Item Open AccessDensity functional theory investigation of linear carbon chains(Bilkent University, 2023-09) Salepci, Efe Dorukhan; Gülseren, OğuzIn this thesis the structural and electronic properties of linear carbon chains are investigated using density functional theory. Polyyne structure of alternating single and triple bonds was shown to be energetically favored structure compared to successive double-double bonded cumulene structure. Band calculations showed that polyyne is a semiconductor whereas cumulene is a metal. Phonon calculations showed that cumulene is unstable. When put in a hexagonal formation these chains are found to form three possibly stable structures, one tightly bound hexagonal tube, and two loosely bound structures one which can be described as a hexagonal assembly of polyyne chains and one which can be considered stacks of hexagonal carbon flakes. Electronic band structure calculations showed that all three structures are semiconductors. Charge density profile showed strong chemical bonds both in vertical and horizontal directions for the first structure, whereas second structure of polyyne chains had no strong bonds between chains and third structure of hexagon flakes showed no strong bond between hexagon flakes. It is also found that as hexagon size shrinks the favored structure of chains changes from polyyne to cumulene and a band structure calculation showed that a semiconductor to metal transition happens. Item Open AccessNanomechanical strain testing of low dimensional materials with micro-electro mechanical system (MEMS) chips(Bilkent University, 2023-09) Başcı, Uğur; Kasırga, Talip SerkanThis thesis explores nanomechanical strain testing of low-dimensional materials. The limitations of existing experimental environments for testing low-dimensional materials are discussed. To overcome these limitations, the study proposes the use of self-designed Micro-Electro Mechanical Systems (MEMS) chips. The fabrication methods and advantages of MEMS chips are explained. The investigation involves studying few-layer 2H-MoS2 crystals using MEMS chips. Device preparation techniques, such as mechanical exfoliation and all-dry transfer, are outlined. Raman measurements are conducted on MoS2 to analyze its response to strain, specifically focusing on the E12g mode Raman peak. The piezoelectric properties of MoS2 are extensively discussed, including piezo voltage-resistivity and IV mea-surements. An interesting thermoelectric bipolar photocurrent response in MoS2 is explored using scanning photocurrent microscopy (SPCM). Possible contributions of different mechanisms such as the Photothermoelectric Effect (PTE) or Flexo-photovoltaic effect of Bipolar Photocurrent response are discussed. The contribution of stress on the recently shown substrate effect is tested in this work. The growth and transfer optimization of V2O3 crystals which have a strain-dependent phase transition properties is explored, with a focus on adapting growth to a conventional CVD chamber. Polymer-assisted transfer techniques and passivation methods are investigated. Raman spectroscopy results demon-strate a shift in the Raman spectrum, and completed V2O3 MEMS devices are showcased. In addition, some preliminary work upon V2O3 growth in different substrates (Mica) is tested. Finally, some small top-gate modulations of V2O3 exploiting Metal-insulator transition property is shown. Overall, this thesis contributes to the field of nanomechanical strain testing of low-dimensional materials by introducing MEMS chips as an effective experimental platform. The investigations provide valuable insights into the mechanism of the substrate-engineered photocurrent generation analysis of 2H-MoS2. The thesis also provides a device fabrication methodology to study interesting phase transitions in strongly-correlated materials. These findings have implications for understanding the properties and potential applications of low-dimensional materials. Item Open AccessLiquid-interface orientation-dictated self-assembly of colloidal semiconductor nanocrystals and its applications(Bilkent University, 2023-08) Waris, Mohsin; Demir, Hilmi VolkanOver the past, different techniques have been used for the self-assembly of nanocrystals (NCs). Recently, the orientation control over the assembly of anisotropic NCs has been achieved using liquid-interface self-assembly, which is a simple yet vastly applicable technique. Here, we propose and show the first account of the application of this method to assemble multi-layered alternating-orientation NC films, with distinct orientation control of our choice over the NCs in each layer. Being laterally atomically flat, these anisotropic NCs belong to a class of quasi-two-dimensional nanocrystals with one confined dimension. Exhibiting extraordinarily large absorption cross-sections, ultra-narrow emission linewidths, and intrinsic structural anisotropy, these nanoplatelets (NPLs) possess characteristics comparable to those of epitaxially grown quantum wells, though while offering low-cost solution-based synthesis and processability at the same time. Due to this anisotropy, the emission of these NPLs is directional with mostly in-plane transition dipole moments, making them favorable for a variety of optoelectronic active media with orientation control over their deposited films. To achieve this, we have assembled the NPL films with one defined orientation and successfully attained their orientation control using macroscopic parameters, including the evaporation rate of the solvent and subphase selection to be used as the active layers for a number of optoelectronic devices. We demonstrated different multi-layered structures of these NPLs with varying orientations. The resulting surface roughness in all these films was successfully kept, on average, with Sq smoother than 2 nm. We further extended this self-assembly technique to different classes of nanocrystals including large hexagonal NPLs (with around 100 nm in lateral dimensions) and cubic quantum dots (with around 15 nm on each side) to show the versatility of our method. The findings of this thesis indicate that our orientation-dictated self-assembly approach holds great promise for constructing complex colloidal structures made of these oriented nanocrystals as the building blocks. Item Open AccessNeural-network quantum states for a two-leg bose-hubbard ladder under a synthetic magnetic field(Bilkent University, 2023-07) Çeven, Kadir; Oktel, Mehmet ÖzgürThis thesis explores novel quantum phases in a two-leg Bose-Hubbard ladder, achieved using neural-network quantum states. The remarkable potential of quantum gas systems for analog quantum simulation of strongly correlated quantum matter is well-known; however, it is equally evident that new theoretical bases are urgently required to comprehend their intricacies fully. While simple one dimensional models have served as valuable test cases, ladder models naturally emerge as the next step, enabling studying higher dimensional effects, including gauge fields. Utilizing the paper [Çeven et al., Phys. Rev. A 106, 063320 (2022)], this thesis investigates the application of neural-network quantum states to a two leg Bose-Hubbard ladder in the presence of strong synthetic magnetic fields. This paper showcased the reliability of variational neural networks, such as restricted Boltzmann machines and feedforward neural networks, in accurately predicting the phase diagram exhibiting superfluid-Mott insulator phase transition under strong interaction. Moreover, the neural networks successfully identified other intriguing many-body phases in the weakly interacting regime. These exciting findings firmly designate a two-leg Bose-Hubbard ladder with magnetic flux as an ideal testbed for advancing the field of neural-network quantum states. By expanding these previous results, this thesis contains various essential aspects, including a comprehensive introduction and analysis of the vanilla Bose-Hubbard model and the two-leg Bose-Hubbard ladder under magnetic flux, an in-depth overview of neural-network quantum states tailored for bosonic systems, and a thorough presentation and analysis of the obtained results using neural-network quantum states for these two Bose-Hubbard models. Item Open AccessSpatial and temporal symmetry breaking in nonlinear laser lithography(Bilkent University, 2023-01) Bin Aamir, Abdullah; İlday, Fatih ÖmerSymmetry breaking is ubiquitous in nonlinear systems. This is also the case for Nonlinear Laser Lithography (NLL), in which an ultrafast laser beam incident on a material surface causes the infinite fold rotational symmetry of the material surface to be broken. In the case of linear polarization, line like structures are obtained that possess 2-fold rotational symmetry. We discuss two types of NLL, one due to the formation of oxide structures (Oxidation NLL) and the other due to material ablation (Ablation NLL). The existence of both types of structures is known for many years, however, although the regularity of oxidative structures has been significantly improved by our group earlier, the same was not true for ablative structures. Here, using the technique for Oxidation NLL and the parameters for ablative structures, we were able to achieve highly regular ablative structures which we call Ablation NLL. We demonstrate the coexistence of these two NLL structures on the same surface and how a plane can be tiled using them. Furthermore, we explore the phase space of NLL and determine the regions of the phase space occupied by the two NLL structures. We also demonstrate the versatility of NLL by obtaining Oxidation and Ablation NLL structures on several metals as well as on Silicon. We also discuss temporal symmetry breaking in NLL. If the laser beam is not incident normal to the surface and is tilted towards or away from the scanning direction, it can cause the period of the NLL structures to decrease or increase respectively. One can thus discern if a video of the beam creating a pattern while scanning over the surface along a line is run forward or backward. This dependence on the scanning direction leads to temporal symmetry breaking and is reminiscent of the Doppler effect. These symmetry breakings can be important for future research in this field along with possible commercial applications, some of which we have discussed here. Item Open AccessCumulants associated with geometric phases and their implementation in modern theory of crystalline polarization(Bilkent University, 2022-09) Cengiz, Sertac; Hetenyi, BalazsMany fields have been influenced by Berry's geometric phase because of its physical meaning and observable effects. One of the breakthroughs that stem from geometric phases is the modern theory of polarization. The expectation value of the position was not possible to calculate for crystalline structures because of ill-defined position operator. The modern theory of polarization showed that the geometric phase obtained by Zak phase, integral across the Brillouin zone, gives thefirst cumulants so that polarization is obtainable by the geometric phase. This indicates that cumulants are essential for studies such as polarization, charge transport, and electron localization. In the context of the modern theory of polarization, gauge-invariant cumulants are derived but they are not geometric even though they are physically well defined. In order to deal with this issue, a Binder cumulant associated with the adiabatic cycle is introduced, so called geometric Binder cumulant. Since the definition of Binder cumulants is based on a ratio of two cumulants, it is possible to eliminate factors that prevent the quantity to become geometric. An alternative way to extract cumulants associated with the adiabatic cycle is proposed as well. Error terms of the Cumulants are improved when they are extracted in an alternative way. Distortion around the transition points which modern theory of polarization has been reduced significantly. Geometric Binder cumulant is implemented to observe the difference between gapped and gapless band structures. One-dimensional and two-dimensional models are investigated and phase transition between metallic and insulating states is clearly observed. SSH model is investigated to make a comparison with the modern theory of polarization and development in the formalism is shown. Geometric Binder cumulant also lets us observe the correlated model and a method based on renormalization group theory is used to locate transition points in the correlated model. Results are in good agreement with each other. An alternative way to extract cumulants is also extended to two-dimensional systems and phase transition is observed in two-dimensional systems with the usage of geometric Binder cumulant. Regardless of whether the two-dimensional system has a zero-dimensional or one-dimensional Fermi surface, Geometric Binder cumulant is a quantity that is sensitive for the metallic and insulating cases. For the open gap case, geometric Binder cumulant is affected by the system size, and the effect of the system size is distinct. An increase in the system size improves the quantity. Item Open AccessDynamics of sliding and loading bilayer graphene(Bilkent University, 2022-09) Edun, Benjamin; Gülseren, OğuzSliding and loading bilayer graphene is investigated using the Tight Binding method. We develop interaction-distance dependent tight binding parameter functions to allow for the calculation of band structure for different interacting distances. We investigate the band structures of sliding graphene and loading bilayer graphene, in which case the latter consists of varying interlayer distances between monolayers. We show that based on developed parameter models, band splittings can be seen to emerge in the band structures, which follow different patterns for different sliding directions. As expected we con rm that for varying vertical interlayer distances, monolayer graphene band structure is the limit for both AA and AB stacking con gurations. By applying a quadratic energy model to the curvature of the band structures in the vicinity of the K-point for AB stacking con guration we predict the effective mass of electrons and holes in bilayer graphene, and electrons in monolayer graphene. We also show the pattern of change of effective mass with respect to changing interlayer distance, and try to investigate where our prescribed quadractic energy model breaks down, as we approach the limit of the monolayer band structure. Item Open AccessA continuum equation displaying Tracy-Widom distribution in the spatial and temporal fluctuations of growing interfaces(Bilkent University, 2022-09) Liçkollari, Xhulian; İlday, Fatih ÖmerA wide variety of surface growth phenomena involves random processes that result in correlated stochastic dynamics. Such dynamics is most succinctly described by a nonlinear equation known as the Kardar-Parisi-Zhang (KPZ) equation. It is of particular interest that the random fluctuations observed along a growing interface described by the KPZ equation turn out to be correlated, with statistics that match the so-called Tracy-Widom distribution. The correlated fluctuations pertain only to the space dimension, namely, along the growing interface. The fluctuations of any given point along the interface over time remain uncorrelated, thus exhibiting Gaussian fluctuations. This is to be expected since the KPZ equation and the experimental systems where the Tracy-Widom statistics have been observed lack mechanisms to induce temporal correlations. Recently, a new mechanism of dissipative self-assembly has been reported, where the self-assembly process is driven by an intrinsic feedback mechanism that is expected to induce temporal correlations. Indeed, such correlations have been experimentally observed with statistics that match the Tracy-Widom probability distribution. Here, we explore the theory of the emergence of correlated temporal fluctuations in such a system when a simplified feedback mechanism is introduced. We develop a highly simplified model, which formally constitutes a modified KPZ equation. We, then, show that this modified equation exhibits temporal fluctuations that are well described by Tracy-Widom fluctuations, up to at least the eight moment, in excellent agreement with the experimental results. Item Open AccessA study of the modern theory of polarization on extensions of one dimensional topological insulators and disordered systems(Bilkent University, 2021-12) Parlak, Selçuk; Hetenyi, BalazsWe work on identifying topological and quantum phase transition via the modern theory of polarization. We go through the problem of electrostatics definition of absolute polarization via a discrete chain of anions and cations. We move from this discrete approach to a continuous one and prove the emergence of the Berry phase under adiabatic evolution. Introducing the Resta's position operator, we show the correspondence to the definition of polarization and go through the polarization distribution of the system. Using these concepts we studied band structures, topological invariants, and symmetries in the Su-Schrie er-Heeger model. With these basics, we analyzed the emergence of torus knots and its identification of topological transition on the distance-dependent SSH model. We go through the formal definitions of knot theory and how to identify them to establish a new system using Klein bottle knots. Following the distance vector structure in the distance-dependent SSH model, we try to establish a real-life system using Klein bottle parametrizations; Pinched torus, figure 8, and the bottle shape. In all of the parametrizations, the interpretation of the real-life system had hoppings on empty sites. Klein bottle knots are tried to observe via parametrizations of the Klein bottle. In all cases, due to the four-dimensional nature of the Klein bottle, we encountered intersecting curves on 3-dimensional interpretations of the Klein bottle. To understand the system better, we go through the Berry phase and dispersion relation of the system. After not encountering anything significant, we try to acquire a knot structure on fundamental polygons. We obtain a Hopf link and unlink with a possible intersection point. The intersection becomes hard to judge due to computational approximation on determining the knot diagrams. Due to the complexity of the project, we go through the Anderson model to study the modern theory of polarization. A background on Anderson localization with a computational method: Transfer matrix method is given. We state Mott's relation of conductivity and discuss the concept of mobility edge. We show the localization theory of Resta by introducing the complex number z. With this, we prove that the jzj becomes 1 when the states are localized and 0 when we have extended states. We also go through the scaling theory of localization. To understand the scaling theory, we introduce the concept of the renormalization group and discuss how this idea is used in the gang of four paper. We go through the assumptions and results of the gang of four by observing that the scaling exponent of conductance exhibits a critical value only in the three dimensions. Using Resta's quantity, we try to establish the gang of four results by examining the size scaling of the variance of polarization of the system and introducing a renormalization flow with Resta's quantity. We observe the low-temperature limit by examining a single state in the ground state. With this, we recover the results of the gang of four. Based on the discussion of Mott's on mobility edge, we further examine the high-temperature limit, where the system is in the average of all states. We identify the transition point via two fixed points(repulsive and attractive) on flow diagrams and size scaling exponent in all dimensions. We recover the behavior of the gang of four in one and three dimensions by examination of the fixed points, and we state the ambiguity of two-dimensional solutions due to the convergence problem of the fixed points. We further solidify the analogy of conductance and Resta's number by observing the Binder cumulant and analogical mobility edge of the system. We found the same repulsive fixed point on Binder cumulant and analogical behavior on the mobility edge argument. Item Open AccessImprovements in simulating discrete deposition models(Bilkent University, 2021-11) Hashemi, Batoul; İlday, Fatih ÖmerThe main purpose of this work is to describe the surface growth phenomena. Initially, we give a brief introduction to the analytical studies, in particular, done by di erential equations such as Edward-Wilkinson and Kardar-Parisi-Zhang equations, and then introduce the discrete surface growth models as a means to describe these phenomena with a restricted number of rules. The universality properties of these models help us categorize them in three di erent classes, namely Gaussian, Edward-Wilkinson, and Kardar-Parisi-Zhang universality classes. Five di erent numerical growth models are explained, and the statistical properties of the growing interfaces in 1D systems are examined via computational studies. Growth properties of 1D structures are viewed in two di erent ways, one being the scaling exponent of roughness changing with respect to time, and the other the distribution of height uctuations. In this research, we show that our numerical simulation findings are in accord with the theoretical and analytical predictions. In addition, for the ballistic deposition and restricted solid-on-solid models, we introduce a binning method  which improves our numerical results. Moreover, we propose a novel modification on the ballistic deposition model by detecting the thin-deep wells on the interface and average them out which enables us to report an improvement in our numerical results with a noteworthy development on physical properties of the system. Furthermore, we investigate the e ect of the change of the deposition rate on the universal behavior of the system, as a result, we introduce critical values for the deposition rate with respect to the size of the system. With these modifications, we are one step closer to defining the complex behavior of the growth phenomena. Item Open AccessPlasmonic metamaterial based structures for designing of multiband and thermally tunable light absorbers, multiple thermal infrared emitter, and high-contrast asymmetric transmission optical diode(Bilkent University, 2021-07) Osgouei, Ataollah Kalantari; Özbay, EkmelMetamaterials with sub-wavelength nanostructures refer to a class of synthetic materials that possess exotic electromagnetic properties which cannot be observed with natural materials. Negative refractive index, asymmetric light transmission, invisible cloaking, and lasing are examples of these attributes. Among these possible applications, the concept of light confinement and harvesting by subwavelength structures have attracted considerable attention due to their widespread applications ranging from thermal emission, optical modulator, sensing, and photodetectors. Here, we propose and design plasmonic metamaterials with subwavelength structures in four different application areas, namely 1) Hybrid indium tin oxide-Au metamaterial absorber in the visible and near-infrared ranges for selective thermal emissions and sensors. 2) Active tuning from narrowband to broadband absorbers using a sub-wavelength VO2 for optical modulator. 3) A spectrally selective nanoantenna emitter compatible with multiple thermal infrared applications. 4) Diode like high-contrast asymmetric transmission of linearly polarized waves. In the first work, we propose a multi-band Metamaterial Perfect absorber (MPA) with two narrowband absorption responses that are centered on the visible and near-infrared (NIR) wavelengths [773 and 900 , respectively] and a broadband absorptive characteristic in another window in the NIR region [ranging from 1,530 to 2,700 with a bandwidth of 1,170 ]. The MPA comprises a periodic array of self-aligned hybrid indium tin oxide (ITO)-Au split-ring-resonators that are separated from an optically thick bottom reflector with a SiO2 layer. Based on numerical calculations, which are accompanied with a semi-analytical examination, we find that the dual narrowband and broadband responses are attributed to the hybridization of the optical responses of gold as a plasmonic material with the ones of ITO. Note that ITO acts as a low-loss dielectric in the visible range and a lossy plasmonic material in the NIR region. Moreover, due to the applied symmetry in the unit cell of the metamaterial, the proposed MPA represents polarization insensitive and omnidirectional absorptive features. The proposed metastructure can find potential applications in selective thermophotovoltaic devices, thermal emitters, and sensors. In the second work, we propose an MPA with diverse functionalities enabled by vanadium dioxide (VO2) embedded in a metal-dielectric plasmonic structure. For the initial design purpose, a Silicon (Si) nanograting on a Silver (Ag) mirror is proposed to have multiple resonant responses in the near infrared (NIR) region. Then, the insertion of a thin VO2 layer at the right position enables the design to act as an on/off switch and resonance tuner. In the insulator phase of VO2, in which the permittivity data of VO2 is similar to that of Si, a double strong resonant behavior is achieved within the NIR region. By increasing the temperature, the state of VO2 transforms from insulator to metallic so that the absorption bands turn into three distinct resonant peaks with close spectral positions. Upon this transformation, a new resonance emerges and the existing resonance features experience blue/red shifts in the spectral domain. The superposition of these peaks makes the overall absorption bandwidth broad. Although Si has a small thermo-optic coefficient, owing to strong light confinement in the ultrasmall gaps, a substantial tuning can be achieved within the Si nanogratings. Therefore, the proposed hybrid design can provide multi-resonance tunable features to cover a broad range and can be a promising strategy for the design of linearly thermal-tunable and broadband MPAs. Owing to the proposed double tuning feature, the resonance wavelengths exhibits great sensitivity to temperature, covering a broad wavelength range. Overall, the proposed design strategy demonstrates diverse functionalities enabled by the integration of a thin VO2 layer with plasmonic absorbers. In the third work, we design a wavelength-selective nanoantenna emitter based on the excitation of gap-surface plasmon modes using a metal–insulator–metal configuration (silicon dioxide (SiO2) sandwiched between silver (Ag) layers) for satisfying multiple infrared applications. The proposed design, which is called design I, realizes triple narrowband perfect absorptions at the resonance wavelengths of 1524 nm, 2279 nm, and 6000 nm, which perfectly match the atmospheric absorption bands while maintaining relatively low emissivity in the atmospheric transparency windows of 3 − 5 m and 8 − 12 m. Later, the functionality of design I is extended, which is called design II, to include a broadband absorption at the near-infrared region to minimize the solar irradiation reflection from the nanoantenna emitter. Finally, single- and three-layer graphene are introduced to provide a real-time tuning of the infrared signature of the proposed nanoantenna emitter (design II). It is also demonstrated that the three-layer graphene structure can suppress an undesired absorption resonance wavelength related to the intrinsic vibrational modes (optical phonons) of the SiO2 layer by 53.19% compared to 25.53% for the single-layer one. The spectral analysis of design I is validated using both analytical and numerical approaches where the numerical simulation domain is extended for the analysis of design II. The thermal characteristic analyses of design I and design II (without/with graphene layers) reveal that infrared signatures of the blackbody radiation are significantly reduced for the whole wavelength spectrum at least by 96% and 91% within a wide temperature ranging from room temperature to 500 , respectively. In the fourth and final work, we present a narrow-band optical diode with a high-contrast forward-to-backward ratio at the near-infrared (NIR) region. The design has a forward transmission of approximately 88%, and a backward one of less than 3%, yielding a contrast ratio of greater than 14.5 dB at a wavelength of 1550 nm. The structure is composed of a one-dimensional diffraction grating on top of a dielectric slab waveguide, both of which are made of silicon nitride (Si3N4), and all together are placed over a silver (Ag) thin film embedded on a dielectric substrate. Utilizing a dielectric-based diffraction grating waveguide on a thin silver layer leads to the simultaneous excitation of two surface plasmon modes known as long- and short-range surface plasmon polaritons (SPPs) at both interfaces of the metallic layer. The plasmon-tunneling effect, which is the result of the coupling of SPPs excited at the upper interface of the metallic layer to the radiation modes, provides a high asymmetric transmission (AT) property. The spectral response of the proposed high-contrast AT device is verified using both rigorous coupled-wave analysis as an analytical approach and finite difference time domain as a numerical one. Item Open AccessExtensions of one-dimensional topological insulator models and their properties(Bilkent University, 2021-04) Pulcu, Yetkin; Hetenyi, BalazsWe mainly study the SSH model, a one dimensional topological insulator. As a start, we give a brief introduction about the model and theoretically showed that it should have at least 2 distinct states using Jackiw-Rebbi model. Instead of us-ing only the periodic boundary conditions, we also use open boundary conditions which revealed the zero energy edge states. Introducing the spectral symmetries, we show how a given system can be characterized using the periodic table of topo-logical insulators  and depending on the symmetries we discuss which invariant can be used to determine diﬀerent topological states. Using an enlarged system for a certain symmetry class Z, we show that polarization or Berry phase fails to distinguish diﬀerent topological states. Subsequently, we implement a similar idea that Haldane used , breaking the time-reversal symmetry via introducing the complex next nearest neighbor hopping and ﬁnd that the system is charac-terized by Z2 invariant. Moving away from the ”textbook” way of writing the Bloch states, we introduce the distance dependent SSH model where the distance between A and B sublattice is p/q with p and q are being co-primes. We ﬁnd that the polarization can be found using the inversion symmetry of the wannier centers, which characterize the topological index. Plotting the curve in the pa-rameter space, we come to conclusion that Brillouin zone must be extended q times in order for the system to conserve its periodicity, which brings the knot behaviour of the curves that can be used to distinguish the topological state. At last, we make the SSH model spinful by introducing the time-reversal symmetry protecting Rashba spin-orbit coupling. Due to the Kramers’ theorem, degenerate states occur and non-Abelian Berry connection must be constructed to analyze the system. We ﬁnd that Kato propagator is suitable and gauge invariant way of doing this and computed the time-reversal polarization of the system. Item Open AccessElectrostatics of polymer translocation through membrane nanopores in electrolyte solutions(Bilkent University, 2021-02) Mohamed, Ghada Mahmoud Abdullah; Büyükdağlı, ŞahinThe transport of polymers across membranes in electrolyte solutions happens in most biological systems and is necessary for cells to function. Moreover, the poly-mer translocation process has proven to be very important in experiments and applications as well, providing a rich source of information about the polymer’s size and composition , , making the polymer translocation procedure a po-tential sequencing method that is eﬃcient, cheap, and quick , . However, no consensus on the theoretical understanding of the translocation mechanism has been reached yet , leaving it a major challenge for theoretical modelling due to its steric, hydrodynamic, and electrostatic interactions , . Here, we calculate the electrostatic energy cost of the translocating polymer in both the approach and translocation phases and investigate the dependence of the poly-mer’s grand potential on diﬀerent model tunable parameters. In the case of neu-tral membranes, low permittivity carbon-based membranes repel the approaching polymer with energy magnitude between ∼ 11 kBT and ∼ 27 kBT , while high permittivity engineered membranes attract the approaching polymer with almost the same energy magnitude. This behavior can be attributed to polymer image-charge interactions, which become ampliﬁed with low permittivity membranes. In strong salt solutions, the membrane exhibits a repulsive barrier that turns to a metastable well in dilute solutions. In pure solvents, the metastable well becomes a deep, stable well that traps the polymer in the pore for some time, where the translocation phase is mainly governed by the attractive trans-cis side interac-tion. For weakly charged membranes, the membrane charge attraction wins over the image-charge repulsion, leading to an attractive minimum at zt ≈ −1 nm followed by a repulsive barrier at lt = L/2 while for stronger membrane charges, the attractive well turns to a metastable point followed by an attractive, stable well. These results suggest that, in translocation experiments, DNA motion can be controlled by tuning the system parameters, such as the solution concentration or the membrane charge. Item Open AccessA Monte Carlo study of Maxwell’s demon coupled to finite quantum heat baths(Bilkent University, 2020-08) Güler, Umutcan; Yalabık, CemalWhen Maxwell’s demon was introduced, it raised the question: Is there a way to decrease an isolated system’s entropy, even though it was forbidden by the second law of thermodynamics. Then, a new idea which considered information as a physical entity was emerged, and an equivalence between information entropy and thermodynamic entropy was suggested. Under the light of new understandings, the original question modified into "Is there a way to decrease thermodynamic entropy of a system by using information entropy?" This work aims to demonstrate such a machinery is possible to exist in real world. Building on the model of Mandal et al. , it inquires whether if such a system is possible to build in nano scales. According to the theoretical relations, the correspondences between internal energy and effective temperature of finite fermionic and bosonic gases for varying number of particles and volumes were tabulated. Subsequently, a series of Monte Carlo simulations were executed under different circumstances. The outcomes of the simulations illustrate that production of information entropy can be used to compensate the decrease of thermodynamic entropy. The results indicate that using either one of the quantum gases as a finite quantum heat bath does affect the efficiency of the refrigerator. Based on this, using fermionic gas is superior to bosonic gas in terms of swiftness of the refrigeration, if all other variables are identical. Further research is needed to analyze the behaviour of the finite quantum heat baths at extremely low temperatures. Item Open AccessInvestigation of the low temperature dynamics of a modified toric code(Bilkent University, 2020-08) Yousuf, Noor Al Huda; Yalabık, CemalTopological quantum systems were introduced as an attempt to overcome the challenge of decoherence due to the self-correcting properties of their energy eigenstates. One of the simplest and most popular topologically ordered systems is known as “Kitaev’s toric code.” We study the dynamics of the quasiparticle excitations that live on the two-dimensional surface of the toric code in the zero temperature limit. We also look at a modified version of the toric code in which the continuity of the system is retained in one direction and removed in the other, thus forming a cylindrical surface. We argue that the main process that can result in a logical error in this limit would be a random walker of quasiparticles that can move around the surface in a topologically non-trivial manner. Using a discrete Monte Carlo method, we find the probability of the occurrence of a logical error as a function of the number of steps taken by the walker and the system size. We find that the cylindrical code does indeed show a notable advantage in its passive fault-tolerance when compared to the toric code. Item Open AccessOptomechanically induced transparency in a PT symmetric system(Bilkent University, 2020-08) Sütlüoğlu, Beyza; Bulutay, CeyhunOptomechanical systems have attracted attention recently in various areas of physics, and are widely used with the purpose of laser cooling, gravitational wave detection, preparation of entangled states, cooling of mechanical mode to its ground state of motion. Some associated remarkable phenomena are optomechanically induced transparency and slow light. Here, we investigate these features in the context of parity-time (PT ) symmetry. For that purpose, we analyze a system composed of a cavity coupled to pair of PT symmetric mechanical resonators, and investigate the first-order sidebands induced by the radiation pressure on the cavity end-mirror. System is driven by a strong control field and a weak probe field. Using a perturbative method in resolved sideband regime, we observe the transmission of the probe field and slow light around the exceptional point. System exhibits different behaviors in PT broken and PT unbroken phases. In addition to these, we apply polaron transformation, and compare our results with the previous approach. Finally, we offer a preliminary exposition of phase relations for a ternary coupled PT symmetric system, where both mechanical resonators are coupled to the electromagnetic cavity which exemplifies higher-order exceptional points. Predominantly, our results highlight the effects of PT symmetry and exceptional points on the optomechanically induced transparency. Item Open AccessJanus particles in a Gaussian optical potential: a comparative experimental study(Bilkent University, 2020-07) Bilgin, Muhammed; Gülseren, OğuzIt has been shown recently that gold coated silica Janus particles can cluster when subject to a smooth optical ﬁeld due to the presence of an attractive interaction of hydrodynamic nature (1). Such an interaction comes from the simultaneous presence of various factors: the thermophoretic ﬂow around the Janus particle itself by the temperature gradient due to the partial absorption of the optical intensity on the gold cap of the particle, the presence of a boundary near the particle, the particular orientation (cap down) due to the gravity and the distinctive property of silica particles in water to move from colder to hotter regions. The model presented in the article suggests that there are various possibilities for driving the behaviour of the system: if the material constituting the particle had opposite thermophoretic features (particle moving from hotter to colder regions) then the sign of the hydrodynamic interaction would be reversed and we wouldn’t observe any tendence to form clusters. In this study we investigate the two cases stated above: we compared the behaviour of gold coated silica Janus particles with the behaviour of gold coated polystyrene Janus particles under the eﬀect of a Gaussian optical potential, for two diﬀerent kind of boundaries (glass slide, polymer slide). We ﬁnd that in the case of polymer slide there is evidence of a repulsive hydrodynamic interaction among gold coated polystyrene Janus particles, which is less pronounced for gold coated silica Janus particles. Moreover, the interplay of optical forces and repulsive hydrodynamic interaction is such that, in case of a mixed solution with Janus colloids and normal colloids, we obtain a relatively fast separation of the two species, that might ﬁnd applications for particles sorting. Though relatively simple in the experimental realisation, this study shows how varied can be the interplay of diﬀerent eﬀects of diﬀerent nature, i.e., due to external ﬁelds (optical, thermophoretic, hydrodynamic forces related to the beam itself) and due to the self-generated ﬁeld (thermophoretic, hydrodynamic interaction due to the absorption by the gold cap). Understanding and engineering the experimental conditions might lead to realise systems where one can switch from clustering to sorting, opening possibilities for the realisation of reconﬁgurable colloidal structures, that might be interesting for cargo deliveries, or the realisation of micro-rotors. Item Open AccessAtomic force microscopy experiments on atomically thin materials(Bilkent University, 2020-06) Sheraz, Ali; Kasırga, Talip SerkanIn 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 AccessInvestigation of dual-narrowband plasmonic perfect absorbers at visible frequencies for biosensing(Bilkent University, 2019-12) Ali, Farhan; Gülseren, OğuzSince the introduction of first plasmonic perfect absorber (PA) in early 2008 by Landy et al., numerous studies have demonstrated their superior optical performance in frequencies ranging from terahertz to visible region of electromagnetic spectrum. In the literature broadband PAs are studied in more detail compared to narrowband PAs as their large absorption bandwidths make them a prime candidate for energy harvesting applications or security and defense. Recently scientists have shown a great interest in designing narrowband PAs by controlling the optical losses of the plasmonic materials as the narrowband resonances with a high quality-factor is particularly important for label-free biosensing. However, given the lossy optical properties of metals, this task has been challenging and requires delicate investigation and parameter control in contrast to broadband perfect absorbers. In this research, we numerically studied and experimentally fabricated a narrow-band plasmonic perfect absorber based on a metal-insulator-metal con- figuration. We analyzed the origin of perfect absorption for our proposed system and investigated the parameters that effect the optical properties. The purposed plasmonic structure comes up with a dual narrow-band absorption peaks at visible and near-infrared region of electromagnetic spectrum with near unity absorption e ciency. The physical origin of these absorption peaks is shown to be the excitation of propagating and localized surface plasmon resonances at certain individual frequencies, that leads to impedance matching and critical coupling when certain conditions are satisfied. Finally, we analyzed the sensing capabilities of PA by embedding nanostructure into different background refractive index, resulting in sensitivity of 500 nm/RIU, making such a platform suitable for biosensing and spectroscopic applications. This work analyzes the perfect absorption phenomena in visible frequencies in detail and will be a go to guide for researchers in the perfect absorber community. Item Open AccessA novel method for thermal conductivity measurement of two dimensional materials(Bilkent University, 2019-09) Çakıroğlu, Onur; Kasırga, Talip SerkanThermal conductivity is a quantity which governs the heat transfer in a material. After increasing importance of efficiency in power generation systems and cooling mechanisms in micro-structures, many measurement methods have been developed to explore the thermal conductivity in micro and nano-sized materials. However, complexity in experimental setups, difficulties in the fabrication of devices required for measurements, and lacking exact solutions to thermal equations limit the usability of the methods to a class of materials. It is particularly challenging to study atomically thin metallic materials. To tackle this challenge, we have developed a new thermal conductivity measurement method based on the temperature dependent electrical resistance change and analyzed our method analytically and numerically by finite element method. We applied our method to 2H-TaS2 and found thermal conductivity as 9.55 1.27 W/m.K. Thermal conductivity value of TaS2, a metallic transition metal dichalcogenide was measured for the first time. This is supported by Wiedemann-Franz law and thermal conductivity of similar materials such as 2H-TaSe2 and 1T-TaS2. The method can be applied to semiconducting thin materials as well and is superior to other methods in various ways.