Onset of turbulence in a regular porous medium : An experimental study

Peer reviewedPublisher PD

On the role of infiltration and exfiltration in swash zone boundary layer dynamics

Funded by Mexican National Council of Science and Technology (CoNACyT) . Grant Number: 490080 Fulbright-Garcia Robles grant Instituto de Ingeniería UNAM International Collaborative Research project University of Delaware DGAPA UNAM National Science Foundation . Grant Numbers: OCE-0845004 , OCE-1332703 University of Delaware UK Engineering and Physical Sciences Research Council ‘Flood MEMORY: Multi-Event Modelling Of Risk & recoverY’ . Grant Number: EP EP/K013513/1Peer reviewedPublisher PD

Investigations on the Oligomerization of Pyolysin, a Cholesterol-Dependent Cytolysin

The bacterial toxin pyolysin (PLO) is a member of the family of Cholesterol-Dependent Cytolysins, which form large, oligomeric pores in cholesterol-containing membranes. The general CDC structure has an elongated shape and consists of four domains rich in β-sheet structure. Upon binding to a membrane, molecules diffuse laterally on the surface and oligomerize to form a pre-pore complex, then insert into the membrane yielding pores of unusually large size, approximately 30 nm in diameter. In this work, the oligomerization properties of PLO were investigated. In particular, the role of the C-terminal domain in the oligomerization process, the effects of a disulphide-tethered mutant on the activity of the wild type toxin, and the pore-forming ability of oligomers pre-formed in solution were characterized. Chapter 2 characterizes the functional properties of a recombinant fragment that corresponds to the C-terminal domain 4 of PLO. It is shown that this fragment can form hybrid oligomers with intact PLO toxin molecules, and is also capable of self-oligomerization. The fragment has no haemolytic activity of its own; nevertheless, it can to some degree increase the haemolytic activity of the wild type toxin. In addition, in a mixture domain 4 and wild type interact in such a way as to form unusual shapes on cholesterol crystals that have not been previously observed. Chapter 3 describes the effects of a disulphide bond linking domain 2 to a membrane-inserting region of domain 3 on the oligomerization process. The disulphide mutant was not able to oligomerize on its own, and when combined with active PLO toxin, the haemolytic activity of wild type was significantly inhibited. Also, the combination of the disulphide-tethered mutant with intact toxin resulted in the formation of hybrid oligomers. This, in turn, caused an increase in incomplete ring formations on cholesterol surfaces which correlate to a reduction in functional pore size, suggesting that insertion of subunits is partially cooperative. The results of the investigation of the pore-forming ability of solution-derived oligomers (SDO) are described in Chapter 4. Here, the fluorescence emission of an environmentally-sensitive probe on the SDO after membrane insertion was a fraction of that observed with the monomeric control, which was supported by hydrophobic quenching analyses. This suggests that the formation of SDO may block necessary conformational changes in the intact toxin to allow membrane insertion

Three-dimensional in situ observations of compressive damage mechanisms in syntactic foam using X-ray microcomputed tomography

Royal Society Grant number RG140680 Lloyd's Register Foundation (GB) Oil and Gas Academy of Scotland Open access via Springer Compact AgreementPeer reviewedPublisher PD

Experimental study of bore-driven swash hydrodynamics on impermeable rough slopes

Copyright 2012 Elsevier B.V., All rights reserved.Peer reviewedPublisher PD

Turbulence structure of open channel flows over permeable and impermeable beds : A comparative study

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Bed-load effects on hydrodynamics of rough-bed open-channel flows

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The structure of gravel-bed flow with intermediate submergence: a laboratory study

The paper reports an experimental study of the flow structure over an immobile gravel bed in open channel at intermediate submergence, with particular focus on the near-bed region. The experiments consisted of velocity measurements using three-component (stereoscopic) Particle Image Velocimetry (PIV) in near-bed horizontal plane and two-component PIV in three vertical planes that covered three distinctly different hydraulic scenarios where the ratio of flow depth to roughness height (i.e., relative submergence) changes from 7.5 to 10.8. Detailed velocity measurements were supplemented with fine-scale bed elevation data obtained with a laser scanner. The data revealed longitudinal low-momentum and high-momentum "strips'' in the time-averaged velocity field, likely induced by secondary currents. This depth-scale pattern was superimposed with particle-scale patches of flow heterogeneity induced by gravel particle protrusions. A similar picture emerged when considering second-order velocity moments. The interaction between the flow field and gravel-bed protrusions is assessed using cross correlations of velocity components and bed elevations in a horizontal plane just above gravel particle crests. The cross correlations suggest that upward and downward fluid motions are mainly associated with upstream-facing and lee sides of particles, respectively. Results also show that the relative submergence affects the turbulence intensity profiles for vertical velocity over the whole flow depth, while only a weak effect, limited to the near-bed region, is noticed for streamwise velocity component. The approximation of mean velocity profiles with a logarithmic formula reveals that log-profile parameters depend on relative submergence, highlighting inapplicability of a conventional "universal'' logarithmic law for gravel-bed flows with intermediate submergence

Temporal acceleration of a turbulent channel flow

We report new laboratory experiments of a flow accelerating from an initially turbulent state following the opening of a valve, together with large eddy simulations of the experiments and extended Stokes first problem solutions for the early stages of the flow. The results show that the transient flow closely resembles an accelerating laminar flow superimposed on the original steady turbulent flow. The primary consequence of the acceleration is the temporal growth of a boundary layer from the wall, gradually leading to a strong instability causing transition. This extends the findings of previous direct numerical simulations of transient flow following a near-step increase in flow rate. In this interpretation, the initial turbulence is not the primary characteristic of the resulting transient flow, but can be regarded as noise, the evolution of which is strongly influenced by the development of the boundary layer. We observe the spontaneous appearance of turbulent spots and discontinuities in the velocity signals in time and space, revealing rich detail of the transition process, including a striking contrast between streamwise and wall-normal fluctuating velocities