Dept. of Physics - Ph.D. / Sc.D.

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  • ItemOpen Access
    Ten million-atom InGaAs embedded quantum dot electron g factor calculations using semi-empirical pseudopotentials
    (Bilkent University, 2022-10) Kahraman, Mustafa; Bulutay, Ceyhun
    Quantum technologies rely on key capabilities such as electron spin control over the full-Bloch sphere, generation of indistinguishable single photons, or entangled photon pairs. For all these purposes, arguably the most established semiconductor structure currently is the self-assembled InGaAs quantum dots (QDs). In this thesis, electron ground state g tensors of embedded InGaAs QDs are calculated employing an atomistic empirical pseudopotential method. Computed QDs have varied size, shape, indium molar fraction but uniform strain. The components of the g tensor do not show appreciable deviation even though the shape is anisotropic for some of the studied QDs. Universality is observed when family of g factor curves is plotted with respect to energy gap which generalizes the findings of a recent study under more restricted conditions. Our work expands its applicability to alloy QDs with different shapes, and finite confinement putting it on a more realistic foundation by allowing penetration to the matrix material. Our regression model shows that the effect of magnetic field on the electron in an InGaAs QD will be the minimal when the so-called, s-shell optical transition energy is around 1.13 eV. Furthermore, low indium molar fraction is unfavorable in terms of g factor tunability. Our findings could be beneficial in the fabrication of g-near-zero QDs or other desired g values aimed for spintronic or electron spin resonance applications.
  • ItemEmbargo
    Many-body theory explored optical properties of selected 2D group II-VI monochalcogenides
    (Bilkent University, 2022-09) Seyedmohammadzadeh, Mahsa; Gülseren, Oğuz
    Two-dimensional (2D) metal oxides (MOs) and metal chalcogenides (MChs) are emerging classes of 2D materials. Depending on the constituent elements, these materials can display various electronic and optical properties making them promising candidates in many device applications, such as solar cells and transparent circuits. Binary graphene-like structures of II-VI are the most straightforward structures of 2D MOs and MChs. We systematically examined the electronic and optical properties of selected 2D structures from this category: BeO, BaTe, CdO, CaO, CaS, MgO, SrS, SrSe and ZnO. The dynamical stability of these materials has been reported in previous studies. In 2D semiconductors, excitonic effects dominate the optical properties. Theoretical investigation of such phenomena requires employing many-body approaches beyond standard density functional theory. We utilized a single shot of GW approximation to predict the electronic band structure and solved the Bethe- Salpeter equation in the Tamm-Dancoff approximation to consider excitonic effects. Our results show that all structures possess indirect band gaps except ZnO and CdO. Furthermore, the considered structures have large exciton binding energies ranging from 0.72 eV in CdO to 2.84 eV in BeO. CdO has the smallest calculated optical band gap with a value of 1.43 eV. Analyzing the optical absorption spectra reveals that the CdO can absorb 7.9 % of the incident light in its optical band gap. The maximum amount of absorption appears in BeO, which can absorb 28% of incident light in the ultraviolet region. Among the structure mentioned above, there is a close matching between the lattice constants of ZnO and MgO, promising for creating lateral and vertical heterostructures. Due to the enhanced performance resulting from mixing distinct properties of individual monolayers, van der Waals heterostructures (vdWHs) are regarded as a revolutionary class among a plethora of presently fabricated or predicted 2D materials. Alongside vdWHs, recent studies have also reported 2D heterostructures with interlayer bonding. Motivated by the flourishing properties of vertical heterostructures, we comprehensively examined the mechanical, electronic and optical properties of ZnO/MgO structures in four different stackings. Structural relaxation has indicated two vdWHs and two structures with interlayer binding. All considered structures are mechanically stable. In addition, phonon dispersion curves show that the AB stacking formed by placing the Mg atom on top of the O atom of the ZnO layer is also dynamically stable at zero temperature. The s orbital of Zn atom dominates the minimum of the first conduction band of these structures. The optical absorbance spectra show that strong excitonic effects reduce the optical band gap to the visible light spectrum range, and all structures can absorb around 8% of incident light.
  • ItemOpen Access
    Electronic structure and optical properties of monolayer semiconductors: a computational study
    (Bilkent University, 2021-09) Korkmaz, Yağmur Aksu; Bulutay, Ceyhun
    Interest on monolayer semiconductors is rapidly growing in recent years. One of the prominent members is hexagonal boron nitride (h-BN). At room tem-perature, it harbors an environment similar to semiconductor vacuum for point defects which is crucial for stable and controllable spin states. This qualification makes h-BN a suitable medium for quantum technological applications. First-principles calculations are essential in order to characterize such systems. Density functional theory (DFT) is one of the most reliable methods used for these type of calculations. Recently, a variant called as DFT-1/2, has been proposed to calculate the band gaps of the materials more accurately without a significant additional computational cost. In the first part of thesis, we have compared the results of DFT and DFT-1/2 for carbon impurities (CB, CN ), single vacan-cies (VB, VN ), double vacancy (divacancy) and Stone-Wales defect in monolayer h-BN. Subsequently, results from computationally expensive techniques such as hybrid or GW are presented and compared with the obtained DFT-1/2 results. Especially for the defect states seemingly hidden in valence or conduction band, DFT-1/2 technique is instrumental in revealing these states while widening the band gap. Thus, we recommend the DFT-1/2 method for a quick screening of candidate band gap defect states. Another outstanding group of semiconductors is transition metal dichalco-genides (TMDs). They owe their advantages to optically addressable valley and bringing optics and mechanics together as in valleytronics, thanks to their high flexibility. In the second part of this thesis, ten TMDs including their janus coun-terparts (JTMDs), namely, MoS2, MoSe2, MoTe2, WS2, WSe2, WTe2, MoSSe, MoSeTe, WSSe, and WSeTe have been computationally studied. To begin with, the electronic band structure of the specified materials have been computed using DFT followed by hybrid calculations over these, with the addition of spin-orbit coupling. Biaxial and uniaxial strain calculations are subsequently performed. JTMDs were previously proclaimed to have a good piezoelectric characteristic. According to our DFT results, JTMDs exhibit band structure and electronic properties in between its constituent TMDs, and in this respect they do not dis-play an outstanding behaviour. Based on the acquired DFT data, spinless and spinful k · p parameters are extracted by fitting around optically active K valley. With the help of k·p parametrization, linear and circular dichroic behaviours are studied for unstrained and strained cases. In consideration of all these materials, WTe2 displays the largest linear dichroic responsitivity for uniaxial strain, since it has the smallest band gap and the greatest uniaxial deformation potential at the K valley. Thus, we propose monolayer WTe2 membranes to be considered for optical polarization based strain measurements, as well as, strain adjustable optical polarizers.
  • ItemOpen Access
    A theoretical study of strained monolayer transition metal dichalcogenides based on simple band structures
    (Bilkent University, 2019-10) Aas, Shahnaz; Bulutay, Ceyhun
    This doctoral thesis deals with optoelectronic and geometric band properties of two-dimensional transition metal dichalcogenides (TMDs) under applied strain. First, we analyze various types of strain for the K valley optical characteristics of a freestanding monolayer MoS2, MoSe2, WS2 and WSe2 within a two-band k p method. By this simple bandstructure combined with excitons at a variational level, we reproduce wide range of available strained-sample photoluminescence data. According to this model strain affects optoelectronic properties. Shear strain only causes a rigid wavevector shift of the valley without any alternation in the bandgap or the effective masses. Also, for exible substrates under applying stress the presence of Poisson's effect or the lack of it are investigated individually for the reported measurements. Furthermore, we show that circular polarization selectivity decreases/increases by tensile/compressive strain for energies above the direct transition onset. TMDs in addition to their different other attractive properties have rendered the geometric band effects directly accessible. The tailoring and enhancement of these features by strain is an ongoing endeavor. In the second part of this thesis, we consider spinless two and three band, and spinful four band bandstructure techniques appropriate to evaluate circular dichroism, Berry curvature and orbital magnetic moment of strained TMDs. First, we establish a new k p parameter set for MoS2, MoSe2, WS2 and WSe2 based on recently released ab initio and experimental band properties. For most of these TMDs its validity range extend from K valley edge to several hundreds of millielectron volts for both valence and conduction band. We introduce strain to an available three band tight-binding Hamiltonian to extend this over a larger part of the Brillouin zone. Based on these we report that by applying a 2:5% biaxial tensile strain, both the Berry curvature and the orbital magnetic moment can be doubled compared to their unstrained values. These simple bandstructure tools can be suitable for the device modeling of the geometric band effects in strained monolayer TMDs.
  • ItemOpen Access
    Development of force fields for novel 2D materials for temperature dependent vibrational properties
    (Bilkent University, 2019-09) Mobaraki, Arash; Gülseren, Oğuz
    A new era of nanodevice engineering has been started after fabricating graphene. This motivated vast number of researches for predicting, fabricating and utilizing 2D materials. Temperature dependent properties are essential for device applications. Although rigorous density functional theory based approaches are able to predict electronic and mechanical properties accurately, but they are mostly limited to zero temperature and ab initio based molecular dynamics are computationally very demanding. Classical molecular dynamics is a very powerful alternative, however its accuracy is basically depend on the interatomic potential used for describing the considered system and therefore constructing accurate force fields is always an open problem, especially for the emerging 2D materials with extra ordinary properties. Single-layer transition metal dichalcogenides (TMDs) are new class of 2D materials which are shown to be good candidates for thermoelectric applications, flexible electronic and optoelectronic devices. In order to investigate thermal properties of TMDs, Stillinger-Weber type potentials are developed using particle swarm optimization method. These potentials are validated by comparing the resulted phonon dispersion curves and thermal conductivities with available first principle and experimental results. In addition, for understanding the anharmonic effects imposed by the generated force fields the trends of the shifts of the optical phonon frequencies at 􀀀 point with variation in the temperature are compared with available experimental data. In all cases, optimized potentials generate results which are in agreement with the target data. In the second step, spectral energy density method together with phonon mode decomposition is used for obtaining temperature dependent phonon frequencies and lifetimes in entire Brillouin zone. The contribution of each phonon branch in thermal conductivity is predicted utilizing the obtained phonon lifetimes and group velocities within the framework of relaxation time approximation. Eventually, with the aim of constructing transferable potentials for describing 2D and bulk structures, a very fast and reliable optimization method is presented. Combining local and global optimization methods and utilizing the energy curves obtained from first principle method, novel Stillinger-Weber type potentials for graphene, silicene and group III nitrides are developed. The proposed approach provides a solid framework for parameter selection and investigating the role of each parameter in the resulted phonon dispersion curves.
  • ItemOpen Access
    Quantum Monte Carlo simulations of ultracold atomic systems
    (Bilkent University, 2019-07) Akatürk, Emre; Tanatar, Bilal
    Here, we present our work and findings on ultracold atomic systems. We first present a semi-analytical work on density wave instability (DWI) and collective modes of a bilayer dipolar system of bosons and fermions. We then show our results for quantum Monte Carlo (QMC) simulations on a bosonic system with an impurity in two-dimensions (2D). We investigate DWI on two parallel layers with antiparallel dipoles that have little to no pairing between interlayer particles. We observe that for both fermionic and bosonic bilayers, below a threshold intralayer coupling strength, no density wave instability emerges. At higher couplings, DWI forms below a critical layer spacing. We also investigate collective modes in this system. For the second problem, we present our investigations of a 2D Bose polaron, which is a system with bosonic particles and a mobile impurity. We use diffusion Monte Carlo (DMC) simulations to calculate physical quantities such as polaron energy and effective mass of the polaron as well as quantities that give insight to structural properties of the system such as pair correlation function and density profile. We model the boson-boson and boson-impurity interaction with hard spheres.
  • ItemOpen Access
    Intracavity optical trapping with fiber laser
    (Bilkent University, 2019-06) Kalantarifard, Fatemeh; Volpe, Giovanni
    After Ashkin's seminal works, optical trapping has been a powerful technique for capturing and manipulating sub micro particles not only in physics research fields but also in biology and photonics. Standard optical tweezers consists of a single beam with Gaussian or profile which focused by a high numerical aperture (NA) water or oil immersion microscope objective. Typically, objective with NA>1.2 is used to provide strong enough gradient forces being able to overcome Brownian uctuations and gravity and trap the particle stably. On the other hand, compare with high NA, trapping with low NA, has its own advantage and among all the advantages, low local heating of the sample has a particular interest in molecular biology and manipulating living cells. The main concern is that the interaction of trapping laser beam and biological object induces a damage on the specimen which is mainly due to light absorption of the sample. It is, therefore, recommended to use NIR (near infrared ) wavelength due to its minimal absorption by water and biological objects. Other important factors that must be considered, to secure the viability of the cell, are spot size of the focused beam and laser power at the sample plane. Thus, it deserves an effort to look for new configurations with low NA with the capability of creating 3D confinement. Standard optical tweezers rely on optical forces that arise when a focused laser beam interacts with a microscopic particle: scattering forces, which push the particle along the beam direction, and gradient forces, which attract it towards the high-intensity focal spot. Importantly, the incoming laser beam is not affected by the particle position because the particle is outside the laser cavity. Here, we demonstrate that intracavity nonlinear feedback forces emerge when the particle is placed inside the optical cavity, resulting in orders-of-magnitude higher confinement per unit laser intensity on the sample. We first present a toy model that intuitively explains how the microparticle position and the laser power become nonlinearly coupled: The loss of the laser cavity depends on the particle position due to scattering, so the laser intensity grows whenever the particle tries to escape. We describe a simple toy model to clarify how the nonlinear feedback forces emerge as a result of the interplay between the particle's motion and the laser's dynamics. It also quantifies how and to what extent this scheme reduces the average laser power to which a trapped particle is exposed. In this model, the power and hence trapping force are considered to be zero for small particle displacements. However, in reality they have small values that do operate the trap even when the particle is near the equilibrium position. Thus, we need an accurate description of the coupling between the laser and the trapped particle thermal dynamics at equilibrium to compare with experiments. In particular, accurate simulations can help to associate an effective harmonic potential to the optical trap for small displacements from the equilibrium position, and hence to define a meaningful stiffness using the standard calibration methods based on the thermal uctuations of a trapped particle. We therefore present a series of numerical simulations based on an extended theoretical model, including highly realistic descriptions of the laser dynamics, optical losses incurred by the particle, and the particle's Brownian motion in order to gain a quantitative understanding of the dynamics of intracavity optical trapping and to guide the experiments. Finally, guided by the simulation results, we have built an experimental setup to prove the operational principle of intracavity optical trapping and experimentally realize this concept by optically trapping microscopic polystyrene and silica particles inside the ring cavity of a fiber laser. One of the major advantages of the intracavity optical trapping scheme is that it can operate with very low-NA lenses, with a consequent large field-of-view, and at very low average power, resulting in about two orders of magnitude reduction in exposure to laser intensity compared to standard optical tweezers. When compared to other low-NA optical trapping schemes, positive and negative aspects can be considered, such as in terms of trap stiffness and average irradiance of the sample. These features can yield advantages when dealing with biological samples. Ultra-low intensity at our wavelength can grant a safe, temperature controlled environment, away from surfaces for micro uidics manipulation of biosamples. Accurate studies on Saccharomices cerevisiae yeast cells in near-infrared counterpropagating traps and standard optical tweezers have found no evidence for a lower power threshold for phototoxicity. We observed that we can 3D trap single yeast cells with about 0:47 mW, corresponding to an intensity of 0:036 mW m􀀀2, that is more than a tenfold less intensity than standard techniques.
  • ItemOpen Access
    Topological aspects of charge transport in quantum many-body systems
    (Bilkent University, 2019-01) Yahyavi, Mohammad; Hetenyi, Balazs
    Motivated by the recent proposals and developments of topological insulators and topological superconductors for their potential applications in electronic devices and quantum computing, we have theoretically studied topological properties of quantum many-body systems. First, we calculate the gauge-invariant cumulants (and moments) associated with the Zak phase. The first cumulant corresponds to the Berry phase itself, the others turn out to be the associated spread, skew, kurtosis, etc. The cumulants are shown to be gauge invariant. We reconstruct the underlying probability distribution of the polarization by maximizing the information entropy and applying the moments as constraints in the Rice-Mele model and in the interacting, spinless Su-Schrieffer-Heeger model. When the Wannier functions are localized within one-unit cell, the probability distribution so obtained corresponds to that of the Wannier function. We follow the probability distribution of the polarization in cycles around the topologically nontrivial point of these models. Secondly, we have constructed a topological one-dimensional analog of the Haldane and Kane-Mele models in two dimensions, with hexagonal lattices. Our Haldane one-dimensional analog model belongs to the C and CI symmetry classes, depending on the parameters, but, due to re ection, it exhibits topological insulation. The model consists of two superimposed Creutz models with onsite potentials. The topological invariants of each Creutz model sum to give the mirror winding number, with winding numbers which are nonzero individually but equal and opposite in the topological phase, and both zero in the trivial phase. We also construct a topological one-dimensional ladder model following the steps which lead to the Kane-Mele model in two dimensions. We couple two Haldane-type ladder models, one for each spin channel, in such a way that time-reversal invariance is restored. We also add a Rashba spin-orbit coupling term. The model falls in the CII symmetry class. We demonstrate the presence of edge states and quantized Hall response in the topological region. Our model exhibits two distinct topological regions, distinguished by the different types of re ection symmetries. Thirdly, we consider the edge at the interface of a simple tight-binding model and a band insulator. We find that crossings in the band structure (one dimensional Dirac points) appear when an interface is present in the system. We calculate the hopping energy resolved along lines of bonds parallel to the interface as a function of distance from the interface. Similarly, we introduce a transport coe cient (Drude weight) for charge currents running parallel to the interface. We find that charge mobility (both the kinetic energy and the Drude weight) is significantly enhanced in the surface of the tight-binding part of the model near the interface. Finally, we study a variant of the generalized Aubry-Andre-Harper model with the effect of introducing next nearest-neighbor p-wave superconducting pairing with incommensurate and commensurate cosine modulations. We extend generalized Aubry-Andr e-Harper model with p-wave superconducting to topologically equivalent and nontrivial "anancestor" two-dimensional p-wave superconducting model. It is found that in incommensurate (commensurate) modulation, by varying next nearest-neighbor p-wave pairing order parameter, the system can switch between extended states and localized states (fully gapped phase and a gapless phase).
  • ItemOpen Access
    Novel concepts in high power semiconductor lasers
    (Bilkent University, 2018-11) Arslan, Seval; Gülseren, Oğuz
    This doctoral thesis deals with innovations to the cavity optics of high power semiconductor lasers emitting light at 9xx nm. High power laser diodes are complex electronic and photonic systems. Developments in epitaxial crystal growth techniques and the quality that ensued has been the driving force in the progress of the field. Semiconductor lasers with high output powers and high efficiencies have thus become possible. Commercial single emitters each with over 10 watts output with efficiencies reaching 60% is available.Even higher output powers have been demonstrated in the lab. High power semiconductor lasers have many applications such as acting as optical pumps in other lasers, range finding, optical storage, light sources in sensors and medical tools. The demand for higher powers and efficiencies continues. Among several possibilities, one of the main limits of maximum output power is the catastrophic optical mirror damage (COMD). At high pump currents and hence output powers, facet absorption leads to temperatures high enough to damage the cavity mirrors. This thesis is focused on novel approaches to increase the COMD threshold. We demonstrate design, fabrication and characterization of the high power strained InGaAs/AlGaAs lasers emitting light at 9xx nm. To prevent facet absorption which decreases the laser efficiency especially at high injection currents, band gaps in the vicinity of the laser facet are increased using impurity-free vacancy disordering (IFVD) while preserving the band gap in the lasing region away from the facets. A record large bandgap at the facet region, relative to that of the lasing region is achieved by thermal stress management of a bilayer dielectric structure. We demonstrate excellent optical loss and optical power output with this bilayer approach. Further, positive feedback cycle during absorption at the facets is broken by keeping the facets cold, by design. Thus, in this cold window approach, we extend the passive unpumped windows to keep the heat source from the main body of the cavity away from the facets while eliminating the additional loss incurred by biasing this section to transparency. This new biased window approach leads to much cooler facet temperatures while reducing the bulk temperatures as well. Thus, we use thermore ectance spectroscopy to measure facet temperature as a function of pump and bias current. We clearly demonstrate that, for the first time, facet temperatures have been decreased below the bulk temperature without penalty on the output power.
  • ItemOpen Access
    Optical and thermal dynamics of long wave quantum cascade lasers
    (Bilkent University, 2018-09) Gündoğdu, Sinan; Gülseren, Oğuz
    Quantum Cascade Lasers (QCLs) are coherent light sources that make use of intraband transitions of wavefunction engineered semiconductor quantum wells. They have been designed to emit light in a wide spectral range; from mid-wave infrared to terahertz. Long wave QCLs are a subject of interest for some applications such as remote detection of harmful chemicals. These applications demand higher optical powers at room temperature. In this thesis we demonstrate simulation, design, fabrication and characterization of long-wave QCLs that emit light around 9.2 m. To increase optical power and enhance thermal performance, we explore the optical and thermal properties of QCLs. Thermal characteristics of QCLs are analyzed by nite element methods. We developed a spectral technique that relies on analysis of Fabry-Perot modes to measure cavity temperatures experimentally. By combining the simulations and experimental results we scrutinized the thermal properties of QCLs, and estimated the active region thermal conductivity. To increase the optical power, we conducted optical calculations and investigated the sources of loss. As a result of a search for alternative electrical passivation materials, we fabricated HfO2 passivated lasers and demonstrated about to two-fold reduction in optical loss and increase in optical power.
  • ItemOpen Access
    The adiabatic and non-adiabatic behavior of a particle in optical lattices
    (Bilkent University, 2018-06) Yılmaz, Fırat; Oktel, Mehmet Özgür
    The 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.
  • ItemOpen Access
    Deformation and finite size effects in cooperative molecular motors
    (Bilkent University, 2002-07) Taneri, Sencer; Yalabık, M. Cemal
    Motor protein systems have been of considerable interest lately. In these studies muscle contraction is modeled as the sliding of two filaments made of protein particles over one another, that is the sliding of the backbone filament on the track filament. In order to make the analytical analysis easy these filaments are assumed to be of infinite length or mass. This enables the understanding of the sliding of motility assays with constant velocity and generation of constant force. However, finite size in length and mass brings fluctuationsuctuations in velocity around certain values, and changes in direction through intermittent transitions. It is possible to associate time constants to this kind of behavior. It turns out that the magnitude of the time constant being created during the process is proportional to both the length of the filament and the mass of the protein particles. Deformation phenomenon stems from internally generated forces which so far has been examined as axonemal deformations. The elastic coupling of the protein particles to the backbone has been studied separately, which in fact is also related to the generation of internal forces. Instead of focusing on the axonemal deformations, we implemented an Ising-like potential contribution to our computation to study the elastic coupling which makes the computation easier. We found out that for certain range of parameters that measures the deformation strength, one attains a better motor because of more intense force generation at the expanse of getting a lower sliding velocity.
  • ItemOpen Access
    Unconventional superconductivity in two dimensional time reversal symmetric noncentrosymmetric superconductors
    (Bilkent University, 2017-08) Günay, Mehmet; Hetenyi, Balazs
    In this thesis we study unconventional pairing observed in noncentrosymmetric superconductors by using spin dependent pairing potentials under the maximal C∞v and the time reversal symmetries (Θ-phase). The lack of inversion symmetry in these materials induces spin orbit interaction which removes the spin degeneracy and splits the Fermi surface into two branches. We demonstrated that in such systems mixed parity in the superconducting order parameter is present. Recently a large number of noncentrosymmetric superconductors appeared with anomalous behavior of a double and isotropic full energy gap present indicating a large inversion symmetry breaking, at the same time displaying an exponentially suppressed low temperature thermodynamic response pointing at a BCS like s-wave pairing. We clarify in this thesis that an isotropic energy gap can accommodate a parity mixed condensate with a comparably strong singlet and triplet pairings. The topology of such a configuration can be nontrivial although the system can have an exponentially suppressed temperature dependence in the thermodynamic response. We investigate other implications of such a behavior and suggest that some of the recent controversial experiments can be explained by the existence of nodal structure in the superconducting pair potential. We also investigate tunneling spectroscopy of different type of pairs by calculating differential conductance through a normal metal superconductor junctions. It is shown that each type of pairs have distinct behavior in the picture of Andreev reflection spectroscopy which is an effective tool to clarify order parameter especially for superconductors having nodal structure in superconducting gap. The zero bias conductance is observed for d wave superconductors and its origin is discussed. Furter it is showed that the neglected term in the theory of Andreev reflection in Josephson junctions with d-wave superconductors can change drastically the appearance of zero bias anomalies.
  • ItemOpen Access
    Size controlled germanium nanocrystals in dielectrics : structural and optical analysis and stress evolution
    (Bilkent University, 2017-08) Bahariqushchi, Rahim; Gülseren, Oğuz
    Group IV semiconductor nanocrystals, namely silicon and germanium have attracted much interest in the past two decades due to their broad applications in photovoltaic, memory, optoelectronic, medical imaging and photodetection devices. Generally, there are two major features of semiconducor nanocrystals: First, spatial confinement of charge carriers which leads to the significant changes in optical and electronic properties of materials as a function of size. This effect gives the possibility to use the size and shape of the nanocrystals to tune the energy of electronic energy states. Second feature of nanocrystals, is the increased of surface area to volume ratio of the nanocrystal with reducing size. This leads to an enhanced role of the effects related to surface and interface of the nanocrystal. Furthermore, stress on the nanocrystals can lead modification of the band structure as well as in uencing the crystallization of the nanomaterials. Recent works show that measurement and control of the stress can open the way for strain engineering of the electronic band structure, thereby opening the way for new physics and applications. In this thesis, we first carry out a study on the synthesis of germanium embedded in silicon nitride and oxide matrices. In uence of the annealing method as well as germanium concentration on the formation of nanocrystals is discussed. It was found that Ge concentration and annealing play important roles in the formation of the Ge nanocrystals. With crystallographic data obtained from high resolution transmission electron microscopy, quantitative analysis of stress state of germanium nanocrystals have been done by analyzing Raman peak shift of embedded nanocrystals taking into account the phonon confinement effect. Finally, using stressors as buffer layers, superlattices of Ge nanosheets were studied to understand the effects of the stressors on the stress state of Ge nanocrystals. We demonstrate that it is possible to tune the stress on the Ge nanocrystals from compressive to tensile. Finally we showed a three dimensional Ge quantum solid that can be used in optoelectronic applications.
  • ItemOpen Access
    Nonlinear and far-from-equilibrium dynamics of optical pulses in fiber oscillators
    (Bilkent University, 2017-08) Teamir, Tesfay Gebremedhin; Ilday, Fatih Ömer
    Fundamentals of mode locking of lasers have been extensively studied and well established for the last three decades. However, it continues to be an intensely studied field. The continued interest is, in part, due to the scientific and technological applications enabled by the generation of ultrashort pulses of light using mode-locking. There is also a deeper reason for the interest. Despite decades of effort, there is still no encompassing theory of mode-locking that applies to the broad range of dynamics displayed by modern mode-locked lasers, in particular, fiber lasers. Mode-locking is a collective phenomenon that arises from the nonlinear interactions between thousands of optical modes supported by a laser cavity, which is typically initiated from laser noise in the cavity. In addition to many unanswered questions from a nonlinear dynamics perspective, there has been limited progress from the point of the thermodynamics, even though mode-locking corresponds to a far-from-equilibrium steady state of a laser. The central premise of this thesis is that mode-locked lasers are invaluable as experimental platforms not only for nonlinear phenomena, but also for far-fromequilibrium dynamics of nonlinear systems, where there is a particular shortage of convenient platforms for experimentation, in addition to the practical interest in development of technically superior lasers. After introductory discussions, we report the direct generation of sub-hundred femtosecond pulses through the interaction of third order dispersion (TOD) and self-phase modulation (SPM) by using two dispersion delay lines (DDLs) inside a laser cavity. Moreover, we report dynamics that are consistent with an effective negative nonlinearity, which is explained through an interplay between self-phase modulation (SPM) and second order dispersion (GVD) for a chirped pulse. Despite numerous studies on their nonlinear dynamics, relatively little is known about the thermodynamics and fluctuations-induced dynamics of mode-locking. We investigate transitions from CW to single pulsing, and then to multipulsing states in the presence of nonlinearity, feedback mechanisms, laser noise (as a source of fluctuations) and the laser’s response to externally injected modulations or fluctuations. Near critical points (instability attractors), dissipative soliton (DS) states are observed to interact between themselves and with their environment which is often followed by random transitions among different pulsing states. This critical behavior appears to be caused by soliton-soliton or solitongenerated dispersive wave interactions in addition to periodic breathing, due to the periodic boundary conditions of the cavity, leading to bifurcations and the onset of chaos. Irrespective of specifics parameters of states, measured noise level (i.e., the strength of fluctuations) of the laser usually starts at a low value, and then slightly reduced as the DSs energy is increased. Further increases in power (nonlinearity) drive it towards a noisy critical state, where random creation or annihilation of pulses occur just before a new steady state is formed. These noiseinduced transitions between steady states far from equilibrium could conceivably shed light on the thermodynamics of other far-from-equilibrium systems. Finally, we demonstrate direct electronic control over mode-locking states using spectral amplitude and phase modulation by incorporating a spatial light modulator (SLM) at a Fourier plane inside the cavity. The modulation enables us to halt and restart mode locking, suppress instabilities, induce controlled reversible and irreversible transitions between mode-locking states, and perform advanced pulse shaping inside a cavity. We also introduce a simple method to manipulate femtosecond optical pulses by directly applying dynamic periodic phase modulation mask on the optical spectrum inside oscillator. With the application of such dynamic periodic linear spectral phase mask we can control the pulse dynamics, demonstrating the capability to tune the pulse-to-pulse separation time, pulse tweezing, blue- and red-shifting of spectral components and pulse splitting. This technique, which is introduced for the first time to our knowledge, may be used in a range of applications such as coherent quantum control, nonlinear spectroscopy, microscopy, in data storage, in the switching of optical and magnetic properties of materials, as well as studies on the fundamentals of oscillator dynamics and other self-organized phenomena in spatiotemporally extended systems.
  • ItemOpen Access
    Mixtures of charged-neutral superfluids
    (Bilkent University, 2016-12) Ünal, Fatmanur; Oktel, Mehmet Özgür
    Motivated by the developments of artificial magnetic fields (AMFs) enabling cou- pling to the neutral particles of ultracold quantum gases, we have theoretically studied charged-neutral mixtures in various settings. The techniques that have been used to manufacture these AMFs are highly sensitive to the internal de- grees of freedom of the atoms, resulting in unequal coupling to the components of a mixture. We demonstrate the possible consequences of this unequal coupling by considering two different systems. First, we examine an impurity problem in a fermion background under an AMF coupling selectively to the impurity in a ring trap. We calculate the response of the system exactly by using Bethe Ansatz and argue that the AMF can be employed as a probe to analyze polaron formation. Secondly, we explore Bardeen-Cooper-Schrieffer theory of supercon- ductivity in the presence of a charge imbalance under an AMF. We analytically calculate the gap equation for any degree of asymmetry between the Landau level spectra of up and down spin particles, and show that the system displays reentrant superconductivity both in magnetic field and temperature. Apart from mixtures, we also investigate the non-equilibrium Hall response of a topological system. The strength of an AMF applied on a optical lattice can be suddenly changed without creating Eddy currents, allowing us to quench the system across a topological phase boundary. We report a fractional Hall response for the result- ing non-equilibrium system and discuss possible implementations for cold atom experiments.
  • ItemOpen Access
    Analysis of nonequilibrium steady-states
    (Bilkent University, 2016-11) Yeşil, Ayşe Ferhan; Yalabık, Mehmet Cemal
    Non-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.
  • ItemOpen Access
    Manipulation and control of collective behavior in active matter systems
    (Bilkent University, 2016-10) Pinçe, Erçağ; Volpe, Giovanni
    Active matter systems consist of active constituents that transform energy into directed motion in a non-equilibrium setting. The interaction of active agents with each other and with their environment results in collective motion and emergence of long-range ordering. Examples to such dynamic behaviors in living active matter systems are pattern formation in bacterial colonies, ocking of birds and clustering of pedestrian crowds. All these phenomena stem from far-from-equilibrium interactions. The governing dynamics of these phenomena are not yet fully understood and extensively studied. In this thesis, we studied the role that spatial disorder can play to alter collective dynamics in a colloidal living active matter system. We showed that the level of heterogeneity in the environment in uences the long-range order in a colloidal ensemble coupled to a bacterial bath where the non-equilibrium forces imposed by the bacteria become pivotal to control switching between gathering and dispersal of colloids. Apart from studying environmental factors in a complex active matter system, we also focused on a new class of active particles, \bionic microswimmers", and their clustering behavior. We demonstrated that spherical bionic microswimmers which are fabricated by attaching motile E. coli bacteria on melamine particles can agglomerate in large colloidal structures. Finally, we observed the emergence of swimming clusters as a result of the collective motion of bionic microswimmers. Our results provide insights about statistical behavior and far-from-equilibrium interactions in an active matter system.
  • ItemOpen Access
    Novel approaches to ultrafast fiber laser design for ablation-cooled material removal
    (Bilkent University, 2016-09) Yılmaz, Saniye Sinem; İlday, Fatih Ömer
    The past few decades in particular have witnessed the tremendous beneficial impact of innovations in laser technology ranging from biomedical to industrial applications in response to enhancing community's quality of life. From the beginning, laser technology, especially ultrafast lasers have provided a very convenient platform for producing need-based laser signals, which are addressed to a wide variety of scientific and technological problems. However, there is a scarcity of utilization of ultrafast lasers as well-developed tools for various applications, mostly in industry and research laboratories due to their complexity, low reliability and high cost as a result of the dominance of solid-state lasers. Fiber lasers, on the other hand, are inherently inexpensive, compact in size and robust in their operation under harsh conditions. Applications of ultrafast laser material processing have become extremely diverse, yet ultrafast material processing is still extremely complex, costly and quite slow in terms of material removal, which is particularly taxing for biological tissue removal, rendering ultrafast lasers uncompetitive compared to mechanical techniques. This thesis represents a series of work about developing fiber laser systems which address this technological problem. The motivation of this thesis is to develop fiber laser systems for applying the ablation cooled laser material removal idea which has recently proposed by our group [1] for tissue and material processing. Ablation cooling becomes significant above a certain repetition rate, which depends on the thermal diffusivity of the target material. Besides, the speed with which the laser beam can be repositioned over a target is limited. As a remedy, burst-mode operation, also proposed by our group [2] has been implemented, where the laser produces groups of high repetition rate pulses, which are, in turn, repeated with a lower frequency. Consequently, the burst-mode fiber laser system operating at 1 µm was demonstrated with an all-fiber architecture and we scaled it to 100 MHz intra-burst repetition rate and 1 MHz burst repetition rate with the average power of 150 W for high power applications. Additionally, a detailed investigation on the limits of continuously-pumped all-fiber burst mode laser system was reported. Besides all the practical advantages of the ablation cooling idea compared to other laser-material interactions, laser ablation depends on laser operating wavelength because materials have wavelength dependent absorption and scattering values. In terms of underlying laser technology, ultrafast tissue ablation experiments require a laser system operating around 2 µm where laser tissue interaction is much stronger due to the local peak of water absorption for achieving a high ablation efficiency. Therefore, this thesis also focuses on transferring know-how on burst-mode operation to the Tm/Ho doped fiber system, operating around 2µm, which addresses requirements for an effcient tissue ablation process without any collateral damage. The physics of the laser-material interaction assisted by ablation cooling idea is also valid for tissue ablation, so the repetition rates of several GHz are necessary for fully exploiting this effect. Toward this goal, we developed core technologies, which were constituted by three different stages: (i) starting from a novel mode-locked oscillator with a repetition rate in the GHz range, (ii) followed by the construction of a Tm-doped pump source based on the WDM cascade architecture and (iii) finally the amplification of the Ho-doped fiber with a dual wavelength pumping concept.
  • ItemOpen Access
    Graphene-based electrically tunable terahertz optoelectronics
    (Bilkent University, 2016-09) Kakenov, Nurbek; Kocabaş, Coşkun
    Advances in terahertz (THz) research and technology, has bridged the gap between radio-frequency electronics and optics. More efficient control of THz waves would highly benefit noninvasive, high-resolution imaging and ultra-fast wireless communications. However, lack of active materials in THz, hinders the realization of these technologies. Graphene, 2d-crystal of carbon atoms, is a promising candidate for reconfigurable THz optoelectronics due to its unique electronic band structure which yields gate-tunable optical response. Here, we studied gate-tunable optical properties of graphene in THz frequencies. Using time-domain and continuous wave THz spectroscopy techniques, tunable Drude response of graphene is investigated at very high doping levels with Fermi energies up to 1 eV. Our results show that, transport scattering time decreases significantly with doping. Unlike conventional semiconductors, we observed nearly perfect electron-hole symmetry even at very high doping levels. In the second part, we implemented using these unique tunable properties for novel THz optoelectronic devices such as THz intensity modulators and THz spatial light modulators. These devices are based on various designs of mutually gated capacitive structures consisting of ionic liquid electrolyte sandwiched between graphene and metallic electrodes. Low insertion losses (<2 dB), high modulation depth (>50 %) over a broad spectrum (0.1-2 THz), and the simplicity of the device structure are the key attributes of graphene based THz devices. Furthermore, with the optimized device architectures, gate tunable coherent perfect absorption is observed in THz which yields modulation depth of nearly 100 %. The approaches developed in this work surpass the challenges of generating high carrier densities on graphene, and introduce low-loss devices with practical fabrication methods which we believe can lead to more responsive and sophisticated optoelectronic devices.