At the forefront of biological experimentation and simulation technology is the attempt to understand the biological mesoscale, the regime in which thermal fluctuations are still vital for function but atomic resolution may no longer be required. There is a wealth of low-resolution biomolecular structural data of macromolecules available for study, and experimental developments are allowing these biomolecules to be visualised to near-atomic resolution without the need for crystallisation. It is clear that a new form of simulation is required to take advantage of this structural data in order to better understand the dynamics of proteins at the biological mesoscale, and their relationship to dynamics at both the microscale and the macroscale. The work presented in this thesis concerns the development of Fluctuating Finite Element Analysis (FFEA), a mesoscale simulation technique that treats globular macromolecules as visco-elastic continuum objects subject to an additional thermal stress, satisfying our definition of the mesoscale. I have further developed the constitutive continuum model to better represent biological macromolecules, and designed a new solution procedure in order to both increase the computational efficiency of the algorithm and to remove superfluous dynamical information. I also introduce a completely new kinetic framework that couples to the underlying simulation protocol, enabling us to simulate discrete biological events, such as conformational changes, within a continuous dynamical simulation. I apply FFEA to the molecular motor cytoplasmic dynein, a mesoscopic system exhibiting dynamical features that are beyond the scope of standard molecular dynamics simulations, but well within the mesoscopic regime FFEA was designed for. I determine the physical parameters that an FFEA model of dynein requires for consistency with both experimental and high-resolution molecular dynamics simulations. Finally, I consider the diffusional properties of dynein with respect to its microtubule track, with the aim of understanding the potential mechanisms that enable the motor to be processive.

This thesis investigates domain dynamics in one of the most well-known ferroelectric materials – polycrystalline BaTiO₃ ceramics, and one of today’s most promising ferroelectric materials for future device applications – mixed-phase BiFeO₃ thin films. The investigations use primarily TEM techniques accompanied by relevant theory and AFM techniques. The study on polycrystalline BaTiO₃ (FIB lamellae) aims to further understand the link between domains coupling across adjacent grains and to explore the domains’ re-ordering as a function of heating through T_C. Two cases were explored: domains coupling across a single grain boundary, and a more complex case of domains within adjacent grains meeting around a junction (or pore). Analysis using martensite crystallography theory demonstrated that domains sharing a single grain boundary do on average arrange themselves in a compatible and stress-free manner. For the example of grains arranged around a junction, a computational example was created, given the complexity of the case. It was demonstrated that the relaxation of the out-of-plane constraint gives rise to an undetermined set of linear equations which can be solved for compatible domain wall orientations and volume fractions of domains, indicating that groups of adjacent grains can form stress-free domain patterns. STEM in-situ heating cycle experiments, heating and cooling through T_C, showed that the re-configuration of the domain structure (domain density, favourable domain orientations and presence of domain bundles) was directly influenced by the rate and continuous/dis-continuous nature of the performed heating cycles. Furthermore, this material was explored with focus on the functionality of its positive temperature coefficient of resistivity (PTCR) effect. Aberration-corrected STEM and EELS revealed a grain boundary PbTiO₃-like region (~10-15 nm), which was associated with an increased local polarisation in that region. The chemical and electronic heterogeneity of the ceramic was linked to the changes in potential barrier at the grain boundary, theorised by the Heywang-Jonker model. It was inferred that the confined PbTiO₃ rich grain boundary region would have a higher spontaneous polarisation (than BaTiO₃), thus reducing the grain boundary barrier potential further below T_C, augmenting electronic transport and enhancing the magnitude of resistivity jump at T_C, and so justifying the optimised PTCR effect exhibited by this ceramic. For the study on phase reversibility in BiFeO₃ thin films, the native polymorphs, known as T and R, were initially identified. The thermal activation phase transformation was investigated by STEM in-situ heating cycle experiments; showing a lateral growth of the highly-strained T phase above 400°C. Additionally, an AFM tip was used to locally apply electric field and stress, demonstrating reversible switching between the native mixed-phase and a pure T phase state. Energy-based effective Hamiltonian simulations verified phase competition under the application of electric field and stress, comparable to experimental data. The stress-written phase boundaries (R’/T’) were investigated via c-AFM showing enhanced conductivity. TEM analysis of cross-sectional lamellae from pre-written AFM regions revealed that the stress-written R’ and T’ polymorphs differ in structure from the native polymorphs and, the R’/T’ boundaries have higher in-plane strain gradients compared to the native R/T boundaries, rationalising the enhanced conductivity as a strain mediated effect.

This thesis focuses on proving a finite domination condition on bounded chain complexes of finitely generated free R-modules where R is a strongly Zn-graded ring.

Nanostructured materials have recently attracted much interest due to their unique properties which make them appealing for the next generation of efficient and novel optical/electrical devices. In particular, two-dimensional (atomically thin) materials such as transition metal dichalcogenides (TMDs) have been extensively researched and shown to exhibit, e.g., strong optical absorption when compared to their bulk counterparts, with potential applications in photovoltaics for solar energy. The optical absorption in such materials may be further improved by decoration with metal nanoparticles (MNPs) due to a plasmonic enhancement effect. While such an effect has been demonstrated experimentally, it is hard to show theoretically from an ab initio point of view due to the computational demand of such calculations: the state-of- the-art approaches commonly used to determine the optical spectra of, e.g, the semiconducting TMD (i.e. density functional theory (DFT) and many-body perturbation theory) may not be applied to the full TMD-MNP structure as the MNP is often on a much larger scale than the semiconductor rendering the ab initio methods infeasible. In this thesis, we develop a dynamical, hybrid approach (the projected equations of motion (PEOM) method) where a composite material is split into subsystems which are then coupled electromagnetically. The primary system (e.g., the TMD) may be treated using any time- dependent theory, while the secondary system (e.g., the MNP) is modelled entirely through its frequency-dependent polarisability which is fitted to obtain parameters which enter into the PEOMs. As a proof of concept, the PEOM method is first applied to a semiconducting quantum dot- MNP system and the obtained energy absorption rates and population dynamics are compared with results from existing analytical approaches. Good agreement between the two methods is shown, while the PEOM proves to be an improvement when investigating ultrafast excitations in such systems. The method is then further tested by comparing absorption spectra in bilayers of hexagonal boron nitride and MoS2 obtained via the PEOM approach with those obtained by time-dependent DFT and the Bethe-Salpeter equation. Again, the two approaches are in good, qualitative agreement. The thesis is left open as a starting point towards investigating the TMD-MNP structures, as well as stating the limitations of the PEOM method and suggesting possible improvements.

No description available.

This thesis focuses on the phenomena of ionised jets associated with massive young stellar objects. Firstly a study was conducted with the aim to establish a statistical sample of such objects. Radio observations towards a sample of 49 MYSOs resulted in the detection of 28 objects classified as ionised jets. The jets' radio luminosities scaled with their MYSOs' bolometric luminosities in the same way as for low-mass examples. This infers that the jet launching and collimation mechanisms of high-mass jets are very similar to that in their low-mass counterparts and they are ejected for the last < 65000yr of the MYSO phase. Interestingly non-thermal emission was regularly detected towards spatially distinct radio lobes (associated with 50% of the jets), suggesting the presence of synchrotron emission and therefore, magnetic fields. With an average spectral index of -0.55 (indicative of the 1st order Fermi acceleration mechanism) it is concluded these lobes are the result of shocks in the jets' stream. My second science chapter is a study of radio variability, precession and proper motions towards a subset of objects from the first chapter. Over a two year time period, no significant variability and only one example of proper motion (1800+/-600 km/s) was detected. Precession was found to be commonplace however and if it arises as the result of binary interactions, we infer orbital radii between 30 and 1800 au for the binary companions. Lastly, high-resolution, VLA observations at C and Q-bands were analysed to extend the known sample of MYSOs harbouring ionised jets into the northern hemisphere. Only 3 radio sources were detected possessing jet-like characteristics towards the work's sub-sample of 8 IRDCs containing 44 mm-cores (in our field of view), highlighting the radio-quiet (> 30 microJy) nature of this early phase in massive star formation. Towards the RMS survey derived sample of 48 MYSOs, a total of 38 radio sources with jet-like characteristics were detected, of which 14 were bona-fide jets (10 of which were associated with shock-ionised lobes). Comparing the analysis of the MYSO sample to statistical surveys of molecular outflows, it was inferred from their total momenta that the jets alone are mechanically capable of entraining the outflows. Measurement of the physical extent of the radio emission showed no evolution of the opening angle with bolometric luminosity, and that a trapped HII region alone was not enough to explain the radio emission. Most interestingly, jets associated with shock ionised lobes were found to occupy later evolutionary IR colours than those without, suggesting them to be an evolutionary stage in ionised jet, and MYSO, evolution.

This thesis presents a study of protoplanetary discs around young, low mass protostars. Such discs are believed to be massive enough to develop gravitational instabilities, which subsequently form spiral structures. The dynamical and chemical evolutions of a protosolar-like, gravitationally unstable disc are explored and the spiral structure in the disc is found to shock-heat material. This affects the chemical composition via enhanced desorption rates and endothermic reaction rates and through global mixing of the disc. As a result, the gravitational instability in the model disc leads to transient and permanent changes in the disc chemistry, and also provides a chemically-rich midplane in contrast to simulations of more evolved discs. Secondly, radiative transfer calculations are performed for the dust continuum, and model-tailored grid construction is found to improve the accuracy of the resultant flux images. Continuum observations of the model disc are synthesised and the spiral structure (driven by the gravitational instability) is shown to be readily detectable with ALMA across a range of frequencies, disc inclinations and dust opacities. The derivation of disc mass from the observed flux densities is explored but the method commonly utilised is found to be unreliable and underestimate the disc mass. Therefore, it is concluded that gravitational instabilities could be retrospectively validated in discs previously thought not massive enough to be self-gravitating. Finally, radiative transfer calculations are performed for molecular line transitions. Methods for improving the accuracy of line flux images are explored and the validity of assuming local thermodynamic equilibrium is assessed. Observations of the line fluxes are synthesised without noise and the spiral structure is found to be traced to an extent by all transitions considered, which is not necessarily congruent with the underlying distribution of the molecular species. The disc is seen in absorption in all transitions considered, due to the global mixing of the disc, which suggests absorption features could be a signature of gravitational instability in young protoplanetary discs. The sensitivities required to detect flux originating in spiral features are determined and it is found that a dedicated observation with ALMA should be capable of spatially resolving spiral structure in a Class 0 disc. Whether the spiral structure can be also be determined from spectral features is explored, which is shown to only be reliable with PV diagrams of nearly edge-on discs. The derivation of protostellar mass from PV diagrams is also explored and found to most likely be unreliable for gravitationally unstable discs.

The phenomenon of distinct conductivity at certain ferroelectric domain walls has the potential to revolutionise nanoelectronics. Complete control over their local carrier properties would allow two-dimensional analogues of semiconducting devices to be dynamically written, effectively supplanting modern printed circuit design. However, despite a growing array of ferroelectric materials found to exhibit domain wall conductance, the most fundamental carrier measurements have not been performed with neither local carrier types, mobilities or densities explicitly determined for any domain wall system. This thesis details the development of a scanning probe microscopy technique that facilitates spatial mapping of the Hall effect within conducting domain walls. The measurements presented herein represent the first explicit characterisation of the carriers involved in conducting ferroelectric domain walls. Studying YbMnO3 single crystals, the Hall potential developed within tail-to-tail charged domain walls was imaged by its influence on an intermittent-contact atomic force microscopy topography profile, confirming the local conduction was mediated by p-type carriers. By calibration of the AFM signal, an estimate of ~ 1x10¹⁶ cm⁻³ is calculated for the mobile carrier density in the wall, around four orders of magnitude below that required for complete screening of the polar discontinuity. A carrier mobility of ∼ 60cm²V⁻¹s⁻¹ is calculated, about an order of magnitude below equivalent carrier mobilities in p-type silicon, but sufficiently high to preclude carrier-lattice coupling associated with small polarons. The technique was further developed by utilising Kelvin probe force microscopy to map the topographic and electrostatic signal in isolation. Surface potential mapping of an ErMnO₃ single crystal confirms quantitative accuracy is maintained under a range of magnetic and electric field states, with distinct wall contrast observed at both charged wall types. Lastly, the alternating polarity method was demonstrated as an simple means of signal demodulation to precisely measure the typically minute conductance of individual domain walls.

We have grown epitaxial single-phase B20 Fe(1−x)Co(x)Ge films on Si (111) substrates films by molecular beam epitaxy. This method is able to produce the whole range of Fe(1−x)Co(x)Ge which are of high quality due to homogeneous layer growth with low surface roughness of 1-2 nm. The films grown are racemic, showing an equal mix of left-handed and right-handed chiral grains, and are strained due the lattice mismatch between the film and substrate. Magnetic measurements showed the FeGe films grown (~ 70 nm thickness) have a saturation moment, Ms = 0.982(7) μB, and ordering temperature, Tc = 280(2) K, both close to bulk value. Ms and Tc were found to decrease monotonically with increasing x and all films were found to have an easy-plane anisotropy. A helical magnetic structure was observed using polarised neutron reflectometry and we found the helix wavelength to vary with composition. A divergence in the wavelength was found at a critical composition xc = 0.5 where a transition from helimagnet to collinear ferromagnet occurred. The temperature dependent resistivity, ρxx(T), was found to be metallic for all compositions and a broad peak with magnetic origin was found to arise for intermediate compositions 0.2 < x < 0.7. The magnetoresistance in Fe(1−x)Co(x)Ge with 0.1 < x < 1 was found to behave similarly to FeGe, however many differences were observed, such as a positive linear magnetoresistance for Fe(0.4)Co(0.6)Ge and a change in conical magnetoresistance scaling beyond Fe(0.5)Co(0.5)Ge. The Hall resistivity showed an increase as well as a sign change in the ordinary Hall effect coefficient, R0, from 0.0122 μΩ cm/T for FeGe to -0.6808 μΩ cm/T for Fe(0.5)Co(0.5)Ge, at 5 K, indicating a large reduction in the carrier concentration and change of carrier type. The anomalous Hall effect was found to increase dramatically on the introduction of Co, increasing by an order of magnitude from FeGe to Fe(0.9)Co(0.1)Ge at 5 K. We find evidence of potential skyrmion structures through the measurement of the topological Hall effect, with features as large as -0.39 μΩ cm for Fe(0.6)Co(0.4)Ge at 5 K. We conclude Fe(1−x)Co(x)Ge is a potential material for further skyrmion study, but direct observation of these topological structures are required to fully attribute the measured effect and progress further.

This thesis presents near-infrared spectroscopy and imaging on large samples of Massive Young Stellar Objects (MYSOs) drawn from the Red MSX (RMS) survey. Low resolution spectra of 92 MYSOs in the near-infrared (NIR) H and K spectral bands taken at the Anglo-Australian Telescope (AAT) are presented. The targets are classified under the (Cooper, 2013) MYSO evolutionary scheme. Based on the presence or absence of H2, HI and FeII lines, MYSOs are placed in an evolutionary sequence ranging from Type Is, which are embedded and show strong shocks to the evolved Type IVs, which are the least embedded. Bolometric luminosity and distance are excluded as drivers of the evolutionary sequence through Kolmogoroff-Smirnoff tests. The different MYSO classes segregate in mid-IR colour space, with the youngest sources being the most embedded, and the more evolved sources bluer. The results from the spectroscopy are compared with radio data on ionised jets in MYSOs and with submilimetre data on star-forming clumps. The lowest jet detection rates are found in evolved MYSOs. The youngest sources are located in the most massive clumps. Next, medium-resolution spectra from Gemini are presented for 36 MYSOs. This is the largest sample of MYSOs observed at this resolution in the NIR. One MYSO showed intrinsic stellar absorption lines, and was assigned a spectral type of an early A giant/supergiant with added continuum dust excess emission. This is consistent with the swollen up MYSOs found in the simulations of (Hosokawa et al, 2010), and is the first time observational evidence for swollen up MYSOs has been found. Line luminosities and accretion rates deduced from Br gamma emission are consistent with values from low-mass YSOs, supporting theories of scaled-up high mass star formation. The luminosities of various lines show strong correlations with each other, even when accounting for distance and line flux biases. This may be due to the luminosities being proportional to the stellar mass. The detection rates of P Cygni and inverse P Cygni are lower in MYSOs than in low-mass YSOs. This is consistent with a change in the accretion mechanism from magnetospheric accretion in T Taus/HAe stars to disc accretion in HBes/MYSOs. Velocity-resolved Br gamma/Br12 ratios are analysed, revealing that the observed ratio features do not correlate with bolometric luminosity, NIR colour or the (Cooper, 2013) evolutionary sequence. The mechanism that causes the variation in profile ratio features is not clear from this data, but it may be a consequence of the variety in inclination with respect to the line of sight of the MYSOs. Finally, a pilot adaptive optics survey in the K band has been performed on 32 MYSOs in order to search for binary companions. This is the first ever systematic study of multiplicity in MYSOs. 18 new companions are found within 3", corresponding to a raw multiplicity fraction of 31% and a companion fraction of 53%. MYSOs have larger multiplicity fractions than their lower mass or more evolved counterparts at these scales. This indicates that multiplicity increases with mass and decreases with evolutionary stage, similar to trends seen for field stars. Lower limits to companion masses and mass ratios are obtained from the K band magnitudes, correcting only for foreground extinction. Results indicate that a larger fraction than expected of the companions have high mass ratios (q > 0.5), in disagreement with the idea that the companions are randomly captured field sources. In summary, this thesis presents a large amount of spectra of MYSOs, forming a census of massive star formation in different environments throughout the Galaxy, probing the circumstellar region and evolution throughout the MYSO phase. Accretion rates from Br gamma support high mass star formation theories based on scaling up from the low mass case. The first ever detection of a swollen up MYSO is found in this sample. The first systematic search for multiplicity in the MYSO phase is reported, and results from this investigation prove that many massive stars form as part of multiple systems.