Topological side-chain classification of beta-turns: Ideal motifs for peptidomimetic development

beta-turns are important topological motifs for biological recognition of proteins and peptides. Organic molecules that sample the side chain positions of beta-turns have shown broad binding capacity to multiple different receptors, for example benzodiazepines. beta-turns have traditionally been classified into various types based on the backbone dihedral angles (phi 2, psi 2, phi 3 and psi 3). Indeed, 57-68% of beta-turns are currently classified into 8 different backbone families (Type I, Type II, Type I', Type II', Type VIII, Type VIa1, Type VIa2 and Type VIb and Type IV which represents unclassified beta-turns). Although this classification of beta-turns has been useful, the resulting beta-turn types are not ideal for the design of beta-turn mimetics as they do not reflect topological features of the recognition elements, the side chains. To overcome this, we have extracted beta-turns from a data set of non-homologous and high-resolution protein crystal structures. The side chain positions, as defined by C-alpha-C-beta vectors, of these turns have been clustered using the kth nearest neighbor clustering and filtered nearest centroid sorting algorithms. Nine clusters were obtained that cluster 90% of the data, and the average intra-cluster RMSD of the four C-alpha-C-beta vectors is 0.36. The nine clusters therefore represent the topology of the side chain scaffold architecture of the vast majority of beta-turns. The mean structures of the nine clusters are useful for the development of beta-turn mimetics and as biological descriptors for focusing combinatorial chemistry towards biologically relevant topological space.

Structural and functional characterization of the conserved salt bridge in mammalian Paneth cell alpha-defensins - Solution structures of mouse cryptdin-4 AND (E15D)-cryptdin-4

Defensins are mediators of mammalian innate immunity, and knowledge of their structure-function relationships is essential for understanding their mechanisms of action. We report here the NMR solution structures of the mouse Paneth cell α-defensin cryptdin-4 (Crp4) and a mutant (E15D)-Crp4 peptide, in which a conserved Glu15 residue was replaced by Asp. Structural analysis of the two peptides confirms the involvement of this Glu in a conserved salt bridge that is removed in the mutant because of the shortened side chain. Despite disruption of this structural feature, the peptide variant retains a well defined native fold because of a rearrangement of side chains, which result in compensating favorable interactions. Furthermore, salt bridge-deficient Crp4 mutants were tested for bactericidal effects and resistance to proteolytic degradation, and all of the variants had similar bactericidal activities and stability to proteolysis. These findings support the conclusion that the function of the conserved salt bridge in Crp4 is not linked to bactericidal activity or proteolytic stability of the mature peptide.

Trainer talk:structures of interaction in teacher training classrooms

The subject of this research is interaction and language use in an institutional context, the teacher training classroom. Trainer talk is an interactional accomplishment and the research question is: what structures of talk-in-interaction characterise trainer talk in this institutional setting? While there has been research into other kinds of classroom and into other kinds of institutional talk, this study is the first on trainer discourse. The study takes a Conversation Analysis approach to studying institutional interaction and aims to identify the main structures of sequential organization that characterize teacher trainer talk as well as the tasks and identities that are accomplished in it. The research identifies three main interactional contexts in which trainer talk is done: expository, exploratory and experiential. It describes the main characteristics of each and how they relate to each other. Expository sequences are the predominant interactional contexts for trainer talk. But the research findings show that these contexts are flexible and open to the embedding of the other two contexts. All three contexts contribute to the main institutional goal of teaching teachers how to teach. Trainer identity is related to the different sequential contexts. Three main forms of identity in interaction are evidenced in the interactional contexts: the trainer as trainer, the trainer as teacher and the trainer as colleague. Each of them play an important role in teacher trainer pedagogy. The main features of trainer talk as a form of institutional talk are characterised by the following interactional properties: 1. Professional discourse is both the vehicle and object of instruction - the articulation of reflection on experience. 2. There is a reflexive relationship between pedagogy and interaction. 3. The professional discourse that is produced by trainees is not evaluated by trainers but, rather, reformulated to give it relevant precision in terms of accuracy and appropriacy.

Effects of vehicle speed in structural health monitoring from operational conditions of bridges

The effects of vehicle speed for Structural Health Monitoring (SHM) of bridges under operational conditions are studied in this paper. The moving vehicle is modelled as a single degree oscillator traversing a damaged beam at a constant speed. The bridge is modelled as simply supported Euler-Bernoulli beam with a breathing crack. The breathing crack is treated as a nonlinear system with bilinear stiffness characteristics related to the opening and closing of crack. The unevenness of the bridge deck is modelled using road classification according to ISO 8606:1995(E). The stochastic description of the unevenness of the road surface is used as an aid to monitor the health of the structure in its operational condition. Numerical simulations are conducted considering the effects of changing vehicle speed with regards to cumulant based statistical damage detection parameters. The detection and calibration of damage at different levels is based on an algorithm dependent on responses of the damaged beam due to passages of the load. Possibilities of damage detection and calibration under benchmarked and non-benchmarked cases are considered. Sensitivity of calibration values is studied. The findings of this paper are important for establishing the expectations from different vehicle speeds on a bridge for damage detection purposes using bridge-vehicle interaction where the bridge does not need to be closed for monitoring. The identification of bunching of these speed ranges provides guidelines for using the methodology developed in the paper.

Gravity collapse structures in the Central Precordillera fold-andthrust belt, Argentina

Several landforms found in the fold-and-thrust belt area of Central Precordillera, Pre-Andes of Argentina, which were often associated with tectonic efforts, are in fact related to non-tectonic processes or gravitational superficial structures. These second-order structures, interpreted as gravitational collapse structures, have developed in the western flank of sierras de La Dehesa and Talacasto. These include rock-slides, rock falls, wrinkle folds, slip sheets and flaps, among others; which together constitute a monoclinal fold dipping between 30º and 60º to the west. Gravity collapse structures are parallel to the regional strike of the Sierra de la Dehesa and are placed in Ordovician limestones and dolomites. Their sloping towards the west, the presence of bed planes, fractures and joints; and the lithology (limestone interbedded with incompetent argillaceous banks) would have favored their occurrence. Movement of the detached structures has been controlled by lithology characteristics, as well as by bedding and joints. Detachment and initial transport of gravity collapse structures and rockslides in the western flank of the Sierra de la Dehesa were tightly controlled by three structural elements: 1) sliding surfaces developed on parallel bedded strata when dipping >30° in the slope direction; 2) Joint’s sets constitute lateral and transverse traction cracks which release extensional stresses and 3) Discontinuities fragmenting sliding surfaces.  Some other factors that could be characterized as local (lithology, structure and topography) and as regional (high seismic activity and possibly wetter conditions during the postglacial period) were determining in favoring the steady loss of the western mountain side in the easternmost foothills of Central Precordillera.

Shock Train/Boundary-Layer Interaction in Rectangular Scramjet Isolators

Numerous studies of the dual-mode scramjet isolator, a critical component in preventing inlet unstart and/or vehicle loss by containing a collection of flow disturbances called a shock train, have been performed since the dual-mode propulsion cycle was introduced in the 1960s. Low momentum corner flow and other three-dimensional effects inherent to rectangular isolators have, however, been largely ignored in experimental studies of the boundary layer separation driven isolator shock train dynamics. Furthermore, the use of two dimensional diagnostic techniques in past works, be it single-perspective line-of-sight schlieren/shadowgraphy or single axis wall pressure measurements, have been unable to resolve the three-dimensional flow features inside the rectangular isolator. These flow characteristics need to be thoroughly understood if robust dual-mode scramjet designs are to be fielded. The work presented in this thesis is focused on experimentally analyzing shock train/boundary layer interactions from multiple perspectives in aspect ratio 1.0, 3.0, and 6.0 rectangular isolators with inflow Mach numbers ranging from 2.4 to 2.7. Secondary steady-state Computational Fluid Dynamics studies are performed to compare to the experimental results and to provide additional perspectives of the flow field. Specific issues that remain unresolved after decades of isolator shock train studies that are addressed in this work include the three-dimensional formation of the isolator shock train front, the spatial and temporal low momentum corner flow separation scales, the transient behavior of shock train/boundary layer interaction at specific coordinates along the isolator's lateral axis, and effects of the rectangular geometry on semi-empirical relations for shock train length prediction. A novel multiplane shadowgraph technique is developed to resolve the structure of the shock train along both the minor and major duct axis simultaneously. It is shown that the shock train front is of a hybrid oblique/normal nature. Initial low momentum corner flow separation spawns the formation of oblique shock planes which interact and proceed toward the center flow region, becoming more normal in the process. The hybrid structure becomes more two-dimensional as aspect ratio is increased but corner flow separation precedes center flow separation on the order of 1 duct height for all aspect ratios considered. Additional instantaneous oil flow surface visualization shows the symmetry of the three-dimensional shock train front around the lower wall centerline. Quantitative synthetic schlieren visualization shows the density gradient magnitude approximately double between the corner oblique and center flow normal structures. Fast response pressure measurements acquired near the corner region of the duct show preliminary separation in the outer regions preceding centerline separation on the order of 2 seconds. Non-intrusive Focusing Schlieren Deflectometry Velocimeter measurements reveal that both shock train oscillation frequency and velocity component decrease as measurements are taken away from centerline and towards the side-wall region, along with confirming the more two dimensional shock train front approximation for higher aspect ratios. An updated modification to Waltrup \& Billig's original semi-empirical shock train length relation for circular ducts based on centerline pressure measurements is introduced to account for rectangular isolator aspect ratio, upstream corner separation length scale, and major- and minor-axis boundary layer momentum thickness asymmetry. The latter is derived both experimentally and computationally and it is shown that the major-axis (side-wall) boundary layer has lower momentum thickness compared to the minor-axis (nozzle bounded) boundary layer, making it more separable. Furthermore, it is shown that the updated correlation drastically improves shock train length prediction capabilities in higher aspect ratio isolators. This thesis suggests that performance analysis of rectangular confined supersonic flow fields can no longer be based on observations and measurements obtained along a single axis alone. Knowledge gained by the work performed in this study will allow for the development of more robust shock train leading edge detection techniques and isolator designs which can greatly mitigate the risk of inlet unstart and/or vehicle loss in flight.

DESIGN, FABRICATION, AND PERFORMANCE CHARACTERIZATION OF MULTIFUNCTIONAL STRUCTURES TO HARVEST SOLAR ENERGY FOR FLAPPING WING AERIAL VEHICLES

Flapping Wing Aerial Vehicles (FWAVs) have the capability to combine the benefits of both fixed wing vehicles and rotary vehicles. However, flight time is limited due to limited on-board energy storage capacity. For most Unmanned Aerial Vehicle (UAV) operators, frequent recharging of the batteries is not ideal due to lack of nearby electrical outlets. This imposes serious limitations on FWAV flights. The approach taken to extend the flight time of UAVs was to integrate photovoltaic solar cells onto different structures of the vehicle to harvest and use energy from the sun. Integration of the solar cells can greatly improve the energy capacity of an UAV; however, this integration does effect the performance of the UAV and especially FWAVs. The integration of solar cells affects the ability of the vehicle to produce the aerodynamic forces necessary to maintain flight. This PhD dissertation characterizes the effects of solar cell integration on the performance of a FWAV. Robo Raven, a recently developed FWAV, is used as the platform for this work. An additive manufacturing technique was developed to integrate photovoltaic solar cells into the wing and tail structures of the vehicle. An approach to characterizing the effects of solar cell integration to the wings, tail, and body of the UAV is also described. This approach includes measurement of aerodynamic forces generated by the vehicle and measurements of the wing shape during the flapping cycle using Digital Image Correlation. Various changes to wing, body, and tail design are investigated and changes in performance for each design are measured. The electrical performance from the solar cells is also characterized. A new multifunctional performance model was formulated that describes how integration of solar cells influences the flight performance. Aerodynamic models were developed to describe effects of solar cell integration force production and performance of the FWAV. Thus, performance changes can be predicted depending on changes in design. Sensing capabilities of the solar cells were also discovered and correlated to the deformation of the wing. This demonstrated that the solar cells were capable of: (1) Lightweight and flexible structure to generate aerodynamic forces, (2) Energy harvesting to extend operational time and autonomy, (3) Sensing of an aerodynamic force associated with wing deformation. Finally, different flexible photovoltaic materials with higher efficiencies are investigated, which enable the multifunctional wings to provide enough solar power to keep the FWAV aloft without batteries as long as there is enough sunlight to power the vehicle.

High performance terahertz resonant tunnelling diode sources and broadband antenna for air-side radiation

Resonant tunnelling diode (RTD) is known to be the fastest electronics device that can be fabricated in compact form and operate at room temperature with potential oscillation frequency up to 2.5 THz. The RTD device consists of a narrow band gap quantum well layer sandwiched between two thin wide band gap barriers layers. It exhibits negative differential resistance (NDR) region in its current-voltage (I-V) characteristics which is utilised in making oscillators. Up to date, the main challenge is producing high output power at high frequencies in particular. Although oscillation frequencies of ~ 2 THz have been already reported, the output power is in the range of micro-Watts. This thesis describes the systematic work on the design, fabrication, and characterisation of RTD-based oscillators in microwave/millimetre-wave monolithic integrated circuits (MMIC) form that can produce high output power and high oscillation frequency at the same time. Different MMIC RTD oscillator topologies were designed, fabricated, and characterised in this project which include: single RTD oscillator which employs one RTD device, double RTDs oscillator which employs two RTD devices connected in parallel, and coupled RTD oscillators which combine the powers of two oscillators over a single load, based on mutual coupling and which can employ up to four RTD devices. All oscillators employed relatively large size RTD devices for high power operation. The main challenge was to realise high oscillation frequency (~ 300 GHz) in MMIC form with the employed large sized RTD devices. To achieve this aim, proper designs of passive structures that can provide small values of resonating inductances were essential. These resonating inductance structures included shorted coplanar wave guide (CPW) and shorted microstrip transmission lines of low characteristics impedances Zo. Shorted transmission line of lower Zo has lower inductance per unit length. Thus, the geometrical dimensions would be relatively large and facilitate fabrication by low cost photolithography. A series of oscillators with oscillation frequencies in the J-band (220 – 325 GHz) range and output powers from 0.2 – 1.1 mW have been achieved in this project, and all were fabricated using photolithography. Theoretical estimation showed that higher oscillation frequencies (> 1 THz) can be achieved with the proposed MMIC RTD oscillators design in this project using photolithography with expected high power operation. Besides MMIC RTD oscillators, reported planar antennas for RTD-based oscillators were critically reviewed and the main challenges in designing high performance integrated antennas on large dielectric constant substrates are discussed in this thesis. A novel antenna was designed, simulated, fabricated, and characterised in this project. It was a bow-tie antenna with a tuning stub that has very wide bandwidth across the J-band. The antenna was diced and mounted on a reflector ground plane to alleviate the effect of the large dielectric constant substrate (InP) and radiates upwards to the air-side direction. The antenna was also investigated for integration with the all types of oscillators realised in this project. One port and two port antennas were designed, simulated, fabricated, and characterised and showed the suitability of integration with the single/double oscillator layout and the coupled oscillator layout, respectively.

Analyzing downloaded data from road side units

En el contexto de las redes vehiculares, analizamos una aplicación de descarga de mapas, donde cada vehículo descarga datos de mapas relevantes según su posición. Entre las estrategias propuestas está la de utilizar las redes con infraestructura (I2V) además de las redes vehículo a vehículo (V2V). En este trabajo comparamos dos métodos de fragmentación de archivos, para el segmento I2V; los métodos son Random Sort Strategy (RSS) y Network Coding (NC). Encontramos que: cuando se utiliza NC la distribución de los diferentes fragmentos recibidos es independiente del tamaño del archivo. Cuando se utiliza RSS, la media y la desviación estándar dependen del tamaño del archivo. Estos resultados serán utilizados para el análisis del segmento V2V de la red.

Fire analysis of car park building structures

The thermal loading of an open car park building structure is going to be analysed, based on different fire scenarios that depend on the type of vehicle (different heat release rate). The compartment is going to be fixed and the thermal effect on beams is going to be analysed, depending on the vehicle position. The result of simple calculation method will be used to determine several temperature-time curves. The simple calculation method (Hasemi method) is also to be compared with the calculations of the Elefir-EN calculation program to analyse the thermal effect of the localized fire on beams.