Gold ion implantation into alumina using an “inverted ion source” configuration.

We describe an approach to ion implantation in which the plasma and its electronics are held at ground potential and the ion beam is injected into a space held at high negative potential, allowing considerable savings both economically and technologically. We used an “inverted ion implanter” of this kind to carry out implantation of gold into alumina, with Au ion energy 40 keV and dose (3–9) × 1016 cm−2. Resistivity was measured in situ as a function of dose and compared with predictions of a model based on percolation theory, in which electron transport in the composite is explained by conduction through a random resistor network formed by Au nanoparticles. Excellent agreement is found between the experimental results and the theory.

Stopping power and depth dose profile of H+ and He+ ion beams in hydroxyapatite thin films.

Hadron therapy is a promising technique to treat deep-seated tumors. For an accurate treatment planning, the energy deposition in the soft and hard human tissue must be well known. Water has been usually employed as a phantom of soft tissues, but other biomaterials, such as hydroxyapatite (HAp), used as bone substitute, are also relevant as a phantom for hard tissues. The stopping power of HAp for H+ and He+ beams has been studied experimentally and theoretically. The measurements have been done using the Rutherford backscattering technique in an energy range of 450-2000 keV for H+ and of 400-5000 keV for He+ projectiles. The theoretical calculations are based in the dielectric formulation together with the MELF-GOS (Mermin Energy-Loss Function – Generalized Oscillator Strengths) method [1] to describe the target excitation spectrum. A quite good agreement between the experimental data and the theoretical results has been found. The depth dose profile of H+ and He+ ion beams in HAp has been simulated by the SEICS (Simulation of Energetic Ions and Clusters through Solids) code [2], which incorporates the electronic stopping force due to the energy loss by collisions with the target electrons, including fluctuations due to the energy-loss straggling, the multiple elastic scattering with the target nuclei, with their corresponding nuclear energy loss, and the dynamical charge-exchange processes in the projectile charge state. The energy deposition by H+ and He+ as a function of the depth are compared, at several projectile energies, for HAp and liquid water, showing important differences.

Autoionizing states and their relevance in electron-ion recombination

Atomic physics plays an important role in determining the evolution stages in a wide range of laboratory and cosmic plasmas. Therefore, the main contribution to our ability to model, infer and control plasma sources is the knowledge of underlying atomic processes. Of particular importance are reliable low temperature dielectronic recombination (DR) rate coefficients. This thesis provides systematically calculated DR rate coefficients of lithium-like beryllium and sodium ions via ∆n = 0 doubly excited resonant states. The calculations are based on complex-scaled relativistic many-body perturbation theory in an all-order formulation within the single- and double-excitation coupled-cluster scheme, including radiative corrections. Comparison of DR resonance parameters (energy levels, autoionization widths, radiative transition probabilities and strengths) between our theoretical predictions and the heavy-ion storage rings experiments (CRYRING-Stockholm and TSRHeidelberg) shows good agreement. The intruder state problem is a principal obstacle for general application of the coupled-cluster formalism on doubly excited states. Thus, we have developed a technique designed to avoid the intruder state problem. It is based on a convenient partitioning of the Hilbert space and reformulation of the conventional set of pairequations. The general aspects of this development are discussed, and the effectiveness of its numerical implementation (within the non-relativistic framework) is selectively illustrated on autoionizing doubly excited states of helium.

Lithogenic flux and textural analysis of the sediment trap samples collected at 150m in the Canary basin, Spain

Trabajo Finde Título para obtener el Grado en Ciencia del Mar

Computational analyses on the structure-function relation in ion channels

Ion channels are protein molecules, embedded in the lipid bilayer of the cell membranes. They act as powerful sensing elements switching chemicalphysical stimuli into ion-fluxes. At a glance, ion channels are water-filled pores, which can open and close in response to different stimuli (gating), and one once open select the permeating ion species (selectivity). They play a crucial role in several physiological functions, like nerve transmission, muscular contraction, and secretion. Besides, ion channels can be used in technological applications for different purpose (sensing of organic molecules, DNA sequencing). As a result, there is remarkable interest in understanding the molecular determinants of the channel functioning. Nowadays, both the functional and the structural characteristics of ion channels can be experimentally solved. The purpose of this thesis was to investigate the structure-function relation in ion channels, by computational techniques. Most of the analyses focused on the mechanisms of ion conduction, and the numerical methodologies to compute the channel conductance. The standard techniques for atomistic simulation of complex molecular systems (Molecular Dynamics) cannot be routinely used to calculate ion fluxes in membrane channels, because of the high computational resources needed. The main step forward of the PhD research activity was the development of a computational algorithm for the calculation of ion fluxes in protein channels. The algorithm - based on the electrodiffusion theory - is computational inexpensive, and was used for an extensive analysis on the molecular determinants of the channel conductance. The first record of ion-fluxes through a single protein channel dates back to 1976, and since then measuring the single channel conductance has become a standard experimental procedure. Chapter 1 introduces ion channels, and the experimental techniques used to measure the channel currents. The abundance of functional data (channel currents) does not match with an equal abundance of structural data. The bacterial potassium channel KcsA was the first selective ion channels to be experimentally solved (1998), and after KcsA the structures of four different potassium channels were revealed. These experimental data inspired a new era in ion channel modeling. Once the atomic structures of channels are known, it is possible to define mathematical models based on physical descriptions of the molecular systems. These physically based models can provide an atomic description of ion channel functioning, and predict the effect of structural changes. Chapter 2 introduces the computation methods used throughout the thesis to model ion channels functioning at the atomic level. In Chapter 3 and Chapter 4 the ion conduction through potassium channels is analyzed, by an approach based on the Poisson-Nernst-Planck electrodiffusion theory. In the electrodiffusion theory ion conduction is modeled by the drift-diffusion equations, thus describing the ion distributions by continuum functions. The numerical solver of the Poisson- Nernst-Planck equations was tested in the KcsA potassium channel (Chapter 3), and then used to analyze how the atomic structure of the intracellular vestibule of potassium channels affects the conductance (Chapter 4). As a major result, a correlation between the channel conductance and the potassium concentration in the intracellular vestibule emerged. The atomic structure of the channel modulates the potassium concentration in the vestibule, thus its conductance. This mechanism explains the phenotype of the BK potassium channels, a sub-family of potassium channels with high single channel conductance. The functional role of the intracellular vestibule is also the subject of Chapter 5, where the affinity of the potassium channels hEag1 (involved in tumour-cell proliferation) and hErg (important in the cardiac cycle) for several pharmaceutical drugs was compared. Both experimental measurements and molecular modeling were used in order to identify differences in the blocking mechanism of the two channels, which could be exploited in the synthesis of selective blockers. The experimental data pointed out the different role of residue mutations in the blockage of hEag1 and hErg, and the molecular modeling provided a possible explanation based on different binding sites in the intracellular vestibule. Modeling ion channels at the molecular levels relates the functioning of a channel to its atomic structure (Chapters 3-5), and can also be useful to predict the structure of ion channels (Chapter 6-7). In Chapter 6 the structure of the KcsA potassium channel depleted from potassium ions is analyzed by molecular dynamics simulations. Recently, a surprisingly high osmotic permeability of the KcsA channel was experimentally measured. All the available crystallographic structure of KcsA refers to a channel occupied by potassium ions. To conduct water molecules potassium ions must be expelled from KcsA. The structure of the potassium-depleted KcsA channel and the mechanism of water permeation are still unknown, and have been investigated by numerical simulations. Molecular dynamics of KcsA identified a possible atomic structure of the potassium-depleted KcsA channel, and a mechanism for water permeation. The depletion from potassium ions is an extreme situation for potassium channels, unlikely in physiological conditions. However, the simulation of such an extreme condition could help to identify the structural conformations, so the functional states, accessible to potassium ion channels. The last chapter of the thesis deals with the atomic structure of the !- Hemolysin channel. !-Hemolysin is the major determinant of the Staphylococcus Aureus toxicity, and is also the prototype channel for a possible usage in technological applications. The atomic structure of !- Hemolysin was revealed by X-Ray crystallography, but several experimental evidences suggest the presence of an alternative atomic structure. This alternative structure was predicted, combining experimental measurements of single channel currents and numerical simulations. This thesis is organized in two parts, in the first part an overview on ion channels and on the numerical methods adopted throughout the thesis is provided, while the second part describes the research projects tackled in the course of the PhD programme. The aim of the research activity was to relate the functional characteristics of ion channels to their atomic structure. In presenting the different research projects, the role of numerical simulations to analyze the structure-function relation in ion channels is highlighted.

Pattern recognition analysis on heavy ion reaction data

One of the problems in the analysis of nucleus-nucleus collisions is to get information on the value of the impact parameter b. This work consists in the application of pattern recognition techniques aimed at associating values of b to groups of events. To this end, a support vec- tor machine (SVM) classifier is adopted to analyze multifragmentation reactions. This method allows to backtracing the values of b through a particular multidimensional analysis. The SVM classification con- sists of two main phase. In the first one, known as training phase, the classifier learns to discriminate the events that are generated by two different model:Classical Molecular Dynamics (CMD) and Heavy- Ion Phase-Space Exploration (HIPSE) for the reaction: 58Ni +48 Ca at 25 AMeV. To check the classification of events in the second one, known as test phase, what has been learned is tested on new events generated by the same models. These new results have been com- pared to the ones obtained through others techniques of backtracing the impact parameter. Our tests show that, following this approach, the central collisions and peripheral collisions, for the CMD events, are always better classified with respect to the classification by the others techniques of backtracing. We have finally performed the SVM classification on the experimental data measured by NUCL-EX col- laboration with CHIMERA apparatus for the previous reaction.

Analysis of ion channel stochastic signals for biosensing

In biological world, life of cells is guaranteed by their ability to sense and to respond to a large variety of internal and external stimuli. In particular, excitable cells, like muscle or nerve cells, produce quick depolarizations in response to electrical, mechanical or chemical stimuli: this means that they can change their internal potential through a quick exchange of ions between cytoplasm and the external environment. This can be done thanks to the presence of ion channels, proteins that span the lipid bilayer and act like switches, allowing ionic current to flow opening and shutting in a stochastic way. For a particular class of ion channels, ligand-gated ion channels, the gating processes is strongly influenced by binding between receptive sites located on the channel surface and specific target molecules. These channels, inserted in biomimetic membranes and in presence of a proper electronic system for acquiring and elaborating the electrical signal, could give us the possibility of detecting and quantifying concentrations of specific molecules in complex mixtures from ionic currents across the membrane; in this thesis work, this possibility is investigated. In particular, it reports a description of experiments focused on the creation and the characterization of artificial lipid membranes, the reconstitution of ion channels and the analysis of their electrical and statistical properties. Moreover, after a chapter about the basis of the modelling of the kinetic behaviour of ligand gated ion channels, a possible approach for the estimation of the target molecule concentration, based on a statistical analysis of the ion channel open probability, is proposed. The fifth chapter contains a description of the kinetic characterisation of a ligand gated ion channel: the homomeric α2 isoform of the glycine receptor. It involved both experimental acquisitions and signal analysis. The last chapter represents the conclusions of this thesis, with some remark on the effective performance that may be achieved using ligand gated ion channels as sensing elements.

Elf magnetic field influence on ION Channels studied by Patch Clamp Technique: exposure set up and "Whole Cell" measurements on Potassium currents

The aim of this thesis was to study the effects of extremely low frequency (ELF) electromagnetic magnetic fields on potassium currents in neural cell lines ( Neuroblastoma SK-N-BE ), using the whole-cell Patch Clamp technique. Such technique is a sophisticated tool capable to investigate the electrophysiological activity at a single cell, and even at single channel level. The total potassium ion currents through the cell membrane was measured while exposing the cells to a combination of static (DC) and alternate (AC) magnetic fields according to the prediction of the so-called ‘ Ion Resonance Hypothesis ’. For this purpose we have designed and fabricated a magnetic field exposure system reaching a good compromise between magnetic field homogeneity and accessibility to the biological sample under the microscope. The magnetic field exposure system consists of three large orthogonal pairs of square coils surrounding the patch clamp set up and connected to the signal generation unit, able to generate different combinations of static and/or alternate magnetic fields. Such system was characterized in term of field distribution and uniformity through computation and direct field measurements. No statistically significant changes in the potassium ion currents through cell membrane were reveled when the cells were exposed to AC/DC magnetic field combination according to the afore mentioned ‘Ion Resonance Hypothesis’.

Optical Microring Resonators based on ion-implanted LiNbO3 ridge waveguides

The growing interest for Integrated Optics for sensing, telecommunications and even electronics is driving research to find solutions to the new challenges issued by a more and more fast, connected and smart world. This thesis deals with the design, the fabrication and the characterisation of the first prototypes of Microring Resonators realised using ion implanted Lithium Niobate (LiNbO3) ridge waveguides. Optical Resonator is one among the most important devices for all tasks described above. LiNbO3 is the substrate commonly used to fabricate optical modulators thanks to its electro-optic characteristics. Since it is produced in high quantity, good quality and large wafers its price is low compared to other electro-optic substrate. We propose to use ion implantation as fabrication technology because in the other way standard optical waveguides realised in LiNbO3 by Proton Exchange (PE) or metal diffusion do not allow small bending radii, which are necessary to keep the circuit footprint small. We will show in fact that this approach allows to fabricate waveguides on Lithium Niobate that are better than PE or metal diffused waveguides as it allows smaller size devices and tailoring of the refractive index profile controlling the implantation parameters. Moreover, we will show that the ridge technology based on enhanced etching rate via ion implantation produces a waveguide with roughness lower than a dry etched one. Finally it has been assessed a complete technological process for fabrication of Microring Resonator devices in Lithium Niobate by ion implantation and the first prototypes have been produced.

Doppelresonanzmessungen an in einer Penningfalle gespeicherten Europium-Ionen zur Bestimmung des Kern-g-Faktors

Die differentielle Hyperfeinanomalie beschreibt den Isotopieeffekt der magnetischen Hyperfeinwechselwirkung und stellt eine Testmöglichkeit für Kernmodelle dar. Nachdem in einer Reihe von Messungen die A-Faktoren der Hyperfeinwechselwirkung im Grundzustand von zwei stabilen und fünf instabilen Europium-Isotopen bestimmt wurden, sollen nun die Kern-g-Faktoren der gleichen Isotope bestimmt werden.Um die Kern-g-Faktoren zu bestimmen, wurden zunächst die Termschemata des Grundzustandesder stabilen Isotope 151,153Eu+ simuliert. Wegen der hohen Kern- und Hüllenspins I=5/2, J=4 ergeben sich 54 Zeemanzustände und ein komplexes optisches Spektrum.Etwa 10^6 Ionen der beiden stabilen Isotope 151,153Eu+ werden in einer Penningfalle beieinem Magnetfeld von ca. 1.5T gespeichert. Durch Puffergas und Anregung einer Seitenbandfrequenzder Ionenbewegung wird optisches Pumpen in metastabile D-Zustände bei gleichzeitiger Kühlung der Ionenwolke verhindert.Bei Verstimmung eines frequenzverdoppelten Ti:Sa-Lasers wurde die Ionenfluoreszenz aufgenommen. Durch die Simulation der optischen Spektren gelang es, einzelne Übergänge des Isotopes 151Eu+ zu identifizieren. Mit Laser/Mikrowellen-Doppelresonanzmessungen erhält man ein in erster Ordnung dopplerfreies Mikrowellenspektren eines Überganges zwischen zwei Zeemanzuständen im Grundzustand.Durch Messung der Übergangsfrequenzen von insgesamt fünf Delta mI=+1 Übergängen und Bestimmung des Magnetfeldes durch Messung der Zyklotronfrequenz gespeicherter Elektronen konnte der gI-Faktor des Isotopes151Eu zu 151gI = 1.37734(6) bestimmt werden.

Untersuchungen an gespeicherten 40 Ca +-Ionen in einer linearen Paulfalle

In Experimenten an lasergekühlten, in einer linearen Paulfalle gespeicherten $Ca^+$-Ionen wurde dieLebensdauer des metastabilen $3D_{5/2}$-Niveaus durch Beobachtung von Quantensprüngen einzelner Ionen zu 1100(18)msbestimmt. Systematische Fehler durch quenchende Stöße oder Stark-Mischen durch das Speicherfeld liegen unterhalb dererreichten Genauigkeit. Abweichungen von früheren Messungen konnten durch eine vernachlässigte Abhängigkeit derLebensdauer von der Laserleistung des Rückpumplasers erklärt werden. Das Endergebnis zeigt gute Übereinstimmung mitneueren theoretischen Werten. In weiteren Messungen an zehn Ionen wurde in einigen Messreihen eine deutliche Reduktionder Lebensdauer gegenüber einem einzelnen Ion festgestellt. Dabei wurden mehr koinzidente Zerfälle von zwei und dreiIonen beobachtet als für unabhängige Teilchen zu erwarten. In einem Ionenkristall wurde eine räumliche Trennung atomarer Zustände erreicht. Dabei wurde ein Teil der Ionen einesKristalls aus einigen hundert Ionen in den metastabilen Zustand gepumpt, der von den Kühllasern vollständig entkoppeltist. Durch sympathetische Kühlung werden diese Ionen weiterhin gekühlt und der Kristall schmilzt nicht. Durch denLichtdruck, den die Kühllaser ausgeüben, werden die Ionen nach atomaren Zuständen sortiert, weil die lasergekühltenIonen einen Rückstoß erfahren, die übrigen aber nicht. Für zukünftige Experimente wurden Verbesserungen des experimentellen Aufbaus auf den Weg gebracht. So wurden Methodenund Komponenten für eine verbesserte Frequenzstabilisierung der Diodenlaser entwickelt.

Messung des Landé-gJ-Faktors im Grundzustand von Ca + und Untersuchung des Speicherverhaltens von Elektronen in einem Penningkäfig

Ionenkäfige und speziell Penningfallen stellen sich in der Atomphysik als außergewöhnliche Werkzeuge heraus. Zum einen bieten diese 'Teilchencontainer' die Möglichkeit atomphysikalische Präzisionsmessungen durchzuführen und zum anderen stellen Penningfallen schwingungsfähige Systeme dar, in welchen nichtlineare dynamische Prozesse an gespeicherten Teilchen untersucht werden können. In einem ersten Teil der Arbeit wurde mit der in der Atomphysik bekannten Methode der optischen Mikrowellen-Doppelresonanz Spektroskopie der elektronische g-Faktor von Ca+ mit einer Genauigkeit von 4*10^{-8} zu gJ=2,00225664(9) bestimmt. g-Faktoren von Elektronen in gebundenen ionischen Systemen sind fundamentale Größen der Atomphysik, die Informationen über die atomare Wellenfunktion des zu untersuchenden Zustandes liefern. In einem zweiten Teil der Arbeit wurde hinsichtlich der Untersuchungen zur nichtlinearen Dynamik von parametrisch angeregten gespeicherten Elektronen beobachtet, dass ab bestimmten kritischen Teilchendichten in der Penningfalle die gespeicherten Elektronen kollektive Eigenschaften manifestieren. Weiterhin wurde bei der Anregung der axialen Eigenbewegung ein Schwellenverhalten der gemessenen Subharmonischen zur 2*omega_z-Resonanz beobachtet. Dieser Schwelleneffekt lässt sich mit der Existenz eines Dämpfungsmechanismus erklären, der auf die Elektronenwolke einwirkt, so dass eine Mindestamplitude der Anregung erforderlich ist, um diese Dämpfung zu überwinden. Durch Bestimmung der charakteristischen Kurven der gedämpften Mathieuschen Differentialgleichung konnte das beobachtete Phänomen theoretisch verstanden werden.

Numerical simulation of ion transport through ion channels and solid-state nanopores

Ion channels are pore-forming proteins that regulate the flow of ions across biological cell membranes. Ion channels are fundamental in generating and regulating the electrical activity of cells in the nervous system and the contraction of muscolar cells. Solid-state nanopores are nanometer-scale pores located in electrically insulating membranes. They can be adopted as detectors of specific molecules in electrolytic solutions. Permeation of ions from one electrolytic solution to another, through a protein channel or a synthetic pore is a process of considerable importance and realistic analysis of the main dependencies of ion current on the geometrical and compositional characteristics of these structures are highly required. The project described by this thesis is an effort to improve the understanding of ion channels by devising methods for computer simulation that can predict channel conductance from channel structure. This project describes theory, algorithms and implementation techniques used to develop a novel 3-D numerical simulator of ion channels and synthetic nanopores based on the Brownian Dynamics technique. This numerical simulator could represent a valid tool for the study of protein ion channel and synthetic nanopores, allowing to investigate at the atomic-level the complex electrostatic interactions that determine channel conductance and ion selectivity. Moreover it will provide insights on how parameters like temperature, applied voltage, and pore shape could influence ion translocation dynamics. Furthermore it will help making predictions of conductance of given channel structures and it will add information like electrostatic potential or ionic concentrations throughout the simulation domain helping the understanding of ion flow through membrane pores.

Mode coupling for precise measurements of the electronic g-factor of hydrogen-like ions in Penning traps

The g-factor is a constant which connects the magnetic moment $vec{mu}$ of a charged particle, of charge q and mass m, with its angular momentum $vec{J}$. Thus, the magnetic moment can be writen $ vec{mu}_J=g_Jfrac{q}{2m}vec{J}$. The g-factor for a free particle of spin s=1/2 should take the value g=2. But due to quantum electro-dynamical effects it deviates from this value by a small amount, the so called g-factor anomaly $a_e$, which is of the order of $10^{-3}$ for the free electron. This deviation is even bigger if the electron is exposed to high electric fields. Therefore highly charged ions, where electric field strength gets values on the order of $10^{13}-10^{16}$V/cm at the position of the bound electron, are an interesting field of investigations to test QED-calculations. In previous experiments [H"aff00,Ver04] using a single hydrogen-like ion confined in a Penning trap an accuracy of few parts in $10^{-9}$ was obtained. In the present work a new method for precise measurement of magnetic the electronic g-factor of hydrogen-like ions is discussed. Due to the unavoidable magnetic field inhomogeneity in a Penning trap, a very important contribution to the systematic uncertainty in the previous measurements arose from the elevated energy of the ion required for the measurement of its motional frequencies. Then it was necessary to extrapolate the result to vanishing energies. In the new method the energy in the cyclotron degree of freedom is reduced to the minimum attainable energy. This method consist in measuring the reduced cyclotron frequency $nu_{+}$ indirectly by coupling the axial to the reduced cyclotron motion by irradiation of the radio frequency $nu_{coup}=nu_{+}-nu_{ax}+delta$ where $delta$ is, in principle, an unknown detuning that can be obtained from the knowledge of the coupling process. Then the only unknown parameter is the desired value of $nu_+$. As a test, a measurement with, for simplicity, artificially increased axial energy was performed yielding the result $g_{exp}=2.000~047~020~8(24)(44)$. This is in perfect agreement with both the theoretical result $g_{theo}=2.000~047~020~2(6)$ and the previous experimental result $g_{exp1}=2.000~047~025~4(15)(44).$ In the experimental results the second error-bar is due to the uncertainty in the accepted value for the electron's mass. Thus, with the new method a higher accuracy in the g-factor could lead by comparison to the theoretical value to an improved value of the electron's mass. [H"af00] H. H"affner et al., Phys. Rev. Lett. 85 (2000) 5308 [Ver04] J. Verd'u et al., Phys. Rev. Lett. 92 (2004) 093002-1