Researcher:
Aral, Neşe

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PhD Student

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Neşe

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Aral

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Aral, Neşe

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2009 - 200912010 - 20162

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Researcher Of Publications: search.filters.isAuthorOfPublication.dbee48dc-05f1-4b3e-b3ba-b8d56a4db7d3

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    Coherent organization in gene regulation: a study on six networks
    (Iop Publishing Ltd, 2016) N/A; Department of Physics; Aral, Neşe; Kabakçıoğlu, Alkan; PhD Student; Faculty Member; Department of Physics; Graduate School of Sciences and Engineering; College of Sciences; N/A; 49854
    Structural and dynamical fingerprints of evolutionary optimization in biological networks are still unclear. Here we analyze the dynamics of genetic regulatory networks responsible for the regulation of cell cycle and cell differentiation in three organisms or cell types each, and show that they follow a version of Hebb's rule which we have termed coherence. More precisely, we find that simultaneously expressed genes with a common target are less likely to act antagonistically at the attractors of the regulatory dynamics. We then investigate the dependence of coherence on structural parameters, such as the mean number of inputs per node and the activatory/repressory interaction ratio, as well as on dynamically determined quantities, such as the basin size and the number of expressed genes.
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    Coherent regulation in yeast's cell-cycle network
    (Iop Publishing Ltd, 2015) N/A; Department of Physics; Aral, Neşe; Kabakçıoğlu, Alkan; PhD Student; Faculty Member; Department of Physics; Graduate School of Sciences and Engineering; College of Sciences; N/A; 49854
    We define a measure of coherent activity for gene regulatory networks, A property that reflects the unity of purpose between the regulatory agents with a common target. We propose that such harmonious regulatory action is desirable under a demand for energy efficiency and may be selected for under evolutionary pressures. We consider two recent models of the cell-cycle regulatory network of the yeast, Saccharomyces cerevisiae as a case study and calculate their degree of coherence. a comparison with random networks of similar size and composition reveals that the yeast's cell-cycle regulation is wired to yield an exceptionally high level of coherent regulatory activity. We also investigate the mean degree of coherence as a function of the network size, connectivity and the fraction of repressory/activatory interactions.
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    PublicationOpen Access
    Chaotic spin correlations in frustrated Ising hierarchical lattices
    (American Physical Society (APS), 2009) Berker, A. Nihat; Department of Physics; Aral, Neşe; Department of Physics; College of Sciences
    Spin-spin correlations are calculated in frustrated hierarchical Ising models that exhibit chaotic renormalization-group behavior. The spin-spin correlations, as a function of distance, behave chaotically. The far correlations, but not the near correlations, are sensitive to small changes in temperature or frustration, with temperature changes having a larger effect. On the other hand, the calculated free energy, internal energy, and entropy are smooth functions of temperature. The recursion-matrix calculation of thermodynamic densities in a chaotic band is demonstrated. The leading Lyapunov exponents are calculated as a function of frustration.