No description available.

DNA origami is a method for constructing 2-dimensional nanostructures with arbitrary shapes, by folding a long piece of viral genomic DNA into an extended pattern (Rothemund, 2006). In this thesis DNA origami nanostructures that in- corporate active transport are developed, by combining rectangular DNA origami tiles with either synthetic DNA motors, or the protein motor F1-ATPase. The transport of an autonomous, unidirectional, and processive 'burnt-bridges' DNA motor across an extended linear track anchored to a DNA origami tile is demonstrated. Ensemble fluorescence measurements are used to characterise motor transport, and are compared to a simple deterministic model of stepping. The motor moves 100 nm along a track at 0.1 nms-1 Atomic force microscopy (AFM) is used to study the transport of individual motor molecules along the track with single-step resolution. A DNA origami track for a 'two-foot' DNA motor is also developed, and is characterised by AFM and ensemble fluorescence measurements. The burnt-bridges DNA motor is then directed through a track network with either 1 or 3 bifurcations. Ensemble fluorescence measurements demonstrate that the path taken can be controlled by the addition of external control strands, or pre-programmed into the motor. A method for attaching the rotary motor protein F1-ATPase to DNA origami tiles is developed. Different bulk and single-molecule methods for demonstrat- ing protein binding are explored. Single-molecule observations of rotation of the protein motor on a DNA origami substrate are made, and are of equivalent data quality to existing techniques.

No description available.

No description available.

Many-core architectures are more promising hardware to design real-time systems than multi-core systems as they should enable an easier mastered integration of a higher number of applications, potentially of different level of criticalities. In embedded real-time systems, these architectures will be integrated within backbone Ethernet networks, as they mostly provide Ethernet controllers as Input/Output(I/O) interfaces. Thus, a number of applications of different level of criticalities could be allocated on the Network-on-Chip (NoC) and required to communicate with sensors and actuators. However, the worst-case behavior of NoC for both inter-core and core-to-I/O communications must be established. Several NoCs targeting hard real-time systems, made of specific hardware extensions, have been designed. However, none of these extensions are currently available in commercially available NoC-based many-core architectures, that instead rely on wormhole switching with round-robin arbitration. Using this switching strategy, interference patterns can occur between direct and indirect flows on many-cores. Besides, the mapping over the NoC of both critical and non-critical applications has an impact on the network contention these core-to-I/O communications exhibit. These core-to-I/O flows (coming from the Ethernet interface of the NoC) cross two networks of different speeds: NoC and Ethernet. On the NoC, the size of allowed packets is much smaller than the size of Ethernet frames. Thus, once an Ethernet frame is transmitted over the NoC, it will be divided into many packets. When all the data corresponding to this frame are received by the DDR-SDRAM memory on the NoC, the frame is removed from the buffer of the Ethernet interface. In addition, the congestion on the NoC, due to wormhole switching, can delay these flows. Besides, the buffer in the Ethernet interface has a limited capacity. Then, this behavior may lead to a problem of dropping Ethernet frames. The idea is therefore to analyze the worst case transmission delays on the NoC and reduce the delays of the core-to-I/O flows. In this thesis, we show that the pessimism of the existing Worst-Case Traversal Time (WCTT) computing methods and the existing mapping strategies lead to drop Ethernet frames due to an internal congestion in the NoC. Thus, we demonstrate properties of such NoC-based wormhole networks to reduce the pessimism when modeling flows in contentions. Then, we propose a mapping strategy that minimizes the contention of core-to-I/O flows in order to solve this problem. We show that the WCTT values can be reduced up to 50% compared to current state-of-the-art real-time packet schedulability analysis. These results are due to the modeling of the real impact of the flows in contention in our proposed computing method. Besides, experimental results on real avionics applications show significant improvements of core-to-I/O flows transmission delays, up to 94%, without significantly impacting transmission delays of core-to-core flows. These improvements are due to our mapping strategy that allocates the applications in such a way to reduce the impact of non-critical flows on critical flows. These reductions on the WCTT of the core-to-I/O flows avoid the drop of Ethernet frames.

The growth of the nuclear power industry has provided a considerable stimulus for investigations into fluid-structure interaction problems. The safety case for nuclear reactors requires an understanding of the impact response of structures enclosing or surrounded by fluids. In many cases the structural response is in excess of that which can be predicted by elastic analyses and both material and geometrical non-linearities must be considered. The understanding of the interaction between the structure and the contained fluid poses additional problems which, in the extreme loading conditions envisaged, have received little attention. There is a lack of data relating to basic fluid-structure interaction problems involving dynamic plastic structural impact. Two sets of experiments are described which were carried out to provide some such data. The first set of experiments considered beams, both fully clamped (leading to large membrane forces) and partially clamped (preventing rotational and transverse motion while allowing the beam material to be fed in from the supports), struck centrally by a projectile. The second set of experiments considered a circular plate clamped around its periphery, sealing a volume of fluid, and struck centrally by a projectile. The shape of the plates and beams as they deformed were recorded, as were the pressure variations during the tests. In both sets of experiments the main contribution of the fluid to the beam or plate response was to localise the deformations. The early deformation of the beams was limited to the centre half span and the deformation only spread to the ends of the beams as the supporting effect of the fluid was lost due to the fluid escaping. In the plate experiments, where a good seal could be achieved, the deformation throughout was localised compared with a similar plate in air. The deformation in these cases was limited to a central disc of approximately half the plate diameter. The pressures recorded during the tests suggest that the fluid response was predominantly incompressible. A finite element program was written to model the response of beams and circular plates (axisymmetric problems). A brief history of the finite element method, the background theory and the development of the method to treat non-linear, large displacement, dynamic problems are given. The results are presented for a number of beam and plate problems, both those described above and other problems for which data was available. The finite element program was found to give good predictions of the deforming shapes of both the beams and the plates. No detailed analysis of the fluid was carried out, but two types of approximation to the effect of the fluid were investigated. Firstly a time varying pressure pulse (based on the measured pressure pulses) or a pressure loading derived from the beam velocity (acoustic and incompressible fluid approximations) were used to represent the loading on the beam due to the fluid. Secondly a mass was added to the plate mass to represent the inertia of the fluid. The applied pressure loading worked to a limited extent for the beams but no one pressure pulse shape gave good results for both end fixities. The best results for the plate problem were achieved with the added mass approach. Finally a number of areas of experimental and computational work are identified, which it is felt would benefit from further study.

No description available.

Early studies of mid-ocean ridges suggest a fundamental difference between crustal accretionary processes at slow- and fast-spreading ridges. Accretion, and the supply of melt to the crust itself, is thought to be highly episodic at slow-spreading ridges but steady-state at fast-spreading ridges. However, recent studies are beginning to question this model, with evidence for the temporal variation in crustal accretionary processes at all spreading rates emerging. This study provides evidence from bathymetry, TOBI sidescan, gravity and magnetic data, collected during different cruises to the Reykjanes Ridge, for the temporal nature of crustal accretion and its relationship to segmentation. Interpretation of TOBI images indicates that individual adjacent axial volcanic ridges (AVRs) vary in relative age, suggesting that they are at various stages of an evolutionary lifecycle, with episodic cycles of magmatic and tectonic activity. However, prior to investigating the possible effects of tectonomagmatic cycles on the crustal structure of AVRs, the effect of the Iceland hotspot on the ridge is examined. The along-axis free-air gravity anomaly is forward modelled in 2-D, revealing an along-axis increase in crustal thickness towards Iceland from 7.5 km to 10.5 km and a decrease in mantle densities from 3.30 to 3.23 g cm"^ between 57 30'N and 62 N. Calculation of the residual mantle Bouguer Anomaly (RMBA) and inversion of magnetic anomaly data, reveal intermediate-wavelength fluctuations in RMBA amplitude and magnetization intensity respectively that are attributed to hotspot pulses, with 59 N marking the southern most extent of the most recent pulse. Removal of the hotspot effect on the gravity data reveals short-wavelength RMBA lows, associated with individual AVRs, superimposed on a broad ridge-trending low. Along-AVR-axis gravity modelling shows that a number of these RMBA lows can be explained by a 200-800 m thickening of the crust and/or by the presence of 5-20% partial melt in the mid-crust. A correlation between relative AVR age and crustal structure is established, with longer, more mature AVRs having a thicker crust and shorter, younger AVRs having more partial melt in the mid-crust. Short-wavelength magnetization intensity highs, associated with younger AVRs, corroborate the TOBI age interpretations. Local spreading rate calculations reveal that total spreading rates for younger AVRs are up to 20% faster than for older AVRs over the last 1.42 Ma. On the basis of these results a model for the cyclicity of crustal accretion is presented, whereby far-field tectonic stresses result in spreading-orthogonal brittle deformation of the crust in the neovolcanic zone, and 3-D mantle upwelling, with a wavelength of -70 km, follows the ridge trend and results in second order segments that comprise ~5 AVRs. It is proposed that along-axis migration of melt within such a segment results in the observed variations in AVR age, length, RMBA amplitude, magnetization intensity and local spreading rate. The proposed model has implications for the temporal variability of crustal accretion at all spreading rates.

Detailed mapping of the rocks to the north and south of Plymouth reveals a sedimentary sequence deformed by a series of folds and thrusts. Two structural zones exist each with a different style of deformation. In the Lower to Upper Devonian rocks of the southern zone, slip vectors, vergence and facing of D 1 folds indicate that the transport direction is to the north west. The northern zone, comprising Upper Devonian and lower Carboniferous strata, extends into central Devon and east Cornw~ll and the geometry and facing of the early folds in these rocks indicate a transport direction to the south or south east. Dl folds generally verge north but are downward facing towards the south. The two structural zones confront each other at an E-W trending line which passes through Cargreen to the north of Plymouth. The confrontation is interpreted as a northerly dipping backthrust produced by underthrusting of the Carboniferous foreland basin flysch deposits which become inverted and backthrust towards the south. The above sequence of events is dependent on a thin-skinned tectonic model and can be incorporated into the well established Early Carboniferous plate tectonic setting. Parameters indicating strike slip movement can also be incorporated within the envisaged thrust regime. These are thought to have been generated by differential movement related to the shape of the Variscan Front. The oblique trend of the Variscan Front to the regional transport direction observed in Southern Ireland, Wales and England, where it trends WNWESE, is thought to be a function of lateral buttressing against the Irish and LondonlBrabant Massifs during NW transport of thrust sheets. Re-mapping in the Plymouth area has also led to modifications of the Devonian stratigraphy and sedimentology of the Lower Devonian. The previously named Dartmouth Beds/Slates have been re-named the Dartmouth Group and comprise the Renney Rocks, Wembury, Yealm and Warren Formations. The latter pass upwards, by interdigitation, into the Meadfoot Group which in turn consists of the Bovisand and Staddon Grit Formations. Overlying the Meadfoot Group is the Plymouth Group which is divided into the Jennycliff Slate Formation, Plymouth Limestone Formation, Compton Slate Formation and the Saltram Slate Formation. The division of the previously named Plympton Formation into the two latter formations has allowed more control on structural mapping in the area north of Plymouth. The recognition of repeated stratigraphy and its further subdivision indicates that, due to thrusting, the sequences are much thinner than previously thought. The sedimentological character of the Dartmouth Group implies deposition in an alluvial setting and sub-environments include channels, sheetflow, overbank flow and lake deposition. Debris flows indicate that the area was periodically unstable. It is envisaged that deposition took place on a wet alluvial plain with rare drying out. The deposits probably represent a distal setting to the more proximal Old Red Sandstone alluvial deposits of South Wales. Higher up the sequence the Meadfoot Group records a major marine transgression across the area (Bovisand Formation) with a minor regressive pulse represented by the Staddon Grit Formation. The boundary conditions of these two formations has been examined and the sedimentology of this part of the sequence indicates the presence of a series of offshore bar forms. They are thought to represent mouth bar sequences related to the overlying deltaic sequence of the Staddon Grit Formation. Analysis of the onshore New Red Sandstone indicates the presence of a topographic high in the Start area. This local palaeogeographic detail can be related to the regional offshore Permian Basin form.

A thesis submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Philosophy. Johannesburg, 2014. / This investigation involves a survey of the fine structure phenomenon of the Isovector Giant Dipole Resonance (IVGDR) over a wide mass range of nuclei, from 27Al, 40Ca, 56Fe, 58Ni to 208Pb, using inelastic proton scattering at 200 MeV. Proton detection is accomplished using the recently commissioned zero-degree facility of the K600 magnetic spectrometer at iThemba LABS. Inelastic proton experiments at zero degrees are very selective to excitations with low angular momentum transfer, and therefore ideal for studies of the IVGDR. This is because such experiments simplify the analysis of the many contributions to the spectra due to the complex nature of the nuclear interaction. The ability to make precise measurements of the properties of the IVGDR demonstrated by this work opens up new challenges to both experimental and theoretical work in nuclear structure. This is a survey of the (p,p′) reaction at zero degrees as a probe to study properties of the GDR and also the low energy E1 strength with high energy-resolution. Such a data base will provide more stringent tests of nuclear theory and the progress is seen in the details obtained. These tests can only be described by microscopic models including complex degrees-of-freedom. This should lead to new insights into the underlying interactions responsible for the nature of the electric dipole strength in nuclei. In the present study, double-differential cross-sections were converted to equivalent photo-absorption cross-sections and their results compared to previously published photo-absorption data. An excellent correspondence in the excitation-energy region of the Giant Dipole Resonance (GDR) was noticed between the two data sets. The fine structure observed can be described using characteristic energy scales, arising mainly from Landau damping (even though the spreading width may also play a role). The extraction of these characteristic energy scales which are a signature for the decay process was achieved through the use of wavelet analysis. Furthermore, thanks to the recent advances in computational power and techniques, microscopic shell model-based calculations lead to new insights into the underlying properties of the nuclear interaction which are responsible for the collective behaviour evidenced by the existence and properties of the IVGDR. In addition to the extraction of characteristic energy scales, this study also provides level densities of J = 1− states. In order to extract nuclear level densities, there is need to eliminate instrumental background and other contributions to the spectra from (p,p′) scattering using the model-independent Discrete Wavelet Transform (DWT) method. Level densities of J = 1− states are determined using the fluctuation analysis technique and comparisons are made with the phenomenological Back Shifted Fermi Gas (BSFG) model predictions, calculations of the Hartree Fock- Bogoluibov (HFB) microscopic model and Hartree Fock-Bardeen-Cooper-Schrieffer (HF-BCS) predictions. Finally, this survey will simultaneously provide bench-marks on the capabilities and limitations of the new zero-degree facility important for planning of the future experimental work.