Identifiying human MHC supertypes using bioinformatic methods

Classification of MHC molecules into supertypes in terms of peptide-binding specificities is an important issue, with direct implications for the development of epitope-based vaccines with wide population coverage. In view of extremely high MHC polymorphism (948 class I and 633 class II HLA alleles) the experimental solution of this task is presently impossible. In this study, we describe a bioinformatics strategy for classifying MHC molecules into supertypes using information drawn solely from three-dimensional protein structure. Two chemometric techniques–hierarchical clustering and principal component analysis–were used independently on a set of 783 HLA class I molecules to identify supertypes based on structural similarities and molecular interaction fields calculated for the peptide binding site. Eight supertypes were defined: A2, A3, A24, B7, B27, B44, C1, and C4. The two techniques gave 77% consensus, i.e., 605 HLA class I alleles were classified in the same supertype by both methods. The proposed strategy allowed “supertype fingerprints” to be identified. Thus, the A2 supertype fingerprint is Tyr9/Phe9, Arg97, and His114 or Tyr116; the A3-Tyr9/Phe9/Ser9, Ile97/Met97 and Glu114 or Asp116; the A24-Ser9 and Met97; the B7-Asn63 and Leu81; the B27-Glu63 and Leu81; for B44-Ala81; the C1-Ser77; and the C4-Asn77. action fields calculated for the peptide binding site. Eight supertypes were defined: A2, A3, A24, B7, B27, B44, C1, and C4. The two techniques gave 77% consensus, i.e., 605 HLA class I alleles were classified in the same supertype by both methods. The proposed strategy allowed “supertype fingerprints” to be identified. Thus, the A2 supertype fingerprint is Tyr9/Phe9, Arg97, and His114 or Tyr116; the A3-Tyr9/Phe9/Ser9, Ile97/Met97 and Glu114 or Asp116; the A24-Ser9 and Met97; the B7-Asn63 and Leu81; the B27-Glu63 and Leu81; for B44-Ala81; the C1-Ser77; and the C4-Asn77.

Computing and Visualizing Solution Sets of Interval Linear Systems

The paper has been presented at the 12th International Conference on Applications of Computer Algebra, Varna, Bulgaria, June, 2006

Almost Conformal Transformation in a Class of Riemannian Manifolds

We consider a 3-dimensional Riemannian manifold V with a metric g and an a±nor structure q. The local coordinates of these tensors are circulant matrices. In V we define an almost conformal transformation. Using that definition we construct an infinite series of circulant metrics which are successively almost conformaly related. In this case we get some properties.

On Affine Connections in a Riemannian Manifold with a Circulant Metric and two Circulant Affinor Structures

Ива Р. Докузова, Димитър Р. Разпопов - В настоящата статия е разгледан клас V оттримерни риманови многообразия M с метрика g и два афинорни тензора q и S. Дефинирана е и друга метрика ¯g в M. Локалните координати на всички тези тензори са циркулантни матрици. Намерени са: 1) зависимост между тензора на кривина R породен от g и тензора на кривина ¯R породен от ¯g; 2) тъждество за тензора на кривина R в случая, когато тензорът на кривина ¯R се анулира; 3) зависимост между секционната кривина на прозволна двумерна q-площадка {x, qx} и скаларната кривина на M.

Carbon nanotube based systems for high energy efficient applications

In the current age of fast-depleting conventional energy sources, top priority is given to exploring non-conventional energy sources, designing highly efficient energy storage systems and converting existing machines/instruments/devices into energy-efficient ones. ‘Energy efficiency’ is one of the important challenges for today’s scientific and research community, worldwide. In line with this demand, the current research was focused on developing two highly energy-efficient devices – field emitters and Li-ion batteries, using beneficial properties of carbon nanotubes (CNT). Interface-engineered, directly grown CNTs were used as cathode in field emitters, while similar structure was applied as anode in Li-ion batteries. Interface engineering was found to offer minimum resistance to electron flow and strong bonding with the substrate. Both field emitters and Li-ion battery anodes were benefitted from these advantages, demonstrating high energy efficiency. Field emitter, developed during this research, could be characterized by low turn-on field, high emission current, very high field enhancement factor and extremely good stability during long-run. Further, application of 3-dimensional design to these field emitters resulted in achieving one of the highest emission current densities reported so far. The 3-D field emitter registered 27 times increase in current density, as compared to their 2-D counterparts. These achievements were further followed by adding new functionalities, transparency and flexibility, to field emitters, keeping in view of current demand for flexible displays. A CNT-graphene hybrid structure showed appreciable emission, along with very good transparency and flexibility. Li-ion battery anodes, prepared using the interface-engineered CNTs, have offered 140% increment in capacity, as compared to conventional graphite anodes. Further, it has shown very good rate capability and an exceptional ‘zero capacity degradation’ during long cycle operation. Enhanced safety and charge transfer mechanism of this novel anode structure could be explained from structural characterization. In an attempt to progress further, CNTs were coated with ultrathin alumina by atomic layer deposition technique. These alumina-coated CNT anodes offered much higher capacity and an exceptional rate capability, with very low capacity degradation in higher current densities. These highly energy efficient CNT based anodes are expected to enhance capacities of future Li-ion batteries.

Seismic Response Analysis of a Full-Scale Base-Isolated Structure via Measurements and Modeling

The full-scale base-isolated structure studied in this dissertation is the only base-isolated building in South Island of New Zealand. It sustained hundreds of earthquake ground motions from September 2010 and well into 2012. Several large earthquake responses were recorded in December 2011 by NEES@UCLA and by GeoNet recording station nearby Christchurch Women's Hospital. The primary focus of this dissertation is to advance the state-of-the art of the methods to evaluate performance of seismic-isolated structures and the effects of soil-structure interaction by developing new data processing methodologies to overcome current limitations and by implementing advanced numerical modeling in OpenSees for direct analysis of soil-structure interaction.

This dissertation presents a novel method for recovering force-displacement relations within the isolators of building structures with unknown nonlinearities from sparse seismic-response measurements of floor accelerations. The method requires only direct matrix calculations (factorizations and multiplications); no iterative trial-and-error methods are required. The method requires a mass matrix, or at least an estimate of the floor masses. A stiffness matrix may be used, but is not necessary. Essentially, the method operates on a matrix of incomplete measurements of floor accelerations. In the special case of complete floor measurements of systems with linear dynamics, real modes, and equal floor masses, the principal components of this matrix are the modal responses. In the more general case of partial measurements and nonlinear dynamics, the method extracts a number of linearly-dependent components from Hankel matrices of measured horizontal response accelerations, assembles these components row-wise and extracts principal components from the singular value decomposition of this large matrix of linearly-dependent components. These principal components are then interpolated between floors in a way that minimizes the curvature energy of the interpolation. This interpolation step can make use of a reduced-order stiffness matrix, a backward difference matrix or a central difference matrix. The measured and interpolated floor acceleration components at all floors are then assembled and multiplied by a mass matrix. The recovered in-service force-displacement relations are then incorporated into the OpenSees soil structure interaction model.

Numerical simulations of soil-structure interaction involving non-uniform soil behavior are conducted following the development of the complete soil-structure interaction model of Christchurch Women's Hospital in OpenSees. In these 2D OpenSees models, the superstructure is modeled as two-dimensional frames in short span and long span respectively. The lead rubber bearings are modeled as elastomeric bearing (Bouc Wen) elements. The soil underlying the concrete raft foundation is modeled with linear elastic plane strain quadrilateral element. The non-uniformity of the soil profile is incorporated by extraction and interpolation of shear wave velocity profile from the Canterbury Geotechnical Database. The validity of the complete two-dimensional soil-structure interaction OpenSees model for the hospital is checked by comparing the results of peak floor responses and force-displacement relations within the isolation system achieved from OpenSees simulations to the recorded measurements. General explanations and implications, supported by displacement drifts, floor acceleration and displacement responses, force-displacement relations are described to address the effects of soil-structure interaction.

Interference lithography for optical devices and coatings

Interference lithography can create large-area, defect-free nanostructures with unique optical properties. In this thesis, interference lithography will be utilized to create photonic crystals for functional devices or coatings. For instance, typical lithographic processing techniques were used to create 1, 2 and 3 dimensional photonic crystals in SU8 photoresist. These structures were in-filled with birefringent liquid crystal to make active devices, and the orientation of the liquid crystal directors within the SU8 matrix was studied. Most of this thesis will be focused on utilizing polymerization induced phase separation as a single-step method for fabrication by interference lithography. For example, layered polymer/nanoparticle composites have been created through the one-step two-beam interference lithographic exposure of a dispersion of 25 and 50 nm silica particles within a photopolymerizable mixture at a wavelength of 532 nm. In the areas of constructive interference, the monomer begins to polymerize via a free-radical process and concurrently the nanoparticles move into the regions of destructive interference. The holographic exposure of the particles within the monomer resin offers a single-step method to anisotropically structure the nanoconstituents within a composite. A one-step holographic exposure was also used to fabricate self- healing coatings that use water from the environment to catalyze polymerization. Polymerization induced phase separation was used to sequester an isocyanate monomer within an acrylate matrix. Due to the periodic modulation of the index of refraction between the monomer and polymer, the coating can reflect a desired wavelength, allowing for tunable coloration. When the coating is scratched, polymerization of the liquid isocyanate is catalyzed by moisture in air; if the indices of the two polymers are matched, the coatings turn transparent after healing. Interference lithography offers a method of creating multifunctional self-healing coatings that readout when damage has occurred.

Microfluidic platforms for the characterization of in meso membrane protein crystallization

Membrane proteins, which reside in the membranes of cells, play a critical role in many important biological processes including cellular signaling, immune response, and material and energy transduction. Because of their key role in maintaining the environment within cells and facilitating intercellular interactions, understanding the function of these proteins is of tremendous medical and biochemical significance. Indeed, the malfunction of membrane proteins has been linked to numerous diseases including diabetes, cirrhosis of the liver, cystic fibrosis, cancer, Alzheimer's disease, hypertension, epilepsy, cataracts, tubulopathy, leukodystrophy, Leigh syndrome, anemia, sensorineural deafness, and hypertrophic cardiomyopathy.1-3 However, the structure of many of these proteins and the changes in their structure that lead to disease-related malfunctions are not well understood. Additionally, at least 60% of the pharmaceuticals currently available are thought to target membrane proteins, despite the fact that their exact mode of operation is not known.4-6 Developing a detailed understanding of the function of a protein is achieved by coupling biochemical experiments with knowledge of the structure of the protein. Currently the most common method for obtaining three-dimensional structure information is X-ray crystallography. However, no a priori methods are currently available to predict crystallization conditions for a given protein.7-14 This limitation is currently overcome by screening a large number of possible combinations of precipitants, buffer, salt, and pH conditions to identify conditions that are conducive to crystal nucleation and growth.7,9,11,15-24 Unfortunately, these screening efforts are often limited by difficulties associated with quantity and purity of available protein samples. While the two most significant bottlenecks for protein structure determination in general are the (i) obtaining sufficient quantities of high quality protein samples and (ii) growing high quality protein crystals that are suitable for X-ray structure determination,7,20,21,23,25-47 membrane proteins present additional challenges. For crystallization it is necessary to extract the membrane proteins from the cellular membrane. However, this process often leads to denaturation. In fact, membrane proteins have proven to be so difficult to crystallize that of the more than 66,000 structures deposited in the Protein Data Bank,48 less than 1% are for membrane proteins, with even fewer present at high resolution (< 2Å)4,6,49 and only a handful are human membrane proteins.49 A variety of strategies including detergent solubilization50-53 and the use of artificial membrane-like environments have been developed to circumvent this challenge.43,53-55 In recent years, the use of a lipidic mesophase as a medium for crystallizing membrane proteins has been demonstrated to increase success for a wide range of membrane proteins, including human receptor proteins.54,56-62 This in meso method for membrane protein crystallization, however, is still by no means routine due to challenges related to sample preparation at sub-microliter volumes and to crystal harvesting and X-ray data collection. This dissertation presents various aspects of the development of a microfluidic platform to enable high throughput in meso membrane protein crystallization at a level beyond the capabilities of current technologies. Microfluidic platforms for protein crystallization and other lab-on-a-chip applications have been well demonstrated.9,63-66 These integrated chips provide fine control over transport phenomena and the ability to perform high throughput analyses via highly integrated fluid networks. However, the development of microfluidic platforms for in meso protein crystallization required the development of strategies to cope with extremely viscous and non-Newtonian fluids. A theoretical treatment of highly viscous fluids in microfluidic devices is presented in Chapter 3, followed by the application of these strategies for the development of a microfluidic mixer capable of preparing a mesophase sample for in meso crystallization at a scale of less than 20 nL in Chapter 4. This approach was validated with the successful on chip in meso crystallization of the membrane protein bacteriorhodopsin. In summary, this is the first report of a microfluidic platform capable of performing in meso crystallization on-chip, representing a 1000x reduction in the scale at which mesophase trials can be prepared. Once protein crystals have formed, they are typically harvested from the droplet they were grown in and mounted for crystallographic analysis. Despite the high throughput automation present in nearly all other aspects of protein structure determination, the harvesting and mounting of crystals is still largely a manual process. Furthermore, during mounting the fragile protein crystals can potentially be damaged, both from physical and environmental shock. To circumvent these challenges an X-ray transparent microfluidic device architecture was developed to couple the benefits of scale, integration, and precise fluid control with the ability to perform in situ X-ray analysis (Chapter 5). This approach was validated successfully by crystallization and subsequent on-chip analysis of the soluble proteins lysozyme, thaumatin, and ribonuclease A and will be extended to microfluidic platforms for in meso membrane protein crystallization. The ability to perform in situ X-ray analysis was shown to provide extremely high quality diffraction data, in part as a result of not being affected by damage due to physical handling of the crystals. As part of the work described in this thesis, a variety of data collection strategies for in situ data analysis were also tested, including merging of small slices of data from a large number of crystals grown on a single chip, to allow for diffraction analysis at biologically relevant temperatures. While such strategies have been applied previously,57,59,61,67 they are potentially challenging when applied via traditional methods due to the need to grow and then mount a large number of crystals with minimal crystal-to-crystal variability. The integrated nature of microfluidic platforms easily enables the generation of a large number of reproducible crystallization trials. This, coupled with in situ analysis capabilities has the potential of being able to acquire high resolution structural data of proteins at biologically relevant conditions for which only small crystals, or crystals which are adversely affected by standard cryocooling techniques, could be obtained (Chapters 5 and 6). While the main focus of protein crystallography is to obtain three-dimensional protein structures, the results of typical experiments provide only a static picture of the protein. The use of polychromatic or Laue X-ray diffraction methods enables the collection of time resolved structural information. These experiments are very sensitive to crystal quality, however, and often suffer from severe radiation damage due to the intense polychromatic X-ray beams. Here, as before, the ability to perform in situ X-ray analysis on many small protein crystals within a microfluidic crystallization platform has the potential to overcome these challenges. An automated method for collecting a "single-shot" of data from a large number of crystals was developed in collaboration with the BioCARS team at the Advanced Photon Source at Argonne National Laboratory (Chapter 6). The work described in this thesis shows that, even more so than for traditional structure determination efforts, the ability to grow and analyze a large number of high quality crystals is critical to enable time resolved structural studies of novel proteins. In addition to enabling X-ray crystallography experiments, the development of X-ray transparent microfluidic platforms also has tremendous potential to answer other scientific questions, such as unraveling the mechanism of in meso crystallization. For instance, the lipidic mesophases utilized during in meso membrane protein crystallization can be characterized by small angle X-ray diffraction analysis. Coupling in situ analysis with microfluidic platforms capable of preparing these difficult mesophase samples at very small volumes has tremendous potential to enable the high throughput analysis of these systems on a scale that is not reasonably achievable using conventional sample preparation strategies (Chapter 7). In collaboration with the LS-CAT team at the Advanced Photon Source, an experimental station for small angle X-ray analysis coupled with the high quality visualization capabilities needed to target specific microfluidic samples on a highly integrated chip is under development. Characterizing the phase behavior of these mesophase systems and the effects of various additives present in crystallization trials is key for developing an understanding of how in meso crystallization occurs. A long term goal of these studies is to enable the rational design of in meso crystallization experiments so as to avoid or limit the need for high throughput screening efforts. In summary, this thesis describes the development of microfluidic platforms for protein crystallization with in situ analysis capabilities. Coupling the ability to perform in situ analysis with the small scale, fine control, and the high throughput nature of microfluidic platforms has tremendous potential to enable a new generation of crystallographic studies and facilitate the structure determination of important biological targets. The development of platforms for in meso membrane protein crystallization is particularly significant because they enable the preparation of highly viscous mixtures at a previously unachievable scale. Work in these areas is ongoing and has tremendous potential to improve not only current the methods of protein crystallization and crystallography, but also to enhance our knowledge of the structure and function of proteins which could have a significant scientific and medical impact on society as a whole. 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POSE ESTIMATION AND 3D RECONSTRUCTION USING SENSOR FUSION

A camera maps 3-dimensional (3D) world space to a 2-dimensional (2D) image space. In the process it loses the depth information, i.e., the distance from the camera focal point to the imaged objects. It is impossible to recover this information from a single image. However, by using two or more images from different viewing angles this information can be recovered, which in turn can be used to obtain the pose (position and orientation) of the camera. Using this pose, a 3D reconstruction of imaged objects in the world can be computed. Numerous algorithms have been proposed and implemented to solve the above problem; these algorithms are commonly called Structure from Motion (SfM). State-of-the-art SfM techniques have been shown to give promising results. However, unlike a Global Positioning System (GPS) or an Inertial Measurement Unit (IMU) which directly give the position and orientation respectively, the camera system estimates it after implementing SfM as mentioned above. This makes the pose obtained from a camera highly sensitive to the images captured and other effects, such as low lighting conditions, poor focus or improper viewing angles. In some applications, for example, an Unmanned Aerial Vehicle (UAV) inspecting a bridge or a robot mapping an environment using Simultaneous Localization and Mapping (SLAM), it is often difficult to capture images with ideal conditions. This report examines the use of SfM methods in such applications and the role of combining multiple sensors, viz., sensor fusion, to achieve more accurate and usable position and reconstruction information. This project investigates the role of sensor fusion in accurately estimating the pose of a camera for the application of 3D reconstruction of a scene. The first set of experiments is conducted in a motion capture room. These results are assumed as ground truth in order to evaluate the strengths and weaknesses of each sensor and to map their coordinate systems. Then a number of scenarios are targeted where SfM fails. The pose estimates obtained from SfM are replaced by those obtained from other sensors and the 3D reconstruction is completed. Quantitative and qualitative comparisons are made between the 3D reconstruction obtained by using only a camera versus that obtained by using the camera along with a LIDAR and/or an IMU. Additionally, the project also works towards the performance issue faced while handling large data sets of high-resolution images by implementing the system on the Superior high performance computing cluster at Michigan Technological University.

Development of Novel Time-Domain Electromagnetic Methods for Offshore Groundwater Studies: A Data Application from Bat Yam, Israel

Recent marine long-offset transient electromagnetic (LOTEM) measurements yielded the offshore delineation of a fresh groundwater body beneath the seafloor in the region of Bat Yam, Israel. The LOTEM application was effective in detecting this freshwater body underneath the Mediterranean Sea and allowed an estimation of its seaward extent. However, the measured data set was insufficient to understand the hydrogeological configuration and mechanism controlling the occurrence of this fresh groundwater discovery. Especially the lateral geometry of the freshwater boundary, important for the hydrogeological modelling, could not be resolved. Without such an understanding, a rational management of this unexploited groundwater reservoir is not possible. Two new high-resolution marine time-domain electromagnetic methods are theoretically developed to derive the hydrogeological structure of the western aquifer boundary. The first is called Circular Electric Dipole (CED). It is the land-based analogous of the Vertical Electric Dipole (VED), which is commonly applied to detect resistive structures in the subsurface. Although the CED shows exceptional detectability characteristics in the step-off signal towards the sub-seafloor freshwater body, an actual application was not carried out in the extent of this study. It was found that the method suffers from an insufficient signal strength to adequately delineate the resistive aquifer under realistic noise conditions. Moreover, modelling studies demonstrated that severe signal distortions are caused by the slightest geometrical inaccuracies. As a result, a successful application of CED in Israel proved to be rather doubtful. A second method called Differential Electric Dipole (DED) is developed as an alternative to the intended CED method. Compared to the conventional marine time-domain electromagnetic system that commonly applies a horizontal electric dipole transmitter, the DED is composed of two horizontal electric dipoles in an in-line configuration that share a common central electrode. Theoretically, DED has similar detectability/resolution characteristics compared to the conventional LOTEM system. However, the superior lateral resolution towards multi-dimensional resistivity structures make an application desirable. Furthermore, the method is less susceptible towards geometrical errors making an application in Israel feasible. In the extent of this thesis, the novel marine DED method is substantiated using several one-dimensional (1D) and multi-dimensional (2D/3D) modelling studies. The main emphasis lies on the application in Israel. Preliminary resistivity models are derived from the previous marine LOTEM measurement and tested for a DED application. The DED method is effective in locating the two-dimensional resistivity structure at the western aquifer boundary. Moreover, a prediction regarding the hydrogeological boundary conditions are feasible, provided a brackish water zone exists at the head of the interface. A seafloor-based DED transmitter/receiver system is designed and built at the Institute of Geophysics and Meteorology at the University of Cologne. The first DED measurements were carried out in Israel in April 2016. The acquired data set is the first of its kind. The measured data is processed and subsequently interpreted using 1D inversion. The intended aim of interpreting both step-on and step-off signals failed, due to the insufficient data quality of the latter. Yet, the 1D inversion models of the DED step-on signals clearly detect the freshwater body for receivers located close to the Israeli coast. Additionally, a lateral resistivity contrast is observable in the 1D inversion models that allow to constrain the seaward extent of this freshwater body. A large-scale 2D modelling study followed the 1D interpretation. In total, 425 600 forward calculations are conducted to find a sub-seafloor resistivity distribution that adequately explains the measured data. The results indicate that the western aquifer boundary is located at 3600 m - 3700 m before the coast. Moreover, a brackish water zone of 3 Omega*m to 5 Omega*m with a lateral extent of less than 300 m is likely located at the head of the freshwater aquifer. Based on these results, it is predicted that the sub-seafloor freshwater body is indeed open to the sea and may be vulnerable to seawater intrusion.

Condylar displacement between centric relation and maximum intercuspation in symptomatic and asymptomatic individuals

Objective: To measure condylar displacement between centric relation (CR) and maximum intercuspation (MIC) in symptomatic and asymptomatic subjects. Materials and Methods: The sample comprised 70 non-deprogrammed individuals, divided equally into two groups, one symptomatic and the other asymptomatic, grouped according to the research diagnostic criteria for temporomandibular disorders (RDC/TMD). Condylar displacement was measured in three dimensions with the condylar position indicator (CPI) device. Dahlberg's index, intraclass correlation coefficient, repeated measures analysis of variance, analysis of variance, and generalized estimating equations were used for statistical analysis. Results: A greater magnitude of difference was observed on the vertical plane on the left side in both symptomatic and asymptomatic individuals (P = .033). The symptomatic group presented higher measurements on the transverse plane (P = .015). The percentage of displacement in the mesial direction was significantly higher in the asymptomatic group than in the symptomatic one (P = .049). Both groups presented a significantly higher percentage of mesial direction on the right side than on the left (P = .036). The presence of bilateral condylar displacement (left and right sides) in an inferior and distal direction was significantly greater in symptomatic individuals (P = .012). However, no statistical difference was noted between genders. Conclusion: Statistically significant differences between CR and MIC were quantifiable at the condylar level in asymptomatic and symptomatic individuals. (Angle Orthod. 2010;80:835-842.)

Morphology and biology of a new Pseudopolydora (Annelida: Spionidae) species from Brazil

Adults of Pseudopolydora rosebelae sp. nov. inhabit silty tubes on muddy bottoms in shallow water in southern Brazil, states of Sao Paulo and Rio de Janeiro. They are rare and extremely delicate, attaining 20 mm long for 55 chaetigers. The worms are distinctive by their colourful yellow and black pigmentation on the anterior part of body and palps, prominent transverse hood on the dorsal anterior edge of chaetiger 3, and lack of coloured respiratory pigment in blood. Of 12 examined individuals, all were females. Oogenesis is intraovarian; oocytes develop from chaetigers 14-15 to chaetigers 24-36. Recently laid oocytes were about 150 mu m in diameter, with embryos and developing larvae found in capsules inside female tubes in March-June. Broods comprised up to 23 capsules with 400 propagules. Capsules were joined to each other in a string and each attached by a single thin stalk to the inner wall of the tube. Larvae hatched at the 4-chaetiger stage and fed on plankton. Pelagic larvae are unique among Pseudopolydora in having large ramified mid-dorsal melanophores from chaetiger 3 onwards. Competent larvae are able to settle and metamorphose at the 15-chaetiger stage, but can remain planktonic up to 18 chaetigers. They have one pair of unpigmented ocelli and three pairs of black eyes in the prostomium, unpaired ramified mid-dorsal melanophores on chaetiger 1 and on the pygidium, ramified lateral melanophores on chaetigers 5-10, prominent yellow chromatophores in the prostomium, peristomium, on dorsal and ventral sides of chaetigers and in the pygidium. Branchiae are present on chaetigers 7-10, and gastrotrochs are arranged on chaetigers 3, 5, 7 and 12. Provisional serrated bristles are present in all notopodia, and hooks are present in neuropodia from chaetiger 8 onwards. Two pairs of provisional protonephridia are present in chaetigers 1 and 2, and adult metanephridia are present from chaetiger 4.

A FEM procedure based on positions and unconstrained vectors applied to non-linear dynamic of 3D frames

This study presents an alternative three-dimensional geometric non-linear frame formulation based on generalized unconstrained vector and positions to solve structures and mechanisms subjected to dynamic loading. The formulation is classified as total Lagrangian with exact kinematics description. The resulting element presents warping and non-constant transverse strain modes, which guarantees locking-free behavior for the adopted three-dimensional constitutive relation, Saint-Venant-Kirchhoff, for instance. The application of generalized vectors is an alternative to the use of finite rotations and rigid triad`s formulae. Spherical and revolute joints are considered and selected dynamic and static examples are presented to demonstrate the accuracy and generality of the proposed technique. (C) 2010 Elsevier B.V. All rights reserved.

Secondary instabilities in the flow around two circular cylinders in tandem

Direct stability analysis and numerical simulations have been employed to identify and characterize secondary instabilities in the wake of the flow around two identical circular cylinders in tandem arrangements. The centre-to-centre separation was varied from 1.2 to 10 cylinder diameters. Four distinct regimes were identified and salient cases chosen to represent the different scenarios observed, and for each configuration detailed results are presented and compared to those obtained for a flow around an isolated cylinder. It was observed that the early stages of the wake transition changes significantly if the separation is smaller than the drag inversion spacing. The onset of the three-dimensional instabilities were calculated and the unstable modes are fully described. In addition, we assessed the nonlinear character of the bifurcations and physical mechanisms are proposed to explain the instabilities. The dependence of the critical Reynolds number on the centre-to-centre separation is also discussed.