Antisense RNAs regulate gene expression in many bacterial systems. The best characterized examples are from prokaryotic accessory elements such as phages, plasmids and transposons. Many of these antisense RNAs have been identified as plasmid copy number regulators where they regulate the replication frequency of the plasmid by negative feedback. Instability and fast binding kinetics is crucial for the regulatory efficiency of these antisense RNAs. In this thesis, the interaction of the cis-encoded antisense RNA CopA with its target CopT was studied in detail using in vivo reporter gene fusion expression and different in vitro methods, such as surface plasmon resonance, fluorescence resonance energy transfer, and gel-shift assays. Formation of inhibitory complexes differs from simple hybridization reactions between complementary strands. E.g., the binding pathway of CopA and CopT proceeds through a hierarchical order of steps. It initiates by reversible loop-loop contacts, resulting in a helix nucleus of two or three base pairs. This is followed by rapid unidirectional helix progression into the upper stems, resulting in a four-way helical junction structure. It had been suggested that the loop of CopT carries a putative U-turn, a structure first found in tRNA anticodon loops. We showed that this putative U-turn is one of the structural elements of CopA/CopT required to achieve fast binding kinetics. Furthermore, the hypothetical U-turn structure determines the direction of helix progression when the kissing complex progresses to a four-way helical junction structure. Another structural element in CopT is the helical stem adjacent to the recognition loop. This stem is important to present the recognition loop appropriately to provide a scaffold for the U-turn. Furthermore, the role of protein Hfq in the interaction of antisense/target RNA was investigated, since several trans-encoded antisense RNAs had been shown to need this protein to exert their function. In contrast, studies of two cis-encoded antisense RNA systems showed that these antisense RNAs do not rely on Hfq for activity. In this study it was also shown that MicF, a trans-encoded antisense RNA which is dependent on Hfq, is greatly stabilized by this protein.

This thesis presents the results of an experimental study on single-charge effects in nanoscale Josephson junctions and Cooper pair transistors (CPTs). In nanoscale Josephson junctions the charging energy EC becomes significant at sub-Kelvin temperatures and single-charge effects, such as the Coulomb blockade of Cooper pair tunneling, influence the transport properties. In order to observe charging effects in a single Josephson junction, the impedance of the electromagnetic environment surrounding the junction has to be larger than the quantum resistance (RQ=h/4e2≈6.45kΩ). In this work the high impedance environment is obtained by biasing the sample under test (single Josephson junction or CPT) with four one-dimensional Josephson junction arrays having SQUID geometry. The advantage of this configuration is the possibility of tuning in situ the effective impedance of the electromagnetic environment. By applying a magnetic field perpendicular to the SQUID loops, the Josephson energy EJ of the SQUIDs is suppressed, resulting in an increase of the measured zero bias resistance of the arrays of several orders of magnitude (104< R0 (Ω) <109). This bias method enables the measurement of the same sample in environments with different impedance. As the impedance of the environment is increased, the current-voltage characteristics (IVCs) of the single Josephson junction and of the CPT show a well defined Coulomb blockade feature with a region of negative differential resistance, signature of the coherent tunneling of single Cooper pairs. The measured IVCs of a single Josephson junction with SQUID geometry in the high impedance environment show a qualitative agreement with the Bloch band theory as the EJ/EC ratio of the junction is tuned with the magnetic field. We also studied a single nontunable Josephson junction with strong coupling (EJ/EC > 1), where the exact dual of the overdamped Josephson effect is realized, resulting in a dual shape of the IVC, where the roles of current and voltage are exchanged. Here, we make for the first time a detailed quantitative comparison with a theory which includes the effect of fluctuations due to the finite temperature of the environment. The measurements on CPTs in the high impedance environment showed that the Coulomb blockade voltage is modulated periodically by the gate-induced charge. The gate-voltage dependence of the CPT changes from e-periodic to 2e-periodic as the impedance of the environment is increased. The high impedance environment reduces quasiparticle tunneling rates, thereby restoring the even parity of the CPT island. This behavior suggests that high impedance leads can be used to effectively suppress quasiparticle poisoning. / QC 20100928

Josephson junction qubits are promising candidates for a scalable quantum processor. Such qubits are commonly manipulated by means of sequences of rf-pulses and different methods are used to determine their quantum state. The readout should be able to distinguish the two qubit states with high accuracy and be faster than the relaxation time of the qubit. We discuss and experiment with a readout method based on the switching of a Josephson junction from the zero voltage state to a finite voltage state. The Josephson junction circuit has a non-linear dynamics and when it is brought to a bifurcation point, it can be made arbitrarily sensitive to small perturbations. This extreme sensitivity at a bifurcation point can be used to distinguish the two quantum states if the topology of the phase space of the circuit leads to a quick separation into the final states where re-crossings of the bifurcation point are negligible. We optimize a switching current detector by analyzing the phase space of a Josephson junction circuit with frequency dependent damping. A pulse and hold technique is used where an initial current pulse brings the junction close to its bifurcation point and the subsequent hold level is used to give the circuit enough time to evolve until the two states can be distinguished by the measuring instrument. We generate the pulse and hold waveform by a new technique where a voltage step with following linear voltage rise is applied to a bias capacitor. The frequency dependent damping is realized by an on-chip RC-environment fabricated with optical lithography. Josephson junction circuits are added on by means of e-beam lithography. Measurements show that switching currents can be detected with pulses as short as 5 ns and a resolution of 2.5% for a sample directly connected to the measurement leads of the cryostat. Detailed analysis of the switching currents in the RC-environment show that pulses with a duration of 20 us can be explained by a generalization of Kramers' escape theory, whereas switching the same sample with 25 ns pulses occurs out of thermal equilibrium, with sensitivity and speed adequate for qubit readout. / QC 20100924

In this thesis, various issues regarding normally-ON silicon carbide (SiC)Junction Field-Effect Transistors (JFETs) are treated. Silicon carbide powersemiconductor devices are able to operate at higher switching frequencies,higher efficiencies, and higher temperatures compared to silicon counterparts.From a system perspective, these three advantages of silicon carbide can determinethe three possible design directions: high efficiency, high switchingfrequency, and high temperature.The structure designs of the commercially-available SiC power transistorsalong with a variety of macroscopic characteristics are presented. Apart fromthe common design and performance problems, each of these devices suffersfrom different issues and challenges which must be dealt with in order to pavethe way for mass production. Moreover, the expected characteristics of thefuture silicon carbide devices are briefly discussed. The presented investigationreveals that, from the system point-of-view, the normally-ON JFET isone of the most challenging silicon carbide devices. There are basically twoJFET designs which were proposed during the last years and they are bothconsidered.The state-of-the-art gate driver for normally-ON SiC JFETs, which wasproposed a few years ago is briefly described. Using this gate driver, theswitching performance of both Junction Field-Effect Transistor designs wasexperimentally investigated.Considering the current development state of the available normally-ONSiC JFETs, the only way to reach higher current rating is to parallel-connecteither single-chip discrete devices or to build multichip modules. Four deviceparameters as well as the stray inductances of the circuit layout might affectthe feasibility of parallel connection. The static and dynamic performance ofvarious combinations of parallel-connected normally-ON JFETs were experimentallyinvestigated using two different gate-driver configurations.A self-powered gate driver for normally-ON SiC JFETs, which is basicallya circuit solution to the “normally-ON problem” is also shown. This gatedriver is both able to turn OFF the shoot-through current during the startupprocess, while it also supplies the steady-state power to the gate-drivecircuit. From experiments, it has been shown that in a half-bridge converterconsisting of normally-ON SiC JFETs, the shoot-through current is turnedOFF within approximately 20 μs.Last but not least, the potential benefits of employing normally-ON SiCJFETs in future power electronics applications is also presented. In particular,it has been shown that using normally-ON JFETs efficiencies equal 99.8% and99.6% might be achieved for a 350 MW modular multilevel converter and a40 kVA three-phase two-level voltage source converter, respectively.Conclusions and suggestions for future work are given in the last chapterof this thesis. / I denna avhandling behandlas olika aspekter av normally–ON junction–field–effect–transistorer (JFETar) baserade på kiselkarbid (SiC). Effekthalvledarkomponenteri SiC kan arbeta vid högre switchfrekvens, högre verkningsgradoch högre temperatur än motsvarigheterna i kisel. Ur ett systemperspektivkan de tre nämnda fördelarna användas i omvandlarkonstruktionen för attuppnå antingen hög verkningsgrad, hög switchfrekvens eller hög temperaturtålighet.Såväl halvledarstrukturen som de makroskopiska egenskaperna för kommersiellttillgängliga SiC–transistorer presenteras. Bortsett från de vanligakonstruktions–och prestandaproblemen lider de olika komponenterna av ettantal tillkortakommanden som måste övervinnas för att bana väg för massproduktion.Även framtida SiC–komponenter diskuteras.Ur ett systemperspektiv är normally-ON JFETen en av de mest utmanandeSiC-komponenterna. De två varianter av denna komponent som varittillgängliga de senaste åren har båda avhandlats.State–of–the–art–drivdonet för normally-ON JFETar som presenteradesför några år sedan beskrivs i korthet. Med detta drivdon undersöks switchegenskapernaför båda JFET-typerna experimentellt.Vid beaktande av det aktuella utvecklingsstadiet av de tillgängliga normally–ON JFETarna i SiC, är det möjligt att uppnå höga märkströmmar endastom ett antal single–chip–komponenter parallellkopplas eller om multichipmodulerbyggs. Fyra komponentparametrar samt strö-induktanser för kretsenkan förutses påverka parallellkopplingen. De statiska och dynamiska egenskapernaför olika kombinationer av parallellkopplade normally-ON JFETarundersöks experimentellt med två olika gate–drivdonskonfigurationer.Ett självdrivande gate-drivdon för normally-ON JFETar presenteras också.Drivdonet är en kretslösning till “normally–ON–problemet”. Detta gatedrivdonkan både stänga av kortslutningsströmmen vid uppstart och tillhandahållaströmförsörjning vid normal drift. Med hjälp av en halvbrygga medkiselkarbidbaserade normally–ON JFETar har det visats att kortslutningsströmmenkan stängas av inom cirka 20 μs.Sist, men inte minst, presenteras de potentiella fördelarna med användningenav SiC-baserade normally-ON JFETar i framtida effektelektroniskatillämpningar. Speciellt visas att verkningsgrader av 99.8% respektive 99.5%kan uppnås i fallet av en 350 MW modular multilevel converter och i en40 kVA tvånivåväxelriktare. Sista kaplitet beskriver slutsatser och föreslagetframtida arbete. / <p>QC 20130527</p>

Road design with focus to safety has been extensively developed in last decades in Nordic and some other EU countries with the main aim to achieve a decrease in a number of accidents and fatalities on the roads. These countries gained many valuable experiences, but they had to sacrifice great effort, expenses, and time to reach the present art-of-state. The purpose of the Master’s Thesis is to review some design approaches with focus to safety and discuss the general way that they may be applied. The Master’s Thesis studies safety in three levels: (i) general - design standards, national safety policies and road hierarchy; (ii) local authority and road administrator; and (iii) three specific safety countermeasures - junctions, pedestrian crossings and traffic calming. The first part of Master’s Thesis describes the general road design standards background and their art of state. Furthermore, it discusses the new approaches in road design standard such as Dutch classification of road standards. Safety policies and programs are discussed and the concept of human imperfection is explained. Road safety policy and road hierarchy in Sweden and Denmark is described. The second part is devoted to the planning process on local authority and road administrator level. The phases of planning process are described. Special attention is paid to ranking process when choosing most effective countermeasures, next to black spot programs and also to public attitudes to safety countermeasures. The focus of the last part is in specific designs for safer road environment. There are discussed three groups of road facilities and countermeasures; unctions, pedestrian crossings and traffic calming. The cost, effectiveness, suitability, possible side effects and other properties of individual types of countermeasures are discussed.

Gap junctions provide direct electrical and biochemical communication between cardiomyocytes in the heart. Connexin40 (Cx40) is the major connexin in the atria of the heart and little is known regarding its regulation. Thus, the goal was to investigate the regulation of Cx40 in both physiological and pathophysiological conditions. The first objective of this thesis was to determine whether Cx40 gap junctions were regulated by â-adrenergic receptor activation. Cx40 has previously been shown to be acutely activated by cAMP, this cAMP-induced increase in Cx40-mediated cell-to-cell dye transfer has been shown to be effected through the â-adrenergic receptor-adenylyl cyclase- Protein Kinase A (PKA) pathway in Cx40-transfected HeLa cells. The second objective of this thesis was to determine whether Cx40 gap junctions were regulated by intracellular Ca2+ concentration ([Ca2+]i ). [Ca2+]i was increased by addition of the ionophore ionomycin and elevating extracellular calcium [Ca2+]o from 1.8 mM to 21.8 mM. This resulted in an elevation of [Ca2+]i and effected an inhibition of Cx40-mediated cell-to-cell dye transfer (IC50 of 500 ± 0.72 nM) which was Calmodulin-dependent. The third objective of this thesis was to determine whether Cx40 gap junctions were regulated by ischemia. Inducing ischemia chemically by inhibiting the electron transport chain with sodium cyanide and glycolysis with iodoacetate and 2-deoxyglucose effected an inhibition of Cx40-mediated cell-to-cell dye transfer that was shown to be Calmodulin dependent. The main conclusions of this thesis were: (1) â-adrenergic receptor activation increases Cx40-mediated cell-to-cell dye transfer which requires the activation of PKA; (2) A sustained elevation in [Ca2+]i causes a partial inhibition of Cx40 gap junction-mediated cell-to-cell dye transfer which was Ca2+-and Calmodulin dependent; (3) Chemical ischemia causes a partial inhibition of Cx40 gap junction-mediated cell-to-cell dye transfer which was shown to be Calmodulin-dependent.

Ca2+, a signal for death and life, is closely involved in the regulation of numerous important cellular events. Ca2+ carries out its function through its binding to Ca2+-receptors or Ca2+-binding proteins. The EF-hand protein, with a helix-loop-helix Ca2+-binding motif, constitutes one of the largest protein families. To facilitate our understanding of the role of Ca2+ in biological systems (denoted as calciomics) using genomic information, an improved pattern search method (http://www.chemistry.gsu.edu/faculty/Yang/Calciomics.htm) for the identification of EF-hand and EF-like Ca2+-binding proteins was developed. This fast and robust method allows us to analyze putative EF-hand proteins at the genome-wide level and further visualize the evolutionary scenario of the EF-hand protein family. This prediction method further enables us to locate a putative viral EF-hand Ca2+-binding motif within the rubella virus nonstructural protease that cleaves the nonstructural protein precursor into two active replicase components. A novel grafting approach has been used to probe the metal-binding properties of this motif by engineering the predicted 12-residue Ca2+-coordinating loop into a non-Ca2+-binding scaffold protein, CD2 domain 1. Structural and conformational studies were further performed on a purified, bacterially-expressed NS protease minimal metal-binding domain spanning the Zn2+- and EF-hand Ca2+-binding motif. It was revealed that Ca2+ binding induced local conformational changes and increased thermal stability. Furthermore, functional studies were carried out using RUB infectious cDNA clone and replicon constructs. Our studies have shown that the Ca2+ binding loop played a structural role in the NS protease and was specifically required for optimal stability under physiological conditions. In addition, we have predicted and characterized a calmodulin-binding domain in the gap junction proteins connexin43 and connexin44. Peptides encompassing the CaM binding motifs were synthesized and their ability to bind CaM was determined using various biophysical approaches. Transient expression in HeLa cells of two mutant Cx43-EYFP constructs without the putative CaM-binding site eliminated the Ca2+-dependent inhibition of gap junction permeability. These results provide the first direct evidence that CaM binds to a specific region of the ubiquitous gap junction protein Cx43 and Cx44 in a Ca2+-dependent manner, providing a molecular basis for the well-characterized Ca2+-dependent inhibition of Cx43-containing gap junctions.

Present day data processing technology requires very high speed signal processing and data conversion rates. One such application which requires high speed is switched capacitor circuits used in Sigma-Delta modulators. A major active component of switched capacitor circuits is the monolithic operational amplifier(opamp). Because of the relatively poor speed performance of the currently available silicon based technology, such high speed circuits can not be designed. GaAs technology appears to be a promising alternative technology for high speed switched capacitor circuits. One problem with GaAs is the lack of complementary technology. Until now, most of the design of GaAs analog integrated circuits has been implemented using depletion mode n-MESFETs, where operational amplifiers and switched capacitors have been developed by various groups. This thesis develops the techniques for implementation of analog integrated circuits using complementary GaAs Heterojunction Field Effect Transistors(HFETs). Several operational amplifiers have been designed and their performance studied via simulation. The designs studied predict superior high frequency performance for C-HFETs over conventional GaAs MESFET and Silicon CMOS technology. The opamp designs are currently being implemented at Oregon State University for fabrication in the future. / Graduation date: 1993

A study of deep levels of the emitter region of a heterojunction bipolar transistor is investigated using deep level transient spectroscopy (DLTS), deep level admittance spectroscopy (DLAS), thermally stimulated capacitance (TSCAP), and capacitance-voltage (C-V) profiling. The DX center, with an activation energy of 0.45 eV, is the only deep level detected. By varying the DLTS rate window and filling pulse widths, DX is found to be comprise of two closely spaced DX centers, denoted DX1 and DX2. A positive peak observed in the DLTS spectra is attributed to electron capture, not minority carrier emission, and, thus, is an experimental artifact. Finally, the reduction of current gain (β) at low collector current and the effect of the DX center on the switching characteristics of HBTs are briefly discussed. / Graduation date: 1993

This thesis has investigated skeletal muscle fibers and neuromuscular junctions of the reptile Anolis carolinensis. The extensor digitorum communis and gastrocnemmius externus were used for observations and characterization. Cross sections were stained for oxidative and glycolytic activities and for contractile properties by the use of four histochemical stains. This revealed the extensor digitorum communis to be composed of predominately fast glycolytic fibers, with a central core of fast oxidative-glycolytic and slow oxidative fibers. The gastrocnemius externus exhibited a majority of fast oxidative-glycolytic fibers and random slow oxidative fibers.Ultra structural examination of the extensor digitorum communis revealed the nerve terminal of the neuromuscular junction to be smaller than that of the gastrocnemius externus, with junctional folds longer and straighter, and synaptic vesicles smaller and more closely packed. In both muscles, the nerve fibers terminated in a shallow groove of the muscle fiber. The characteristics and heterogeneity that exist are very similar to the homologous mammalian extensor digitorum longus and soleus skeletal muscle.Ball State UniversityMuncie, IN 47306