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.

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.

REXTRAP - ion accumulation, cooling and bunching for REX-ISOLDE

REX-ISOLDE ist ein Pilotexperiment zur Nachbeschleunigung radioaktiver Ionenstrahlen am on-line Massenseparator ISOLDE am CERN. Ein wichtiges Teilprojekt war die Realisierung der effizienten Umwandlung des kontinuierlichen niederenergetischen Ionenstrahles in kurze Ionenpulse hoher Qualität. Zu diesem Zweck wurde im Rahmen dieser Arbeit REXTRAP, eine gasgefüllte Penningfalle entwickelt, in Betrieb genommen und systematisch untersucht.

Computational investigations of ion conduction mechanisms using enhanced sampling methods

Proper ion channels’ functioning is a prerequisite for a normal cell and disorders involving ion channels, or channelopathies, underlie many human diseases. Long QT syndromes (LQTS) for example may arise from the malfunctioning of hERG channel, caused either by the binding of drugs or mutations in HERG gene. In the first part of this thesis I present a framework to investigate the mechanism of ion conduction through hERG channel. The free energy profile governing the elementary steps of ion translocation in the pore was computed by means of umbrella sampling simulations. Compared to previous studies, we detected a different dynamic behavior: according to our data hERG is more likely to mediate a conduction mechanism which has been referred to as “single-vacancy-like” by Roux and coworkers (2001), rather then a “knock-on” mechanism. The same protocol was applied to a model of hERG presenting the Gly628Ser mutation, found to be cause of congenital LQTS. The results provided interesting insights about the reason of the malfunctioning of the mutant channel. Since they have critical functions in viruses’ life cycle, viral ion channels, such as M2 proton channel, are considered attractive targets for antiviral therapy. A deep knowledge of the mechanisms that the virus employs to survive in the host cell is of primary importance in the identification of new antiviral strategies. In the second part of this thesis I shed light on the role that M2 plays in the control of electrical potential inside the virus, being the charge equilibration a condition required to allow proton influx. The ion conduction through M2 was simulated using metadynamics technique. Based on our results we suggest that a potential anion-mediated cation-proton exchange, as well as a direct anion-proton exchange could both contribute to explain the activity of the M2 channel.

Tuning of magnetic exchange interactions between organic radicals through bond and space

The dissertation entitled "Tuning of magnetic exchange interactions between organic radicals through bond and space" comprises eight chapters. In the initial part of chapter 1, an overview of organic radicals and their applications were discussed and in the latter part motivation and objective of thesis was described. As the EPR spectroscopy is a necessary tool to study organic radicals, the basic principles of EPR spectroscopy were discussed in chapter 2. rnAntiferromagnetically coupled species can be considered as a source of interacting bosons. Consequently, such biradicals can serve as molecular models of a gas of magnetic excitations which can be used for quantum computing or quantum information processing. Notably, initial small triplet state population in weakly AF coupled biradicals can be switched into larger in the presence of applied magnetic field. Such biradical systems are promising molecular models for studying the phenomena of magnetic field-induced Bose-Einstein condensation in the solid state. To observe such phenomena it is very important to control the intra- as well as inter-molecular magnetic exchange interactions. Chapters 3 to 5 deals with the tuning of intra- and inter-molecular exchange interactions utilizing different approaches. Some of which include changing the length of π-spacer, introduction of functional groups, metal complex formation with diamagnetic metal ion, variation of radical moieties etc. During this study I came across two very interesting molecules 2,7-TMPNO and BPNO, which exist in semi-quinoid form and exhibits characteristic of the biradical and quinoid form simultaneously. The 2,7-TMPNO possesses the singlet-triplet energy gap of ΔEST = –1185 K. So it is nearly unrealistic to observe the magnetic field induced spin switching. So we studied the spin switching of this molecule by photo-excitation which was discussed in chapter 6. The structural similarity of BPNO with Tschitschibabin’s HC allowed us to dig the discrepancies related to ground state of Tschitschibabin’s hydrocarbon(Discussed in chapter 7). Finally, in chapter 8 the synthesis and characterization of a neutral paramagnetic HBC derivative (HBCNO) is discussed. The magneto liquid crystalline properties of HBCNO were studied by DSC and EPR spectroscopy.rn

Proposal of a Continuous Read-out Implementation in the ALICE-TOF detector

The main purpose of ultrarelativistic heavy-ion collisions is the investigation of the QGP. The ALICE experiment situated at the CERN has been specifically designed to study heavy-ion collisions for centre-of-mass energies up to 5.5 per nucleon pair. Extended particle identification capability is one of the main characteristics of the ALICE experiment. In the intermediate momentum region (up to 2.5 GeV/c for pi/K and 4 GeV/c for K/p), charged particles are identified in the ALICE experiment by the Time of Flight (TOF) detector. The ALICE-TOF system is a large-area detector based on the use of Multi-gap Resistive Plate Chamber (MRPC) built with high efficiency, fast response and intrinsic time resolution better than 40 ps. This thesis work, developed with the ALICE-TOF Bologna group, is part of the efforts carried out to adapt the read-out of the detector to the new requirements after the LHC Long Shutdown 2. Tests on the feasibility of a new read-out scheme for the TOF detector have been performed. In fact, the achievement of a continuous read-out also for the TOF detector would not be affordable if one considers the replacement of the TRM cards both for hardware and budget reasons. Actually, the read-out of the TOF is limited at 250 kHz i.e. it would be able to collect up to just a fourth of the maximum collision rate potentially achievable for pp interactions. In this Master’s degree thesis work, I discuss a different read-out system for the ALICE-TOF detector that allows to register all the hits at the interaction rate of 1 MHz foreseen for pp interactions after the 2020, by using the electronics currently available. Such solution would allow the ALICE-TOF detector to collect all the hits generated by pp collisions at 1 MHz interaction rate, which corresponds to an amount four times larger than that initially expected at such frequencies with the triggered read-out system operated at 250 kHz for LHC Run 3. The obtained results confirm that the proposed read-out scheme is a viable option for the ALICE TOF detector. The results also highlighted that it will be advantageous if the ALICE-TOF group also implement an online monitoring system of noisy channels to allow their deactivation in real time.

Modification of the magnetic properties of a heterometallic wheel by inclusion of a Jahn-Teller distorted Cu(II) ion

An investigation into the physical consequences of including a Jahn-Teller distorted Cu(II) ion within an antiferromagnetically coupled ring, [R(2)NH(2)][Cr(7)CuF(8)((O(2)C(t)Bu)(16))] is reported. Inelastic neutron scattering (INS) and electron paramagnetic resonance (EPR) spectroscopic data are simulated using a microscopic spin Hamiltonian, and show that the two Cr-Cu exchange interactions must be inequivalent. One Cr-Cu exchange is found to be antiferromagnetic and the other ferromagnetic. The geometry of the Jahn-Teller elongation is deduced from these results, and shows that a Jahn-Teller elongation axis must lie in the plane of the Cr(7)Cu wheel; the elongation is not observed by X-ray crystallography, due to positional disorder of the Cu site within the wheel. An electronic structure calculation confirms the structural distortion of the Cu site.

A versatile gas interface for routine radiocarbon analysis with a gas ion source

In 2010 more than 600 radiocarbon samples were measured with the gas ion source at the MIni CArbon DAting System (MICADAS) at ETH Zurich and the number of measurements is rising quickly. While most samples contain less than 50 mu g C at present, the gas ion source is attractive as well for larger samples because the time-consuming graphitization is omitted. Additionally, modern samples are now measured down to 5 per-mill counting statistics in less than 30 min with the recently improved gas ion source. In the versatile gas handling system, a stepping-motor-driven syringe presses a mixture of helium and sample CO2 into the gas ion source, allowing continuous and stable measurements of different kinds of samples. CO2 can be provided in four different ways to the versatile gas interface. As a primary method. CO2 is delivered in glass or quartz ampoules. In this case, the CO2 is released in an automated ampoule cracker with 8 positions for individual samples. Secondly, OX-1 and blank gas in helium can be provided to the syringe by directly connecting gas bottles to the gas interface at the stage of the cracker. Thirdly, solid samples can be combusted in an elemental analyzer or in a thermo-optical OC/EC aerosol analyzer where the produced CO2 is transferred to the syringe via a zeolite trap for gas concentration. As a fourth method, CO2 is released from carbonates with phosphoric acid in septum-sealed vials and loaded onto the same trap used for the elemental analyzer. All four methods allow complete automation of the measurement, even though minor user input is presently still required. Details on the setup, versatility and applications of the gas handling system are given. (C) 2012 Elsevier B.V. All rights reserved.

Continuous Flow Analysis Method for Determination of Dissolved Reactive Phosphorus in Ice Cores

Phosphorus (P) is an essential macronutrient for all living organisms. Phosphorus is often present in nature as the soluble phosphate ion PO43– and has biological, terrestrial, and marine emission sources. Thus PO43– detected in ice cores has the potential to be an important tracer for biological activity in the past. In this study a continuous and highly sensitive absorption method for detection of dissolved reactive phosphorus (DRP) in ice cores has been developed using a molybdate reagent and a 2-m liquid waveguide capillary cell (LWCC). DRP is the soluble form of the nutrient phosphorus, which reacts with molybdate. The method was optimized to meet the low concentrations of DRP in Greenland ice, with a depth resolution of approximately 2 cm and an analytical uncertainty of 1.1 nM (0.1 ppb) PO43–. The method has been applied to segments of a shallow firn core from Northeast Greenland, indicating a mean concentration level of 2.74 nM (0.26 ppb) PO43– for the period 1930–2005 with a standard deviation of 1.37 nM (0.13 ppb) PO43– and values reaching as high as 10.52 nM (1 ppb) PO43–. Similar levels were detected for the period 1771–1823. Based on impurity abundances, dust and biogenic particles were found to be the most likely sources of DRP deposited in Northeast Greenland.

Continuous eclogite melting and variable refertilisation in upwelling heterogeneous mantle

Large-scale tectonic processes introduce a range of crustal lithologies into the Earth's mantle. These lithologies have been implicated as sources of compositional heterogeneity in mantle-derived magmas. The model being explored here assumes the presence of widely dispersed fragments of residual eclogite (derived from recycled oceanic crust), stretched and stirred by convection in the mantle. Here we show with an experimental study that these residual eclogites continuously melt during upwelling of such heterogeneous mantle and we characterize the melting reactions and compositional changes in the residue minerals. The chemical exchange between these partial melts and more refractory peridotite leads to a variably metasomatised mantle. Re-melting of these metasomatised peridotite lithologies at given pressures and temperatures results in diverse melt compositions, which may contribute to the observed heterogeneity of oceanic basalt suites. We also show that heterogeneous upwelling mantle is subject to diverse local freezing, hybridization and carbonate-carbon-silicate redox reactions along a mantle adiabat.

ROSINA/DFMS and IES observations of 67P: Ion-neutral chemistry in the coma of a weakly outgassing comet

Context. The Rosetta encounter with comet 67P/Churyumov-Gerasimenko provides a unique opportunity for an in situ, up-close investigation of ion-neutral chemistry in the coma of a weakly outgassing comet far from the Sun. Aims. Observations of primary and secondary ions and modeling are used to investigate the role of ion-neutral chemistry within the thin coma. Methods. Observations from late October through mid-December 2014 show the continuous presence of the solar wind 30 km from the comet nucleus. These and other observations indicate that there is no contact surface and the solar wind has direct access to the nucleus. On several occasions during this time period, the Rosetta/ROSINA/Double Focusing Mass Spectrometer measured the low-energy ion composition in the coma. Organic volatiles and water group ions and their breakup products (masses 14 through 19), CO2+ (masses 28 and 44) and other mass peaks (at masses 26, 27, and possibly 30) were observed. Secondary ions include H3O+ and HCO+ (masses 19 and 29). These secondary ions indicate ion-neutral chemistry in the thin coma of the comet. A relatively simple model is constructed to account for the low H3O+/H2O+ and HCO+/CO+ ratios observed in a water dominated coma. Results from this simple model are compared with results from models that include a more detailed chemical reaction network. Results. At low outgassing rates, predictions from the simple model agree with observations and with results from more complex models that include much more chemistry. At higher outgassing rates, the ion-neutral chemistry is still limited and high HCO+/CO+ ratios are predicted and observed. However, at higher outgassing rates, the model predicts high H3O+/H2O+ ratios and the observed ratios are often low. These low ratios may be the result of the highly heterogeneous nature of the coma, where CO and CO2 number densities can exceed that of water.

N budget and NH3 exchange of a grass/clover crop at two levels of N application

Atmospheric ammonia (NH3) exchange during a single growing season was measured over two grass/clover fields managed by cutting and treated with different rates of mineral nitrogen (N) fertilizer. The aim was to quantify the total NH3 exchange of the two systems in relation to their N budget, the latter was split into N derived from symbiotic fixation, from fertilization, and from the soil. The experimental site was located in an intensively managed agricultural area on the Swiss plateau. Two adjacent fields with mixtures of perennial ryegrass (Lolium perenne L.), cocks foot (Dactylis glomerata L.), white clover (Trifolium repens L.) and red clover (Trifolium pratense L.) were used. These were treated with either 80 or 160 kg N ha−1 applied as NH4NO3 fertilizer in equal portions after each of four cuts. Continuous NH3 flux measurements were carried out by micrometeorological techniques. To determine the contribution of each species to the overall NH3 canopy compensation point, stomatal NH3 compensation points of the individual plant species were determined on the basis of NH4+ + NH3 (NHx) concentrations and pH in the apoplast. Symbiotic N2 fixation was measured by the 15N dilution method.

Charge exchange in cometary coma: Discovery of H- ions in the solar wind close to comet 67P/Churyumov-Gerasimenko

As Rosetta was orbiting comet 67P/Churyumov-Gerasimenko, the Ion and Electron Sensor detected negative particles with angular distributions like those of the concurrently measured solar wind protons but with fluxes of only about 10% of the proton fluxes and energies of about 90% of the proton energies. Using well-known cross sections and energy-loss data, it is determined that the fluxes and energies of the negative particles are consistent with the production of H- ions in the solar wind by double charge exchange with molecules in the coma.

Continuous 25-years aerosol records at coastal Antarctica: Part I. Variability and climate implications of ionic compounds

The aerosol climatology at the coastal Antarctic Neumayer Station (NM) was investigated based on continuous, 25-yr long observations of biogenic sulphur components (methanesulfonate and non-sea salt sulphate), sea salt and nitrate. Although significant long-term trends could only be detected for nitrate (-3.6 ± 2.5% per year between 1983 and 1993 and +4.0 ± 3.2% per year from 1993-2007), non-harmonic periodicities between 2 and 5 yr were typical for all species. Dedicated time series analyses revealed that relations to sea ice extent and various circulation indices are weak at best or not significant. In particular, no consistent link between sea ice extent and sea salt loadings was evident suggesting only a rather local relevance of the NM sea salt record. Nevertheless, a higher Southern Annular Mode index tended to entail a lower biogenic sulphur signal. In examining the spatial uniformity of the NM findings we contrasted them to respective 17 yr records from the coastal Dumont d'Urville Station. We found similar long-term trends for nitrate, indicating an Antarctic-wide but not identifiable atmospheric signal, although any significant impact of solar activity or pollution could be ruled out. No inter-site variability on the multiannual scale was evident for the other ionic compounds.

Major ion concentrations in rain water and atmospheric moisture above the Atlantic Ocean

Concentratios of Cl-, Mg2+, Ca2+, and HCO3- ions were studied in rain waters and condensed atmospheric moisture above the Atlantic Ocean. Maximal number of samples was collected in the eastern tropical North Atlantic. Concentration of chloride ions ranged from 1 to 28 mg/l in rain waters (average 4.3 mg/l) and ranged from 0.3 to 2 mg/l in condensed atmospheric moisture with the average about one order of magnitude less than that for rain waters. Chloride normalized concentrations of magnesium and calcium are greater in rain waters and condensed atmospheric moisture than in ocean water due to more intensive subtraction of these ions as compared to chloride ions. Chloride normalized HCO3- concentration is one order of magnitude greater in atmospheric moisture than in seawater, possibly because of volatile component CO2 taking part in exchange between the ocean and the atmosphere.