher Ts. With respect to the bulk, the HF dissociation in HF(H₂O)₇ is about one order of magnitude faster. This is due to a lower free energy barrier for dissociation in the cluster.

Spin correlations for tau lepton decays are included in the Pythia 8 event generation software with a framework which can be expanded to include the decays of particles other than the tau lepton. The spin correlations for the decays of tau leptons produced from electroweak and Higgs bosons are calculated. Decays of the tau lepton using sophisticated resonance models are included in Pythia 8 for all channels with experimentally observed branching fractions greater than 0.04%. The mass distributions for the decay products of these channels calculated with Pythia 8 are validated against the equivalent distributions from the Herwig++ and Tauola event generators. The technical implementation of the tau lepton spin correlations and decays in Pythia 8 is described.A measurement of the inclusive Z to di-tau cross-section using 1.0 inverse fb of data from pp collisions at sqrt(s) = 7 TeV collected with the LHCb detector is presented. Reconstructed final states containing two muons, a muon and an electron, a muon and a charged hadron, or an electron and a charged hadron are selected as Z to di-tau candidates. The cross-section for Z bosons with a mass between 60 and 120 GeV decaying into tau leptons with pseudo-rapidities between 2.0 and 4.5 and transverse momenta greater than 20 GeV is measured to be 72.3 +- 3.5 +- 2.9 +- 2.5 pb. The first uncertainty is statistical, the second uncertainty is systematic, and the third is to due the integrated luminosity uncertainty. The Z to di-tau to Z to di-muon cross-section ratio is found to be 0.94 +- 0.09 and the Z to di-tau to Z to di-electron cross-section ratio is found to be 0.95 +- 0.07. The uncertainty on these ratios is the combined statistical, systematic, and luminosity uncertainties.Limits on the production of neutral Higgs bosons decaying into tau lepton pairs with pseudo-rapidities between 2.0 and 4.5 are set at a 95% confidence level using the same LHCb dataset. A model independent upper limit on the production of neutral Higgs bosons decaying into tau leptons is set and ranges between 8.6 pb for a Higgs boson mass of 90 GeV to 0.7 pb for a Higgs boson mass of 250 GeV. This limit is compared to the expected standard model cross-section. An upper limit on tan-beta in the CP-odd Higgs mass and tan-beta plane is set for the mh-max scenario of the minimal supersymmetric model and varies from 34 for a CP-odd Higgs boson mass of 90 GeV to 70 for a CP-odd Higgs boson mass of 140 GeV.

Electromechanical coupling is ubiquitous in nature and is a functional characteristic in a large range of inorganic and organic materials, including collagen type I - a fibrous protein abundant in mammals. Understanding the biofunctionality of electromechanical coupling in its linear form - piezoelectricity, has been a topic of research spanning over seven decades and yet many questions still remain unanswered. Piezoelectricity in bone and connective tissues such as tendon has been investigated at the macroscopic scale since the discovery of piezoelectricity in bone in 1957 and induced currents via the piezoelectric effect have been shown to activate the healing process in tissues under tension. Biological systems consist of complex hierarchical structures which results from a high degree of organization from the macroscale down to the nanoscale. These complex structures, however, make quantitative piezoelectric measurements difficult. Therefore, there exists a need to understand these processes at the individual protein level - i.e. at the nanoscale. In this thesis, a voltage-modulated form of atomic force microscopy called piezoresponse force microscopy is utilized to investigate the counterpart which is responsible for piezoelectricity in bone and connective tissues - collagen. The polar properties of collagen were revealed at the nanoscale and were shown to result in a highly complex polar architecture in natural tissue, which is important for understanding tissue development. Shear piezoelectricity was discovered to persist in engineered collagen hydrogels, a study intended to highlight the importance of replicating both structural and functional properties in replacement tissues. The electromechanical properties of collagen type II were investigated which were previously unknown. Collagen type II was shown to be a shear piezoelectric, exhibiting an angle dependence of the piezoelectric signal with cantilever-fibril angle. In addition, the piezoelectric tensor of collagen type I was determined at the nanoscale. Most piezoelectric coefficients measured were higher than those previously reported at the macroscopic scale. The new local tensor here will be useful for future studies which are concerned with the biofunctional implications of piezoelectrically-induced charges in collagen at the nanoscale.

This thesis concerns the study of inverse-Compton emission from two astrophysical sources. The first object, 1ES 1959+650, is a nearby active galactic nucleus. This source was observed as part of the VERITAS blazar monitoring programme in the hopes of detecting it in the midst of a dramatic flaring event. Over the course of these monitoring observations which span four years, a significant detection of the source in its low state was accumulated. The spectral energy distribution of this source was analysed from optical to VHE and was modelled with a synchrotron self-Compton model with an additional external Compton component. The parameters obtained cannot be fully explained by first-order Fermi acceleration at parallel shocks, and instead may suggest particle acceleration at oblique subluminal shocks, or that 1ES 1959+650 may consist of an inhomogeneous jet with a fast inner spine and slower-moving outer cocoon.The second source is the famous Crab Nebula, for years considered the standard candle of X-ray to VHE gamma-ray astronomy. VERITAS observed the Crab Nebula during the recent flare of the high-energy synchrotron component of the source in March 2013. No enhanced VHE emission was detected, but the observations facilitated the calculation of upper limits on any extra VHE spectral component emerging during the flare. A wealth of archival VHE Crab Nebula data also exists, spanning many years. An extended VHE data set of the source from 2000 to 2013 was compiled from Whipple 10m Telescope and VERITAS observations. This data set was searched for short-term flaring activity, but no evidence of this behaviour was found. A slight decrease in the long-term flux of the nebula was detected in the VERITAS data in 2011. This could possibly be correlated with increasing instability of the aerosol content of the local atmosphere around the VERITAS site.

The work presented in this thesis is primarily focused on the use of a laserproduced plasma as a source of protons, ions and X-rays. It explores highimpact applications of both high power ultrafast lasers and nanosecond lasers.Section 1 gives a general introduction to the physics governing the experimentsand the lasers in the following sections. The physics of plasmas isdescribed in Section 1.1. The physics of ultrafast lasers is described in detailin Section 1.2 from the theory of mode locking of oscillators to the compressionof high power ultrafast systems. The physics and mechanisms of X-raylasers are then explained in Section 1.3. Both the collisional excitation mechanismand the Linford gain equation are described along with a summery ofthe challenges in pumping X-ray lasers. Next in Section 1.4 laser acceleratedprotons are described in detail. Acceleration mechanisms are described andthe interaction mechanism with insulators is introduced. Finally, a numberof tools for photoabsorption studies are described in Section 1.5. In this Sectionthe dual laser plasma technique for obtaining photoabsorption spectra isdescribed along with the atomic structure codes (the Cowan and RTDLDAcodes) used to simulate the spectra.Section 2 describes all the laser systems used in this thesis. The variouscomponents of the Quantronix ultrafast laser system from UCD includingthe oscillator, the Odin-II amplifier and the Thor amplifier are described inSection 2.2, Section 2.3 and Section 2.4. The operation of the Surelite III andthe Spectron SL805 Q-switched nanosecond lasers are described in Section2.5 and Section 2.6. Finally, the TARANIS multi-terrawatt system and itsdifferent components are described in Section 2.7.Section 3 is covers two different experiments involving the generation ofX-rays from a laser produced plasma. The first technique described in Section3.3 is the generation of coherent X-rays by pumping a preformed laser plasmawith the TARANIS laser system. A Ni-like Mo laser was successfully pumpedyielding energies of 2 x 10-7 J with a gain length product of 3000.The second technique described in Section 3.5, involved inner shell X-rayemission from an indium target irradiated by the Quantronix laser system.The indium K series emission was observed using a lithium-drifted silicondetector. Seven counts of K_ emission was detected under the followingconditions (12000 shots through a 0.5 mm pin hole filtered with a 60_m Alfoil and a laser energy of 30 mJ). Due to the laser reliability this experimentis only a preliminary one which is intended to be continued at a later stage.Section 4 describes a laser accelerated proton experiment conducted in theCenter for Plasma Research in Queens University Belfast, using the TARANISlaser system. In this experiment 13 MeV protons were accelerated from10 μm gold foil targets into a sample of BK-7 glass. The interaction of theprotons with the glass were observed by taking spatially resolved images ofthe transient opacity induced by the protons interacting with the BK-7 Glassand an optical probe beam. These spatially resolved images are presented inSection 4.3.In Section 4.4.2 an optical streaking technique experiment is described tocalculate the lifetime of the transient opacity induced by the proton interaction.This process showed that the opacity in the glass began to occur 62ps after the TARANIS main pulse was _red and reaches 30% transmission88 ps after the firing of the TARANIS main pulse. Due to the limited timewindow available, the exact lifetime of the opacity is not known, howeverglass is seen to de-excite after 138 ps and has returned to 50 % transmissionby 175 ps.Section 5 describes the refurbishment of the 1-m normal incidence VUVspectrometer. It describes the replacement of a photographic plate based detectionsystem with a linear CCD array. The CCD array can detect the VUVradiation through a sodium salicylate phosphor coating which emits at 410nm on interacting with VUV radiation. Different phosphors are compared interms of sensitivity and ease of coating and the grounds for choosing sodiumsalicylate are explained. The adaptations to the spectrometer to use the linearCCD array are described and the details on calibrating the spectrometerare explained.Finally, Section 6 describes a set of spectroscopic experiments which usethe refurbished 1-m normal incidence spectrometer. First Section 6.2 describesa repeat of the photoabsorption of indium and indium plus whichwas conducted previously on the spectrometer. This was designed as a proofof principle of the working of the new phosphor based linear CCD arraysystem.Next, Section 6.3, describes the photoabsorption of thulium in the 23 eVto 40 eV region. The experimental spectrum is compared to the RTDLDAcalculations and to the autoionized Cowan code calculations. The simulationssuccessfully describe the observed absorption structure and 5p → nd and5p → ms transitions are identified.In Section 6.4 an indium laser produced plasma is successfully reheatedusing the Odin-II first amplifier of the Quantronix laser system. An experimentis described which shows emission from an indium plasma fromtransitions which are normally observed in absorption. This reheating wasoptimized with a specific set of target parameters (a delay of Δτ= 500 nsbetween the lasers, the Odin was focused into the center of the absorbing lineplasma, which was set at a height of Δz = -0:2 mm from the optical axis of the spectrometer).

The research presented here focuses on the theoretical investigation of spinons in quasi one-dimensional quantum spin chains from the perspective of neutron scattering, with emphasis placed on the calculation of dynamic spin structure factors for both unpolarised and polarised incident neutrons. Two anisotropic versions of the Heisenberg spin chain are considered for such an examination: the spin-$1/2$ antiferromagnetic $XXZ$ model and the spin-$1/2$ ferromagnetic $XYZ$ model.The $XYZ$ model supports spinon scattering (modelled at finite temperature) and is related to the so-called Villain mode. The introduction of a perturbation in the form of an external transverse magnetic field or Dzyaloshinskii-Moriya interaction (DMI) leads to the emergence of incommensurability in the system; such a result is a signature of fractional excitations. The presence of these interactions also give rise to a chiral response associated with the spinons in the polarised term of the scattering cross section. The inelastic scattering cross section is computed for both unpolarised and polarised neutrons.In relation to the antiferromagnetic $XXZ$ model, emphasis is on spinon pair creation (modelled at $T = 0\ {\rm K}$). Motivated by the presence of a chiral response in the case of the $XYZ$ model mentioned above, a new technique is developed in order to incorporate DMI and the transverse magnetic field so that one can determine if there is a chiral property associated with the two-spinon system. This technique is numerical in nature and is based on Green function methods. Using the results produced by the Green function approach, the inelastic cross section in the presence of an external transverse magnetic field is computed for the first time. The result is compared with experimental neutron scattering data; good agreement is demonstrated between theory and experiments on ${\rm CsCoBr}_3$.Finally, the Green function approach is generalised to account for the interactions between spin chains in magnetic compounds described by a staggered field. Various dynamic structure factors are computed for this scenario with results compared to experiment; good agreement between the theory and experiments on ${\rm RbCoCl}_3$ is shown.

Corneal Cross-Linking (CXL) is a one hour therapeutic treatment involving epithelial removal, application of riboflavin drops for 30 min. followed by UV light exposure to the cornea for the treatment of keratoconus, ectasia and infection. The photochemical reaction mechanism during CXL effectively halts the progression of corneal disease. The three main components of successful CXL are 1) the diffusion of riboflavin, 2) the presence of molecular oxygen (O2) and the formation of reactive oxygen species, and 3) UV interactions during CXL which results in the biomechanical strengthening in the corneal stroma, thus halting disease progression. Recent applications such as reduced treatment time, epithelial by-passing and the combination of advanced CXL protocols as an alternative to refractive procedures have been investigated. The purposes of this study are to 1) investigate the diffusion of riboflavin using intra-stromal channels in order to determine the effective diffusion coefficients as compared to traditional axial diffusion with epithelium on or off, and 2) investigate O2 behaviours during CXL in order to better understand Type I and II photochemical reactions using an established luminescence quenching technique.Measurements of riboflavin diffusion using intra-stromal channels were created by means of a mechanical stromal instrument in whole-mounted post-mortem porcine eyes. The use of fluorescent imaging along with numerical modelling allows determination of effective diffusion coefficients under different conditions.Time-Correlated Single Photon Counting Phosphorescence Lifetime Imaging (TCSPC-PLIM) is an innovative and complex method for fluorescence and phosphorescence lifetime measurements. Phosphorescence sensitive O2 based probes in soluble form have the ability to detect O2 concentrations repeatedly and non-invasively in living biological tissue. This study investigated the use of O2 sensitive phosphorescent probes using three models: (i) O2-sensitive nanoparticles in soluble solution of riboflavin without collagen, (ii) collagen type-I gel with O2-sensitive nanoparticles and riboflavin, and (iii) porcine eyes stained with O2-sensitive nanoparticles and riboflavin. Several O2-sensitive nanoparticle probes were evaluated. One probe was chosen (SII-A), displaying sufficient brightness, photostability and efficient in-depth staining. Results showed O2 behaviour after UV- induced CXL in all samples measured, concluding TCSPC-PLIM to be a novel, effective method in measuring CXL.

This thesis presents work done on investigating colliding laser-produced plasmas with time-resolved, UV-visible spectroscopy and time-resolved visible imaging. A nanosecond Nd:YAG laser pulse was split with a wedge prism and the two laser pulses created were focused onto the target surface, with power densities of ϕ = 1:6 x 10^12 W/cm2. The separation between the two plasmas was 2.6 mm and in between them a stagnation layer was formed. Plasmas of silicon (Si, Z=14), tin (Sn, Z=50) and lead (Pb, Z=82) were investigated. Time-resolved spectroscopy was used to determine the expansion velocities for different ion stages of Si and Pb, for both single plasmas as well as in the case where two plasmas collided to yield stagnation layers. Time-resolved visible imaging was used to obtain the expansion velocities of both seed plasmas and stagnation layers plasma-plume front. Colliding plasmas of different elements, Pb and Si, were studied and expansion velocities of different ion stages were compared with those obtained for colliding two identical plasmas. Acceleration of ions due to an electric potential difference is observed in the stagnation layer. Obtaining information about expansion velocities of different ion species provides great insight into the dynamics of laser-produced plasma expansion. Charge and time resolved dynamics have not been used before to study stagnation layers.

Atomic force microscopy (AFM) based techniques have been used widely to study functional properties of ferroelectrics. In this thesis, we investigated the application of AFM tips loaded with different stress ranges (from ~nN to ~µN) on ferroelectric thin films at the nanoscale. AFM tips applied with tens of nN force were used for careful characterization of ferroelectric switching on an inhomogeneous Pb(Zr,Ti)O3 (PZT) thin film. Different switching loops and domains were obtained after performing band excitation piezoelectric spectroscopy (BEPS) on the film at adjacent nanoscale areas. By combining BEPS, piezoresponse force microscopy (PFM), transmission electron microscope (TEM) and machine learning, abnormal loops were clustered and proved to be induced from various mechanisms including electrostatic, ferroelastic, and charge injection, which was mediated by defect-led microstructural variations. Applied stress in a large force range up to ~1 µN on ferroelectric BiFeO3 (BFO) thin films showed significantly enhanced injection currents, much larger than typical switching currents, induced by polarization switching via conductive atomic force microscopy. This injected current can be effectively modulated by applying mechanical force. As the loading force increases from tens of nN to hundreds of nN, the magnitude of the injected current increases and the critical voltage to trigger the current injection decreases. Notably, changing the loading force by an order of magnitude increases the peak current by several orders of magnitude. The mechanically boosted injected current could be useful for the development of high-density FeRAM devices. The mechanical modulation of injected current may be attributed to the mechanical force-induced changes in barrier height and width of the interfacial layer. AFM tips with these forces can characterize or modulate ferroelectric related properties. We therefore expected that larger force (tens of µN) can further remove ferroelectric materials for nanomechanical machining as ferroelectrics are important candidate materials for a wide range of applications including data storage and actuators. AFM-based machining of ferroelectric nanostructures offers advantages such as low damage and low-cost modification for already-fabricated thin films. Through a systematic investigation of a broad range of AFM parameters, we demonstrate that AFM-based machining provides a low-cost option to rapidly modify local regions of the BFO thin film, as well as fabricate a range of different nanostructures, including a nanocapacitor array with individually addressable ferroelectric elements.

A first step towards understanding planetary formation is the characterisation of the structure and evolution of protoplanetary discs. Although the large scale disc is understood in some detail, much less is known about the inner 5 au in which the main physical processes take place: accretion, ejection, and planetary formation. Even in the nearest sites of star formation, this region cannot be spatially resolved by stand-alone telescopes; only in recent years have optical and infrared interferometers been able to achieve this, and only in the case of the brightest sources. Hydrogen recombination lines are present in the spectra of young stars. In particular, the Bracket gamma line is the brightest line in the K-band. HD50138 is a target that exhibits bright Bracket gamma and faint high-n Pfund (from level n=24 to n=19) emission. Our results show that the circumstellar environment of the target is complex and shows asymmetries in both the Bracket gamma and the continuum emitting regions. The Bracket gamma is more compact than the continuum emitting region and originates from a wind with a wide opening angle. The origin of the Bracket gamma line is still controversial and it has been found to be associated with both accretion and ejection processes. Thus, more tracers are needed to better constrain the inner gaseous disc properties. Molecules are also present in this part of the disc. In particular, the CO overtone emission at 2.3\,\mic\ is a good tracer of the inner disc properties. This emission is not common and in the case of T Tauri stars it has been observed in only three sources. RW Aur A is a CTTS that exhibits irregular dimming events. It shows CO overtone emission in both the bright and dim states. Modelling this emission with an LTE CO ring in Keplerian rotation, we find that the CO conditions do not change during the dimming events. Moreover, no significant accretion variation is detected between the two states, leading to the conclusion that the dimmings are caused by occulting material very close to the star (within 1 au). The CO ro-vibrational emission at 2.3\,\mic\ observed with the second generation interferometer VLTI/GRAVITY opens a new window on constraining the physical properties of the inner gaseous disc, by spatially resolving the CO emission. 51Oph is a target which shows bright CO overtone emission. By modelling the CO emission, the CO is found to emitt very close to the star from a warm and dense gas. This is the first observational evidence of the physical properties so close to the star (~0.1 au) where there is no dust. This is consistent with previous LTE models of the physical conditions in the dust-free disc.

Blazars, consisting of flat-spectrum radio quasars (FSRQs) and BL Lacertae objects (BL Lacs), are active galactic nuclei (AGN) defined by a narrow inclination angle between the relativistic jets and our line of sight. While blazars are multiwavelength emitters, their morphological and spectral properties have been poorly explored at ~150 MHz because, generally, low-frequency instruments have lacked the requisite resolution and sensitivity to facilitate studies at this waveband. Such studies are now technically feasible with the Low-Frequency Array (LOFAR). The FSRQ 3C 273 and the BL Lac OJ 287 are notable for their one-sided X-ray jets. LOFAR observations of these blazars are calibrated, and I present the first high-resolution images of these jets at ~150 MHz. The jets consist of compact knots linked by diffuse emission. Studies of blazar samples from the LOFAR Two-Metre Sky Survey are also performed. Flat spectra are typically associated with blazars at gigahertz frequencies, and this was found to be the case at megahertz frequencies too. A tentative link between the flux densities at ~150 MHz and the gamma-ray photon fluxes was identified, suggesting that for a given source, a single population of particles is responsible for some of the emission at both wavebands. It was discovered that the majority of blazars possess complex morphologies at ~150 MHz, which are attributable to beamed jet components and large-scale diffuse emission, with significant variation between sources. The spatial extents of FSRQs are shown to be in concordance with the predictions of the radio-loud AGN unification scheme. Studying the extended low-frequency emission from blazars can improve our understanding of the emission mechanisms that give rise to jet spectra and, ultimately, can help determine the validity of the radio-loud AGN unification scheme.

In this thesis, I investigate the formation of high-mass young stellar objects (HMYSOs) and the properties of their protostellar jets. My first science chapter is a study of the kinematic and dynamic properties of the 20M HMYSO IRAS 13481-6124 (Fedriani et al. 2018). I measured mass-loss and momentum rates on the order of 10^-4M sun yr-1 and 10^-2Msun yr-1 km s-1, respectively. I used Hi emission lines to perform spectro-astrometry to probe the massive protostellar jet at au-scales and connect it with the parsec-scale jet. In the second science chapter, I study the unique case of G35.2-0.74N, a 10M sun HMYSO (Fedriani et al. 2019). I observe, spatially coincident atomic near-infrared (NIR) and ionised radio jet emission. For the first time, the ionisation fraction from a jet driven by a massive protostar has been measured. The value obtained (~10%) is similar to that found in jets driven by low-mass protostars. This suggests a common launching mechanism, i. e., the jet is launched magneto-centrifugally. It was possible to measure mass-loss and momentum rates on the order of 10-5Msun yr-1 and 10-2Msun yr-1 km s-1, respectively, without relying on assumptions on the ionisation fraction. This study also confirms that the ionisation mechanism is related to shocks instead of UV radiation from the central source. The new method used in this paper, which combines NIR and radio measurements, opens up a new way to measure ionisation fraction of jets for both the low- and high-mass regime. Lastly, the jet and the accretion disc of the driving source of the Herbig-Haro object 135/136, IRAS 11101-5829, was investigated in the third science chapter (Fedriani et al. submitted). I found disc emission, for the first time, in this object revealed by the NIR CO overtone bandhead emission at 2.29 - 2.5 microns. By using our own developed LTE model, I infer that the emission is consistent with a relatively warm (T~3000 K) and dense (NCO~10^22 cm-2) disc. Notably, the model also suggests a geometry different from that inferred in the jet, retrieved from both spectral emission lines and imaging. This implies that the disc emission is reflected off the outflow cavity walls. This approach has been used for the first time in this thesis and indicates that to obtain the correct geometry of the system, one needs both high spectral and spatial resolution to avoid retrieving possible erroneous results. The results presented in this thesis show further observational evidence that the formation of high-mass protostars and their jets are a scaled-up version of their low-mass counterparts and that their properties scale with mass. In light of these results, we are then one step closer to confirm that star formation proceeds in a similar fashion independently of mass.

In the recent years, light modulation has been achieved by an array of binary-positioning micromirrors, namely Digital Micromirror Devices (DMD), which have gained popularity in vision science, such as in retinal imaging, psychophysical vision testing or coded wavefront sensing. In this thesis, a DMD is used to measure two aspects of vision characterization: a) retinal directionality through the Stiles-Crawford effect of the first kind (SCE-I) and b) crosstalk-free wavefront sensing for large ocular aberrations. For the first part of this work, a DMD is used as a key component in a uniaxial flicker system to characterize the SCE-I in Maxwellian view, capable of controlling pupil aperture size and location, as well as field intensity by adjusting the duty cycle of the micromirrors. The SCE-I is tested under different conditions including foveal and parafoveal retinal locations, different luminance levels ranging from scotopic to photopic conditions, wavelength dependence through the visible spectrum and into the near infrared, as well as differences for myopic subjects. The SCE-I is also characterized in normal viewing conditions (Newtonian view) by scanning of the pupil with small apertures, where the influence of the SCE-I on visual acuity is analysed. Furthermore, a method to directly measure the integrated SCE-I is described and analysed using a geometrical optics absorption model based on volumetric overlap of incident light with photoreceptor outer segments, without accounting for photoreceptor waveguiding. In the second part, a wavefront sensing system using a digital micromirror device is implemented to achieve a wavefront sensor with high dynamic range and speed, without the use of a lenslet array which, in turn, avoids crosstalk. By sequential scanning of the wavefront, very high sampling densities can be achieved when compromising speed. The system is tested by measuring aberrations in an artificial eye and extended to the human eye.

The effect of organic salts of low melting temperature, called ionic liquids (ILs), on mechanoelasticity of cell membranes and migration of cells have been investigated by a combination of experimental approaches, including neutron scattering and atomic force microscopy (AFM), complemented by biological assays; nanostructuring of ILs in water solution and optical properties of ILs relevant for biological applications have been investigated by computational approaches, including molecular dynamics (MD) simulations and density functional methods. A major part of this Ph.D. work focuses on the effect of sub-toxic concentration of imidazolium ILs of varying chain length ([bmim][Cl] and [dmim][Cl]). At the IL concentrations below their critical micellar concentration, a combined neutron scattering and AFM studies showed insertion of [bmim][Cl] IL-cation into the lipid bilayer and affecting their local mechano-elasticity in IL chain-length dependent manner. Additionally, in-vitro cell migration assay has resulted in the IL-induced enhancement of cell migration rate depending upon their chain-length and concentration. Overall, these effects are stronger for the longer chain-length and the highest sub-toxic concentration of the ILs. Combining these biophysical and biochemical studies, we propose, in the end, a bio-chemical-physical mechanism that relates this IL-induced alteration in the cell membrane with the alteration in the cell migration. The overall result is that IL-concentration and IL-cation chain-length can tune the cell membrane elasticity and cell migration. The chemical-physical manipulations of the lipid-bilayer elasticity hold the promise of effective therapeutic and diagnostic approaches. The chemical-physics background underlying the complex phenomena explored previously by experiments has been investigated by computational means, focusing on the nanostructuring in the water of protic and aprotic ILs. Here, by employing MD simulations based on empirical force fields, we analysed the fluctuations of the ions and water molecule distribution in space in solutions spanning a wide salt concentration range, from 25 to 75 wt%. Depending upon the salt concentration, the transition of nanostructuring from water-rich to salt-rich condition has been observed. Additionally, a combination of density functional methods has been used to compute absorption and luminescence properties of gas-phase single ions and neutral ion pairs from ILs.

In this thesis, the use of convolutional neural networks (CNNs) for identifying muon ring images from the VERITAS gamma-ray telescope is investigated. Muon images are important to identify due to their use in the calibration of the telescope and being a source of background which can sometimes be misidentified as being produced by a gamma ray. Currently muon images are identified using an algorithm in the VEGAS analysis software which was developed for VERITAS. It is hoped that CNNs may be able to improve upon this algorithm and increase the efficiency of the detection of these images. In order to train a convolutional neural network for this purpose, a labelled dataset is required. Multiple datasets were generated and tested for this purpose, using VEGAS-labelled data, simulated data, and data from the Muon Hunters 2 citizen science project. Extra information in the simulations was used to generate labels for the simulated data, while volunteer votes were used to label the Muon Hunters 2 data. For this purpose the volunteer votes were first analysed in order to determine how best to use them to generate hard labels for the images. It was found by applying the trained models to an expert-labelled test dataset that CNNs are more effective than the current algorithm at identifying muon images. Particularly the models trained on Muon Hunters 2 data produced the highest accuracy and AUROC (area under receiver operating characteristic) values, with AUROC being an indication of how well the model can separate muon and non-muon images across a range of output decision boundaries. A model trained on Muon Hunters 2 data identified approximately 30 times the number of muon images that the current algorithm does when applied to an independent expert-labelled test dataset. This was achieved with the output boundary upon which classifications were based adjusted so as to eliminate false positives from the model predictions. One of the benefits of the CNN model is its ability to identify various types of rings other than the full, central rings identified by the current algorithm. For calibration purposes however, more work is required in order to allow these less than full rings to be used. More work is also required in order to be able to separate out muon images which are usable for calibration from those which aren't, without using existing algorithms which may also eliminate some usable images.

A nanoparticle entering the human body results in the formation of a nano-bio interface. This results in a dynamic interaction that takes place amongst the nanoparticle surface and a variety of biomolecules, especially proteins, forming a protein corona (PC). Recently, studies of the nanoparticle protein corona (NP-PC) biophysical properties have become a significant area of research. It is important to understand, characterize and model the biophysical properties and the molecular interactions related to the NP-PC. Protein-nanoparticle interactions are driven largely by corresponding physio-chemical changes. Here, we perform atomistic molecular dynamic (MD) conformational studies of five important proteins that are known to participate in the protein corona around the nanoparticle in the human body: Human Serum Albumin, Apolipoprotein, Human Surfactant Protein D, Alpha-1 antitrypsin, and Mucin 2 D3 domain. Using their structures from the RCSB protein data bank, we perform a statistical analysis of their MD trajectories to determine their representative, average equilibrium structures and their possible outlier structures (i.e., most different from the representative ones). Using these structures in conjunction with docking simulations, we generate both homo-oligomers and hetero-oligomers and analyze their surface biophysical properties such as their hydrophobic fraction of the solvent accessible surface area (SASAH) and surface charges. We also use atomistic models of TiO2 and SiO2 nanoparticles to generate and study the NP-PC interface around these nanoparticles, describe specific residues found in the NP-PC interfaces, and show that accurate SASAH, SASA+, SASA- values, and PC surface charges can be estimated for atomistic models of NP-PCs. The efficient yet accurate characterization of NP-PC biophysical properties should be useful in future studies of NP-NP and NP-biomolecular interactions and their possible effects (e.g., toxicity) in specific biological systems.

The detection of molecules at low concentrations using methods such as surface enhanced Raman spectroscopy (SERS) and surface enhanced fluorescence (SEF) is crucial in many fields, such as medical diagnostics, forensics, security, and environmental monitoring. Traditionally platforms for optical sensing are fabricated using expensive methods, requiring specialized equipment, such as lithography, and rely on the use of noble metals, which are limited by lack of biocompatibility and inertness as well as their large environmental impact. Dielectric materials, in particular semiconductors, have been recently proposed and researched as alternatives for sensing substrate designs, due to their unique properties, such as low cost, ease of manufacturing, recyclability as well as the large versatility of available materials and designs that can be utilized. Although many promising studies have been performed on dielectric-based SERS, the state-of-the-art designs are often very limited, due to the lower signal enhancements generated. The aim of this thesis is to study the efficiency of environmentally friendly dielectric-based platforms for optical sensing applications, fabricated using simple and cost-effective methods. In the thesis, the two main groups of dielectric materials: inorganics and organics are studied by investigating the performance of a representative subgroup. Both groups are studied as dielectric-only platforms, and as components of a metal/dielectric hybrid. The efficiency of the platforms is assessed in terms of signal enhancements of Raman and fluorescence signals and lowest detectable signals obtained, the effectiveness of signal boosting strategies employed, as well as the suitability of the materials for other applications, such as photocatalysis. First, we study metal oxides, which are inorganic semiconductors, largely beneficial in the SERS field due to their charge generation properties. Metal oxide nanowires with a focus on ZnO, TiO2, and WO3 are shown to be efficient SERS platforms, following decoration of the nanowires with silver nanoparticles, as well as without the use of metal. We show that heat treatment in an oxygen atmosphere can be used as an effective method for point defect introduction in the lattice of the semiconductor, which results in significant boosting of the SERS signal intensities generated, due to heat-induced wettability changes and optical gap shrinking that allows for more effective charge transfer. Additionally, for certain wide bandgap semiconductors, these templates can be used as an effective substrate for driving catalytic redox reactions based on a model reaction of oxidation of PATP to PNTP. Subsequently, we utilize cellulose, an abundant, naturally occurring biopolymer, for the design of cost-efficient, recyclable, and biocompatible and for Raman and fluorescence-based detection of molecules. We study the interactions of porphyrins, a representative group of biomolecules with crystalline surfaces of Iß cellulose, and demonstrate the Stranski-Krastanov growth of clusters for complex molecules. We show that randomly distributed cellulose nanofibers as well as other cellulose derivative materials can be used as efficient metal-free SERS platforms for porphyrin molecule detection and as platforms for fluorescence-based molecule detection of a range of biomolecules, including a model immunoassay. Additionally, we demonstrate that cellulose acetate can be shaped into uniform photonic crystals with regular features using a replica moulding method and then, following coating with a thin layer of silver, used as a sensing template characterized by flexibility and high signal reproducibility.