Researcher:
Kabakçıoğlu, Alkan

Profile Picture
ORCID

Job Title

Faculty Member

First Name

Alkan

Last Name

Kabakçıoğlu

Name

Name Variants

Kabakçıoğlu, Alkan

Email Address

Birth Date

Filters

Advanced Search

Filter by

Settings

Researcher Of Publications: search.filters.isAuthorOfPublication.b634c79c-632f-462a-9c70-cbd0455bb63c

Search Results

Now showing 1 - 10 of 30
  • Placeholder
    PublicationMetadata only
    Transcriptional regulatory network topology from statistics of DNA binding sites
    (Elsevier, 2007) N/A; Department of Physics; Kabakçıoğlu, Alkan; Faculty Member; Department of Physics; College of Sciences; 49854
    We show that the out-degree distribution of the gene regulation network of the budding yeast, Saccharomyces cerevisiae, can be reproduced to high accuracy from the statistics of TF binding sequences. Our observation suggests a particular microscopic mechanism for the observed universal global topology in these networks. The numerical data and analytical solution of our model disagree with a simple power-law for the experimentally obtained degree distribution in the case of yeast.
  • Placeholder
    PublicationMetadata only
    Anharmonicity, mode-coupling and entropy in a fluctuating native protein
    (Iop Publishing Ltd, 2010) N/A; Department of Physics; Department of Computer Engineering; N/A; Department of Chemical and Biological Engineering; Kabakçıoğlu, Alkan; Yüret, Deniz; Gür, Mert; Erman, Burak; Faculty Member; Faculty Member; PhD Student; Faculty Member; Department of Physics; Department of Computer Engineering; Department of Chemical and Biological Engineering; College of Sciences; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; 49854; 179996; 216930; 179997
    We develop a general framework for the analysis of residue fluctuations that simultaneously incorporates anharmonicity and mode-coupling in a unified formalism. We show that both deviations from the Gaussian model are important for modeling the multidimensional energy landscape of the protein Crambin (1EJG) in the vicinity of its native state. the effect of anharmonicity and mode-coupling on the fluctuational entropy is in the order of a few percent.
  • Placeholder
    PublicationMetadata only
    Tension propagation during DNA hairpin folding
    (Iop Publishing Ltd, 2019) Li, Huaping; Department of Physics; Kabakçıoğlu, Alkan; Faculty Member; Department of Physics; College of Sciences; 49854
    Characterization of DNA/RNA folding dynamics is an interesting problem involving the complex force balance between the relaxation of the growing duplex and the stretched single-stranded segments. In a previous paper, we reported that the helicity plays an important role in determining the folding time for a chain of size N, where is the Flory exponent. Here we analyze this process in further detail by using molecular dynamics, with particular emphasis on tension propagation along a single strand on the unfolded segment. We directly observe that the single-strand segments are always stretched during the folding process by the tension induced by base pair formation, propagating ahead of the y?-junction. Our molecular dynamics simulations verify the existence of a stem-flower structure in the unfolded segments, with a power-law dependence of the stem length N-s on the duplex length n. For the longest hairpin structures considered, we also find that the power-law regime terminates before the first half of the folding is completed. We demonstrate that the structure?s helicity is an integral aspect of the folding dynamics by comparing our findings with those obtained from a hypothetical non-helical model.
  • Placeholder
    PublicationMetadata only
    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.
  • Placeholder
    PublicationMetadata only
    Functionally important residues from mode coupling during short-time protein dynamics
    (Cell Press, 2015) Varol, Onur; Department of Computer Engineering; Department of Chemical and Biological Engineering; Department of Physics; Yüret, Deniz; Erman, Burak; Kabakçıoğlu, Alkan; Faculty Member; Faculty Member; Faculty Member; Department of Computer Engineering; Department of Chemical and Biological Engineering; Department of Physics; College of Engineering; College of Engineering; College of Sciences; 179996; 179997; 49854
  • Placeholder
    PublicationMetadata only
    Constrained thermal denaturation of DNA under fixed linking number
    (De Gruyter, 2012) Bar, Amir; Mukamel, David; Department of Physics; Kabakçıoğlu, Alkan; Faculty Member; Department of Physics; College of Sciences; 49854
    A DNA molecule with freely fluctuating ends undergoes a sharp thermal denaturation transition upon heating. However, in circular DNA chains and some experimental setups that manipulate single DNA molecules, the total number of turns (linking number) is constant at all times. The consequences of this additional topological invariant on the melting behaviour are nontrivial. Below, we investigate the melting characteristics of a homogeneous DNA where the linking number along the melting curve is preserved by supercoil formation in duplex portions. We obtain the mass fraction and the number of loops and supercoils below and above the melting temperature. We also argue that a macroscopic loop appears at T (c) and calculate its size as a function of temperature.
  • Placeholder
    PublicationMetadata only
    New results on the melting thermodynamics of a circular DNA chain
    (2010) Orlandini, E.; Mukamel, D.; Department of Physics; Kabakçıoğlu, Alkan; Faculty Member; Department of Physics; College of Sciences; 49854
    We investigate the impact of supercoil period and nonzero supercoil formation energy on the thermal denaturation of a circular DNA. Our analysis is based on a recently proposed generalization of the Poland–Scheraga model that allows the DNA melting to be studied for plasmids with circular topology, where denaturation is accompanied by formation of supercoils. We find that the previously obtained first-order melting transition persists under the generalization discussed. The dependence of the size of the order-parameter jump at the transition point and the associated melting temperature are obtained analytically.
  • Placeholder
    PublicationMetadata only
    Function changing mutations in glucocorticoid receptor evolution correlate with their relevance to mode coupling
    (2016) N/A; N/A; N/A; Department of Physics; Kav, Batuhan; Öztürk, Murat; Kabakçıoğlu, Alkan; Master Student; Master Student; Faculty Member; Department of Physics; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; 49854
    Nonlinear effects in protein dynamics are expected to play role in function, particularly of allosteric nature, by facilitatingenergy transfer between vibrational modes. A recently proposed method focusing on the non-Gaussian shape of the configu-rational population near equilibrium projects this information onto real space in order to identify the aminoacids relevantto function. We here apply this method to three ancestral proteins in glucocorticoid receptor (GR) family and show that themutations that restrict functional activity during GR evolution correlate significantly with locations that are highlighted bythe nonlinear contribution to the near-native configurational distribution. Our findings demonstrate that the analysis ofnonlinear effects in protein dynamics can be harnessed into a predictive tool for functional site determination.
  • Placeholder
    PublicationMetadata only
    Robustness of transcriptional regulation in yeast-like model boolean networks
    (World Scientific Publ Co Pte Ltd, 2010) Tugrul, Murat; Department of Physics; Kabakçıoğlu, Alkan; Faculty Member; Department of Physics; College of Sciences; 49854
    We investigate the dynamical properties of the transcriptional regulation of gene expression in the yeast Saccharomyces Cerevisiae within the framework of a synchronously and deterministically updated Boolean network model. With a dynamically determinant subnetwork, we explore the robustness of transcriptional regulation as a function of the type of Boolean functions used in the model that mimic the influence of regulating agents on the transcription level of a gene. We compare the results obtained for the actual yeast network with those from two different model networks, one with similar in-degree distribution as the yeast and otherwise random, and another due to Balcan et al., where the global topology of the yeast network is reproduced faithfully. We, surprisingly, find that the first set of model networks better reproduce the results found with the actual yeast network, even though the Balcan et al. model networks are structurally more similar to that of yeast.
  • Placeholder
    PublicationMetadata only
    Anomalies in the transcriptional regulatory network of the Yeast Saccharomyces cerevisiae
    (Elsevier, 2010) N/A; Department of Physics; Tuğrul, Murat; Kabakçıoğlu, Alkan; N/A; Faculty Member; Department of Physics; Graduate School of Sciences and Engineering; College of Sciences; N/A; 49854
    We investigate the structural and dynamical properties of the transcriptional regulatory network of the Yeast Saccharomyces cerevisiae and compare it with two "unbiased" ensembles: one obtained by reshuffling the edges and the other generated by mimicking the transcriptional regulation mechanism within the cell. Both ensembles reproduce the degree distributions (the first-by construction-exactly and the second approximately), degree-degree correlations and the k-core structure observed in Yeast. An exceptionally large dynamically relevant core network found in Yeast in comparison with the second ensemble points to a strong bias towards a collective organization which is achieved by subtle modifications in the network's degree distributions. We use a Boolean model of regulatory dynamics with various classes of update functions to represent in vivo regulatory interactions. We find that the Yeast's core network has a qualitatively different behavior, accommodating on average multiple attractors unlike typical members of both reference ensembles which converge to a single dominant attractor. Finally, we investigate the robustness of the networks and find that the stability depends strongly on the used function class. The robustness measure is squeezed into a narrower band around the order-chaos boundary when Boolean inputs are required to be nonredundant on each node. However, the difference between the reference models and the Yeast's core is marginal, suggesting that the dynamically stable network elements are located mostly on the peripherals of the regulatory network. Consistently, the statistically significant three-node motifs in the dynamical core of Yeast turn out to be different from and less stable than those found in the full transcriptional regulatory network.