Synthetic presentation of iterative asynchronous parallel algorithms.

Iterative asynchronous parallel methods are nowadays gaining renewed interest in the community of researchers interested in High Performance Computing (HPC), in the specific case of massive parallelism. This is because these methods avoid the deadlock phenomena and that moreover a rigorous load balancing is not necessary, which is not the case with synchronous methods. Such iterative asynchronous parallel methods are of great interest when there are many synchronizations between processors, which in the case of iterative methods is the case when convergence is slow. Indeed in iterative synchronous parallel methods, to respect the task sequence graph that defines in fact the logic of the algorithm used, processors must wait for the results they need and calculated by other processors; such expectations of the results emitted by concurrent processors therefore cause idle times for standby processors. It is to overcome this drawback that asynchronous parallel iterative methods have been introduced first for the resolution of large scale linear systems and then for the resolution of highly nonlinear algebraic systems of large size as well, where the solution may be subject to constraints. This kind of method has been widely studied worldwide by many authors. The purpose of this presentation is to present as broadly and pedagogically as possible the asynchronous parallel iterative methods as well as the issues related to their implementation and application in solving many problems arising from High Performance Computing. We will therefore try as much as possible to present the underlying concepts that allow a good understanding of these methods by avoiding as much as possible an overly rigorous mathematical formalism; references to the main pioneering work will also be made. After a general introduction we will present the basic concepts that allow to model asynchronous parallel iterative methods including as a particular case synchronous methods. We will then present the algorithmic extensions of these methods consisting of asynchronous sub-domain methods, asynchronous multisplitting methods as well as asynchronous parallel methods with flexible communications. In each case an analysis of the behavior of these methods will be presented. Note that the first kind of analysis allows to obtain an estimate of the asymptotic rate of convergence. The difficult problem of the stopping test of asynchronous parallel iterations will be also studied, both by computer sciences considerations and also by numerical aspects related to the mathematical analysis of the behavior of theses iterative parallel methods. The parallel asynchronous methods have been implemented on various architectures and we will present the main principles that made it possible to code them. These parallel asynchronous methods have been used for the resolution of several kind of mathematical problems and we will list the main applications processed. Finally we will try to specify in which cases and on which type of architecture these methods are efficient and interesting to use

Digital Fourier microscopy for soft matter dynamics

Soft matter is studied with a large portfolio of methods. Light scattering and video microscopy are the most employed at optical wavelengths. Light scattering provides ensemble-averaged information on soft matter in the reciprocal space. The wave-vectors probed correspond to length scales ranging from a few nanometers to fractions of millimetre. Microscopy probes the sample directly in the real space, by offering a unique access to the local properties. However, optical resolution issues limit the access to length scales smaller than approximately 200 nm. We describe recent work that bridges the gap between scattering and microscopy. Several apparently unrelated techniques are found to share a simple basic idea: the correlation properties of the sample can be characterized in the reciprocal space via spatial Fourier analysis of images collected in the real space. We describe the main features of such digital Fourier microscopy (DFM), by providing examples of several possible experimental implementations of it, some of which not yet realized in practice. We also provide an overview of experimental results obtained with DFM for the study of the dynamics of soft materials. Finally, we outline possible future developments of DFM that would ease its adoption as a standard laboratory method. \ua9 2014 IOP Publishing Ltd

Methods for Data Management in Multi-Centre MRI Studies and Applications to Traumatic Brain Injury

Neuroimaging studies are becoming increasingly bigger, and multi-centre collaborations to collect data under similar protocols, but different scanning sites, are now commonplace.However, with increasing sample size the complexity of databases and the entailed data management as well as computational burden are growing. This thesis aims to highlight and address challenges faced by large multi-centre magnetic resonance imaging(MRI) studies. The methods implemented are then applied to traumatic brain injury (TBI) data.Firstly, a pre-processing pipeline for both anatomical and diffusion MRI was proposed, that allows for a high throughput of MRI scans. After describing the choices for processing tools,the performance of the integrated quality assurance was assessed based on the results from a large multi-centre dataset for TBI. Secondly, the applicability of the pipelines for processing mild TBI (mTBI) data from three sites was shown in a case study. For this, volumetric and diffusion metrics in the acute phase are analysed for their prognostic potential. Further-more, the cohort was examined for longitudinal changes. Thirdly, independent scan-rescan datasets are examined to gain a better understanding of the degree of reproducibility which can be achieved in imaging studies. This involves analysing the robustness of brain parcellations based on structural or diffusion imaging. The effect of using different MRI scanners or imaging protocols was also assessed and discussed. Fourthly, sources of diffusion MRI variability and different approaches to cope with these are reviewed. Using this foundation,state-of-the art methods for diffusion MRI harmonisation were compared against each other using both a benchmark dataset and mTBI cohort. Lastly, a solution to localise brain lesions was proposed. Its implications for lesion analysis, are assessed in the light of an application to a more severe TBI patient cohort, imaged on two different scanners. Furthermore, a lesion matching algorithm was introduced to automatically examine lesion evolution with time post-injury. In summary, this thesis explored different options for MRI data analysis in the context of large multi-centre studies. Different approaches are studied and compared using a number of different MRI datasets, including scan-rescan data across different MRI scanners and imaging protocols. The potential of the optimised solutions was illustrated through applications to TBI data.CENTER-TB

Surface modification of bioceramics: chemically enhanced laser surface microstructuring of hydroxyapatite

PhDBioceramics have been developed for implants to repair damaged tissues of the human musculo-skeletal system. The clinical success of a bioceramic implant depends largely on the chemical response at the implant interface in addition to the sufficiency of the mechanical properties for the application. The present study combines the developments in the fields of bioceramic materials and laser surface micro structuring of materials. Bioceramic hydroxyapatite powders (HA, Formula: CaIO(PO4)6(OH)2) have been produced by emulsion technology and freeze-drying methods exhibiting BET specific surface areas >148 m2 /g and particle sizes <13 nrn prior to thermal treatment. The powder yield has been doubled using an increased reaction temperature of 25 *C from 17 *C, with a small increase (< 4nm) in the average particle size. HA discs that were >95.5 % dense have been achieved after isostatic pressing with pressure of 0.59 MPa and pressurelesss intering at 1200 *C for 2 hours. No chemical decomposition was detected using X-ray Diffraction Analysis (XRD). Methods of chemically enhanced laser-assisted etching have been developed to produce microstructural features on the surface of bioceramic HA discs that were 78.5 % dense (2482.95 kr , /M3 measured density). The use of 10 MPa SF6 at laser fluencies in the range of 14.50-15.20 W/M2 produced a columnar topography with individual structures featuring 10-20 pm height and 8-12 pm width as characterised by Scanning Electron Microscopy (SEM). Chemical characterisation by X-ray microdiffraction, Energy Dispsersive, X-ray analysis (SEM-EDS), Fourier Transformed Infrared spectroscopy (FTIR) and Raman spectroscopy (Raman) found the microtopography to be composed of fluorine-substituted HA (FHA). Alternatively the use of 80 MPa NH3 at laser fluencies in the range of 17.17-18.50 kj/m 2 produced an irregular surface of scattered porous hillocks that remained chemically unchanged in composition but exhibited four times as many surface hydroxyl groups. In both cases the mechanical and chemical stability of the bulk composition is maintained and the surface of increased surface area, in addition to the presence of concavities and pores is likely to be of enhanced osteoconductivity.IRC in Biomaterial

Charakterisierung funktionaler Nanomaterialien für biomagnetische Sensoren und Atemanalyse

The presented thesis is covering materials aspects for the development of magnetoelectric sensors for biomagnetic sensing and solid state sensors for breath monitoring. The electrophysiological signals of the human body and especially their irregularities provide extremely valuable information about the heart, brain or nerve malfunction in medical diagnostics. Similar and even more detailed information is contained in the generated biomagnetic fields which measurement offers improved diagnostics and treatment of the patients. A new type of room temperature operable magnetoelectric composite sensors is developed in the framework of the CRC1261 Magnetoelectric Sensors: From Composite Materials to Biomagnetic Diagnostics. This thesis focuses on the individual materials structure-property relations and their combination in magnetoelectric composite sensors studied by electron beam based techniques, at lengths scales ranging from micrometers to atomic resolution. The first part of this thesis highlights selected studies on the structural and analytic aspects of single phase materials and their composites using TEM as the primary method of investigation. With respect to the piezoelectric phase, alternatives to AlN have been thoroughly investigated to seek for improvement of specific sensor approaches. In this context, the alloying of Sc into the AlN matrix has been demonstrated to yield high quality films with improved piezoelectric and unprecedented ferroelectric properties grown under the control of deposition parameters. Lead-free titanate films with large piezo-coefficients at the verge of the morphotropic phase boundary as alternative to PZT films have been investigated in terms of crystal symmetry, defect structure and domains of cation ordering. New morphologies of ZnO and GaN semiconductors envisioned for a piezotronic-based sensor approach were subject of in-depth defect and analytical studies describing intrinsic defects and lattice strains upon deposition as well as hollow composite structures. When the dimensions of a materials are reduced, novel exciting properties such as in-plane piezoelectricity can arise in planar transition-metal dichalcogenides. Here, the turbostratic disorder in a few-layered MoSe2 film has been investigated by nanobeam electron diffraction and Fast Fourier Transformations. From the perspective of magnetic materials, the atomic structure of magnetostrictive multilayers of FeCo/TiN showing stability up to elevated temperatures has been analyzed in detail regarding the crystallographic relationship of heteroepitaxy in multilayer composites exhibiting individual layer thicknesses below 1 nm. Further, magnetic hard layers have been investigated in the context of exchange spring concepts and ME composites based on shape memory alloy substrates have been studied regarding structural changes implied by different annealing processes. The second part of this thesis introduces materials aspects and sensor studies on gas detection in the clinical context of breath analysis. The detection of specific vapors in the human breath is of medical relevance, since certain species can be enriched depending on the conditions and processes within the human body. Hence, they can be regarded as biomarkers for the patients condition of health. The selection of suitable materials and the gas measurement working principle are considered and selected studies on solid state sensors with different surface functionalization or targeted application on basis of ZnO or CuO-oxide and Fe-oxide species are presented

Cartilage Tissue Engineering For Rhinoplasty

Nasal surgery (rhinoplasty) has evolved considerably since its origins in Egypt around 1600BCE, yet modern reconstruction still relies on grafts harvested from autologous rib cartilage. Rib cartilage is an excellent graft material, but chest donor site morbidity can be a significant problem. The aim of this thesis was to create a patient specific cartilage surgical product using autologous stem cells that would provide surgeons with an effective alternative to rib cartilage. Adipose-derived stem cells (ADSCs) and cartilage-derived stem/precursor cells (CSPCs) were used in this thesis as they can be harvested through minimally invasive procedures and their chondrogenic potential already widely established. Using a novel tissue clearing protocol for whole mount imaging, primary experiments confirmed the ability of both cell types to self-organize and generate cartilage-like extracellular matrix (ECM) in 3D spheroids. Three different methods of engineering cartilage in 3D were investigated. Firstly, a clinically approved collagen matrix was used as a scaffold and seeded with cells. Immunocytochemistry and histological staining demonstrated cartilage like ECM on the scaffold surface in preference to deeper regions. The collagen matrix proved too be tight and constrictive on cell expansion. Secondly, a 3D bioprinter was used to print cells mixed with cellulose/alginate “bioink” hydrogels. This bioink failed to demonstrate cartilage like ECM in static culture and in a chick embryo chorioallantoic membrane (CAM) model. Lastly, a cell laden fibrin hydrogel was “sandwiched” between 2 layers of polycaprolactone (PCL) sheets to provide mechanical support and grafted onto CAM. Histological analysis of cell laden fibrin confirmed regions of chondrogenesis by positive staining of collagen and glycosaminoglycans. In conclusion, the results provide further understanding of how these cells respond to different 3D environments and the effect on chondrogenesis. Combining 3D bioprinting with a sandwich design may be an effective future approach to product development

Magnetic Nanomaterials

The constant search for innovative magnetic materials increasingly leads to the creation of highly engineered systems built in different forms (films, wires, particles), structured on the nanoscale in at least one spatial direction, and often characterized by the coexistence of two or more phases that are magnetically and/or structurally different. In magnetic systems, the nanometric structural characteristics of the constituent elements, together with the type and strength of the magnetic interactions between them, determine the overall magnetic behavior and can lead to the appearance of unexpected and amazing magnetic phenomena. Indeed, the study of the magnetic properties of nanomaterials continues to arouse great interest for their intriguing fundamental properties and prospective technological applications. This Special Issue contributes to broadening the knowledge on magnetic nanomaterials, demonstrating the breadth and richness of this research field as well as the growing need to address it through an interdisciplinary approach. The papers collected in this book (two reviews and eight regular articles) report cutting-edge studies on the production and characterization of a variety of novel magnetic nanomaterials (nanoparticles, nanocomposites, thin films and multilayers), which have the potential to play a key role in different technologically advanced sectors, such as biotechnology, nanomedicine, energy, spintronics, data storage, and sensors

A Study of bacterial growth and adhesion in environments subjected to flow or surface vibration

This thesis presents investigations into the adhesion of E.coli cells and the growth of such cells into colonies on substrates that are subject to external mechanical perturbations. The first perturbation we introduce is in the form of an applied flow through a microfluidic channel that contains adhered E.coli cells. We show that when the types of appendages present at the cell membrane vary, the flow rate at which the cells become dislodged changes, indicating a change in the strength of the adhesion of the cells to the substrate. This allows for a maximum drag force that cells can withstand before detaching for each E.coli strain to be quantified. We also investigate how the elasticity of the substrate of the microfluidic device plays a role in the adhesion of the cells to the surface. This is achieved by altering the elastomer ratio of the device material, PDMS, and comparing maximum drag forces of the cells for different ratios. This allows for insight into how the stiffness of a surface affects the adhesion of cells, and we ultimately show that a more deformable substrate favours prolonged attachment of cells. The dependence on the cell's orientation with respect to the direction of flow is investigated and linked to the likelihood that a cell will remain attached when exposed to an increasing applied flow rate. Using an agar microfluidic device we further investigate, the role cell appendages play in surface adhesion when bacteria are subjected to flow. We next describe the design of an experiment in which an agar plate is periodically deformed, at frequencies in the range 5-50 Hz, by coupling it to a loudspeaker cone. Colonies grown on the deformed plates were found to exhibit two main effects that differ from control colonies grown on static plates. These effects were: an increase in colony perimeter roughness and an increase in the final diameter of the colony after a fixed period of growth. It was shown that these effects increased with increasing driving frequency. In addition to the acceleration which accompanies the vibration, when the boundary of the plate is fixed there is an induced elastic strain field that varies across the plate. Work was carried out to quantify the effect of the strain and acceleration on colony perimeter roughness and final diameter and attempt to relate each one separately to the observed effects. It was determined that the presence of the strain field was related to the increase in diameter whilst the large increase in acceleration resulted in rougher colonies forming. We hypothesise that both of these effects contribute to a modification of the forces on the bacteria that allow cells at the perimeter of the colony to switch their relative position and orientation which then leads to an increase in colony perimeter roughness and diameter. When colonies formed from two bacterial strains (fluorescent/non-fluorescent) it was observed that the peak sector size remains the same but the distribution of sectors angular size broadens, so that there is an increase in finding larger sectors. Finally, this thesis closes by detailing the development of an in-situ microscope to directly observe bacterial colonies on a deformed agar plate. The microscope was used to quantify the velocity at which the colony perimeter advances and the width of the growing layer. This work was expanded to measure these parameters on agar plates with different elastic properties. It was shown that as the agar becomes stiffer, the expansion velocity of the growing front decreases and with this the total roughness of the colonies also decreases. This was explained as the increasing stiffness of the agar results in a stronger polymer network being formed that offers greater resistance to the applied deformation, reducing the strain field, which results in a decrease in the radial expansion velocity. We also measured the height profiled of colonies grown on static and deformed plates. The observed behaviour is found to be consistent with a computational model in which decreasing the friction coefficient between the cell and the substrate leads to an increase in the colony diameter