The role of water in determining structure and function of macromolecules and macromolecular assemblies /

The interaction of biological molecules with water is an important determinant of structural properties both in molecular assemblies, and in conformation of individual macromolecules. By observing the effects of manipulating the activity of water (which can be accomplished by limiting its concentration or by adding additional solutes, "osmotic stress"), one can learn something about intrinsic physical properties of biological molecules as well as measure an energetic contribution of closely associated water molecules to overall equilibria in biological reactions. Here two such studies are reported. The first of these examines several species of lysolipid which, while present in relatively low concentrations in biomembranes, have been shown to affect many cellular processes involving membrane-protein or membrane-membrane interactions. Monolayer elastic constants were determined by combining X-ray diffraction and the osmotic stress technique. Spontaneous radii of curvature of lysophosphatidylcholines were determined to be positive and in the range +30A to +70A, while lysophosphatidylethanolamines proved to be essentially flat. Neither lysolipid significantly affected the bending modulus of the monolayer in which it was incorporated. The second study examines the role of water in theprocess of polymerization of actin into filaments. Water activity was manipulated by adding osmolytes and the effect on the equilibrium dissociation constant (measured as the criticalmonomer concentration) was determined. As water activity was decreased, the critical concentration was reduced for Ca-actin but not for Mg-actin, suggesting that 10-12 fewer water molecules are associated with Ca-actin in the polymerized state. Thisunexpectedly small amount of water is discussed in the context of the common structural motif of a nucleotide binding cleft.

Characterization of the unfolding of a weak focus and modulus of analytic classification

La thèse présente une description géométrique d’un germe de famille générique déployant un champ de vecteurs réel analytique avec un foyer faible à l’origine et son complexifié : le feuilletage holomorphe singulier associé. On montre que deux germes de telles familles sont orbitalement analytiquement équivalents si et seulement si les germes de familles de difféomorphismes déployant la complexification de leurs fonctions de retour de Poincaré sont conjuguées par une conjugaison analytique réelle. Le “caractère réel” de la famille correspond à sa Z2-équivariance dans R^4, et cela s’exprime comme l’invariance du plan réel sous le flot du système laquelle, à son tour, entraîne que l’expansion asymptotique de la fonction de Poincaré est réelle quand le paramètre est réel. Le pullback du plan réel après éclatement par la projection monoidal standard intersecte le feuilletage en une bande de Möbius réelle. La technique d’éclatement des singularités permet aussi de donner une réponse à la question de la “réalisation” d’un germe de famille déployant un germe de difféomorphisme avec un point fixe de multiplicateur égal à −1 et de codimension un comme application de semi-monodromie d’une famille générique déployant un foyer faible d’ordre un. Afin d’étudier l’espace des orbites de l’application de Poincaré, nous utilisons le point de vue de Glutsyuk, puisque la dynamique est linéarisable auprès des points singuliers : pour les valeurs réels du paramètre, notre démarche, classique, utilise une méthode géométrique, soit un changement de coordonée (coordonée “déroulante”) dans lequel la dynamique devient beaucoup plus simple. Mais le prix à payer est que la géométrie locale du plan complexe ambiante devient une surface de Riemann, sur laquelle deux notions de translation sont définies. Après avoir pris le quotient par le relèvement de la dynamique nous obtenons l’espace des orbites, ce qui s’avère être l’union de trois tores complexes plus les points singuliers (l’espace résultant est non-Hausdorff). Les translations, le caractère réel de l’application de Poincaré et le fait que cette application est un carré relient les différentes composantes du “module de Glutsyuk”. Cette propriété implique donc le fait qu’une seule composante de l’invariant Glutsyuk est indépendante.

Développement d'une nouvelle méthode de caractérisation tissulaire basée sur l'élastographie ultrasonore : application pour le dépistage précoce du cancer du sein

Le cancer du sein est le cancer le plus fréquent chez la femme. Il demeure la cause de mortalité la plus importante chez les femmes âgées entre 35 et 55 ans. Au Canada, plus de 20 000 nouveaux cas sont diagnostiqués chaque année. Les études scientifiques démontrent que l'espérance de vie est étroitement liée à la précocité du diagnostic. Les moyens de diagnostic actuels comme la mammographie, l'échographie et la biopsie comportent certaines limitations. Par exemple, la mammographie permet de diagnostiquer la présence d’une masse suspecte dans le sein, mais ne peut en déterminer la nature (bénigne ou maligne). Les techniques d’imagerie complémentaires comme l'échographie ou l'imagerie par résonance magnétique (IRM) sont alors utilisées en complément, mais elles sont limitées quant à la sensibilité et la spécificité de leur diagnostic, principalement chez les jeunes femmes (< 50 ans) ou celles ayant un parenchyme dense. Par conséquent, nombreuses sont celles qui doivent subir une biopsie alors que leur lésions sont bénignes. Quelques voies de recherche sont privilégiées depuis peu pour réduire l`incertitude du diagnostic par imagerie ultrasonore. Dans ce contexte, l’élastographie dynamique est prometteuse. Cette technique est inspirée du geste médical de palpation et est basée sur la détermination de la rigidité des tissus, sachant que les lésions en général sont plus rigides que le tissu sain environnant. Le principe de cette technique est de générer des ondes de cisaillement et d'en étudier la propagation de ces ondes afin de remonter aux propriétés mécaniques du milieu via un problème inverse préétabli. Cette thèse vise le développement d'une nouvelle méthode d'élastographie dynamique pour le dépistage précoce des lésions mammaires. L'un des principaux problèmes des techniques d'élastographie dynamiques en utilisant la force de radiation est la forte atténuation des ondes de cisaillement. Après quelques longueurs d'onde de propagation, les amplitudes de déplacement diminuent considérablement et leur suivi devient difficile voir impossible. Ce problème affecte grandement la caractérisation des tissus biologiques. En outre, ces techniques ne donnent que l'information sur l'élasticité tandis que des études récentes montrent que certaines lésions bénignes ont les mêmes élasticités que des lésions malignes ce qui affecte la spécificité de ces techniques et motive la quantification de d'autres paramètres mécaniques (e.g.la viscosité). Le premier objectif de cette thèse consiste à optimiser la pression de radiation acoustique afin de rehausser l'amplitude des déplacements générés. Pour ce faire, un modèle analytique de prédiction de la fréquence de génération de la force de radiation a été développé. Une fois validé in vitro, ce modèle a servi pour la prédiction des fréquences optimales pour la génération de la force de radiation dans d'autres expérimentations in vitro et ex vivo sur des échantillons de tissu mammaire obtenus après mastectomie totale. Dans la continuité de ces travaux, un prototype de sonde ultrasonore conçu pour la génération d'un type spécifique d'ondes de cisaillement appelé ''onde de torsion'' a été développé. Le but est d'utiliser la force de radiation optimisée afin de générer des ondes de cisaillement adaptatives, et de monter leur utilité dans l'amélioration de l'amplitude des déplacements. Contrairement aux techniques élastographiques classiques, ce prototype permet la génération des ondes de cisaillement selon des parcours adaptatifs (e.g. circulaire, elliptique,…etc.) dépendamment de la forme de la lésion. L’optimisation des dépôts énergétiques induit une meilleure réponse mécanique du tissu et améliore le rapport signal sur bruit pour une meilleure quantification des paramètres viscoélastiques. Il est aussi question de consolider davantage les travaux de recherches antérieurs par un appui expérimental, et de prouver que ce type particulier d'onde de torsion peut mettre en résonance des structures. Ce phénomène de résonance des structures permet de rehausser davantage le contraste de déplacement entre les masses suspectes et le milieu environnant pour une meilleure détection. Enfin, dans le cadre de la quantification des paramètres viscoélastiques des tissus, la dernière étape consiste à développer un modèle inverse basé sur la propagation des ondes de cisaillement adaptatives pour l'estimation des paramètres viscoélastiques. L'estimation des paramètres viscoélastiques se fait via la résolution d'un problème inverse intégré dans un modèle numérique éléments finis. La robustesse de ce modèle a été étudiée afin de déterminer ces limites d'utilisation. Les résultats obtenus par ce modèle sont comparés à d'autres résultats (mêmes échantillons) obtenus par des méthodes de référence (e.g. Rheospectris) afin d'estimer la précision de la méthode développée. La quantification des paramètres mécaniques des lésions permet d'améliorer la sensibilité et la spécificité du diagnostic. La caractérisation tissulaire permet aussi une meilleure identification du type de lésion (malin ou bénin) ainsi que son évolution. Cette technique aide grandement les cliniciens dans le choix et la planification d'une prise en charge adaptée.

Ultrasonic Study Of The Elastic Properties And Phase Transitions In Selected Mixed Sulphate Crystals

The thesis investigated the elastic properties and phase transitions in selected mixed sulphate crystals – Lithium Hydrazinium Sulphate [LiN2H2SO4], Lithium Ammonium Sulphate [LiNH4SO4] and Lithium Potassium Sulphate [LiKSO4] – using ultrasonic technique. The pulse echo overlap technique has been used for measuring ultrasonic velocity and its dependence on temperature along different directions with waves of longitudinal and transverse polarizations. Two major numerical techniques and the corresponding computer programs developed as part of present work are presented in this thesis. All the 9 elastic constants of LHS are determined accurately from ultrasonic measurements and applying misorientation correction refines the constants. Ultrasonic measurements are performed in LAS to determine the elastic constants and to study the low temperature phase transitions. Temperature variation studies of elastic constant of LAS are performed for 6 different modes of propagation for heating and cooling at low temperatures. All the 5 independent elastic constants of LPS is determined using ultrasonic measurements. It is concluded that LPS crystal does not undergo a phase transition near this temperature. A comparison of the three crystals studied shows that LPS has maximum number of phase transitions and LHS has the least number. It is interesting to note that LPS has the simplest formula unit among the three. There is considerable scope for the future work on these crystals and others belonging to the sulphate family.

Elastic Constants And Structural Parameters Of Selected Polycrystalline Ceramics By Ultrasonic Technique

The present work is an attempt to probe the elastic properties in some dielectric ceramics, by using ultrasonic pulse echo overlap technique. The base Ba6-xSm8+2xTi18O54 and Ca5Nb2TiO12 are very important dielectrics ceramics used for microwave communication as well as for substrate materials. Ultrasonic is one of the most widely used and powerful techniques to measure elastic properties of solids. The ultrasonic technique is nondestructive in nature and the measurements are relatively straightforward to perform. One unique advantantage of the ultrasonic technique is that both static and dynamic properties can be measured simultaneously. The velocity and attenuation coefficients of the ultrasonic waves propagating through a medium are related to the microscopic structure of the material and they provide valuable information about the structural changes in the system. Among the various ultrasonic techniques, the pulse echo overlap method is the most accurate and precise one. In the present case the decreased elastic properties of Cas-XMg,Nb2TiO12 and Cas-,ZnNb2TiO12 ceramics can be attributed to their mixture phases beyond x = 1. Moreover, the abrupt change in elastic properties observed for x >1 can also be correlated to the structural transformation of the materials from their phase pure form to mixture phases for higher extent of substitution of the concerned material . Ca4(ANb2Ti)012 (A = Mg, Zn) is the strongest compound with the maximum values for elastic properties . This could be due to the possible substitution of Mg/Zn ions with lesser radius [25] than Ca2+ in perovskite B-site of Ca(Cali4Nb2i4Tili4) O3 material to contribute more ordering and symmetry to the system [20]. All other compositions (x > 1) contain mixed-phases and for such mixed-phase samples, the mechanical properties are difficult to explain.

Elastic constant measurements of super ionic LiKSO4:Na single crystals

Elastic properties of sodium doped Lithium potassium sulphate, LiK0.9Na0.1SO4, crystal has been studied by ultrasonic Pulse Echo Overlap [PEO] technique and are reported for the first time. The controversy regarding the type of crystal found while growth is performed at 35 °C with equimolar fraction of Li2SO4H2O, K2SO4 and Na2SO4 has been resolved by studying the elastic properties. The importance of this crystal is that it exhibits pyroelectric, ferroelectric and electro optic properties. It is simultaneously ferroelastic and superionic. The elastic properties of LiK0.9Na0.1SO4 crystal are well studied by measuring ultrasonic velocity in the crystal in certain specified crystallographic directions and evaluating the elastic stiffness constants, compliance constants and Poisson’s ratios. The anisotropy in the elastic properties of the crystal are well explained by the pictorial representation of the surface plots of phase velocity, slowness and linear compressibility in a-b and a-c planes.

Young’s modulus of silicon nitride used in scanning force microscope cantilevers

The Young’s modulus and Poisson’s ratio of high-quality silicon nitride films with 800 nm thickness, grown on silicon substrates by low-pressure chemical vapor deposition, were determined by measuring the dispersion of laser-induced surface acoustic waves. The Young’s modulus was also measured by mechanical tuning of commercially available silicon nitride cantilevers, manufactured from the same material, using the tapping mode of a scanning force microscope. For this experiment, an expression for the oscillation frequencies of two-media beam systems is derived. Both methods yield a Young’s modulus of 280–290 GPa for amorphous silicon nitride, which is substantially higher than previously reported (E5146 GPa). For Poisson’s ratio, a value of n 50.20 was obtained. These values are relevant for the determination of the spring constant of the cantilever and the effective tip–sample stiffness

Finite Element Analysis of Warship Structures

Warships are generally sleek, slender with V shaped sections and block coefficient below 0.5, compared to fuller forms and higher values for commercial ships. They normally operate in the higher Froude number regime, and the hydrodynamic design is primarily aimed at achieving higher speeds with the minimum power. Therefore the structural design and analysis methods are different from those for commercial ships. Certain design guidelines have been given in documents like Naval Engineering Standards and one of the new developments in this regard is the introduction of classification society rules for the design of warships.The marine environment imposes subjective and objective uncertainties on ship structure. The uncertainties in loads, material properties etc.,. make reliable predictions of ship structural response a difficult task. Strength, stiffness and durability criteria for warship structures can be established by investigations on elastic analysis, ultimate strength analysis and reliability analysis. For analysis of complicated warship structures, special means and valid approximations are required.Preliminary structural design of a frigate size ship has been carried out . A finite element model of the hold model, representative of the complexities in the geometric configuration has been created using the finite element software NISA. Two other models representing the geometry to a limited extent also have been created —- one with two transverse frames and the attached plating alongwith the longitudinal members and the other representing the plating and longitudinal stiffeners between two transverse frames. Linear static analysis of the three models have been carried out and each one with three different boundary conditions. The structural responses have been checked for deflections and stresses against the permissible values. The structure has been found adequate in all the cases. The stresses and deflections predicted by the frame model are comparable with those of the hold model. But no such comparison has been realized for the interstiffener plating model with the other two models.Progressive collapse analyses of the models have been conducted for the three boundary conditions, considering geometric nonlinearity and then combined geometric and material nonlinearity for the hold and the frame models. von Mises — lllyushin yield criteria with elastic-perfectly plastic stress-strain curve has been chosen. ln each case, P-Delta curves have been generated and the ultimate load causing failure (ultimate load factor) has been identified as a multiple of the design load specified by NES.Reliability analysis of the hull module under combined geometric and material nonlinearities have been conducted. The Young's Modulus and the shell thickness have been chosen as the variables. Randomly generated values have been used in the analysis. First Order Second Moment has been used to predict the reliability index and thereafter, the probability of failure. The values have been compared against standard values published in literature.

Third order elastic constants of bcc Cu-Al-Ni

We have measured the changes in the ultrasonic wave velocity, induced by the application of uniaxial stresses in a Cu-Al-Ni single crystal. From these measurements, the complete set of third-order elastic constants has been obtained. The comparison of results for Cu-Al-Ni with available data for other Cu-based alloys has shown that all these alloys exhibit similar anharmonic behavior. By using the measured elastic constants in a Landau expansion for elastic phase transitions, we have been able to give an estimation of the value of a fourth-order elastic constants combination. The experiments have also shown that the application of a stress in the [001] direction, reduces the material resistance to a (110)[110] shear and thus favors the martensitic transition.

Elastic constants of Ni-Mn-Ga magnetic shape memory alloys

We have measured the adiabatic second order elastic constants of two Ni-Mn-Ga magnetic shape memory crystals with different martensitic transition temperatures, using ultrasonic methods. The temperature dependence of the elastic constants has been followed across the ferromagnetic transition and down to the martensitic transition temperature. Within experimental errors no noticeable change in any of the elastic constants has been observed at the Curie point. The temperature dependence of the shear elastic constant C' has been found to be very different for the two alloys. Such a different behavior is in agreement with recent theoretical predictions for systems undergoing multi-stage structural transitions.

Comment on "Reappraisal of experimental values of third-order elastic constants of some cubic semiconductors and metals"

In a recent paper A. S. Johal and D. J. Dunstan [Phys. Rev. B 73, 024106 (2006)] have applied multivariate linear regression analysis to the published data of the change in ultrasonic velocity with applied stress. The aim is to obtain the best estimates for the third-order elastic constants in cubic materials. From such an analysis they conclude that uniaxial stress data on metals turns out to be nearly useless by itself. The purpose of this comment is to point out that by a proper analysis of uniaxial stress data it is possible to obtain reliable values of third-order elastic constants in cubic metals and alloys. Cu-based shape memory alloys are used as an illustrative example.

Temperature and magnetic-field dependence of the elastic constants of Ni-Mn-Al magnetic Heusler alloy

We report on measurements of the adiabatic second-order elastic constants of the off-stoichiometric Ni54Mn23Al23 single-crystalline Heusler alloy. The variation in the temperature dependence of the elastic constants has been investigated across the magnetic transition and over a broad temperature range. Anomalies in the temperature behavior of the elastic constants have been found in the vicinity of the magnetic phase transition. Measurements under applied magnetic field, both isothermal and variable temperature, show that the value of the elastic constants depends on magnetic order, thus giving evidence for magnetoelastic coupling in this alloy system.

Shot noise anomalies in elastic nondegenerate diffusive conductors

We present a theoretical investigation of shot-noise properties in nondegenerate elastic diffusive conductors. Both Monte Carlo simulations and analytical approaches are used. Two interesting phenomena are found: (i) the display of enhanced shot noise for given energy dependences of the scattering time, and (ii) the recovery of full shot noise for asymptotic high applied bias. The first phenomenon is associated with the onset of negative differential conductivity in energy space that drives the system towards a dynamical electrical instability in excellent agreement with analytical predictions. The enhancement is found to be strongly amplified when the dimensionality in momentum space is lowered from three to two dimensions. The second phenomenon is due to the suppression of the effects of long-range Coulomb correlations that takes place when the transit time becomes the shortest time scale in the system, and is common to both elastic and inelastic nondegenerate diffusive conductors. These phenomena shed different light in the understanding of the anomalous behavior of shot noise in mesoscopic conductors, which is a signature of correlations among different current pulses.