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Publication Open Access A compressed sensing framework for efficient dissection of neural circuits(Nature Publishing Group (NPG), 2019) Lee, Jeffrey B.; Yonar, Abdullah; Hallacy, Timothy; Shen, Ching-Han; Milloz, Josselin; Srinivasan, Jagan; Ramanathan, Sharad; Department of Physics; Kocabaş, Aşkın; Department of Physics; College of Sciences; 227753A fundamental question in neuroscience is how neural networks generate behavior. The lack of genetic tools and unique promoters to functionally manipulate specific neuronal subtypes makes it challenging to determine the roles of individual subtypes in behavior. We describe a compressed sensing-based framework in combination with non-specific genetic tools to infer candidate neurons controlling behaviors with fewer measurements than previously thought possible. We tested this framework by inferring interneuron subtypes regulating the speed of locomotion of the nematode Caenorhabditis elegans. We developed a real-time stabilization microscope for accurate long-term, high-magnification imaging and targeted perturbation of neural activity in freely moving animals to validate our inferences. We show that a circuit of three interconnected interneuron subtypes, RMG, AVB and SIA control different aspects of locomotion speed as the animal navigates its environment. Our work suggests that compressed sensing approaches can be used to identify key nodes in complex biological networks.Publication Open Access A divergence-free parametrization for dynamical dark energy(Institute of Physics (IOP) Publishing, 2015) Vazquez, J. Alberto; Department of Physics; Dereli, Tekin; Akarsu, Özgür; Faculty Member; Department of Physics; College of Sciences; 201358; N/AWe introduce a new parametrization for the dark energy, led by the same idea to the linear expansion of the equation of state in scale factor a and in redshift z, which diverges neither in the past nor future and contains the same number of degrees of freedom with the former two. We present constraints of the cosmological parameters using the most updated baryon acoustic oscillation (BAO) measurements along with cosmic microwave background (CMB) data and a recent reanalysis of Type Ia supernova (SN) data. This new parametrization allowed us to carry out successive observational analyses by decreasing its degrees of freedom systematically until ending up with a dynamical dark energy model that has the same number of parameters with ACDM. We found that the dark energy source with a dynamical equation of state parameter equal 2/3 at the early universe and -1 today fits the data slightly better than A.Publication Metadata only A micropillar-based microfluidic viscometer for newtonian and non-newtonian fluids(Elsevier, 2020) Tanyeri, Melikhan; Erten, Ahmet; Department of Physics; N/A; N/A; N/A; N/A; Kiraz, Alper; Yalçın, Özlem; Mustafa, Adil; Aksu, Ali Cenk; Eser, Ayşenur; Faculty Member; Faculty Member; PHD Student; PHD Student; Master Student; Department of Physics; College of Sciences; School of Medicine; Graduate School of Sciences and Engineering; School of Medicine; Graduate School of Sciences and Engineering; 22542; 218440; N/A; N/A; N/AIn this study, a novel viscosity measurement technique based on measuring the deflection of flexible (poly) dimethylsiloxane (PDMS) micropillars is presented. The experimental results show a nonlinear relationship between fluid viscosity and the deflection of micropillars due to viscoelastic properties of PDMS. A calibration curve, demonstrating this nonlinear relationship, is generated, and used to determine the viscosity of an unknown fluid. Using our method, viscosity measurements for Newtonian fluids (glycerol/water solutions) can be performed within 2-100 cP at shear rates gamma = 60.5-398.4 s(-1). We also measured viscosity of human whole blood samples (non-Newtonian fluid) yielding 2.7-5.1 cP at shear rates gamma = 120-345.1 s(-1), which compares well with measurements using conventional rotational vis-cometers (3.6-5.7 cP). With a sensitivity better than 0.5 cP, this method has the potential to be used as a portable microfluidic viscometer for real-time rheological studies. (C) 2020 Elsevier B.V. All rights reserved.Publication Open Access Acoustic superradiance from an optical-superradiance-induced vortex in a Bose-Einstein condensate(American Physical Society (APS), 2014) Ghazanfari, Nader; Department of Physics; Müstecaplıoğlu, Özgür Esat; Faculty Member; Department of Physics; College of Sciences; 1674We consider the scattering of an acoustic wave from a vortex induced by optical superradiance. The vortex is created by pumping a large amount of angular momentum with a Laguerre-Gaussian light beam in an atomic Bose-Einstein condensate. We derive the mean-field dynamical equations of the light-superfluid system, and obtain the equations governing the elementary excitation of the system, which result in a massless Klein-Gordon equation with source terms. This equation describes the propagation of the sound wave in an effective space-time. Employing a simplifying draining bathtub model for the vortex, we investigate the scattering of the acoustic wave in the vortex phase and obtain a condition for the acoustic superradiance. We conclude that Laguerre-Gaussian-beam-induced sudden transition from homogeneous to vortex state in the superfluid leads to a prominent observation of the acoustic superradiance.Publication Open Access Active invisibility cloaks in one dimension(American Physical Society (APS), 2015) Department of Mathematics; Department of Physics; Mostafazadeh, Ali; Faculty Member; Department of Mathematics; Department of Physics; College of Sciences; 4231We outline a general method of constructing finite-range cloaking potentials which render a given finite-range real or complex potential, v(x), unidirectionally reflectionless or invisible at a wave number, k(0), of our choice. We give explicit analytic expressions for three classes of cloaking potentials which achieve this goal while preserving some or all of the other scattering properties of v(x). The cloaking potentials we construct are the sum of up to three constituent unidirectionally invisible potentials. We discuss their utility in making v(x) bidirectionally invisible at k(0) and demonstrate the application of our method to obtain antireflection and invisibility cloaks for a Bragg reflector.Publication Open Access Algorithmic quantum heat engines(American Physical Society (APS), 2019) Çakmak, Selçuk; Gençten, Azmi; Kominis, Iannis K.; Department of Physics; Müstecaplıoğlu, Özgür Esat; Faculty Member; Department of Physics; College of Sciences; Graduate School of Sciences and Engineering; 1674; N/AWe suggest alternative quantum Otto engines, using heat bath algorithmic cooling with a partner pairing algorithm instead of isochoric cooling and using quantum SWAP operations instead of quantum adiabatic processes. Liquid state nuclear magnetic resonance systems in a single entropy sink are treated as working fluids. The extractable work and thermal efficiency are analyzed in detail for four-stroke and two-stroke types of alternative quantum Otto engines. The role of the heat bath algorithmic cooling in these cycles is to use a single entropy sink instead of two so that a single incoherent energy resource can be harvested and processed using an algorithmic quantum heat engine. Our results indicate a path to programmable quantum heat engines as analogs of quantum computers beyond traditional heat engine cycles. We find that for our NMR system example implementation of quantum algorithmic heat engine stages yields more power due to increased cycle speeds.Publication Metadata only An animal model of fetishism(Pergamon-Elsevier Science Ltd, 2004) Köksal, Falih; Domcan, Michael; Orung, S.; Bowers,Robert; Kumru, Gülsen; Sertel, Berk Özlem; Department of Physics; Kurt, Adnan; Teaching Faculty; Department of Physics; College of Sciences; 194455An animal model of sexual fetishism was developed with male Japanese quail based on persistence of conditioned sexual responding during extinction to an inanimate object made of terrycloth (Experiments 1 and 3). This persistent responding occurred only in subjects that came to copulate with the terrycloth object, suggesting that the copulatory behavior served to maintain the fetishistic behavior. Sexual conditioning was carried out by pairing a conditioned stimulus (CS) with the opportunity to copulate with a female (the unconditioned stimulus or US). Copulation with the CS object and persistent responding did not develop if the CS was a light (Experiment 1) or if conditioning was carried out with a food US (Experiment 2). In addition, subjects that showed persistence in responding to the terrycloth CS did not persist in their responding to a light CS (Experiment 3). The results are consistent with the hypothesis that conditioned copulatory behavior creates a form of self-maintenance that leads to persistent responding to an inanimate object. The development of an animal model of such fetishistic behavior should facilitate experimental analysis of the phenomenon. (C) 2003 Elsevier Ltd. All rights reserved.Publication Open Access Anisotropic inflation with a non-minimally coupled electromagnetic field to gravity(Institute of Physics (IOP) Publishing, 2017) Adak, Muzaffer; Akarsu, Özgür; Sert, Özcan; Department of Physics; Dereli, Tekin; PhD Student; Department of Physics; College of Sciences; 201358We consider the non-minimal model of gravity in Y (R) F-2-form. We investigate a particular case of the model, for which the higher order derivatives are eliminated but the scalar curvature R is kept to be dynamical via the constraint YRFmn F-mn = -2/k(2) The ff ective fluid obtained can be represented by interacting electromagnetic field and vacuum depending on Y (R), namely, the energy density of the vacuum tracks R while energy density of the conventional electromagnetic field is dynamically scaled with the factor Y (R) 2. We give exact solutions for anisotropic inflation by assuming the volume scale factor of the Universe exhibits a power-law expansion. The directional scale factors do not necessarily exhibit power-law expansion, which would give rise to a constant expansion anisotropy, but expand nontrivially and give rise to a non-monotonically evolving expansion anisotropy that eventually converges to a non-zero constant. Relying on this fact, we discuss the anisotropic e-fold during the inflation by considering observed scale invariance in CMB and demanding the Universe to undergo the same amount of e-folds in all directions. We calculate the residual expansion anisotropy at the end of inflation, though as a result of non-monotonic behaviour of expansion anisotropy all the axes of the Universe undergo the same of amount of e-folds by the end of inflation. We also discuss the generation of the modified electromagnetic field during the first few e-folds of the inflation and its persistence against to the vacuum till end of inflation.Publication Open Access Antibunching via cooling by heating(American Physical Society (APS), 2022) Department of Physics; Müstecaplıoğlu, Özgür Esat; Naseem, Muhammad Tahir; Faculty Member; Department of Physics; College of Sciences; 1674; N/AWe investigate statistics of the photon (phonon) field undergoing linear and nonlinear damping processes. An effective two-photon (phonon) nonlinear "cooling by heating"process is realized from linear damping by spectral filtering of the heat baths present in the system. This cooling process driven by incoherent quantum thermal noise can create quantum states of the photon field. In fact, for high temperatures of the spectrally filtered heat baths, sub-Poissonian statistics with strong antibunching in the photon (phonon) field are reported. This notion of the emergence and control of quantumness by incoherent thermal quantum noise is applied to a quantum system comprised of a two-level system and a harmonic oscillator or analogous optomechanical setting. Our analysis may provide a promising direction for the preparation and protection of quantum features via nonlinear damping that can be controlled with incoherent thermal quantum noise.Publication Metadata only Are dark energy models with variable EoS parameter w compatible with the late inhomogeneous Universe?(Institute of Physics (IOP) Publishing, 2015) Bouhmadi-Lopez, Mariam; Brilenkov, Maxim; Brilenkov, Ruslan; Eingorn, Maxim; Zhuk, Alexander; Department of Physics; Akarsu, Özgür; Researcher; Department of Physics; College of Sciences; N/AWe study the late-time evolution of the Universe where dark energy (DE) is presented by a barotropic fluid on top of cold dark matter (CDM). We also take into account the radiation content of the Universe. Here by the late stage of the evolution we refer to the epoch where CDM is already clustered into inhomogeneously distributed discrete structures (galaxies, groups and clusters of galaxies). Under this condition the mechanical approach is an adequate tool to study the Universe deep inside the cell of uniformity. More precisely, we study scalar perturbations of the FLRW metric due to inhomogeneities of CDM as well as fluctuations of radiation and DE. For an arbitrary equation of state for DE we obtain a system of equations for the scalar perturbations within the mechanical approach. First, in the case of a constant DE equation of state parameter w, we demonstrate that our method singles out the cosmological constant as the only viable dark energy candidate. Then, we apply our approach to variable equation of state parameters in the form of three different linear parametrizations of w, e.g., the Chevallier-Polarski-Linder perfect fluid model. We conclude that all these models are incompatible with the theory of scalar perturbations in the late Universe.