Photolithography based patterning of bacteriorhodopsin films

The patterning of photoactive purple membrane (PM) films onto electronic substrates to create a biologically based light detection device was investigated. This research is part of a larger collaborative effort to develop a miniaturized toxin detection platform. This platform will utilize PM films containing the photoactive protein bacteriorhodopsin to convert light energy to electrical energy. Following an effort to pattern PM films using focused ion beam machining, the photolithography based bacteriorhodopsin patterning technique (PBBPT) was developed. This technique utilizes conventional photolithography techniques to pattern oriented PM films onto flat substrates. After the basic patterning process was developed, studies were conducted that confirmed the photoelectric functionality of the PM films after patterning. Several process variables were studied and optimized in order to increase the pattern quality of the PM films. Optical microscopy, scanning electron microscopy, and interferometric microscopy were used to evaluate the PM films produced by the patterning technique. Patterned PM films with lateral dimensions of 15 μm have been demonstrated using this technique. Unlike other patterning techniques, the PBBPT uses standard photolithographic processes that make its integration with conventional semiconductor fabrication feasible. The final effort of this research involved integrating PM films patterned using the PBBPT with PMOS transistors. An indirect integration of PM films with PMOS transistors was successfully demonstrated. This indirect integration used the voltage produced by a patterned PM film under light exposure to modulate the gate of a PMOS transistor, activating the transistor. Following this success, a study investigating how this PM based light detection system responded to variations in light intensity supplied to the PM film. This work provides a successful proof of concept for a portion of the toxin detection platform currently under development.

Hall-effect thruster-cathode coupling : the effect of cathode position and magnetic field topology

Hall-effect thruster (HET) cathodes are responsible for the generation of the free electrons necessary to initiate and sustain the main plasma discharge and to neutralize the ion beam. The position of the cathode relative to the thruster strongly affects the efficiency of thrust generation. However, the mechanisms by which the position affects the efficiency are not well understood. This dissertation explores the effect of cathode position on HET efficiency. Magnetic field topology is shown to play an important role in the coupling between the cathode plasma and the main discharge plasma. The position of the cathode within the magnetic field affects the ion beam and the plasma properties of the near-field plume, which explains the changes in efficiency of the thruster. Several experiments were conducted which explored the changes of efficiency arising from changes in cathode coupling. In each experiment, the thrust, discharge current, and cathode coupling voltage were monitored while changes in the independent variables of cathode position, cathode mass flow and magnetic field topology were made. From the telemetry data, the efficiency of the HET thrust generation was calculated. Furthermore, several ion beam and plasma properties were measured including ion energy distribution, beam current density profile, near-field plasma potential, electron temperature, and electron density. The ion beam data show how the independent variables affected the quality of ion beam and therefore the efficiency of thrust generation. The measurements of near-field plasma properties partially explain how the changes in ion beam quality arise. The results of the experiments show that cathode position, mass flow, and field topology affect several aspects of the HET operation, especially beam divergence and voltage utilization efficiencies. Furthermore, the experiments show that magnetic field topology is important in the cathode coupling process. In particular, the magnetic field separatrix plays a critical role in impeding the coupling between cathode and HET. Suggested changes to HET thruster designs are provided including ways to improve the position of the separatrix to accommodate the cathode.

Immobilizing bacteriorhodopsin on a single electron transistor

As awareness of potential human and environmental impacts from toxins has increased, so has the development of innovative sensors. Bacteriorhodopsin (bR) is a light activated proton pump contained in the purple membrane (PM) of the bacteria Halobacterium salinarum. Bacteriorhodopsin is a robust protein which can function in both wet and dry states and can withstand extreme environmental conditions. A single electron transistor(SET) is a nano-scale device that exploits the quantum mechanical properties of electrons to switch on and off. SETs have tremendous potential in practical applications due to their size, ultra low power requirements, and electrometer-like sensitivity. The main goal of this research was to create a bionanohybrid device by integrating bR with a SET device. This was achieved by a multidisciplinary approach. The SET devices were created by a combination of sputtering, photolithography, and focused ion beam machining. The bionanomaterial bacteriorhodopsin was created through oxidative fermentation and a series of transmembrane purification processes. The bR was then integrated with the SET by electrophoretic deposition, creating a bionanohybrid device. The bionanohybrid device was then characterized using a semiconductor parametric analyzer. Characterization demonstrated that the bR modulated the operational characteristics of the SET when bR was activated with light within its absorbance spectrum. To effectively integrate bacteriorhodopsin with microelectromechanical systems (MEMS) and nanoelectromechanical systems (NEMS), it is critical to know the electrical properties of the material and to understand how it will affect the functionality of the device. Tests were performed on dried films of bR to determine if there is a relationship between inductance, capacitance, and resistance (LCR) measurements and orientation, light-on/off, frequency, and time. The results indicated that the LCR measurements of the bR depended on the thickness and area of the film, but not on the orientation, as with other biological materials such as muscle. However, there was a transient LCR response for both oriented and unoriented bR which depended on light intensity. From the impedance measurements an empirical model was suggested for the bionanohybrid device. The empirical model is based on the dominant electrical characteristics of the bR which were the parallel capacitance and resistance. The empirical model suggests that it is possible to integrate bR with a SET without influencing its functional characteristics.

Structural and surface property characterization of titanium dioxide nanotubes for orthopedic implants

This research focused on the to modification of the surface structure of titanium implants with nanostructured morphology of TiO2 nanotubes and studied the interaction of nanotubes with osteoblast cells to understand the parameters that affect the cell growth. The electrical, mechanical, and structural properties of TiO2 nanotubes were characterized to establish a better understanding on the properties of such nanoscale morphological structures. To achieve the objectives of this research work I transformed the titanium and its alloys, either in bulk sheet form, bulk machined form, or thin film deposited on another substrate into a surface of titania nanotubes using a low cost and environmentally friendly process. The process requires only a simple electrolyte, low cost electrode, and a DC power supply. With this simple approach of scalable nanofabrication, a typical result is nanotubes that are each approximately 100nm in diameter and have a wall thickness of about 20nm. By changing the fabrication parameters, independent nanotubes can be fabricated with open volume between them. Titanium in this form is termed onedimensional since electron transport is narrowly confined along the length of the nanotube. My Ph.D. accomplishments have successfully shown that osteoblast cells, the cells that are the precursors to bone, have a strong tendency to attach to the inside and outside of the titanium nanotubes onto which they are grown using their filopodia – cell’s foot used for locomotion – anchored to titanium nanotubes. In fact it was shown that the cell prefers to find many anchoring sites. These sites are critical for cell locomotion during the first several weeks of maturity and upon calcification as a strongly anchored bone cell. In addition I have shown that such a surface has a greater cell density than a smooth titanium surface. My work also developed a process that uses a focused and controllably rastered ion beam as a nano-scalpel to cut away sections of the osteoblast cells to probe the attachment beneath the main cell body. Ultimately the more rapid growth of osteoblasts, coupled with a stronger cell-surface interface, could provide cost reduction, shorter rehabilitation, and fewer follow-on surgeries due to implant loosening.

Integration of room temperature single electron transistor with CMOS subsystem

The single electron transistor (SET) is a charge-based device that may complement the dominant metal-oxide-semiconductor field effect transistor (MOSFET) technology. As the cost of scaling MOSFET to smaller dimensions are rising and the the basic functionality of MOSFET is encountering numerous challenges at dimensions smaller than 10nm, the SET has shown the potential to become the next generation device which operates based on the tunneling of electrons. Since the electron transfer mechanism of a SET device is based on the non-dissipative electron tunneling effect, the power consumption of a SET device is extremely low, estimated to be on the order of 10^-18J. The objectives of this research are to demonstrate technologies that would enable the mass produce of SET devices that are operational at room temperature and to integrate these devices on top of an active complementary-MOSFET (CMOS) substrate. To achieve these goals, two fabrication techniques are considered in this work. The Focus Ion Beam (FIB) technique is used to fabricate the islands and the tunnel junctions of the SET device. A Ultra-Violet (UV) light based Nano-Imprint Lithography (NIL) call Step-and-Flash- Imprint Lithography (SFIL) is used to fabricate the interconnections of the SET devices. Combining these two techniques, a full array of SET devices are fabricated on a planar substrate. Test and characterization of the SET devices has shown consistent Coulomb blockade effect, an important single electron characteristic. To realize a room temperature operational SET device that function as a logic device to work along CMOS, it is important to know the device behavior at different temperatures. Based on the theory developed for a single island SET device, a thermal analysis is carried out on the multi-island SET device and the observation of changes in Coulomb blockade effect is presented. The results show that the multi-island SET device operation highly depends on temperature. The important parameters that determine the SET operation is the effective capacitance Ceff and tunneling resistance Rt . These two parameters lead to the tunneling rate of an electron in the SET device, Γ. To obtain an accurate model for SET operation, the effects of the deviation in dimensions, the trap states in the insulation, and the background charge effect have to be taken into consideration. The theoretical and experimental evidence for these non-ideal effects are presented in this work.

Development of room temperature operating single electron transistor using FIB etching and deposition technology

The single-electron transistor (SET) is one of the best candidates for future nano electronic circuits because of its ultralow power consumption, small size and unique functionality. SET devices operate on the principle of Coulomb blockade, which is more prominent at dimensions of a few nano meters. Typically, the SET device consists of two capacitively coupled ultra-small tunnel junctions with a nano island between them. In order to observe the Coulomb blockade effects in a SET device the charging energy of the device has to be greater that the thermal energy. This condition limits the operation of most of the existing SET devices to cryogenic temperatures. Room temperature operation of SET devices requires sub-10nm nano-islands due to the inverse dependence of charging energy on the radius of the conducting nano-island. Fabrication of sub-10nm structures using lithography processes is still a technological challenge. In the present investigation, Focused Ion Beam based etch and deposition technology is used to fabricate single electron transistors devices operating at room temperature. The SET device incorporates an array of tungsten nano-islands with an average diameter of 8nm. The fabricated devices are characterized at room temperature and clear Coulomb blockade and Coulomb oscillations are observed. An improvement in the resolution limitation of the FIB etching process is demonstrated by optimizing the thickness of the active layer. SET devices with structural and topological variation are developed to explore their impact on the behavior of the device. The threshold voltage of the device was minimized to ~500mV by minimizing the source-drain gap of the device to 17nm. Vertical source and drain terminals are fabricated to realize single-dot based SET device. A unique process flow is developed to fabricate Si dot based SET devices for better gate controllability in the device characteristic. The device vi parameters of the fabricated devices are extracted by using a conductance model. Finally, characteristic of these devices are validated with the simulated data from theoretical modeling.

Calibration and analysis of the 2007 data

he physics program of the NA61/SHINE (SHINE = SPS Heavy Ion and Neutrino Experiment) experiment at the CERN SPS consists of three subjects. In the first stage of data taking (2007-2009) measurements of hadron production in hadron-nucleus interactions needed for neutrino (T2K) and cosmic-ray (Pierre Auger and KASCADE) experiments will be performed. In the second stage (2009-2010) hadron production in proton-proton and proton-nucleus interactions needed as reference data for a better understanding of nucleus-nucleus reactions will be studied. In the third stage (2009-2013) energy dependence of hadron production properties will be measured in p+p, p+Pb interactions and nucleus-nucleus collisions, with the aim to identify the properties of the onset of deconfinement and find evidence for the critical point of strongly interacting matter. The NA61 experiment was approved at CERN in June 2007. The first pilot run was performed during October 2007. Calibrations of all detector components have been performed successfully and preliminary uncorrected spectra have been obtained. High quality of track reconstruction and particle identification similar to NA49 has been achieved. The data and new detailed simulations confirm that the NA61 detector acceptance and particle identification capabilities cover the phase space required by the T2K experiment. This document reports on the progress made in the calibration and analysis of the 2007 data.

Ultracold Quantum Gases and Lattice Systems: Quantum Simulation of Lattice Gauge Theories

Abelian and non-Abelian gauge theories are of central importance in many areas of physics. In condensed matter physics, AbelianU(1) lattice gauge theories arise in the description of certain quantum spin liquids. In quantum information theory, Kitaev’s toric code is a Z(2) lattice gauge theory. In particle physics, Quantum Chromodynamics (QCD), the non-Abelian SU(3) gauge theory of the strong interactions between quarks and gluons, is nonperturbatively regularized on a lattice. Quantum link models extend the concept of lattice gauge theories beyond the Wilson formulation, and are well suited for both digital and analog quantum simulation using ultracold atomic gases in optical lattices. Since quantum simulators do not suffer from the notorious sign problem, they open the door to studies of the real-time evolution of strongly coupled quantum systems, which are impossible with classical simulation methods. A plethora of interesting lattice gauge theories suggests itself for quantum simulation, which should allow us to address very challenging problems, ranging from confinement and deconfinement, or chiral symmetry breaking and its restoration at finite baryon density, to color superconductivity and the real-time evolution of heavy-ion collisions, first in simpler model gauge theories and ultimately in QCD.

Hot QCD vs cosmology

It is a long-standing dream to “simulate” cosmology in laboratory through heavy ion collision experiments. Although the QCD epoch itself may not leave major cosmological signatures, theoretical methods developed and tested in the context of heavy ion collision experiments could indeed find applications at other energy scales. Here recent progress in this spirit is reviewed.

Measurement of the jet radius and transverse momentum dependence of inclusive jet suppression in lead-lead collisions at sqrtsNN=2.76 TeV with the AT detector

Measurements of inclusive jet suppression in heavy ion collisions at the LHC provide direct sensitivity to the physics of jet quenching. In a sample of lead-lead collisions at root S-NN = 2.76 TeV corresponding to an integrated luminosity of approximately 7 mu b(-1), ATLAS has measured jets with a calorimeter system over the pseudorapidity interval vertical bar eta vertical bar < 2.1 and over the transverse momentum range 38 < pT <210 GeV. Jets were reconstructed using the anti-k(t) algorithm with values for the distance parameter that determines the nominal jet radius of R = 0.2, 0.3, 0.4 and 0.5. The centrality dependence of the jet yield is characterized by the jet "central-to-peripheral ratio," R-CP. Jet production is found to be suppressed by approximately a factor of two in the 10% most central collisions relative to peripheral collisions. R-CP varies smoothly with centrality as characterized by the number of participating nucleons. The observed suppression is only weakly dependent on jet radius and transverse momentum. These results provide the first direct measurement of inclusive jet suppression in heavy ion collisions and complement previous measurements of dijet transverse energy imbalance at the LHC.

Charm contribution to bulk viscosity

In the range of temperatures reached in future heavy ion collision experiments, hadronic pair annihilations and creations of charm quarks may take place within the lifetime of the plasma. As a result, charm quarks may increase the bulk viscosity affecting the early stages of hydrodynamic expansion. Assuming thermalisation, we estimate the charm contribution to bulk viscosity within the same effective kinetic theory framework in which the light parton contribution has been computed previously. The time scale at which this physics becomes relevant is related to the width of the transport peak associated with the trace anomaly correlator and is found to be ≲20 fm/c for T≳600 MeV.

NA61/SHINE facility at the CERN SPS: beams and detector system

NA61/SHINE (SPS Heavy Ion and Neutrino Experiment) is a multi-purpose experimental facility to study hadron production in hadron-proton, hadron-nucleus and nucleus-nucleus collisions at the CERN Super Proton Synchrotron. It recorded the first physics data with hadron beams in 2009 and with ion beams (secondary 7Be beams) in 2011. NA61/SHINE has greatly profited from the long development of the CERN proton and ion sources and the accelerator chain as well as the H2 beamline of the CERN North Area. The latter has recently been modified to also serve as a fragment separator as needed to produce the Be beams for NA61/SHINE. Numerous components of the NA61/SHINE set-up were inherited from its predecessors, in particular, the last one, the NA49 experiment. Important new detectors and upgrades of the legacy equipment were introduced by the NA61/SHINE Collaboration. This paper describes the state of the NA61/SHINE facility — the beams and the detector system — before the CERN Long Shutdown I, which started in March 2013.

AMS-C14 analysis of graphite obtained with an Automated Graphitization Equipment (AGE III) from aerosol collected on quartz filters

AMS-14C applications often require the analysis of small samples. Such is the case of atmospheric aerosols where frequently only a small amount of sample is available. The ion beam physics group at the ETH, Zurich, has designed an Automated Graphitization Equipment (AGE III) for routine graphite production for AMS analysis from organic samples of approximately 1 mg. In this study, we explore the potential use of the AGE III for graphitization of particulate carbon collected in quartz filters. In order to test the methodology, samples of reference materials and blanks with different sizes were prepared in the AGE III and the graphite was analyzed in a MICADAS AMS (ETH) system. The graphite samples prepared in the AGE III showed recovery yields higher than 80% and reproducible 14C values for masses ranging from 50 to 300 lg. Also, reproducible radiocarbon values were obtained for aerosol filters of small sizes that had been graphitized in the AGE III. As a study case, the tested methodology was applied to PM10 samples collected in two urban cities in Mexico in order to compare the source apportionment of biomass and fossil fuel combustion. The obtained 14C data showed that carbonaceous aerosols from Mexico City have much lower biogenic signature than the smaller city of Cuernavaca.

Radiochemical determination of 129I and 36Cl in MEGAPIE, a proton irradiated lead-bismuth eutectic spallation target

The concentrations of the long-lived nuclear reaction products 129I and 36Cl have been measured in samples from the MEGAPIE liquid metal spallation target. Samples from the bulk target material (lead-bismuth eutectic, LBE), from the interface of the metal free surface with the cover gas, from LBE/steel interfaces and from noble metal absorber foils installed in the cover gas system were analysed using Accelerator Mass Spectrometry at the Laboratory of Ion beam Physics at ETH Zürich. The major part of 129I and 36Cl was found accumulated on the interfaces, particularly at the interface of LBE and the steel walls of the target container, while bulk LBE samples contain only a minor fraction of these nuclides. Both nuclides were also detected on the absorber foils to a certain extent (≪ 1% of the total amount). The latter number is negligible concerning the radio-hazard of the irradiated target material; however it indicates a certain affinity of the absorber foils for halogens, thus proving the principle of using noble metal foils for catching these volatile radionuclides. The total amounts of 129I and 36Cl in the target were estimated from the analytical data by averaging within the different groups of samples and summing up these averages over the total target. This estimation could account for about half of the amount of 129I and 36Cl predicted to be produced using nuclear physics modelling codes for both nuclides. The significance of the results and the associated uncertainties are discussed.

U-series ages from calcitic cold-water corals from the Amundsen Sea

Radiocarbon and uranium-thorium dating results are presented from a genus of calcitic Antarctic cold-water octocorals (family Coralliidae), which were collected from the Marie Byrd Seamounts in the Amundsen Sea (Pacific sector of the Southern Ocean) and which to date have not been investigated geochemically. The geochronological results are set in context with solution and laser ablation-based element/Ca ratios (Li, B, Mg, Mn, Sr, Ba, U, Th). Octocoral radiocarbon ages on living corals are in excellent agreement with modern ambient deep-water D14C, while multiple samples of individual fossil coral specimens yielded reproducible radiocarbon ages. Provided that local radiocarbon reservoir ages can be derived for a given time, fossil Amundsen Sea octocorals should be reliably dateable by means of radiocarbon. In contrast to the encouraging radiocarbon findings, the uranium-series data are more difficult to interpret. The uranium concentration of these calcitic octocorals is an order of magnitude lower than in the aragonitic hexacorals that are conventionally used for geochronological investigations. While modern and Late Holocene octocorals yield initial d234U in good agreement with modern seawater, our results reveal preferential inward diffusion of dissolved alpha-recoiled 234U and its impact on fossil coral d234U. Besides alpha-recoil related 234U diffusion, high-resolution sampling of two fossil octocorals further demonstrates that diagenetic uranium mobility has offset apparent coral U-series ages. Combined with the preferential alpha-recoil 234U diffusion, this process has prevented fossil octocorals from preserving a closed system U-series calendar age for longer than a few thousand years. Moreover, several corals investigated contain significant initial thorium, which cannot be adequately corrected for because of an apparently variable initial 232Th/230Th. Our results demonstrate that calcitic cold-water corals are unsuitable for reliable U-series dating. Mg/Ca ratios within single octocoral specimens are internally strikingly homogeneous, and appear promising in terms of their response to ambient temperature. Magnesium/lithium ratios are significantly higher than usually observed in other deep marine calcifiers and for many of our studied corals are remarkably close to seawater compositions. Although this family of octocorals is unsuitable for glacial deep-water D14C reconstructions, our findings highlight some important differences between hexacoral (aragonitic) and octocoral (calcitic) biomineralisation. Calcitic octocorals could still be useful for trace element and some isotopic studies, such as reconstruction of ambient deep water neodymium isotope composition or pH, via boron isotopic measurements.