Researcher:
Sarıyer, Ozan

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Ozan

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Sarıyer

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Sarıyer, Ozan

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2010 - 20123

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Researcher Of Publications: search.filters.isAuthorOfPublication.16db644a-37d4-45b4-8481-898e626602ac

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    Sequence alignment using simulated annealing
    (Elsevier, 2010) Güven, Can; Department of Physics; Sarıyer, Ozan; Researcher; Department of Physics; College of Sciences; 237449
    We apply simulated annealing to amino acid sequence alignment, a fundamental problem in bioinformatics, particularly relevant to evolution. Our goal was obtaining results comparable to those reached through dynamic programming algorithms, like the Needleman-Wunsch algorithm, as well as making a connection between physics and bioinformatics through a representative example.
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    PublicationOpen Access
    Phase separation and charge-ordered phases of the d=3 Falicov-Kimball model at nonzero temperature: temperature-density-chemical potential global phase diagram from renormalization-group theory
    (American Physical Society (APS), 2011) Hinczewski, Michael; Department of Physics; Sarıyer, Ozan; Berker, Ahmet Nihat; Faculty Member; Department of Physics; College of Sciences
    The global phase diagram of the spinless Falicov-Kimball model in d = 3 spatial dimensions is obtained by renormalization-group theory. This global phase diagram exhibits five distinct phases. Four of these phases are charge-ordered (CO) phases, in which the system forms two sublattices with different electron densities. The CO phases occur at and near half filling of the conduction electrons for the entire range of localized electron densities. The phase boundaries are second order, except for the intermediate and large interaction regimes, where a first-order phase boundary occurs in the central region of the phase diagram, resulting in phase coexistence at and near half filling of both localized and conduction electrons. These two-phase or three-phase coexistence regions are between different charge-ordered phases, between charge-ordered and disordered phases, and between dense and dilute disordered phases. The second-order phase boundaries terminate on the first-order phase transitions via critical endpoints and double critical endpoints. The first-order phase boundary is delimited by critical points. The cross-sections of the global phase diagram with respect to the chemical potentials and densities of the localized and conduction electrons, at all representative interactions strengths, hopping strengths, and temperatures, are calculated and exhibit ten distinct topologies.
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    PublicationOpen Access
    Deep spin-glass hysteresis-area collapse and scaling in the three-dimensional +/- J Ising model
    (American Physical Society (APS), 2012) Berker, A. Nihat; Department of Physics; Sarıyer, Ozan; Kabakçıoğlu, Alkan; Faculty Member; Department of Physics; College of Sciences; N/A; 49854
    We investigate the dissipative loss in the +/- J Ising spin glass in three dimensions through the scaling of the hysteresis area, for a maximum magnetic field that is equal to the saturation field. We perform a systematic analysis for the whole range of the bond randomness as a function of the sweep rate by means of frustration-preserving hard-spin mean-field theory. Data collapse within the entirety of the spin-glass phase driven adiabatically (i.e., infinitely slow field variation) is found, revealing a power-law scaling of the hysteresis area as a function of the antiferromagnetic bond fraction and the temperature. Two dynamic regimes separated by a threshold frequency omega(c) characterize the dependence on the sweep rate of the oscillating field. For omega < omega(c), the hysteresis area is equal to its value in the adiabatic limit omega = 0, while for omega > omega(c) it increases with the frequency through another randomness-dependent power law.