Mühendislik ve Doğa Bilimleri Fakültesi

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Citation Count: 2
Cosmic ray intensity variation during a CME
(Pergamon-Elsevier Science Ltd, 2002) Kandemir, Gulcın; Geçkinli, Melih; Fırat, Coşkun; Yılmaz, Melek; Özuğur, B
The June 6 2000 coronal mass ejection was an exceptional full halo which made it possible to measure cosmic ray (CR) decrease with a simple experimental set-up. Variation in the local secondary cosmic ray density has been investigated by means of gamma rays. The experiment site was located in Istanbul (41.1N 29.0E). CR electrons and slow gamma rays have been eliminated. The CR density has dropped drastically starting on June 8 2000. The counts have been compared with the pre-shock levels and some other cases of CMEs. During strong solar modulation the local counts of secondary CR intensity values dropped down as much as 24%. (C) 2002 Elsevier Science Ltd. All rights reserved.
Citation Count: 2
An equivalence class decomposition of finite metric spaces via Gromov products
(Elsevier Science Bv, 2017) Bilge, Ayşe Hümeyra; Çelik, Derya; Koçak, Şahin
Let (X, d) be a finite metric space with elements P-i, i = 1,..., n and with the distance functions d(ij) The Gromov Product of the "triangle" (P-i, P-j, P-k) with vertices P-t, P-j and P-k at the vertex Pi is defined by Delta(ijk) = 1/2(d(ij) + d(ik) - d(jk)). We show that the collection of Gromov products determines the metric. We call a metric space Delta-generic, if the set of all Gromov products at a fixed vertex P-i has a unique smallest element (for i = 1,., n). We consider the function assigning to each vertex P-i the edge {P-i, P-k} of the triangle (P-i, P-j, P-k) realizing the minimal Gromov product at P-i and we call this function the Gromov product structure of the metric space (X, d). We say two Delta-generic metric spaces (X, d) and (X, d') to be Gromov product equivalent, if the corresponding Gromov product structures are the same up to a permutation of X. For n = 3, 4 there is one (Delta-generic) Gromov equivalence class and for n = 5 there are three (Delta-generic) Gromov equivalence classes. For n = 6 we show by computer that there are 26 distinct (Delta-generic) Gromov equivalence classes. (C) 2017 Elsevier B.V. All rights reserved.
Citation Count: 14
Exploration of the binding pocket of histone deacetylases: the design of potent and isoform-selective inhibitors
(Tübitak, 2017) Yelekçi, Kemal; Yelekçi, Kemal
Histone deacetylases (HDACs) are enzymes that act on histone proteins to remove the acetyl group and thereby regulate the chromatin state. HDACs act not only on histone protein but also nonhistone proteins that are key players in cellular processes such as the cell cycle, signal transduction, apoptosis, and more. “Classical” HDACs have been shown to be promising targets for anticancer drug design and development. However, the selectivity of HDAC inhibitors for HDAC isoforms remains the motivation of current research in this field. Here, we explored Class I HDACs and HDAC6 by sequence alignment and structural superimposition, catalytic channel extraction, and identification of critical residues involved in HDAC catalysis. Based on the general pharmacophore features of known HDAC inhibitors, we developed a library of compounds by scaffold hopping on a fragment hit identified via structurebased virtual screening of the molecular fragment library retrieved from the Otava database. Molecular docking assay revealed five of these compounds to have increased potency and selectivity for HDACs 1 and 2. Furthermore, their predicted absorption, distribution, metabolism, elimination, and toxicity (ADMET) properties were consistent with those of drug-like compounds. With further modelingbased and experimental investigations, we believe that these findings may offer additional potential HDAC inhibitors with improved selectivity
Citation Count: 2
Generalized Einstein tensor for a Weyl manifold and its applications
(Springer Heidelberg, 2013) Özdeğer, Abdülkadir
It is well known that the Einstein tensor G for a Riemannian manifold defined by R (alpha) (beta) = g (beta gamma) R (gamma I +/-) where R (gamma I +/-) and R are respectively the Ricci tensor and the scalar curvature of the manifold plays an important part in Einstein's theory of gravitation as well as in proving some theorems in Riemannian geometry. In this work we first obtain the generalized Einstein tensor for a Weyl manifold. Then after studying some properties of generalized Einstein tensor we prove that the conformal invariance of the generalized Einstein tensor implies the conformal invariance of the curvature tensor of the Weyl manifold and conversely. Moreover we show that such Weyl manifolds admit a one-parameter family of hypersurfaces the orthogonal trajectories of which are geodesics. Finally a necessary and sufficient condition in order that the generalized circles of a Weyl manifold be preserved by a conformal mapping is stated in terms of generalized Einstein tensors at corresponding points.
Citation Count: 2
Intrinsic Dynamics and Causality in Correlated Motions Unraveled in Two Distinct Inactive States of Human beta(2)-Adrenergic Receptor
(Amer Chemical Soc, 2019) Söğünmez, Nuray; Akten, Ebru Demet
The alternative inactive state of the human beta(2)-adrenergic receptor originally exposed in molecular dynamics simulations was investigated using various analysis tools to evaluate causality between correlated residue-pair fluctuations and suggest allosteric communication pathways. A major conformational shift observed in the third intracellular loop (ICL3) displayed a novel inactive state featuring an inaccessible G protein binding site blocked by ICL3 and an expanded orthosteric ligand binding site. Residue-based mean square fluctuation and stiffness calculations revealed a significant mobility decrease in ICL3 which induced a mobility increase in the remaining loop regions. This indicates conformational entropy loss in one mobile region being compensated by residual intermolecular motions in other mobile regions. Moreover the extent motions decreased and correlations that once existed between transmembrane helices shifted toward regions with increased mobility. Conditional time-delayed cross-correlation analysis identified distinct driver follower relationship profiles. Prior to its packing freely moving ICL3 was markedly driven by transmembrane helix-8 whereas once packed ICL3 controlled future fluctuations of nearby helices. Moreover two transmembrane helices (H5 and H6) started to control future fluctuations of a remote site the extracellular loop ECL2. This clearly suggests that allosteric coupling between extra- and intracellular parts intensified in agreement with the receptor's well recognized feature which is the inverse proportionality between activity and the degree of coupling.
Citation Count: 1
Orthogonal projection and liftings of Hamilton-decomposable Cayley graphs on abelian groups
(Elsevier Science Bv, 2013) Çalışkan, Cafer; Çalışkan, Cafer; Kreher, Donald L.
In this article we introduce the concept of (p alpha)-switching trees and use it to provide sufficient conditions on the abelian groups G and H for when CAY (G x H
Citation Count: 5
Three-fast-searchable graphs
(Elsevier Science Bv, 2013) Dereniowski, Dariusz; Diner, Öznur Yaşar; Dyer, Danny
In the edge searching problem searchers move from vertex to vertex in a graph to capture an invisible fast intruder that may occupy either vertices or edges. Fast searching is a monotonic internal model in which at every move a new edge of the graph G must be guaranteed to be free of the intruder. That is once all searchers are placed the graph G is cleared in exactly vertical bar E(G)vertical bar moves. Such a restriction obviously necessitates a larger number of searchers. We examine this model and characterize graphs for which 2 or 3 searchers are sufficient. We prove that the corresponding decision problem is NP-complete. (C) 2013 Elsevier B.V. All rights reserved.

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