Magnetic topology and current channels in plasmas with toroidal current density inversions

The equilibrium magnetic field inside axisymmetric plasmas with inversions on the toroidal current density is studied. Structurally stable non-nested magnetic surfaces are considered. For any inversion in the internal current density the magnetic families define several positive current channels about a central negative one. A general expression relating the positive and negative currents is derived in terms of a topological anisotropy parameter. Next, an analytical local solution for the poloidal magnetic flux is derived and shown compatible with current hollow magnetic pitch measurements shown in the literature. Finally, the analytical solution exhibits non-nested magnetic families with positive anisotropy, indicating that the current inside the positive channels have at least twice the magnitude of the central one.

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.

Magnetohydrodynamic Effects On Mixed Convection Flows In Channels And Ducts

This work focuses on magnetohydrodynamic (MHD) mixed convection flow of electrically conducting fluids enclosed in simple 1D and 2D geometries in steady periodic regime. In particular, in Chapter one a short overview is given about the history of MHD, with reference to papers available in literature, and a listing of some of its most common technological applications, whereas Chapter two deals with the analytical formulation of the MHD problem, starting from the fluid dynamic and energy equations and adding the effects of an external imposed magnetic field using the Ohm's law and the definition of the Lorentz force. Moreover a description of the various kinds of boundary conditions is given, with particular emphasis given to their practical realization. Chapter three, four and five describe the solution procedure of mixed convective flows with MHD effects. In all cases a uniform parallel magnetic field is supposed to be present in the whole fluid domain transverse with respect to the velocity field. The steady-periodic regime will be analyzed, where the periodicity is induced by wall temperature boundary conditions, which vary in time with a sinusoidal law. Local balance equations of momentum, energy and charge will be solved analytically and numerically using as parameters either geometrical ratios or material properties. In particular, in Chapter three the solution method for the mixed convective flow in a 1D vertical parallel channel with MHD effects is illustrated. The influence of a transverse magnetic field will be studied in the steady periodic regime induced by an oscillating wall temperature. Analytical and numerical solutions will be provided in terms of velocity and temperature profiles, wall friction factors and average heat fluxes for several values of the governing parameters. In Chapter four the 2D problem of the mixed convective flow in a vertical round pipe with MHD effects is analyzed. Again, a transverse magnetic field influences the steady periodic regime induced by the oscillating wall temperature of the wall. A numerical solution is presented, obtained using a finite element approach, and as a result velocity and temperature profiles, wall friction factors and average heat fluxes are derived for several values of the Hartmann and Prandtl numbers. In Chapter five the 2D problem of the mixed convective flow in a vertical rectangular duct with MHD effects is discussed. As seen in the previous chapters, a transverse magnetic field influences the steady periodic regime induced by the oscillating wall temperature of the four walls. The numerical solution obtained using a finite element approach is presented, and a collection of results, including velocity and temperature profiles, wall friction factors and average heat fluxes, is provided for several values of, among other parameters, the duct aspect ratio. A comparison with analytical solutions is also provided, as a proof of the validity of the numerical method. Chapter six is the concluding chapter, where some reflections on the MHD effects on mixed convection flow will be made, in agreement with the experience and the results gathered in the analyses presented in the previous chapters. In the appendices special auxiliary functions and FORTRAN program listings are reported, to support the formulations used in the solution chapters.

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’.

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.

A hybrid technology for parallel recording of single ion channels

Hybrid technologies, thanks to the convergence of integrated microelectronic devices and new class of microfluidic structures could open new perspectives to the way how nanoscale events are discovered, monitored and controlled. The key point of this thesis is to evaluate the impact of such an approach into applications of ion-channel High Throughput Screening (HTS)platforms. This approach offers promising opportunities for the development of new classes of sensitive, reliable and cheap sensors. There are numerous advantages of embedding microelectronic readout structures strictly coupled to sensing elements. On the one hand the signal-to-noise-ratio is increased as a result of scaling. On the other, the readout miniaturization allows organization of sensors into arrays, increasing the capability of the platform in terms of number of acquired data, as required in the HTS approach, to improve sensing accuracy and reliabiity. However, accurate interface design is required to establish efficient communication between ionic-based and electronic-based signals. The work made in this thesis will show a first example of a complete parallel readout system with single ion channel resolution, using a compact and scalable hybrid architecture suitable to be interfaced to large array of sensors, ensuring simultaneous signal recording and smart control of the signal-to-noise ratio and bandwidth trade off. More specifically, an array of microfluidic polymer structures, hosting artificial lipid bilayers blocks where single ion channel pores are embededed, is coupled with an array of ultra-low noise current amplifiers for signal amplification and data processing. As demonstrating working example, the platform was used to acquire ultra small currents derived by single non-covalent molecular binding between alpha-hemolysin pores and beta-cyclodextrin molecules in artificial lipid membranes.

Ion channels in mixed tethered bilayer lipid membranes

Mixed tethered bilayer lipid membranes (tBLMs) are described based on the self-assembly of a monolayer on template stripped gold, of an archea analogue thiolipid, 2,3-di-o-phytanyl-sn-glycerol-1-tetraethylene glycol-D,L--lipoic acid ester lipid (DPTL), and a newly designed dilution molecule, tetraethylene glycol-D,L--lipoic acid ester (TEGL). The usage of spacer and addition of extra dilution molecules between the substrate and the bilayer is that this architecture provides an ionic reservoir underneath the membrane, avoiding direct contact of the embedded membrane proteins with the gold electrodes and increasing the lateral diffusion of the bilayer, thus allowing for the incorporation of complex channels proteins which are failed in non-diluted systems. The tBLM is completed by fusion of liposomes made from a mixture of 1,2-diphythanolyl-sn-glycero-3-phosphocholine (DPhyPC), cholesterol, and 1,2-diphytanoyl-sn-Glycero-3-phosphate (DPhyPG) in a molar ratio of 6:3:1. Varying the mixing ratio, the optimum mixing ratio was obtained at a dilution factor of DPTL and TEGL at 90%:10%. Only under these conditions, the mixed tBLM showed electrical properties, as shown by EIS, which are comparable to a BLM. With higher dilution factors, a defect-free lipid bilayer was not formed. Formation of bilayers have been characterized by different techniques, such as surface plasmon resonance (SPR), electrochemical impedance spectroscopy (EIS), atomic force microscopy (AFM), and quartz crystal microbalance (QCM). Different proteins such as hemolysin, melittin, gramicidin, M2, Maxi-K, nAChR and bacteriohodopsin are incorporated into these tBLMs as shown by SPR and EIS studies. Ionic conductivity at 0 V vs. Ag|AgCl, 3M KCl were measured by EIS measurements. Our results indicate that these proteins have been successfully incorporated into a very stable tBLM environment in a functionally active form. Therefore, we conclude that the mixed tBLMs have been successfully designed as a general platform for biosensing and screening purposes of membrane proteins.

Coded slotted aloha with multipacket reception over block fading channels (for satellite networks)

Random access (RA) protocols are normally used in a satellite networks for initial terminal access and are particularly effective since no coordination is required. On the other hand, contention resolution diversity slotted Aloha (CRDSA), irregular repetition slotted Aloha (IRSA) and coded slotted Aloha (CSA) has shown to be more efficient than classic RA schemes as slotted Aloha, and can be exploited also when short packets transmissions are done over a shared medium. In particular, they relies on burst repetition and on successive interference cancellation (SIC) applied at the receiver. The SIC process can be well described using a bipartite graph representation and exploiting tools used for analyze iterative decoding. The scope of my Master Thesis has been to described the performance of such RA protocols when the Rayleigh fading is taken into account. In this context, each user has the ability to correctly decode a packet also in presence of collision and when SIC is considered this may result in multi-packet reception. Analysis of the SIC procedure under Rayleigh fading has been analytically derived for the asymptotic case (infinite frame length), helping the analysis of both throughput and packet loss rates. An upper bound of the achievable performance has been analytically obtained. It can be show that in particular channel conditions the throughput of the system can be greater than one packets per slot which is the theoretical limit of the Collision Channel case.

Ubiquitylation and SUMOylation of Cardiac Ion Channels

Cardiac ion channels play an essential role in the generation of the action potential of cardiomyocytes. Over the past 15 years, a new field of research called channelopathies has emerged; it regroups all diseases caused by ion channel dysfunction. Investigators have largely determined the physiological roles of cardiac ion channels, but little is known about the molecular determinants of their regulation. Two post-translational mechanisms that are crucial in determining the fate of proteins are ubiquitylation and the SUMOylation pathways, which lead to the degradation and/or regulation of modified proteins. Recently, several groups have investigated the physiological impacts of these mechanisms on the regulation of different classes of cardiac ion channels. The objective of this review is to summarize and briefly discuss these results.

Suicidal knife wound to the heart: challenges in reconstructing wound channels with post mortem CT and CT-angiography

We present a case of an individual who stabbed himself through the heart with a large knife. Post mortem computed tomography (CT) and CT-angiography were used to assess the stab channel and to reconstruct the sequence of events. After penetrating injuries to the chest, both the intra-thoracic organs and the injury causing instrument may shift (e.g. from pnemothorax) and render forensic reconstructions more challenging. This case report illustrates the potentials and the pitfalls of CT for the reconstruction of penetrating injures to the chest.

Channels and transporters. Mini-symposium of the Division of Medicinal Chemistry (DMC) of the Swiss Chemical Society (SCS) at the Department of Chemistry, University of Basel, May 27, 2010

During a half-day symposium, the topic 'Channels and Transporters' was covered with five lectures, including a presentation on 'Introduction and Basics of Channels and Transporters' by Beat Ernst, lectures on structure, function and physiology of channels and transporters ('The Structural Basis for Ion Conduction and Gating in Pentameric Ligand-Gated Ion Channels' by Raimund Dutzler and 'Uptake and Efflux Transporters for Endogenous Substances and for Drugs' by Dietrich Keppler), and a case study lecture on 'Avosentan' by Werner Neidhart. The program was completed by Matthias Hediger who introduced to the audience the National Center of Competence in Research (NCCR)-TransCure in his lecture entitled 'From Transport Physiology to Identification of Therapeutic Targets'.

Monepantel allosterically activates DEG-3/DES-2 channels of the gastrointestinal nematode Haemonchus contortus

Monepantel is the first drug of a new family of anthelmintics, the amino acetonitrile derivatives (AAD), presently used to treat ruminants infected with gastrointestinal nematodes such as Haemonchus contortus. Monepantel shows an excellent tolerability in mammals and is active against multidrug-resistant parasites, indicating that its molecular target is absent or inaccessible in the host and is different from those of the classic anthelmintics. Genetic approaches with mutant nematodes have suggested acetylcholine receptors of the DEG-3 subfamily as the targets of AADs, an enigmatic clade of ligand-gated ion channels that is specific to nematodes and does not occur in mammals. Here we demonstrate direct interaction of monepantel, its major active metabolite monepantel sulfone, and other AADs with potential targets of the DEG-3 subfamily of acetylcholine receptors. H. contortus DEG-3/DES-2 receptors were functionally expressed in Xenopus laevis oocytes and were found to be preferentially activated by choline, to permeate monovalent cations, and to a smaller extent, calcium ions. Although monepantel and monepantel sulfone did not activate the channels by themselves, they substantially enhanced the late currents after activation of the channels with choline, indicating that these AADs are type II positive allosteric modulators of H. contortus DEG-3/DES-2 channels. It is noteworthy that the R-enantiomer of monepantel, which is inactive as an anthelmintic, inhibited the late currents after stimulation of H. contortus DEG-3/DES-2 receptors with choline. In summary, we present the first direct evidence for interaction of AADs with DEG-3-type acetylcholine receptors and discuss these findings in the context of anthelmintic action of AADs.

Acid-sensing channels in human bladder: expression, function and alterations during bladder pain syndrome

We examined the possible role of H(+) activated acid-sensing ion channels in pain perception. We characterized expression in bladder dome biopsies from patients with bladder pain syndrome and controls, in cultured human urothelium and in urothelial TEU-2 cells.