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Item Open Access 33 Femtosecond Yb-doped optical frequency comb for frequency metrology applications(Bilkent University, 2013) Şenel, ÇağrıOptical frequency combs have enabled many applications (high precision spectroscopy, table-top optical frequency metrology, optical atomic clocks, etc.), received considerable attention and a Nobel Prize. In this thesis, the development of a stabilized Yb-doped femtosecond optical frequency comb is presented. As a starting point in the development of the frequency comb, a new type of fiber laser has been designed using numerical simulations and realized experimentally. The developed laser is able to produce pulses that can be compressed to 33 fs without higher-order dispersion compensation. After realization of the laser, a new type of fiber amplifier has been developed to be used for supercontinuum generation. The amplifier produces 6.8 nJ pulses that can be compressed to 36 fs without higher-order dispersion compensation. The dynamics of supercontinuum generation have been studied by developing a separate simulation program which solves the generalized nonlinear Schr¨odinger equation. Using the simulation results, appropriate photonic crystal fiber was chosen and octave-spanning supercontinuum was generated. Carrier-envelope-offset frequency of the laser has been obtained by building an f-2f interferometer. Repetition rate and carrier-envelope offset frequency of the laser have been locked to Cs atomic clock using electronic feedback circuits, resulting in a fully stabilized optical frequency comb. The noise performance and stability of the system have been characterized. Absolute frequency measurement of an Nd:YAG laser, which was stabilized using iodine gas, has been performed using the developed optical frequency comb.Item Open Access A1GaN UV photodetectors : from micro to nano(Bilkent University, 2011) Bütün, SerkanThe absorption edge of AlGaN based alloys can be tuned from deep UV to near UV by changing the composition. This enables the use of the material in various technological applications such as military, environmental monitoring and biological imaging. In this thesis, we proposed and demonstrated various UV photodetectors for different purposes. The multi-band photodetectors have the unique ability to sense the UV spectrum in different portions at the same time. We demonstrated monolithically integrated dual and four-band photodetectors with multi layer structures grown on sapphire. This was achieved through epitaxial growth of multi AlGaN layers with decreasing Al content. We suggested two different device architectures. First one has separate filter and active layers, whereas the second one has all active layers which are used as filter layers as well. The full width at half maximum (FWHM) values for the dual band photodetector was 11 and 22 nm with more than three orders of magnitude inter-band rejection ratio. The self-filtering four band photodetector has FWHMs of 18, 17, 22 and 9 nm from longer to shorter bands. Whereas photodetector with separate filter layers has FWHMs of 8, 12, 11 and 8 nm, from longer to shorter bands. The overall inter-band rejection ration was increased from about one to two of magnitude after incorporating the passive filter layers. The plasmonic enhancement of photonic devices has attracted much attention for the past decade. However, there is not much research that has been conducted in UV region. In the second part of this thesis, we fabricated nanostructures on GaN based photodetectors and improved the responsivity of the device. We have fabricated Al nano-particles on sapphire with e-beam lithography. We characterized their response via spectral extinction measurements. We integrated these particles with GaN photodetectors and had enhancement of %50 at the plasmonic resonance of the nano-particles. Secondly, we have fabricated sub-wavelength photodetectors on GaN coupled with linear gratings. We had 8 fold enhancement in the responsivity at the plasmonic resonance frequency of the grating at normal incidence. Numerical simulations revealed that both surface plasmons and the unbound leaky surface waves played a role in the enhancement. We, finally, conducted basic research on the current transport mechanisms in Schottky barriers of AlGaN based materials. Experiments revealed that the tunneling current plays a major role in current transport. In addition incorporation, of a thin insulator between metalsemiconductor interface reduces the undesired surface states thereby improving the device performance.Item Open Access Ab-initio study of iridium on silicon (001) surface(Bilkent University, 2013) Oğuz, İsmail CanSelf-assembled nanowire growth on semiconductor surface is based on deposing sub-monolayer material over the surface. Even though high resolution STM image gives plausible surface analysis, determination of the nanowire structure is the most difficult part of these experiments. Due to the this reason, first-principles investigation is essential to understand the one dimensional nanowire structure grown over the surface as well as the STM images of these structures. Recently, iridium silicide nanowire on Si (001) surface is observed. In this thesis, we study formation of the nanowire after deposition of Ir on Si(001). Ab-initio plane wave pseudopotential calculations are performed for number of iridium silicide nanowires generated by increasing iridium coverage on Si(001) surface. For the iridium coverage as 0.125 ML, the possible nanowire formation is analyzed and its calculated STM images are compared with experimental STM image. As a result of our detailed analysis, we suggest that the STM image observed at experiment doesn’t consist of Ir atoms since Ir atom tends to be buried into the Si bulk. We model the possible nanowire formation which is consistent with pseudo-STM calculation. According to our model, iridium is placed at the troughs between the dimer rows on the surface and it creates a structure by breaking the Si dimer bonds. The coverage implied by the model, is consistent with experimental numbers.Item Open Access The adiabatic and non-adiabatic behavior of a particle in optical lattices(Bilkent University, 2018-06) Yılmaz, FıratThe cold atom experiments provide a clean and controlled environment for realizing many body systems. Recent realizations of artificial gauge fields and adjustable optical lattices paved the way for the study of effectively charged particles with neutral atoms in various lattice and continuum systems. Moreover, it is possible to precisely control the external system parameters, i.e. the artificial gauge fields much faster or slower than the time scales associated with atomic motion in the lattice. It still needs further analysis to fully understand how the adiabatic and non-adiabatic changes affect the stationary and dynamical behavior of the system. We first investigate the effect of the adiabatic changes in the artificial gauge fields, and focus on the famous problem: A charged particle in a periodic potential under magnetic field. This simple system leads a complicated and involved selfsimilar energy spectrum, the Hofstadter butterfly. The whole structure of this energy spectrum is determined by the lattice geometry as well as the external field. In this regard, we consider all possible Bravais lattices in two dimensions and investigate the structure of the Hofstadter butterfly as the different point symmetry groups of the lattices are adiabatically deformed from one into another. We find that each 2D Bravais lattice is uniquely mapped to a fractal energy spectrum and it is possible to understand the interplay between the point symmetry groups and the energy spectrum. This beautiful spectrum, in addition, consists of infinitely many topologically distinct regions as a function of magnetic flux and gap number. The topological character of energy bands are determined through their Chern numbers. We calculate the Chern numbers of the major gaps and Chern number transfer between bands during the topological transitions. In the second part, we investigate the dramatic effect of the non-adiabatic changes in the artificial gauge fields. In a synthetic lattice, the precise control over the hopping matrix elements makes it possible to change this artificial magnetic field non-adiabatically even in the quench limit. We consider such a magneticflux quench scenario in synthetic dimensions. Sudden changes have not been considered for real magnetic fields as such changes in a conducting system would result in large induced currents. Hence we first study the difference between a time varying real magnetic field and an artificial magnetic field using a minimal six-site model which leads to gauge dependent results. This model proves the relation between the gauge dependant dynamics and the absence of scalar potential terms connecting different gauge potentials. In this context, we secondly search for clear indication of the gauge dependent dynamics through magnetic flux quenches of wave packets in two- and three-leg synthetic ladders. We show that the choice of gauge potentials have tremendous effect on the post-quench dynamics of wave packets. Even trivially distinct two vector potentials by an additive constant can produce observable effects, we investigate the effects on the Landau levels and the Laughlin wave function for a filling factor ν = 1/q. We also show that edge solutions in a wide synthetic ladder are protected under a flux quench only if there is another edge state solution in the quenched Hamiltonian.Item Open Access Adsorption and dissociation of hydrogen molecule on carbon nanotubes(Bilkent University, 2004) Öztürk, YavuzEarlier, it has been suggested that carbon nanotubes can provide high storage capacity and other physical properties suitable for the fuel cell technologies. In this thesis we have investigated adsorption, desorption and dissociation of hydrogen molecule on the surface of the zigzag (8,0) single-wall carbon nanotube (SWNT) by carrying out extensive first-principles pseudopotential plane wave calculations within the Density Functional Theory (DFT). We found that while H2 molecule cannot be bound to the surface of bare SWNT, an elastic radial deformation leading to the elliptical deformation of the circular cross-section renders the physisorption of the molecule possible. Coadsorption of Li atom on the SWNT makes the similar effect, and hence enhances the physisorption. That an adsorbed H2 can be desorbed upon releasing the elastic radial strain is extremely convenient for the storage. In addition to that, we found that a Pt atom coadsorbed on the SWNT can form a strong chemisorption bond with a H2 molecule. If a single H2 molecule engages in interactions with more than one coadsorbed Pt atom at its close proximity it dissociates into single H atoms, which, in turn, make Pt-H bonds. The interaction between H2 and coadsorbed Pd atom is similar to Pt, but it is weaker. We believe that these findings clarify earlier controversial results related to the storage of H2 in carbon nanotubes, and makes important contributions to fuel cell technology.Item Open Access Al(x)Ga(1-x)As/GaAs graded index separate confinement heterostructure single quantum well lasers(Bilkent University, 1994) Bozkurt, Mümtaz Koray"Stimulated emission of photons could be produced in semiconductors by recombination of carriers injected across a p-n junction This idea was first suggested by Basov et al} in 1961. Soon afterwards diode lasers were first demonstrated at cryogenic temperatures in pulsed operation in 1962 by separate groups in US.^"® Until the first use of heterostructures in diode lasers^ in 1969, advances in the diode laser area were not as good as was expected. New era of the diode Icisers begin with use of the heterostructures in laser diode technology which allowed them to run at room temperatures in continuous wave operations. Also, introduction of MBE and LPE techniques in crystal growth area supplied the forecoming materials and enabled growing of nanocrystal layers for semiconductor laser diode applications. Reaching to reliable, compact and an efficient components for applications is the major factor which forces the laser diode designs to maturity. In this work, ridge type Single Quantum Well Graded Index Separately Confined Heterostructure lгıser diodes which were made by reactive ion etching in CCI2F2 and lift-off of low temperature PECVD SİO2, is taken from its crystal growth aspects through design and fabrication steps to its characterization.Item Open Access Alteration of self-assembled patterns by microorganisms in evaporating droplets(Bilkent University, 2016-08) Andaç, TuğbaThe science of self-organization comprises a diverse range of processes where a disordered system of components form ordered pattern or structure spontaneously without any external instruction [1]. Plentiful examples of this phenomenon appear in nature at almost all scales [2]. Over the past decades, self-assembly has become the apple of many researchers eye by offering breakthroughs for many applications in not only physics but also chemistry, biology and material sciences [3]. Among several self-assembly methods, using evaporating droplets shines out as it provides ease and simplicity. Along with these advantages, it increases its popularity by providing the opportunity of obtaining a variety of patterns such as uniform depositions, central bumps, polygons and hexagons [4] and more famously (coffee) rings [5]. Nonetheless, most of the studies resulting in these patterns have been carried out by using Brownian particles which uctuate randomly due to the collisions with the molecules of the surrounding uid, while only little is known when it comes to active particles suspended in evaporating droplets. The self-propelling nature of active particles [6] permits them to explore their environment differently from Brownian particles and opens new doors in this research line. Being in the quest of understanding what will happen in the presence of active particles such as the well-studied bacteria Esherichia coli (E.coli ), we investigate and explore the self-assembled patterns in evaporating droplets by using digital video microscopy. We demonstrate that the presence of E.coli bacteria tunes the self-assembled patterns. Moreover, we enrich the patterns by introducing salt. We show that the activity of these microorganisms has an in- uence on salt crystallization based on the characteristic dendritic crystals obtained with active and motile bacteria and unaltered, regular crystals obtained with nonmotile bacteria with inhibited activity. Our results suggest a simpler, faster and cheaper method in which common salt can be used as a biomarker to detect bacterial activity.Item Open Access AlxGa1-xN based solar blind Schottky photodiodes(Bilkent University, 2004) Tut, TurgutPhotodetectors are essential components of optoelectronic integrated circuits and fiber optic communication systems. AlxGa1−xN is a promising material for optoelectronics and electronics. Applications include blue and green LEDs, blue laser diodes, high power-high frequency electronics, and UV photodetectors. Photodetectors that operate only in the λ < 280 nm spectrum are called solarblind detectors due to their blindness to solar radiation within the atmosphere. In this thesis, we present our efforts for the design, fabrication and characterization of Al0.38Ga62N/GaN based solar blind Schottky photodiodes. We obtained very low dark current, high quantum efficiency, high detectivity performance. Under 25 V reverse bias, we measured a maximum quantum efficiency of 71 percent at 254 nm and a maximum responsivity of 0.15 A/W at 253 nm for a 150 micron diameter device. To our knowledge, these are the best values reported in the literature. For a 30 micron device, 50 ps FWHM pulse response is observed. When the scope response is deconvoluted, a maximum 3-dB bandwidth of 4.0 GHz is obtained for 30 micron diameter Schottky photodiodes.Item Open Access Analysis of nonequilibrium steady-states(Bilkent University, 2016-11) Yeşil, Ayşe FerhanNon-equilibrium is the state of the almost all systems in the universe. Unlike equilibrium systems, they interfere with their surroundings which results in never ceasing uxes. There is no unified theory to understand these systems, since their complexity have no bounds. However, there is a restricted subset of them, namely a steady state, in which system maintains constant uxes and its macroscopic observables are not changing in time. Majority of the non-equilibrium problems that the scientific community is interested in comprise systems at steady states or the way such systems relax to steady states, due to their relative ease of analysis. Steady states of Totally Asymmetric Simple Exclusion Processes (TASEPs) are the main focus of this dissertation. We analyze them through Monte Carlo (MC) simulations. The technique is basically a computational experiment done by utilizing random numbers. Performing a computational experiment is a natural way to study these systems since most of the time they are still too complex to have analytical solutions. We present MC simulation results of our studies on the response of TASEP steady states to sinusoidal boundary oscillations. Typically over-damped systems, such as TASEPs, give monotonous frequency response to sinusoidal driving. However, there are exceptions to these all which draw significant attention from the community, e.g., stochastic resonance. We report a novel resonance phenomena on over-damped systems. We present our results in two different but related works. In our first work, we study the motion of shock profiles of TASEP with single class of particles under oscillatory boundary conditions using MC analysis. We also model its dynamics as a Fokker-Planck (FP) system, which incorporates a retarded-oscillatory force with a static single well potential. We solve the FP system by numerical integration. We showed that amplitudes of statistical quantities in both of these systems, (e.g., average position), display resonant effects and their results are qualitatively very similar. In our second work, we showed that by periodically manipulating the boundary conditions of TASEP with two classes of particles, we can achieve otherwise unreachable states of the system by the same parameters. We also report the hysteresis behavior in the same system, existence of which leads to the identifi- cation of typical velocity of the system. All these phenomena are the results of resonant response of the particle number density of the system.Item Open Access Analysis of the magnetic translation group and investigation of a one-dimensional topological model(Bilkent University, 2017-08) Gholizadeh, SinaThe periodicity of a space lattice in presence of a uniform magnetic eld is preserved. During this thesis, we will study a set of modi ed translation operators which commute with the e ective Hamiltonian of an electron in the lattice. Group theory helps us to construct matrix representations of the modi ed translation operators. These operators form ray groups. Using group projection operators, we will nd partner functions for constructed irreducible representation in order to obtain a relation which corresponds to Bloch function in a periodic lattice and is named as Bloch-type function. By multiplying a phase factor to modi ed translation operators, they will be extended to a new set of operators called magnetic translation operators so that they form a full group rather than a ray group. In a similar procedure, we will investigate displacement operators in phase space coordinate to form a full group of them. In another study, we will introduce a one dimensional model derived from Creutz model, called shifted Creutz model, in which a gap closure appears in its ground state band structure leading to timereversal symmetry breaking and subsequently giving rise to a topological phase transition. Adopting spin-orbit coupling to our model, generates a time-reversal symmetric pair of states with two-fold degeneracy. A topological investigation will be carried on both models by analyzing the band structures, phase diagram, edge states, symmetries in the models, and calculating the winding number.Item Open Access Analytic calculation of ground state properties of the 2d and 3d electron gas(Bilkent University, 2015-06) Katı, YağmurThe electron gas (2D and 3D) is a model which consists of interacting electrons moving in a uniform positive background. Its importance stems from the fact that a number of metals behave similarly, it provides the functional used in density functional theory, and that in 2D it can be experimentally realized. Understanding the behavior of this model is of fundamental importance. In this thesis we present an analysis of this model based on the Hypernetted Chain Method in 3D, and 2D. The HNC method is a variational method to calculate the ground state properties of an interacting system, by expressing the ground state energy as a functional of the radial distribution function. Minimizing the energy expression one obtains a zero energy Schr odinger equation for the square root of the radial distribution function. The potential in this equation can include the e ects of fermionic or bosonic exchange. We applied this method to charged boson and electron gas in 2D and 3D systems. On the basis of the results of this research, it can be concluded that we obtained very close correlation energy results compared to Monte Carlo, and FHNC results for the density range when rs is from 0 to 20. This extended range is important for solid state applications.Item Open Access Approximation methods in the polaron theory: applications to low dimensionally confined polarons(Bilkent University, 1996) Senger, R. TuğrulThe pelaron problem has been of interest in condensed matter physics cind held theory tor cibout half a century. Within the framework of Vcist variety of theoreticcil approximations, the bulk polaron properties have been extensively (explored and fairly well understood in the literature. In the last two deccides, with the impressive progress achieved in the mici-ofabrication technology, it became possible to ol)t£iin low dimensional microstructures, in which the charge ca.rriers are confined in one or more spatial dii'ections. Consequently, there has appeared (|uite a large interest in phonon coupling-induced effects and polaronic properties of low dimensionally confined electrons. In this context, this thesis work is devoted to the study of low dimensional optical polaron properties, with the application of several different formal approaches common in the literature, such as perturbation theory, variatioiicil principles and Feynman path integral formalism. The model we adopt in this work consists of an electron, confined within an external potential (quantuni well), and interacting via the Fröhlich Harniltonian with the bulk LO-phonons of the relevant well material. Therefore, our primary concern is to give a clear view of only the bulk phonon effects on an electron in confined media, and we disregard all other complications that may come about from screening effects, phonon confinement, etc. Under these assumptions, we calculate the ground state energy, the effective mass, and some other quantities of polaron in several confinement geometries. We also provide a broad interpolating overview to the one polaxon problem in the overall range of electron-phonon coupling constant and in a general type of confinement, which can be conformed from one geometriccd configuration to another. Another interesting theme of the polaron theory, magneto-polaron, is considered in the context of the confinement effect on the polaron, brought about by the rncignetic field. A detailed analysis is given in the case, where the effect of electron-phonon coupling is dominated over by the magnetic field counterpart of the problem.Item Open Access Atomic force microscopy experiments on atomically thin materials(Bilkent University, 2020-06) Sheraz, AliIn 2004, successful isolation of graphene attracted immense attention of scientists because of atomic scale thickness and exotic functionalities. Regardless of graphene’s thickness and extraordinary properties only reason that limits the usage of graphene in electronics is no band gap. But there is a way to open band gap of graphene by introducing defects or applying electric field but defects introduction can affect its functionality. So, world moved towards transition metal dichalcogenides (TMDCs), new analogs of graphene with thickness dependent band gap option are promising nominee for potential applications in modern physics and electronics. Besides electronic properties, TMDCs depict excellent mechanical characteristics (in plane elastic modulus, breaking strength/strain and pretension) compared to conventional volumetric counterparts. The objective of this study is to investigate work function and mechanical properties of atomically thin materials using Kelvin probe force microscopy (KPFM) and Nanoindentation modes of Asylum Atomic Force Microscopy (AFM) respectively. Firstly, KPFM experiments were performed on CVD grown Vanadium Sesquioxide V2O3 to map surface potential variation and calculated work function value 4.91 eV. This will help in understanding band alignment, contact resistance and appropriate Schottky barrier height (SBH) by choosing metal contacts with closer work function to V2O3. Secondly by using AFM based nanoindentation we first time reported elastic features of metallic TMDCs: 2H-TaS2, 3R-NbS2, 1T-TaTe2 and 1T-NbTe2 with various thickness values suspended over circular holes. Comprehensive measurement was done on 2H-TaS2 and found thickness independent Young’s modulus for 2H-TaS2 is 114 ± 14 GPa, breaking strength 12.6 ± 2.6 GPa corresponds to nominal strain of 11% and ultimate strain of 0.22. Same mechanical features were investigated for other three materials and they also manifested extreme elasticity and high strain values compare to other 2D materials reported so far except graphene. This mechanical analysis of metallic materials will contribute in future flexible nano technological devices (for instance piezo electronics), wearable electronics, resistive coatings in electronic devices, nanoelectromechanical systems (NEMS) and strain sensors.Item Open Access Atomic scale investigation of clean and epi-grown Si(001) surfaces using scanning tunneling microscopy(Bilkent University, 1996) Özer, H. ÖzgürIn this thesis, clean and epi-grown Si(001)(2x1)surfaces are analyzed by Scanning Tunneling Microscopy (STM). The STM and Ultra High Vacuum System (UHV) in which the microscope is installed, are described. A brief history of the studies on the reconstruction and fundamental features of the Si(001) surface is also given. First, the sample and tip preparation techniques were optimized. Sample preparation method, which includes both ex situ chemical and in situ heating cleaning procedures, was found not to give routinely the clean and atomically flat surfaces, because of the criticality of the temperature values used during heat treatments. The monoatomic steps, dimer rows, defects such as missing dimer and dimer groups, were observed on clean Si(001) surfaces. Double height step formation due to contamination was also detected on a few samples. Buckling of dimers, which is believed to be due mainly to either the high defect density or tip-surface interaction, was observed on one sample. Si and Ge were grown epitaxially on the silicon substrate, with 0.11 ML and 3.2 ML coverages, respectively. The Si growth on Si(001) was found to occur as island formation because of the low substrate temperature (ca. 300 degrees C). Strong shape anisotropy and diffusional anistropy in the growth have been observed. On the other hand, the large coverage of Ge on Si(001) at a relatively high substrate temperature (ca. 500 degrees C) resulted in step flow growth rather than individual island formation on the terraces.Item Open Access Atomic theory of the scanning tunneling microscope(Bilkent University, 1988) Tekman, Ahmet ErkanThe Scanning Tunneling Microscope is proven to be one of the most powerful tools for surface structure determination. Present theories are able to explain the operation of the microscope when the tip is far from the surface. For the small tip height case the atomic-scale interaction of the tip and the surface has to be included in the theory. The electronic structure of the combined system of the tip and the surface is calculated with an Empirical Tight Binding approach for graphite. It is found that in the vicinity of the tip some Tip Induced Localized States are formed. These states play an important role in the tunneling phenomenon. The contribution of these states to the tunneling current is calculated.Item Open Access Atomic, electronic, and transport properties of quantum point contacts on graphite surface(Bilkent University, 1997) Kılıç, ÇetinIn this thesis, the variation of conductance through a contact formed by a hard STM tip pressing on a graphite substrate is investigated. Our study involves the molecular dynamics simulations to reveal the evolution of the atomic structure during the growth of the contact, and ab initio electronic structure calculations of graphite that is under expansive and compressive strain along the [0001] axis. Combining the results obtained from these calculations, we propose a mechanism to explain the peculiar variation of the conductance. Owing to the layered structure of graphite, the variation of conductance exhibits dramatic differences from that of normal metals. It is predicted that in graphite, the conductance first increases, and then drops to a lower value with the puncture of the atomic plane. This phenomenon repeats quasi-periodically as the tip continues to press on the surface.Item Open Access Ballistic transport and tunneling in small systems(Bilkent University, 1990) Tekman, A ErkanBallistic transport and tunneling of electrons in mesoscopic systems have become one of the most important subjects of condensed matter physics. The quantum point contacts and scanning tunneling microscope form the basic experimental tools in this area and have been used for understanding many features of small systems. In this work ballistic transport and tunneling in small systems are investigated theoretically. Ballistic transport through narrow constrictions is investigated for a variety of configurations. It is found that for a uniform constriction the conductance is quantized in units of the quantum of conductance (2e^/A) for long channels. The interference of waves in the constriction gives rise to the resonance structure superimposed on the quantized steps. The lack of the resonance structure in the experimental results are attributed to temperature effects and/or adiabatic transport due to tapering of the constriction. It is shown that elastic scattering by an impurity distorts the quantization of conductance. Novel resonant tunneling effects due to formation of bound states are predicted for an attractive impurity or a local widening at the center of the constriction. It is shown that the probing in scanning tunneling microscopy have very much in common with narrow constrictions. The transition from tunneling to point contact regime is explained by the vanishing effective potential barrier as a result of tip-sample interaction. For noble and simple metals it is conjectured that lateral position dependent interaction between the tip and sample leads to corrugation of the potential barrier and in turn to atomic corrugation observed by scanning tunneling microscopy. The focused field emission of electrons from point sources is analyzed in a systematical way. The effective barrier due to the lateral confinement and nonadiabatic transport through the horn-like opening are found to be responsible for focusing. The nonequilibrium nature of transport is investigated by use of Keldysh Green’s function technique. The effects of elastic and inelastic scattering are analyzed in a strictly one-dimensional geometry. The features of voltage and current probes are studied and the Landauer formulae are examined for multiprobe measurements.Item Open Access Beaming and localization of electromagnetic waves in periodic structures(Bilkent University, 2010) Çağlayan, HümeyraWe want to manipulate light for several applications: microscopy, data storage, leds, lasers, modulators, sensor and solarcells to make our life healthier, easier or more comfortable. However, especially in small scales manipulating light have many difficulties. We could not focus or localize light into subwavelength dimensions easily, which is the key solution to beat today’s devices both in performance and cost. Achievements in three key research fields may provide the answer to these problems. These emerging research fields are metamaterials, photonic crystals and surface plasmons. In this thesis, we investigated beaming and localization of electromagnetic waves in periodic structures such as: subwavelength metallic gratings, photonic crystals and metamaterials. We studied off-axis beaming from both a metallic subwavelength aperture and photonic crystal waveguide at microwave regime. The output surfaces are designed asymmetrically to change the beaming angle. Furthermore, we studied frequency dependent beam steering with a photonic crystal with a surface defect layer made of dimmers. The dispersion diagram reveals that the dimer-layer supports a surface mode with negative slope. Thus, a photonic crystal based surface wave structure that acts as a frequency dependent leaky wave antenna was presented. Additionally, we investigated metamaterial based cavity systems. Since the unit cells of metamaterials are much smaller than the operation wavelength, we observed subwavelength localization within these metamaterial cavity structures. Moreover, we introduced coupled-cavity structures and presented the transmission spectrum of metamaterial based coupled-cavity structures. Finally, we demonstrated an ultrafast bioassay preparation method that overcomes the today’s bioassay limitations using a combination of low power microwave heating and split ring resonator structures.Item Open Access Bias voltage control of a molecular spin valve(Bilkent University, 2009) Can, DuyguWith the discovery of giant magneto resistance a new field called spintronics is emerged. Utilizing spin-degree of freedom of the electron as well as its charge, high-speed devices which consumes low energy can be designed. One of the main concerns of spintronics is creating spin polarized currents. Half-metallic materials, which conduct electrons of one spin state but behave as an insulator for the other spin state, are ideal candidates for this purpose. In a way they function as spinvalves, and the current passing through these materials will be spin polarized. The half-metallic property of periodic atomic chains of carbon-transition metal compounds and spin-valve property of transition metal caped finite carbon linear chains motivated our study. In this work, we analyzed the spin dependent transport properties of CrCnCr atomic chains. We connected the magnetic CrCnCr molecules to appropriate electrodes and studied their electronic and magnetic properties under applied bias. All the calculations are carried out using a method which combines density functional theory (DFT) with non-equilibrium Green’s function (NEGF) technique. For CrCnCr molecules with odd n we observed cumulenic bond lengths, while the C−C bonds are in polyynic nature for even n. In these structures Cr atoms induce net magnetic moments on C atoms. The magnetic moment on Cr atoms favors anti-parallel (AF) alignment for even n and parallel (FM) alignment for odd n. This situation is inverted when the molecules are connected to the electrodes. Two-probe conductance calculations of such systems reveal that their conductance properties are also n dependent. Finite bias voltages which create non-equilibrium conditions within the device region, causes the spin-degenerate molecular levels of the device to be separated from each other. Then conductance properties of the device become spin dependent. We observe that the ground state CrCnCr two-probe systems with odd n changes from AF to FM at a critical voltage. Thus, we have a spinvalve which is initially in ”off-state” turned on with applied bias. We achieved to control spin-polarization of the current transmitted through a molecular spinvalve with applied bias voltage. We showed that they are molecular analogues of GMR devices. These molecular spin-valve devices function without any need of an external magnetic field as it is required in conventional GMR devices.Item Open Access Bio-inpired all-polymer 2d photonic crystal fibers = Doğadan esinlenilmiş tamamen polimer 2B fotonik kristal fiberleri(Bilkent University, 2014) Doğan, TamerPhotonic crystals are essential part of the integrated systems which require manipulation of light in a manner that all-optical polarization and re ection properties are completely calibrated to necessary levels. However, beyond scienti c development of photonic crystals, biological systems also provided inspiration for the eld since they perfected the mechanisms in terms of coloration over millions of years. In addition, natural samples are also observed to serve and function for more than single purpose, and this further illuminates the technological designs so as to develop multifunctional structures. Anas Platyrhynchos L. (mallard) is one of the natural examples and detailed investigations yield that its neck feathers have structural coloration, iridescence and hydrophobicity. Being inspired form mallard duck, two-dimensional photonic crystal bers are produced to imitate coloration and surface architecture. The fabrication is established by iterative size reduction technique which, as a top-down method, enables design of nano-scale materials from macro-scale structures. To accurately imitate duck feathers, polycarbonate (PC) and polyvinyldi uoride (PVDF), are characterized and selected for their thermal compatibility and dielectric properties among number of polymers. Produced 2D photonic crystal bers have been demonstrated to re ect color of green like duck feathers, and also shown to have iridescence by optical means. Besides single coloration, all colors of visible spectrum are also obtained to attest potential applicability of fabrication technique and produced bers. It is also substantiated that all colors can be obtained in a single ber by tapering a thick ber. In addition, last but not least, 2D photonic crystal bers are carefully designed to have surface roughness which promoted hydrophobic feature of PVDF and provided better hydrophobicity than natural counterparts. Manufactured structures are also the rst demonstration for production of all-polymer two dimensional photonic crystal bers which may be used in textile or ltering technologies.