Complex chemical dynamics through engineering-like methods

Most of the problems in modern structural design can be described with a set of equation; solutions of these mathematical models can lead the engineer and designer to get info during the design stage. The same holds true for physical-chemistry; this branch of chemistry uses mathematics and physics in order to explain real chemical phenomena. In this work two extremely different chemical processes will be studied; the dynamic of an artificial molecular motor and the generation and propagation of the nervous signals between excitable cells and tissues like neurons and axons. These two processes, in spite of their chemical and physical differences, can be both described successfully by partial differential equations, that are, respectively the Fokker-Planck equation and the Hodgkin and Huxley model. With the aid of an advanced engineering software these two processes have been modeled and simulated in order to extract a lot of physical informations about them and to predict a lot of properties that can be, in future, extremely useful during the design stage of both molecular motors and devices which rely their actions on the nervous communications between active fibres.

Sea level measurement using single GNSS antenna SNR signals

This thesis presents a possible method to calculate sea level variation using geodetic-quality Global Navigate Satellite System (GNSS) receivers. Three antennas are used: two small antennas and a choke ring one, analyzing only Global Positioning System signals. The main goal of the thesis is to test a modified configuration for antenna set up. In particular, measurements obtained tilting one antenna to face the horizon are compared to measurements obtained from antennas looking upward. The location of the experiment is a coastal environment nearby the Onsala Space Observatory in Sweden. Sea level variations are obtained using periodogram analysis of the SNR signal and compared to synthetic gauge generated from two independent tide gauges. The choke ring antenna provides poor result, with an RMS around 6 cm and a correlation coefficients of 0.89. The smaller antennas provide correlation coefficients around 0.93. The antenna pointing upward present an RMS of 4.3 cm and the one pointing the horizon an RMS of 6.7 cm. Notable variation in the statistical parameters is found when modifying the length of the interval analyzed. In particular, doubts are risen on the reliability of certain scattered data. No relation is found between the accuracy of the method and weather conditions. Possible methods to enhance the available data are investigated, and correlation coefficient above 0.97 can be obtained with small antennas when sacrificing data points. Hence, the results provide evidence of the suitability of SNR signal analysis for sea level variation in coastal environment even in the case of adverse weather conditions. In particular, tilted configurations provides comparable result with upward looking geodetic antennas. A SNR signal simulator is also tested to investigate its performance and usability. Various configuration are analyzed in combination with the periodogram procedure used to calculate the height of reflectors. Consistency between the data calculated and those received is found, and the overall accuracy of the height calculation program is found to be around 5 mm for input height below 5 m. The procedure is thus found to be suitable to analyze the data provided by the GNSS antennas at Onsala.

Dynamic development of hydrofractures

Natürliche hydraulische Bruchbildung ist in allen Bereichen der Erdkruste ein wichtiger und stark verbreiteter Prozess. Sie beeinflusst die effektive Permeabilität und Fluidtransport auf mehreren Größenordnungen, indem sie hydraulische Konnektivität bewirkt. Der Prozess der Bruchbildung ist sowohl sehr dynamisch als auch hoch komplex. Die Dynamik stammt von der starken Wechselwirkung tektonischer und hydraulischer Prozesse, während sich die Komplexität aus der potentiellen Abhängigkeit der poroelastischen Eigenschaften von Fluiddruck und Bruchbildung ergibt. Die Bildung hydraulischer Brüche besteht aus drei Phasen: 1) Nukleation, 2) zeitabhängiges quasi-statisches Wachstum so lange der Fluiddruck die Zugfestigkeit des Gesteins übersteigt, und 3) in heterogenen Gesteinen der Einfluss von Lagen unterschiedlicher mechanischer oder sedimentärer Eigenschaften auf die Bruchausbreitung. Auch die mechanische Heterogenität, die durch präexistierende Brüche und Gesteinsdeformation erzeugt wird, hat großen Einfluß auf den Wachstumsverlauf. Die Richtung der Bruchausbreitung wird entweder durch die Verbindung von Diskontinuitäten mit geringer Zugfestigkeit im Bereich vor der Bruchfront bestimmt, oder die Bruchausbreitung kann enden, wenn der Bruch auf Diskontinuitäten mit hoher Festigkeit trifft. Durch diese Wechselwirkungen entsteht ein Kluftnetzwerk mit komplexer Geometrie, das die lokale Deformationsgeschichte und die Dynamik der unterliegenden physikalischen Prozesse reflektiert. rnrnNatürliche hydraulische Bruchbildung hat wesentliche Implikationen für akademische und kommerzielle Fragestellungen in verschiedenen Feldern der Geowissenschaften. Seit den 50er Jahren wird hydraulisches Fracturing eingesetzt, um die Permeabilität von Gas und Öllagerstätten zu erhöhen. Geländebeobachtungen, Isotopenstudien, Laborexperimente und numerische Analysen bestätigen die entscheidende Rolle des Fluiddruckgefälles in Verbindung mit poroelastischen Effekten für den lokalen Spannungszustand und für die Bedingungen, unter denen sich hydraulische Brüche bilden und ausbreiten. Die meisten numerischen hydromechanischen Modelle nehmen für die Kopplung zwischen Fluid und propagierenden Brüchen vordefinierte Bruchgeometrien mit konstantem Fluiddruck an, um das Problem rechnerisch eingrenzen zu können. Da natürliche Gesteine kaum so einfach strukturiert sind, sind diese Modelle generell nicht sonderlich effektiv in der Analyse dieses komplexen Prozesses. Insbesondere unterschätzen sie die Rückkopplung von poroelastischen Effekten und gekoppelte Fluid-Festgestein Prozesse, d.h. die Entwicklung des Porendrucks in Abhängigkeit vom Gesteinsversagen und umgekehrt.rnrnIn dieser Arbeit wird ein zweidimensionales gekoppeltes poro-elasto-plastisches Computer-Model für die qualitative und zum Teil auch quantitativ Analyse der Rolle lokalisierter oder homogen verteilter Fluiddrücke auf die dynamische Ausbreitung von hydraulischen Brüchen und die zeitgleiche Evolution der effektiven Permeabilität entwickelt. Das Programm ist rechnerisch effizient, indem es die Fluiddynamik mittels einer Druckdiffusions-Gleichung nach Darcy ohne redundante Komponenten beschreibt. Es berücksichtigt auch die Biot-Kompressibilität poröser Gesteine, die implementiert wurde um die Kontrollparameter in der Mechanik hydraulischer Bruchbildung in verschiedenen geologischen Szenarien mit homogenen und heterogenen Sedimentären Abfolgen zu bestimmen. Als Resultat ergibt sich, dass der Fluiddruck-Gradient in geschlossenen Systemen lokal zu Störungen des homogenen Spannungsfeldes führen. Abhängig von den Randbedingungen können sich diese Störungen eine Neuausrichtung der Bruchausbreitung zur Folge haben kann. Durch den Effekt auf den lokalen Spannungszustand können hohe Druckgradienten auch schichtparallele Bruchbildung oder Schlupf in nicht-entwässerten heterogenen Medien erzeugen. Ein Beispiel von besonderer Bedeutung ist die Evolution von Akkretionskeilen, wo die große Dynamik der tektonischen Aktivität zusammen mit extremen Porendrücken lokal starke Störungen des Spannungsfeldes erzeugt, die eine hoch-komplexe strukturelle Entwicklung inklusive vertikaler und horizontaler hydraulischer Bruch-Netzwerke bewirkt. Die Transport-Eigenschaften der Gesteine werden stark durch die Dynamik in der Entwicklung lokaler Permeabilitäten durch Dehnungsbrüche und Störungen bestimmt. Möglicherweise besteht ein enger Zusammenhang zwischen der Bildung von Grabenstrukturen und großmaßstäblicher Fluid-Migration. rnrnDie Konsistenz zwischen den Resultaten der Simulationen und vorhergehender experimenteller Untersuchungen deutet darauf hin, dass das beschriebene numerische Verfahren zur qualitativen Analyse hydraulischer Brüche gut geeignet ist. Das Schema hat auch Nachteile wenn es um die quantitative Analyse des Fluidflusses durch induzierte Bruchflächen in deformierten Gesteinen geht. Es empfiehlt sich zudem, das vorgestellte numerische Schema um die Kopplung mit thermo-chemischen Prozessen zu erweitern, um dynamische Probleme im Zusammenhang mit dem Wachstum von Kluftfüllungen in hydraulischen Brüchen zu untersuchen.

Comparative study of the different models for the calculation of BLEVEs overpressure effects

The BLEVE, acronym for Boiling Liquid Expanding Vapour Explosion, is one of the most dangerous accidents that can occur in pressure vessels. It can be defined as an explosion resulting from the failure of a vessel containing a pressure liquefied gas stored at a temperature significantly above its boiling point at atmospheric pressure. This phenomenon frequently appears when a vessel is engulfed by a fire: the heat causes the internal pressure to raise and the mechanical proprieties of the wall to decrease, with the consequent rupture of the tank and the instantaneous release of its whole content. After the breakage, the vapour outflows and expands and the liquid phase starts boiling due to the pressure drop. The formation and propagation of a distructive schock wave may occur, together with the ejection of fragments, the generation of a fireball if the stored fluid is flammable and immediately ignited or the atmospheric dispersion of a toxic cloud if the fluid contained inside the vessel is toxic. Despite the presence of many studies on the BLEVE mechanism, the exact causes and conditions of its occurrence are still elusive. In order to better understand this phenomenon, in the present study first of all the concept and definition of BLEVE are investigated. A historical analysis of the major events that have occurred over the past 60 years is described. A research of the principal causes of this event, including the analysis of the substances most frequently involved, is presented too. Afterwards a description of the main effects of BLEVEs is reported, focusing especially on the overpressure. Though the major aim of the present thesis is to contribute, with a comparative analysis, to the validation of the main models present in the literature for the calculation and prediction of the overpressure caused by BLEVEs. In line with this purpose, after a short overview of the available approaches, their ability to reproduce the trend of the overpressure is investigated. The overpressure calculated with the different models is compared with values deriving from events happened in the past and ad-hoc experiments, focusing the attention especially on medium and large scale phenomena. The ability of the models to consider different filling levels of the reservoir and different substances is analyzed too. The results of these calculations are extensively discussed. Finally some conclusive remarks are reported.

Alpha4beta1 integrin mediates the recruitment of immature dendritic cells across the blood-brain barrier during experimental autoimmune encephalomyelitis

Dendritic cells (DCs) within the CNS are recognized to play an important role in the effector phase and propagation of the immune response in experimental autoimmune encephalomyelitis (EAE), a mouse model for multiple sclerosis. However, the mechanisms regulating DC trafficking into the CNS still need to be characterized. In this study, we show by performing intravital fluorescence videomicroscopy of the inflamed spinal cord white-matter microvasculature in SJL mice with EAE that immature, and to a lesser extent, LPS-matured, bone marrow-derived DCs efficiently interact with the CNS endothelium by rolling, capturing, and firm adhesion. Immature but not LPS-matured DCs efficiently migrated across the wall of inflamed parenchymal microvessels into the CNS. Blocking alpha4 integrins interfered with the adhesion but not the rolling or capturing of immature and LPS-matured DCs to the CNS microvascular endothelium, inhibiting their migration across the vascular wall. Functional absence of beta1 integrins but not of beta7 integrins or alpha4beta7 integrin similarly reduced the adhesion of immature DCs to the CNS microvascular endothelium, demonstrating that alpha4beta1 but not alpha4beta7 integrin mediates this step of immature DCs interaction with the inflamed blood-brain barrier during EAE. Our study shows that during EAE, especially immature DCs migrate into the CNS, where they may be crucial for the perpetuation of the CNS-targeted autoimmune response. Thus therapeutic targeting of alpha4 integrins affects DC trafficking into the CNS and may therefore lead to the resolution of the CNS autoimmune inflammation by reducing the number of CNS professional APCs.

Structural basis for the regulation of cysteine-protease activity by a new class of protease inhibitors in Plasmodium

Plasmodium cysteine proteases are essential for host-cell invasion and egress, hemoglobin degradation, and intracellular development of the parasite. The temporal, site-specific regulation of cysteine-protease activity is a prerequisite for survival and propagation of Plasmodium. Recently, a new family of inhibitors of cysteine proteases (ICPs) with homologs in at least eight Plasmodium species has been identified. Here, we report the 2.6 A X-ray crystal structure of the C-terminal, inhibitory domain of ICP from P. berghei (PbICP-C) in a 1:1 complex with falcipain-2, an important hemoglobinase of Plasmodium. The structure establishes Plasmodium ICP as a member of the I42 class of chagasin-like protease inhibitors but with large insertions and differences in the binding mode relative to other family members. Furthermore, the PbICP-C structure explains why host-cell cathepsin B-like proteases and, most likely, also the protease-like domain of Plasmodium SERA5 (serine-repeat antigen 5) are no targets for ICP.

Cardiac sodium channel NaV1.5 distribution in myocytes via interacting proteins: the multiple pool model

The cardiac sodium current (INa) is responsible for the rapid depolarization of cardiac cells, thus allowing for their contraction. It is also involved in regulating the duration of the cardiac action potential (AP) and propagation of the impulse throughout the myocardium. Cardiac INa is generated by the voltage-gated Na(+) channel, NaV1.5, a 2016-residue protein which forms the pore of the channel. Over the past years, hundreds of mutations in SCN5A, the human gene coding for NaV1.5, have been linked to many cardiac electrical disorders, including the congenital and acquired long QT syndrome, Brugada syndrome, conduction slowing, sick sinus syndrome, atrial fibrillation, and dilated cardiomyopathy. Similar to many membrane proteins, NaV1.5 has been found to be regulated by several interacting proteins. In some cases, these different proteins, which reside in distinct membrane compartments (i.e. lateral membrane vs. intercalated disks), have been shown to interact with the same regulatory domain of NaV1.5, thus suggesting that several pools of NaV1.5 channels may co-exist in cardiac cells. The aim of this review article is to summarize the recent works that demonstrate its interaction with regulatory proteins and illustrate the model that the sodium channel NaV1.5 resides in distinct and different pools in cardiac cells. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Cardiac Pathways of Differentiation, Metabolism and Contraction.

Direction finding in the presence of a more realistic environment model

Direction-of-arrival (DOA) estimation is susceptible to errors introduced by the presence of real-ground and resonant size scatterers in the vicinity of the antenna array. To compensate for these errors pre-calibration and auto-calibration techniques are presented. The effects of real-ground constituent parameters on the mutual coupling (MC) of wire type antenna arrays for DOA estimation are investigated. This is accomplished by pre-calibration of the antenna array over the real-ground using the finite element method (FEM). The mutual impedance matrix is pre-estimated and used to remove the perturbations in the received terminal voltage. The unperturbed terminal voltage is incorporated in MUSIC algorithm to estimate DOAs. First, MC of quarter wave monopole antenna arrays is investigated. This work augments an existing MC compensation technique for ground-based antennas and proposes reduction in MC for antennas over finite ground as compared to the perfect ground. A factor of 4 decrease in both the real and imaginary parts of the MC is observed when considering a poor ground versus a perfectly conducting one for quarter wave monopoles in the receiving mode. A simulated result to show the compensation of errors direction of arrival (DOA) estimation with actual realization of the environment is also presented. Secondly, investigations for the effects on received MC of λ/2 dipole arrays placed near real-earth are carried out. As a rule of thumb, estimation of mutual coupling can be divided in two regions of antenna height that is very near ground 0

QUANTUM CORRELATIONS OF LIGHTS IN MACROSCOPIC ENVIRONMENTS

This dissertation presents a detailed study in exploring quantum correlations of lights in macroscopic environments. We have explored quantum correlations of single photons, weak coherent states, and polarization-correlated/polarization-entangled photons in macroscopic environments. These included macroscopic mirrors, macroscopic photon number, spatially separated observers, noisy photons source and propagation medium with loss or disturbances. We proposed a measurement scheme for observing quantum correlations and entanglement in the spatial properties of two macroscopic mirrors using single photons spatial compass state. We explored the phase space distribution features of spatial compass states, such as chessboard pattern by using the Wigner function. The displacement and tilt correlations of the two mirrors were manifested through the propensities of the compass states. This technique can be used to extract Einstein-Podolsky-Rosen correlations (EPR) of the two mirrors. We then formulated the discrete-like property of the propensity Pb(m,n), which can be used to explore environmental perturbed quantum jumps of the EPR correlations in phase space. With single photons spatial compass state, the variances in position and momentum are much smaller than standard quantum limit when using a Gaussian TEM00 beam. We observed intrinsic quantum correlations of weak coherent states between two parties through balanced homodyne detection. Our scheme can be used as a supplement to decoy-state BB84 protocol and differential phase-shift QKD protocol. We prepared four types of bipartite correlations ±cos2(θ12) that shared between two parties. We also demonstrated bits correlations between two parties separated by 10 km optical fiber. The bits information will be protected by the large quantum phase fluctuation of weak coherent states, adding another physical layer of security to these protocols for quantum key distribution. Using 10 m of highly nonlinear fiber (HNLF) at 77 K, we observed coincidence to accidental-coincidence ratio of 130±5 for correlated photon-pair and Two-Photon Interference visibility >98% entangled photon-pair. We also verified the non-local behavior of polarization-entangled photon pair by violating Clauser-Horne-Shimony-Holt Bell’s inequality by more than 12 standard deviations. With the HNLF at 300 K (77 K), photon-pair production rate about factor 3(2) higher than a 300 m dispersion-shifted fiber is observed. Then, we studied quantum correlation and interference of photon-pairs; with one photon of the photon-air experiencing multiple scattering in a random medium. We observed that depolarization noise photon in multiple scattering degrading the purity of photon-pair, and the existence of Raman noise photon in a photon-pair source will contribute to the depolarization affect. We found that quantum correlation of polarization-entangled photon-pair is better preserved than polarization-correlated photon-pair as one photon of the photon-pair scattered through a random medium. Our findings showed that high purity polarization-entangled photon-pair is better candidate for long distance quantum key distribution.

Combining Monte Carlo methods with coherent wave optics for the simulation of phase-sensitive X-ray imaging

Phase-sensitive X-ray imaging shows a high sensitivity towards electron density variations, making it well suited for imaging of soft tissue matter. However, there are still open questions about the details of the image formation process. Here, a framework for numerical simulations of phase-sensitive X-ray imaging is presented, which takes both particle- and wave-like properties of X-rays into consideration. A split approach is presented where we combine a Monte Carlo method (MC) based sample part with a wave optics simulation based propagation part, leading to a framework that takes both particle- and wave-like properties into account. The framework can be adapted to different phase-sensitive imaging methods and has been validated through comparisons with experiments for grating interferometry and propagation-based imaging. The validation of the framework shows that the combination of wave optics and MC has been successfully implemented and yields good agreement between measurements and simulations. This demonstrates that the physical processes relevant for developing a deeper understanding of scattering in the context of phase-sensitive imaging are modelled in a sufficiently accurate manner. The framework can be used for the simulation of phase-sensitive X-ray imaging, for instance for the simulation of grating interferometry or propagation-based imaging.

Ion channel macromolecular complexes in cardiomyocytes: roles in sudden cardiac death.

The movement of ions across specific channels embedded on the membrane of individual cardiomyocytes is crucial for the generation and propagation of the cardiac electric impulse. Emerging evidence over the past 20 years strongly suggests that the normal electric function of the heart is the result of dynamic interactions of membrane ion channels working in an orchestrated fashion as part of complex molecular networks. Such networks work together with exquisite temporal precision to generate each action potential and contraction. Macromolecular complexes play crucial roles in transcription, translation, oligomerization, trafficking, membrane retention, glycosylation, post-translational modification, turnover, function, and degradation of all cardiac ion channels known to date. In addition, the accurate timing of each cardiac beat and contraction demands, a comparable precision on the assembly and organizations of sodium, calcium, and potassium channel complexes within specific subcellular microdomains, where physical proximity allows for prompt and efficient interaction. This review article, part of the Compendium on Sudden Cardiac Death, discusses the major issues related to the role of ion channel macromolecular assemblies in normal cardiac electric function and the mechanisms of arrhythmias leading to sudden cardiac death. It provides an idea of how these issues are being addressed in the laboratory and in the clinic, which important questions remain unanswered, and what future research will be needed to improve knowledge and advance therapy.

Variedades de uva en Chile y Argentina (1550-1850). Genealogía del torrontés

Cuyo y Chile central constituyen, desde el siglo XVIII hasta hoy, el principal polo vitivinícola de América Latina y uno de los con mayor desarrollo del mundo. Su producción de vinos y aguardientes ha tenido fuertes implicancias sociales, económicas, políticas y culturales en la región. En la base de este proceso se encuentra el cultivo de la vid, trabajo agrícola intensivo y especializado, en el cual los vidueños tienen una relevancia central. Este artículo examina las variedades cultivadas en la región a partir de documentos originales inéditos, sobre todo de fondos notariales y judiciales de archivos de Santiago, Mendoza y San Juan. Sobre esta base se conformó un corpus documental de 3,5 millones de plantas, con vistas a identificar el proceso de ingreso, adaptación y propagación de las variedades de vid, desde la llegada de los españoles hasta el ingreso de las cepas francesas a mediados del siglo XIX. Particular atención se presta al inicio de la coexistencia entre la uva País y la uva de Italia (moscatel de Alejandría), situación que generó las condiciones para el surgimiento del torrontés, única variedad criolla de alto valor enológico y actual cepa emblemática de los vinos blancos argentinos

Variedades de uva en Chile y Argentina (1550-1850). Genealogía del torrontés

Cuyo y Chile central constituyen, desde el siglo XVIII hasta hoy, el principal polo vitivinícola de América Latina y uno de los con mayor desarrollo del mundo. Su producción de vinos y aguardientes ha tenido fuertes implicancias sociales, económicas, políticas y culturales en la región. En la base de este proceso se encuentra el cultivo de la vid, trabajo agrícola intensivo y especializado, en el cual los vidueños tienen una relevancia central. Este artículo examina las variedades cultivadas en la región a partir de documentos originales inéditos, sobre todo de fondos notariales y judiciales de archivos de Santiago, Mendoza y San Juan. Sobre esta base se conformó un corpus documental de 3,5 millones de plantas, con vistas a identificar el proceso de ingreso, adaptación y propagación de las variedades de vid, desde la llegada de los españoles hasta el ingreso de las cepas francesas a mediados del siglo XIX. Particular atención se presta al inicio de la coexistencia entre la uva País y la uva de Italia (moscatel de Alejandría), situación que generó las condiciones para el surgimiento del torrontés, única variedad criolla de alto valor enológico y actual cepa emblemática de los vinos blancos argentinos

Variedades de uva en Chile y Argentina (1550-1850). Genealogía del torrontés

Cuyo y Chile central constituyen, desde el siglo XVIII hasta hoy, el principal polo vitivinícola de América Latina y uno de los con mayor desarrollo del mundo. Su producción de vinos y aguardientes ha tenido fuertes implicancias sociales, económicas, políticas y culturales en la región. En la base de este proceso se encuentra el cultivo de la vid, trabajo agrícola intensivo y especializado, en el cual los vidueños tienen una relevancia central. Este artículo examina las variedades cultivadas en la región a partir de documentos originales inéditos, sobre todo de fondos notariales y judiciales de archivos de Santiago, Mendoza y San Juan. Sobre esta base se conformó un corpus documental de 3,5 millones de plantas, con vistas a identificar el proceso de ingreso, adaptación y propagación de las variedades de vid, desde la llegada de los españoles hasta el ingreso de las cepas francesas a mediados del siglo XIX. Particular atención se presta al inicio de la coexistencia entre la uva País y la uva de Italia (moscatel de Alejandría), situación que generó las condiciones para el surgimiento del torrontés, única variedad criolla de alto valor enológico y actual cepa emblemática de los vinos blancos argentinos