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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access Emergence of correlated proton tunnelling in water ice(The Royal Society, 2019) Farrow, Tristan; Deliduman, Cemsinan; Vedral, Vlatko; Department of Physics; Pusuluk, Onur; Department of Physics; Graduate School of Sciences and EngineeringSeveral experimental and theoretical studies report instances of concerted or correlated multiple proton tunnelling in solid phases of water. Here, we construct a pseudo-spin model for the quantum motion of protons in a hexameric H2O ring and extend it to open system dynamics that takes environmental effects into account in the form of O-H stretch vibrations. We approach the problem of correlations in tunnelling using quantum information theory in a departure from previous studies. Our formalism enables us to quantify the coherent proton mobility around the hexagonal ring by one of the principal measures of coherence, the l(1) norm of coherence. The nature of the pairwise pseudo-spin correlations underlying the overall mobility is further investigated within this formalism. We show that the classical correlations of the individual quantum tunnelling events in long-time limit is sufficient to capture the behaviour of coherent proton mobility observed in low-temperature experiments. We conclude that long-range intra-ring interactions do not appear to be a necessary condition for correlated proton tunnelling in water ice.Publication Open Access Terminal neuron localization to the upper cortical plate is controlled by the transcription factor NEUROD2(Nature Publishing Group (NPG), 2019) Department of Molecular Biology and Genetics; Department of Physics; Akkaya, Cansu; Atak, Dila; Güzelsoy, Gizem; Dunn, Cory David; Dunn, Gülayşe İnce; Kabakçıoğlu, Alkan; Master Student; Faculty Member; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; Department of Physics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/A; N/A; 105301; N/A; 49854Excitatory neurons of the mammalian cerebral cortex are organized into six functional layers characterized by unique patterns of connectivity, as well as distinctive physiological and morphological properties. Cortical layers appear after a highly regulated migration process in which cells move from the deeper, proliferative zone toward the superficial layers. Importantly, defects in this radial migration process have been implicated in neurodevelopmental and psychiatric diseases. Here we report that during the final stages of migration, transcription factor Neurogenic Differentiation 2 (Neurod2) contributes to terminal cellular localization within the cortical plate. In mice, in utero knockdown of Neurod2 resulted in reduced numbers of neurons localized to the uppermost region of the developing cortex, also termed the primitive cortical zone. Our ChIP-Seq and RNA-Seq analyses of genes regulated by NEUROD2 in the developing cortex identified a number of key target genes with known roles in Reelin signaling, a critical regulator of neuronal migration. Our focused analysis of regulation of the Reln gene, encoding the extracellular ligand REELIN, uncovered NEUROD2 binding to conserved E-box elements in multiple introns. Furthermore, we demonstrate that knockdown of NEUROD2 in primary cortical neurons resulted in a strong increase in Reln gene expression at the mRNA level, as well as a slight upregulation at the protein level. These data reveal a new role for NEUROD2 during the late stages of neuronal migration, and our analysis of its genomic targets offers new genes with potential roles in cortical lamination.Publication Open Access The information coded in the yeast response elements accounts for most of the topological properties of its transcriptional regulation network(Public Library of Science, 2007) Balcan, Duygu; Mungan, Muhittin; Erzan, Ayşe; Department of Physics; Kabakçıoğlu, Alkan; Faculty Member; Department of Physics; College of Sciences; 49854The regulation of gene expression in a cell relies to a major extent on transcription factors, proteins which recognize and bind the DNA at specific binding sites (response elements) within promoter regions associated with each gene. We present an information theoretic approach to modeling transcriptional regulatory networks, in terms of a simple "sequence-matching" rule and the statistics of the occurrence of binding sequences of given specificity in random promoter regions. The crucial biological input is the distribution of the amount of information coded in these cognate response elements and the length distribution of the promoter regions. We provide an analysis of the transcriptional regulatory network of yeast Saccharomyces cerevisiae, which we extract from the available databases, with respect to the degree distributions, clustering coefficient, degree correlations, rich-club coefficient and the k-core structure. We find that these topological features are in remarkable agreement with those predicted by our model, on the basis of the amount of information coded in the interaction between the transcription factors and response elements.Publication Open Access Superradiant quantum heat engine(Nature Publishing Group (NPG), 2015) Department of Physics; Hardal, Ali Ümit Cemal; Müstecaplıoğlu, Özgür Esat; Faculty Member; Department of Physics; College of Sciences; N/A; 1674Quantum physics revolutionized classical disciplines of mechanics, statistical physics, and electrodynamics. One branch of scientific knowledge however seems untouched: thermodynamics. Major motivation behind thermodynamics is to develop efficient heat engines. Technology has a trend to miniaturize engines, reaching to quantum regimes. Development of quantum heat engines (QHEs) requires emerging field of quantum thermodynamics. Studies of QHEs debate whether quantum coherence can be used as a resource. We explore an alternative where it can function as an effective catalyst. We propose a QHE which consists of a photon gas inside an optical cavity as the working fluid and quantum coherent atomic clusters as the fuel. Utilizing the superradiance, where a cluster can radiate quadratically faster than a single atom, we show that the work output becomes proportional to the square of the number of the atoms. In addition to practical value of cranking up QHE, our result is a fundamental difference of a quantum fuel from its classical counterpart. KeywordsPublication Open Access Phase diffusion of a q-deformed oscillator(Multidisciplinary Digital Publishing Institute (MDPI), 2009) Birol, Turan; Department of Physics; Müstecaplıoğlu, Özgür Esat; Faculty Member; Department of Physics; College of Sciences; 1674We examine the problem of phase diffusion rate in a U(1) global phase symmetry broken system, from the perspective of q-deformed oscillators where the deformation parameter represents the anharmonicity. It is shown that broken phase symmetry states, described by deformed coherent states, suffer phase diffusion at a rate determined by the deformation parameter. Analytical discussions are given for the case of weak deformations, while detailed numerical results are presented when strong anharmonicity is present in the system.Publication Open Access Evidence for broken ergodicity due to chemical alloying from the dissociation kinetics of binary clusters(American Institute of Physics (AIP) Publishing, 2014) Calvo, Florent; Department of Physics; Yurtsever, İsmail Ersin; Faculty Member; Department of Physics; College of Sciences; 7129The interplay between thermal relaxation and statistical dissociation in binary Morse clusters (AB)N has been investigated using numerical simulations and simple statistical approaches, for a variety of interaction parameters covering miscible and non-miscible regimes. While all clusters exhibit a core/shell phase separation pattern in their most stable, T = 0 structure, different melting mechanisms are identified depending on the ranges and their mismatch, including two-step melting of the surface and the core or premelting as alloying. The preference for emitting A or B particles upon evaporation has been evaluated assuming that the cluster is either thermally equilibrated or vibrationally excited in its ground state structure, and compared to the predictions of theWeisskopf theory. The variations of the dissociation rate constants with increasing energy and the branching ratio between the two channels show significant differences in both cases, especially when the clusters are miscible and bound by short-range forces, which indicates that the time scale for evaporation is much shorter than the equilibration time. Our results suggest that dissociation properties could be used to test the ergodic hypothesis in such compounds. © 2014 AIP Publishing LLC.Publication Open Access All optical control of magnetization in quantum confined ultrathin magnetic metals(Nature Publishing Group (NPG), 2021) Department of Physics; Department of Electrical and Electronics Engineering; N/A; Müstecaplıoğlu, Özgür Esat; Onbaşlı, Mehmet Cengiz; Naseem, Muhammad Tahir; Zanjani, Saeedeh Mokarian; Faculty Member; Faculty Member; Department of Physics; Department of Electrical and Electronics Engineering; College of Sciences; College of Engineering; Graduate School of Sciences and Engineering; 1674; 258783; N/A; N/AAll-optical control dynamics of magnetization in sub-10 nm metallic thin films are investigated, as these films with quantum confinement undergo unique interactions with femtosecond laser pulses. Our theoretical analysis based on the free electron model shows that the density of states at Fermi level (DOSF) and electron-phonon coupling coefficients (G(ep)) in ultrathin metals have very high sensitivity to film thickness within a few angstroms. We show that completely different magnetization dynamics characteristics emerge if DOSF and G(ep) depend on thickness compared with bulk metals. Our model suggests highly efficient energy transfer from femtosecond laser photons to spin waves due to minimal energy absorption by phonons. This sensitivity to the thickness and efficient energy transfer offers an opportunity to obtain ultrafast on-chip magnetization dynamics.Publication Open Access Analog black holes and energy extraction by super-radiance from Bose Einstein condensates (BEC) with constant density(Elsevier, 2019) Department of Physics; Department of Physics; Graduate School of Sciences and Engineering; College of SciencesThis paper investigates the acoustic superradiance of the density and phase fluctuations from the single vortex state of a Bose-Einstein condensate, by employing full time-domain and asymptotic frequency domain numerical calculations. The draining bathtub model of an incompressible barotropic fluid is adopted to describe the vortex. The propagation of the axisymmetric density and phase fluctuations in the condensate are governed by the massless scalar Klein-Gordon wave equation, which establishes the rotating black-hole analogy. Hence, the amplified scattering of these fluctuations from the vortex comprise the superradiance effect. A particular coordinate transformation is applied to reveal the event horizon and the ergosphere termwise in the metric and the respective asymptotic spectral solutions. A comparative analysis of the time domain and asymptotic frequency domain results are given for a range of rotational speed of the vortex and the frequency of the impinging fluctuations. The agreement at low rotational speeds of the vortex is shown to be very good, which starts to deteriorate at higher rotational speeds due to increasing constraint violations of the time-domain calculations. We further demonstrate an asymptotic upper bound for the superradiance as a function of vortex rotational speed, provided that the vortex remains stable.