Sensitivity of a hydraulic model to changes in channel erosion during extreme flooding

Recent research into flood modelling has primarily concentrated on the simulation of inundation flow without considering the influences of channel morphology. River channels are often represented by a simplified geometry that is implicitly assumed to remain unchanged during flood simulations. However, field evidence demonstrates that significant morphological changes can occur during floods to mobilise the boundary sediments. Despite this, the effect of channel morphology on model results has been largely unexplored. To address this issue, the impact of channel cross-section geometry and channel long-profile variability on flood dynamics is examined using an ensemble of a 1D-2D hydraulic model (LISFLOOD-FP) of the 1:2102 year recurrence interval floods in Cockermouth, UK, within an uncertainty framework. A series of hypothetical scenarios of channel morphology were constructed based on a simple velocity based model of critical entrainment. A Monte-Carlo simulation framework was used to quantify the effects of channel morphology together with variations in the channel and floodplain roughness coefficients, grain size characteristics, and critical shear stress on measures of flood inundation. The results showed that the bed elevation modifications generated by the simplistic equations reflected a good approximation of the observed patterns of spatial erosion despite its overestimation of erosion depths. The effect of uncertainty on channel long-profile variability only affected the local flood dynamics and did not significantly affect the friction sensitivity and flood inundation mapping. The results imply that hydraulic models generally do not need to account for within event morphodynamic changes of the type and magnitude modelled, as these have a negligible impact that is smaller than other uncertainties, e.g. boundary conditions. Instead morphodynamic change needs to happen over a series of events to become large enough to change the hydrodynamics of floods in supply limited gravel-bed rivers like the one used in this research.

Study of plasma immersion ion implantation into silicon substrate using magnetic mirror geometry

The effect of magnetic field enhanced plasma immersion ion implantation (PIII) in silicon substrate has been investigated at low and high pulsed bias voltages. The magnetic field in magnetic bottle configuration was generated by two magnetic coils installed outside the vacuum chamber. The presence of both, electric and magnetic field in PIII creates a system of crossed E x B fields, promoting plasma rotation around the target. The magnetized electrons drifting in crossed E x B fields provide electron-neutral collision. Consequently, the efficient background gas ionization augments the plasma density around the target where a magnetic confinement is achieved. As a result, the ion current density increases, promoting changes in the samples surface properties, especially in the surface roughness and wettability and also an increase of implantation dose and depth. (C) 2012 Elsevier B. V. All rights reserved.

Modular Hyperthermostable Bacterial Endo-beta-1, 4-Mannanase: Molecular Shape, Flexibility and Temperature-Dependent Conformational Changes

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Geometry effects on the electronic properties of multi-open dots structures

In this paper we show that the electronic properties of multi-open dots structures are strongly modified by even smalt changes in their geometries. Our discussion of these effects is done in terms of the interaction among localized states (dot-like) and extended states (channel-like), from which a Fano resonance situation arises.

The Oligocene-Neogene deep-sea Columbia Channel system in the South Brazilian Basin: Seismic stratigraphy and environmental changes

The Columbia Channel (CCS) system is a depositional system located in the South Brazilian Basin, south of the Vitoria-Trindade volcanic chain. It lies in a WNW-ESE direction on the continental rise and abyssal plain, at a depth of between 4200 and 5200 m. It is formed by two depocenters elongated respectively south and north of the channel that show different sediment patterns. The area is swept by a deep western boundary current formed by AABW. The system has been previously interpreted has a mixed turbidite-contourite system. More detailed study of seismic data permits a more precise definition of the modern channel morphology, the system stratigraphy as well as the sedimentary processes and control. The modern CCS presents active erosion and/or transport along the channel. The ancient Oligo-Neogene system overlies a ""upper Cretaceous-Paleogene"" sedimentary substratum (Unit U1) bounded at the top by a major erosive ""late Eocene-early Oligocene"" discordance (D2). This ancient system is subdivided into 2 seismic units (U2 and U3). The thick basal U2 unit constitutes the larger part of the system. It consists of three subunits bounded by unconformities: D3 (""Oligocene-Miocene boundary""), D4 (""late Miocene"") and D5 (""late Pliocene""). The subunits have a fairly tabular geometry in the shallow NW depocenter associated with predominant turbidite deposits. They present a mounded shape in the deep NE depocenter, and are interpreted as forming a contourite drift. South of the channel, the deposits are interpreted as a contourite sheet drift. The surficial U3 unit forms a thin carpet of deposits. The beginning of the channel occurs at the end of U1 and during the formation of D2. Its location seems to have been determined by active faults. The channel has been active throughout the late Oligocene and Neogene and its depth increased continuously as a consequence of erosion of the channel floor and deposit aggradation along its margins. Such a mixed turbidite-contourite system (or fan drift) is characterized by frequent, rapid lateral facies variations and by unconformities that cross the whole system and are associated with increased AABW circulation. (C) 2009 Elsevier B.V. All rights reserved.

Fluoropolymer piezoelectrets with tubular channels: resonance behavior controlled by channel geometry

Ferro- or piezoelectrets are dielectric materials with two elastically very different macroscopic phases and electrically charged interfaces between them. One of the newer piezoelectret variants is a system of two fluoroethylenepropylene (FEP) films that are first laminated around a polytetrafluoroethylene (PTFE) template. Then, by removing the PTFE template, a two-layer FEP structure with open tubular channels is obtained. After electrical charging, the channels form easily deformable macroscopic electric dipoles whose changes under mechanical or electrical stress lead to significant direct or inverse piezoelectricity, respectively. Here, different PTFE templates are employed to generate channel geometries that vary in height or width. It is shown that the control of the channel geometry allows a direct adjustment of the resonance frequencies in the tubular-channel piezoelectrets. By combining several different channel widths in a single ferroelectret, it is possible to obtain multiple resonance peaks that may lead to a rather flat frequency-response region of the transducer material. A phenomenological relation between the resonance frequency and the geometrical parameters of a tubular channel is also presented. This relation may help to design piezoelectrets with a specific frequency response.

3-D geometry reconstruction using a color image stereo pair and partial differential equations

[EN] In this work, we present a new model for a dense disparity estimation and the 3-D geometry reconstruction using a color image stereo pair. First, we present a brief introduction to the 3-D Geometry of a camera system. Next, we propose a new model for the disparity estimation based on an energy functional. We look for the local minima of the energy using the associate Euler-Langrage partial differential equations. This model is a generalization to color image of the model developed in, with some changes in the strategy to avoid the irrelevant local minima. We present some numerical experiences of 3-D reconstruction, using this method some real stereo pairs.

Numerical simulations of magma chamber dynamics at Campi Flegrei, and associated seismicity, deformation and gravity changes

Understanding the complex relationships between quantities measured by volcanic monitoring network and shallow magma processes is a crucial headway for the comprehension of volcanic processes and a more realistic evaluation of the associated hazard. This question is very relevant at Campi Flegrei, a volcanic quiescent caldera immediately north-west of Napoli (Italy). The system activity shows a high fumarole release and periodic ground slow movement (bradyseism) with high seismicity. This activity, with the high people density and the presence of military and industrial buildings, makes Campi Flegrei one of the areas with higher volcanic hazard in the world. In such a context my thesis has been focused on magma dynamics due to the refilling of shallow magma chambers, and on the geophysical signals detectable by seismic, deformative and gravimetric monitoring networks that are associated with this phenomenologies. Indeed, the refilling of magma chambers is a process frequently occurring just before a volcanic eruption; therefore, the faculty of identifying this dynamics by means of recorded signal analysis is important to evaluate the short term volcanic hazard. The space-time evolution of dynamics due to injection of new magma in the magma chamber has been studied performing numerical simulations with, and implementing additional features in, the code GALES (Longo et al., 2006), recently developed and still on the upgrade at the Istituto Nazionale di Geofisica e Vulcanologia in Pisa (Italy). GALES is a finite element code based on a physico-mathematical two dimensional, transient model able to treat fluids as multiphase homogeneous mixtures, compressible to incompressible. The fundamental equations of mass, momentum and energy balance are discretised both in time and space using the Galerkin Least-Squares and discontinuity-capturing stabilisation technique. The physical properties of the mixture are computed as a function of local conditions of magma composition, pressure and temperature.The model features enable to study a broad range of phenomenologies characterizing pre and sin-eruptive magma dynamics in a wide domain from the volcanic crater to deep magma feeding zones. The study of displacement field associated with the simulated fluid dynamics has been carried out with a numerical code developed by the Geophysical group at the University College Dublin (O’Brien and Bean, 2004b), with whom we started a very profitable collaboration. In this code, the seismic wave propagation in heterogeneous media with free surface (e.g. the Earth’s surface) is simulated using a discrete elastic lattice where particle interactions are controlled by the Hooke’s law. This method allows to consider medium heterogeneities and complex topography. The initial and boundary conditions for the simulations have been defined within a coordinate project (INGV-DPC 2004-06 V3_2 “Research on active volcanoes, precursors, scenarios, hazard and risk - Campi Flegrei”), to which this thesis contributes, and many researchers experienced on Campi Flegrei in volcanological, seismic, petrological, geochemical fields, etc. collaborate. Numerical simulations of magma and rock dynamis have been coupled as described in the thesis. The first part of the thesis consists of a parametric study aimed at understanding the eect of the presence in magma of carbon dioxide in magma in the convection dynamics. Indeed, the presence of this volatile was relevant in many Campi Flegrei eruptions, including some eruptions commonly considered as reference for a future activity of this volcano. A set of simulations considering an elliptical magma chamber, compositionally uniform, refilled from below by a magma with volatile content equal or dierent from that of the resident magma has been performed. To do this, a multicomponent non-ideal magma saturation model (Papale et al., 2006) that considers the simultaneous presence of CO2 and H2O, has been implemented in GALES. Results show that the presence of CO2 in the incoming magma increases its buoyancy force promoting convection ad mixing. The simulated dynamics produce pressure transients with frequency and amplitude in the sensitivity range of modern geophysical monitoring networks such as the one installed at Campi Flegrei . In the second part, simulations more related with the Campi Flegrei volcanic system have been performed. The simulated system has been defined on the basis of conditions consistent with the bulk of knowledge of Campi Flegrei and in particular of the Agnano-Monte Spina eruption (4100 B.P.), commonly considered as reference for a future high intensity eruption in this area. The magmatic system has been modelled as a long dyke refilling a small shallow magma chamber; magmas with trachytic and phonolitic composition and variable volatile content of H2O and CO2 have been considered. The simulations have been carried out changing the condition of magma injection, the system configuration (magma chamber geometry, dyke size) and the resident and refilling magma composition and volatile content, in order to study the influence of these factors on the simulated dynamics. Simulation results allow to follow each step of the gas-rich magma ascent in the denser magma, highlighting the details of magma convection and mixing. In particular, the presence of more CO2 in the deep magma results in more ecient and faster dynamics. Through this simulations the variation of the gravimetric field has been determined. Afterward, the space-time distribution of stress resulting from numerical simulations have been used as boundary conditions for the simulations of the displacement field imposed by the magmatic dynamics on rocks. The properties of the simulated domain (rock density, P and S wave velocities) have been based on data from literature on active and passive tomographic experiments, obtained through a collaboration with A. Zollo at the Dept. of Physics of the Federici II Univeristy in Napoli. The elasto-dynamics simulations allow to determine the variations of the space-time distribution of deformation and the seismic signal associated with the studied magmatic dynamics. In particular, results show that these dynamics induce deformations similar to those measured at Campi Flegrei and seismic signals with energies concentrated on the typical frequency bands observed in volcanic areas. The present work shows that an approach based on the solution of equations describing the physics of processes within a magmatic fluid and the surrounding rock system is able to recognise and describe the relationships between geophysical signals detectable on the surface and deep magma dynamics. Therefore, the results suggest that the combined study of geophysical data and informations from numerical simulations can allow in a near future a more ecient evaluation of the short term volcanic hazard.

Deep geometry of subduction below the Andean belt of Colombia as revealed by seismic tomography

In this study new tomographic models of Colombia were calculated. I used the seismicity recorded by the Colombian seismic network during the period 2006-2009. In this time period, the improvement of the seismic network yields more stable hypocentral results with respect to older data set and allows to compute new 3D Vp and Vp/Vs models. The final dataset consists of 10813 P- and 8614 S-arrival times associated to 1405 earthquakes. Tests with synthetic data and resolution analysis indicate that velocity models are well constrained in central, western and southwestern Colombia to a depth of 160 km; the resolution is poor in the northern Colombia and close to Venezuela due to a lack of seismic stations and seismicity. The tomographic models and the relocated seismicity indicate the existence of E-SE subducting Nazca lithosphere beneath central and southern Colombia. The North-South changes in Wadati-Benioff zone, Vp & Vp/Vs pattern and volcanism, show that the downgoing plate is segmented by slab tears E-W directed, suggesting the presence of three sectors. Earthquakes in the northernmost sector represent most of the Colombian seimicity and concentrated on 100-170 km depth interval, beneath the Eastern Cordillera. Here a massive dehydration is inferred, resulting from a delay in the eclogitization of a thickened oceanic crust in a flat-subduction geometry. In this sector a cluster of intermediate-depth seismicity (Bucaramanga Nest) is present beneath the elbow of the Eastern Cordillera, interpreted as the result of massive and highly localized dehydration phenomenon caused by a hyper-hydrous oceanic crust. The central and southern sectors, although different in Vp pattern show, conversely, a continuous, steep and more homogeneous Wadati-Benioff zone with overlying volcanic areas. Here a "normalthickened" oceanic crust is inferred, allowing for a gradual and continuous metamorphic reactions to take place with depth, enabling the fluid migration towards the mantle wedge.

Geometry-Aware Multiscale Image Registration via OBBTree-Based Polyaffine Log-Demons

Non-linear image registration is an important tool in many areas of image analysis. For instance, in morphometric studies of a population of brains, free-form deformations between images are analyzed to describe the structural anatomical variability. Such a simple deformation model is justified by the absence of an easy expressible prior about the shape changes. Applying the same algorithms used in brain imaging to orthopedic images might not be optimal due to the difference in the underlying prior on the inter-subject deformations. In particular, using an un-informed deformation prior often leads to local minima far from the expected solution. To improve robustness and promote anatomically meaningful deformations, we propose a locally affine and geometry-aware registration algorithm that automatically adapts to the data. We build upon the log-domain demons algorithm and introduce a new type of OBBTree-based regularization in the registration with a natural multiscale structure. The regularization model is composed of a hierarchy of locally affine transformations via their logarithms. Experiments on mandibles show improved accuracy and robustness when used to initialize the demons, and even similar performance by direct comparison to the demons, with a significantly lower degree of freedom. This closes the gap between polyaffine and non-rigid registration and opens new ways to statistically analyze the registration results.

Risk of target lesion failure in relationship to vessel angiographic geometry and stent conformability using the second generation of drug-eluting stents

Vessel angulation and large changes in vessel geometry after stent implantation have been associated with an increased risk of target lesion failure (TLF) using bare-metal stents. Second-generation drug-eluting stents (DES)offer superior conformability and inhibition of neointima. The aim of the study is to investigate the relationship between pre and post-implant vessel geometry and the occurrence of TLF at 1 year after treatment with second-generation DES; and to compare the conformability of Resolute and Xience stents.

Angiographic geometric changes of the lumen arterial wall after bioresorbable vascular scaffolds and metallic platform stents at 1-year follow-up

The aim of this study was to compare the angiographic changes in coronary geometry of the bioresorbable vascular scaffolds (BVS) and metallic platform stent (MPS) between baseline and follow-up.

Effects of pCO2 and iron on the elemental composition and cell geometry of the marine diatom Pseudo-nitzschia pseudodelicatissima//(Bacillariophyceae)

Partial pressure of CO2 (pCO2) and iron availability in seawater show corresponding changes due to biological and anthropogenic activities. The simultaneous change in these factors precludes an understanding of their independent effects on the ecophysiology of phytoplankton. In addition, there is a lack of data regarding the interactive effects of these factors on phytoplankton cellular stoichiometry, which is a key driving factor for the biogeochemical cycling of oceanic nutrients. Here, we investigated the effects of pCO2 and iron availability on the elemental composition (C, N, P, and Si) of the diatom Pseudo-nitzschia pseudodelicatissima (Hasle) Hasle by dilute batch cultures under 4 pCO2 (~200, ~380, ~600, and ~800 µatm) and five dissolved inorganic iron (Fe'; ~5, ~10, ~20, ~50, and ~100 pmol /L) conditions. Our experimental procedure successfully overcame the problems associated with simultaneous changes in pCO2 and Fe' by independently manipulating carbonate chemistry and iron speciation, which allowed us to evaluate the individual effects of pCO2 and iron availability. We found that the C:N ratio decreased significantly only with an increase in Fe', whereas the C:P ratio increased significantly only with an increase in pCO2. Both Si:C and Si:N ratios decreased with increasing pCO2 and Fe'. Our results indicate that changes in pCO2 and iron availability could influence the biogeochemical cycling of nutrients in future oceans with high- CO2 levels, and, similarly, during the time course of phytoplankton blooms. Moreover, pCO2 and iron availability may also have affected oceanic nutrient biogeochemistry in the past, as these conditions have changed markedly over the Earth's history.

A single point mutation in the pore region of the epithelial Na+ channel changes ion selectivity by modifying molecular sieving

The epithelial Na+ channel (ENaC) belongs to a new class of channel proteins called the ENaC/DEG superfamily involved in epithelial Na+ transport, mechanotransduction, and neurotransmission. The role of ENaC in Na+ homeostasis and in the control of blood pressure has been demonstrated recently by the identification of mutations in ENaC β and γ subunits causing hypertension. The function of ENaC in Na+ reabsorption depends critically on its ability to discriminate between Na+ and other ions like K+ or Ca2+. ENaC is virtually impermeant to K+ ions, and the molecular basis for its high ionic selectivity is largely unknown. We have identified a conserved Ser residue in the second transmembrane domain of the ENaC α subunit (αS589), which when mutated allows larger ions such as K+, Rb+, Cs+, and divalent cations to pass through the channel. The relative ion permeability of each of the αS589 mutants is related inversely to the ionic radius of the permeant ion, indicating that αS589 mutations increase the molecular cutoff of the channel by modifying the pore geometry at the selectivity filter. Proper geometry of the pore is required to tightly accommodate Na+ and Li+ ions and to exclude larger cations. We provide evidence that ENaC discriminates between cations mainly on the basis of their size and the energy of dehydration.

Specific atomic groups and RNA helix geometry in acceptor stem recognition by a tRNA synthetase

Oligonucleotides that recapitulate the acceptor stems of tRNAs are substrates for aminoacylation by many tRNA synthetases in vitro, even though these substrates are missing the anticodon trinucleotides of the genetic code. In the case of tRNAAla a single acceptor stem G⋅U base pair at position 3·70 is essential, based on experiments where the wobble pair has been replaced by alternatives such as I⋅U, G⋅C, and A⋅U, among others. These experiments led to the conclusion that the minor-groove free 2-amino group (of guanosine) of the G⋅U wobble pair is essential for charging. Moreover, alanine-inserting tRNAs (amber suppressors) that replace G⋅U with mismatches such as G⋅A and C⋅A are partially active in vivo and can support growth of an Escherichia coli tRNAAla knockout strain, leading to the hypothesis that a helix irregularity and nucleotide functionalities are important for recognition. Herein we investigate the charging in vitro of oligonucleotide and full-length tRNA substrates that contain mismatches at the position of the G⋅U pair. Although most of these substrates have undetectable activity, G⋅A and C⋅A variants retain some activity, which is, nevertheless, reduced by at least 100-fold. Thus, the in vivo assays are much less sensitive to large changes in aminoacylation kinetic efficiency of 3·70 variants than is the in vitro assay system. Although these functional data do not clarify all of the details, it is now clear that specific atomic groups are substantially more important in determining kinetic efficiency than is a helical distortion. By implication, the activity of mutant tRNAs measured in the in vivo assays appears to be more dependent on factors other than aminoacylation kinetic efficiency.