Experimental and numerical studies of hydrodynamic interaction of two bodies in waves

This thesis focuses on experimental and numerical studies of the hydrodynamic interaction between two vessels in close proximity in waves. In the model tests, two identical box-like models with round corners were used. Regular waves with the same wave steepness and different wave frequencies were generated. Six degrees of freedom body motions and wave elevations between bodies were measured in a head sea condition. Three initial gap widths were examined. In the numerical computations, a panel-free method based seakeeping program, MAPS0, and a panel method based program, WAMIT, were used for the prediction of body motions and wave elevations. The computed body motions and wave elevations were compared with experimental data.

Interaction-free measurements by quantum Zeno stabilization of ultracold atoms

Quantum mechanics predicts that our physical reality is influenced by events that can potentially happen but factually do not occur. Interaction-free measurements (IFMs) exploit this counterintuitive influence to detect the presence of an object without requiring any interaction with it. Here we propose and realize an IFM concept based on an unstable many-particle system. In our experiments, we employ an ultracold gas in an unstable spin configuration, which can undergo a rapid decay. The object-realized by a laser beam-prevents this decay because of the indirect quantum Zeno effect and thus, its presence can be detected without interacting with a single atom. Contrary to existing proposals, our IFM does not require single-particle sources and is only weakly affected by losses and decoherence. We demonstrate confidence levels of 90%, well beyond previous optical experiments.

Three-dimensional kinetic simulations of active suspensions: effect of chemotaxis and steric interaction

In this work, the effects of chemotaxis and steric interactions in active suspensions are analyzed by extending the kinetic model proposed by Saintillan and Shelley [1, 2]. In this model, a conservation equation for the active particle configuration is coupled to the Stokes equation for the flow arising from the force dipole exerted by the particles on the fluid. The fluid flow equations are solved spectrally and the conservation equation is solved by second-order finite differencing in space and second-order Adams-Bashforth time marching. First, the dynamics in suspensions of oxytactic run-and-tumble bacteria confined in thin liquid films surrounded by air is investigated. These bacteria modify their tumbling behavior by making temporal comparisons of the oxygen concentration, and, on average, swim towards high concentrations of oxygen. The kinetic model proposed by Saintillan and Shelley [1, 2] is modified to include run-and-tumble effects and oxygentaxis. The spatio-temporal dynamics of the oxygen and bacterial concentration are analyzed. For small film thicknesses, there is a weak migration of bacteria to the boundaries, and the oxygen concentration is high inside the film as a result of diffusion; both bacterial and oxygen concentrations quickly reach steady states. Above a critical film thickness (approximately 200 micron), a transition to chaotic dynamics is observed and is characterized by turbulent-like 3D motion, the formation of bacterial plumes, enhanced oxygen mixing and transport into the film, and hydrodynamic velocities of magnitudes up to 7 times the single bacterial swimming speed. The simulations demonstrate that the combined effects of hydrodynamic interactions and oxygentaxis create collective three-dimensional instabilities which enhances oxygen availability for the bacteria. Our simulation results are consistent with the experimental findings of Sokolov et al. [3], who also observed a similar transition with increasing film thickness. Next, the dynamics in concentrated suspensions of active self-propelled particles in a 3D periodic domain are analyzed. We modify the kinetic model of Saintillan and Shelley [1, 2] by including an additional nematic alignment torque proportional to the local concentration in the equation for the rotational velocity of the particles, causing them to align locally with their neighbors (Doi and Edwards [4]). Large-scale three- dimensional simulations show that, in the presence of such a torque both pusher and puller suspensions are unstable to random fluctuations and are characterized by highly nematic structures. Detailed measures are defined to quantify the degree and direction of alignment, and the effects of steric interactions on pattern formation will be presented. Our analysis shows that steric interactions have a destabilizing effect in active suspensions.

Complete spin and orbital evolution of close-in bodies using a Maxwell viscoelastic rheology

In this paper, we present a formalism designed to model tidal interaction with a viscoelastic body made of Maxwell material. Our approach remains regular for any spin rate and orientation, and for any orbital configuration including high eccentricities and close encounters. The method is to integrate simultaneously the rotation and the position of the planet as well as its deformation. We provide the equations of motion both in the body frame and in the inertial frame. With this study, we generalize preexisting models to the spatial case and to arbitrary multipole orders using a formalism taken from quantum theory. We also provide the vectorial expression of the secular tidal torque expanded in Fourier series. Applying this model to close-in exoplanets, we observe that if the relaxation time is longer than the revolution period, the phase space of the system is characterized by the presence of several spin-orbit resonances, even in the circular case. As the system evolves, the planet spin can visit different spin-orbit configurations. The obliquity is decreasing along most of these resonances, but we observe a case where the planet tilt is instead growing. These conclusions derived from the secular torque are successfully tested with numerical integrations of the instantaneous equations of motion on HD 80606 b. Our formalism is also well adapted to close-in super-Earths in multiplanet systems which are known to have non-zero mutual inclinations.

Testicular arteries systematization based on different levels of scrotal configuration in caprines

O objetivo deste trabalho foi analisar a distribuição dos vasos arteriais nos testículos em caprinos com diferentes graus de divisão escrotal. A configuração escrotal foi classificada da seguinte forma: Grupo I: constituído por caprinos com escroto único, Grupo II: com escroto separado até a metade do testículo e Grupo III: com separação escrotal estendendo-se além da metade do testículos. As artérias foram injetadas e coradas com solução de acetado de vinil, sendo os orgãos (30 pares) submetidos à corrossão para obtenção dos moldes vasculares. As artérias testiculares emergem da aorta abdominal, com trajeto retilíneo, atravessam o canal inguinal, apresentam-se espiraladas e envolvidas parcialmente pelo plexo pampiniforme. Próximo à extremidade caudada do testículo, dividem-se mais freqüentemente nos ramos cranial e caudal, os quais emitem vasos colaterais, de onde emergem ramos penetrantes. Os testículos dos animais com nível intermediário de divisão escrotal (Grupo II) apresentam menor quantidade destes ramos, sendo os quadrantes mais povoados o ventrolateral e o dorsolateral. Conclui-se que a origem, o trajeto e a distribuição das artérias testiculares não apresentam variações relacionadas ao grau de divisão escrotal em caprinos.

A test method for analysing disturbed ethernet data streams

Ethernet connections, which are widely used in many computer networks, can suffer from electromagnetic interference. Typically, a degradation of the data transmission rate can be perceived as electromagnetic disturbances lead to corruption of data frames on the network media. In this paper a software-based measuring method is presented, which allows a direct assessment of the effects on the link layer. The results can directly be linked to the physical interaction without the influence of software related effects on higher protocol layers. This gives a simple tool for a quantitative analysis of the disturbance of an Ethernet connection based on time domain data. An example is shown, how the data can be used for further investigation of mechanisms and detection of intentional electromagnetic attacks. © 2015 Author(s).

Blade-wake interactions in cross-flow turbines

This paper presents analytical bounds for blade–wake interaction phenomenona occurring in rotating cross-flow turbines for wind and tidal energy generation (e.g. H rotors, Darrieus or vertical axis). Limiting cases are derived for one bladed turbines and extended to the more common three bladed configuration. Additionally, we present a classification of the blade–wake type of interactions in terms of limiting tip speed ratios. These bounds are validated using a high order h=p Discontinuous Galerkin solver with sliding meshes. This computational method enables highly accurate flow solutions and shows that the analytical bounds correspond to limiting blade-wake interactions in fully resolved flow simulations

Sex group composition, social interaction, and metabolism in the fish Nile tilapia

O objetivo deste trabalho foi testar se grupos monossexuais de machos gastam mais energia e exibem perfil agonístico diferente de grupos formados por um macho e uma fêmea na tilápia-do-Nilo (Oreochromis niloticus). Tais diferenças são esperadas, pois machos e fêmeas competem por diferentes recursos reprodutivos. Foram utilizadas duplas de machos (MM) e duplas de macho-fêmea (MF) que permaneceram pareadas por 40 minutos. Durante esse período foi feito o registro da interação agonística (10 minutos iniciais e 10 minutos finais do pareamento) e determinado o gasto energético (consumo de O2) pelo Método de Winckler. A latência para o início dos confrontos (média ± DP, MM = 27,40 ± 25,15 s; MF = 14,22 ± 21,19 s; Mann-Whitney, U = 33,50, P = 0,21) e a freqüência de todas as unidades comportamentais (média ± DP, MM < 72,30 ± 25,29; MF < 73,50 ± 21,65.10/min; Mann-Whitney, P > 0,10) foram semelhantes entre os grupos MM e MF nos 10 minutos iniciais. Isso indica que cada intruso foi considerado um potencial competidor no início da interação. No entanto, a freqüência de ondulação (interação também exibida durante a corte) foi maior para o residente do grupo MF nos 10 minutos finais (média ± DP, MM = 3,56 ± 5,89; MF = 8,56 ± 4,00.10/min; Mann-Whitney, U = 15,50, P = 0,01). A freqüência de fuga, entretanto, foi menor para o intruso do mesmo grupo (média ± DP, MM = 3,90 ± 4,33; MF = 0,44 ± 0,96.10/min; Mann-Whitney, U = 23,50, P = 0,04). Além disso, o perfil agonístico no grupo MM foi composto por um maior número de itens comportamentais do que o MF (para residentes e intrusos). Apesar das diferenças comportamentais, o consumo de O2 não foi afetado pela composição sexual do grupo (média ± DP, MM = 1,93 ± 0,54; MF = 1,77 ± 0,46 mgO2.g peso seco-1.40/min; t-teste de Student, t = 0,71, P = 0,49).

An assisted navigation method for telepresence robots

Telepresence robots have emerged as a new means of interaction in remote environments. However, the use of such robots is still limited due to safety and usability issues when operating in human-like environments. This work addresses these issues by enhancing the robot navigation through a collaborative control method that assists the user to negotiate obstacles. The method has been implemented in a commercial telepresence robot and a user study has been conducted in order to test the suitability of our approach.

A THEORETICAL STUDY OF INTERACTION OF NANOPARTICLES WITH BIOMOLECULE

Many types of materials at nanoscale are currently being used in everyday life. The production and use of such products based on engineered nanomaterials have raised concerns of the possible risks and hazards associated with these nanomaterials. In order to evaluate and gain a better understanding of their effects on living organisms, we have performed first-principles quantum mechanical calculations and molecular dynamics simulations. Specifically, we will investigate the interaction of nanomaterials including semiconducting quantum dots and metallic nanoparticles with various biological molecules, such as dopamine, DNA nucleobases and lipid membranes. Firstly, interactions of semiconducting CdSe/CdS quantum dots (QDs) with the dopamine and the DNA nucleobase molecules are investigated using similar quantum mechanical approach to the one used for the metallic nanoparticles. A variety of interaction sites are explored. Our results show that small-sized Cd4Se4 and Cd4S4 QDs interact strongly with the DNA nucleobase if a DNA nucleobase has the amide or hydroxyl chemical group. These results indicate that these QDs are suitable for detecting subcellular structures, as also reported by experiments. The next two chapters describe a preparation required for the simulation of nanoparticles interacting with membranes leading to accurate structure models for the membranes. We develop a method for the molecular crystalline structure prediction of 1,2-Dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC), 1,2-Dimyristoyl-sn-glycero-3-phosphorylethanolamine (DMPE) and cyclic di-amino acid peptide using first-principles methods. Since an accurate determination of the structure of an organic crystal is usually an extremely difficult task due to availability of the large number of its conformers, we propose a new computational scheme by applying knowledge of symmetry, structural chemistry and chemical bonding to reduce the sampling size of the conformation space. The interaction of metal nanoparticles with cell membranes is finally carried out by molecular dynamics simulations, and the results are reported in the last chapter. A new force field is developed which accurately describes the interaction forces between the clusters representing small-sized metal nanoparticles and the lipid bilayer molecules. The permeation of nanoparticles into the cell membrane is analyzed together with the RMSD values of the membrane modeled by a lipid bilayer. The simulation results suggest that the AgNPs could cause the same amount of deformation as the AuNPs for the dysfunction of the membrane.

DIFFUSE-INTERFACE FIELD APPROACH TO MODELING SELF-ASSEMBLY OF HETEROGENEOUS COLLOIDAL SYSTEMS AND RELATED DIPOLE-DIPOLE INTERACTION PHENOMENA

Colloid self-assembly under external control is a new route to fabrication of advanced materials with novel microstructures and appealing functionalities. The kinetic processes of colloidal self-assembly have attracted great interests also because they are similar to many atomic level kinetic processes of materials. In the past decades, rapid technological progresses have been achieved on producing shape-anisotropic, patchy, core-shell structured particles and particles with electric/magnetic charges/dipoles, which greatly enriched the self-assembled structures. Multi-phase carrier liquids offer new route to controlling colloidal self-assembly. Therefore, heterogeneity is the essential characteristics of colloid system, while so far there still lacks a model that is able to efficiently incorporate these possible heterogeneities. This thesis is mainly devoted to development of a model and computational study on the complex colloid system through a diffuse-interface field approach (DIFA), recently developed by Wang et al. This meso-scale model is able to describe arbitrary particle shape and arbitrary charge/dipole distribution on the surface or body of particles. Within the framework of DIFA, a Gibbs-Duhem-type formula is introduced to treat Laplace pressure in multi-liquid-phase colloidal system and it obeys Young-Laplace equation. The model is thus capable to quantitatively study important capillarity related phenomena. Extensive computer simulations are performed to study the fundamental behavior of heterogeneous colloidal system. The role of Laplace pressure is revealed in determining the mechanical equilibrium of shape-anisotropic particles at fluid interfaces. In particular, it is found that the Laplace pressure plays a critical role in maintaining the stability of capillary bridges between close particles, which sheds light on a novel route to in situ firming compact but fragile colloidal microstructures via capillary bridges. Simulation results also show that competition between like-charge repulsion, dipole-dipole interaction and Brownian motion dictates the degree of aggregation of heterogeneously charged particles. Assembly and alignment of particles with magnetic dipoles under external field is studied. Finally, extended studies on the role of dipole-dipole interaction are performed for ferromagnetic and ferroelectric domain phenomena. The results reveal that the internal field generated by dipoles competes with external field to determine the dipole-domain evolution in ferroic materials.

La pensée mixte : une approche de la composition par l'interaction des pensées instrumentale, électroacoustique et informatique

La « pensée mixte » est une approche de la composition caractérisée par l’interaction de trois pensées: la pensée instrumentale, la pensée électroacoustique et la pensée informatique. Elle prend la forme d’un réseau où le compositeur fait des aller-retours entre les trois pensées et réalise des équivalences paramétriques. La pensée instrumentale se rattache à la tradition de l’écriture occidentale, la pensée électroacoustique fait allusion aux pratiques du studio analogique et de la musique acousmatique, et la pensée informatique fait référence aux pratiques numériques de la programmation visuelle et de l’analyse spectrale. Des lieux communs existent où s’opèrent l’interaction des trois pensées: la notion du studio instrumental de Ivo Malec, la notion de musique concrète instrumentale de Helmut Lachenmann, la composition assistée par ordinateur, la musique spectrale, l’approche instrumentale par montage, la musique acousmatique s’inspirant de la tradition musicale écrite et les musiques mixtes. Ces domaines constituent les influences autour desquelles j’ai composé un corpus de deux cycles d’œuvres: Les Larmes du Scaphandre et le Nano-Cosmos. L’analyse des œuvres met en évidence la notion de « pensée mixte » en abordant la pensée électroacoustique dans ma pratique instrumentale, la pensée informatique dans ma pratique musicale, et la pensée instrumentale dans ma pratique électroacoustique.

La pensée mixte : une approche de la composition par l'interaction des pensées instrumentale, électroacoustique et informatique

La « pensée mixte » est une approche de la composition caractérisée par l’interaction de trois pensées: la pensée instrumentale, la pensée électroacoustique et la pensée informatique. Elle prend la forme d’un réseau où le compositeur fait des aller-retours entre les trois pensées et réalise des équivalences paramétriques. La pensée instrumentale se rattache à la tradition de l’écriture occidentale, la pensée électroacoustique fait allusion aux pratiques du studio analogique et de la musique acousmatique, et la pensée informatique fait référence aux pratiques numériques de la programmation visuelle et de l’analyse spectrale. Des lieux communs existent où s’opèrent l’interaction des trois pensées: la notion du studio instrumental de Ivo Malec, la notion de musique concrète instrumentale de Helmut Lachenmann, la composition assistée par ordinateur, la musique spectrale, l’approche instrumentale par montage, la musique acousmatique s’inspirant de la tradition musicale écrite et les musiques mixtes. Ces domaines constituent les influences autour desquelles j’ai composé un corpus de deux cycles d’œuvres: Les Larmes du Scaphandre et le Nano-Cosmos. L’analyse des œuvres met en évidence la notion de « pensée mixte » en abordant la pensée électroacoustique dans ma pratique instrumentale, la pensée informatique dans ma pratique musicale, et la pensée instrumentale dans ma pratique électroacoustique.

Improvement of The Driver Simulator Control and Comparison Between Driver-Road-Vehicle Interaction in Real and Simulated Environment

The present doctoral thesis discusses the ways to improve the performance of driving simulator, provide objective measures for the road safety evaluation methodology based on driver’s behavior and response and investigates the drivers' adaptation to the driving assistant systems. The activities are divided into two macro areas; the driving simulation studies and on-road experiments. During the driving simulation experimentation, the classical motion cueing algorithm with logarithmic scale was implemented in the 2DOF motion cueing simulator and the motion cues were found desirable by the participants. In addition, it found out that motion stimuli could change the behaviour of the drivers in terms of depth/distance perception. During the on-road experimentations, The driver gaze behaviour was investigated to find the objective measures on the visibility of the road signs and reaction time of the drivers. The sensor infusion and the vehicle monitoring instruments were found useful for an objective assessment of the pavement condition and the drivers’ performance. In the last chapter of the thesis, the safety assessment during the use of level 1 automated driving “ACC” is discussed with the simulator and on-road experiment. The drivers’ visual behaviour was investigated in both studies with innovative classification method to find the epochs of the distraction of the drivers. The behavioural adaptation to ACC showed that drivers may divert their attention away from the driving task to engage in secondary, non-driving-related tasks.

Characterization of DNA sequence properties through network and statistical approaches

In this thesis we will see that the DNA sequence is constantly shaped by the interactions with its environment at multiple levels, showing footprints of DNA methylation, of its 3D organization and, in the case of bacteria, of the interaction with the host organisms. In the first chapter, we will see that analyzing the distribution of distances between consecutive dinucleotides of the same type along the sequence, we can detect epigenetic and structural footprints. In particular, we will see that CG distance distribution allows to distinguish among organisms of different biological complexity, depending on how much CG sites are involved in DNA methylation. Moreover, we will see that CG and TA can be described by the same fitting function, suggesting a relationship between the two. We will also provide an interpretation of the observed trend, simulating a positioning process guided by the presence and absence of memory. In the end, we will focus on TA distance distribution, characterizing deviations from the trend predicted by the best fitting function, and identifying specific patterns that might be related to peculiar mechanical properties of the DNA and also to epigenetic and structural processes. In the second chapter, we will see how we can map the 3D structure of the DNA onto its sequence. In particular, we devised a network-based algorithm that produces a genome assembly starting from its 3D configuration, using as inputs Hi-C contact maps. Specifically, we will see how we can identify the different chromosomes and reconstruct their sequences by exploiting the spectral properties of the Laplacian operator of a network. In the third chapter, we will see a novel method for source clustering and source attribution, based on a network approach, that allows to identify host-bacteria interaction starting from the detection of Single-Nucleotide Polymorphisms along the sequence of bacterial genomes.