Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 3Citation - Scopus: 3Extended Void Merging Tree Algorithm for Self-Similar Models(Oxford University Press, 2014) Russell, EsraIn hierarchical evolution, voids exhibit two different behaviours related with their surroundings and environments, they can merge or collapse. These two different types of void processes can be described by the two-barrier excursion set formalism based on Brownian random walks. In this study, the analytical approximate description of the growing void merging algorithm is extended by taking into account the contributions of voids that are embedded into overdense region(s) which are destined to vanish due to gravitational collapse. Following this, to construct a realistic void merging model that consists of both collapse and merging processes, the twobarrier excursion set formalism of the void population is used. Assuming spherical voids in the Einstein-de Sitter Universe, the void merging algorithm which allows us to consider the two main processes of void hierarchy in one formalism is constructed. In addition to this, the merger rates, void survival probabilities, void size distributions in terms of the collapse barrier and finally, the void merging tree algorithm in the self-similar models are defined and derived.Article Citation - WoS: 21Citation - Scopus: 61Studies of Jet Mass in Dijet and W/Z + Jet Events(Springer Verlag, 2013) CMS Collaboration; Karapınar, GülerInvariant mass spectra for jets reconstructed using the anti-k T and CambridgeAachen algorithms are studied for different jet "grooming" techniques in data corresponding to an integrated luminosity of 5 fb-1, recorded with the CMS detector in proton-proton collisions at the LHC at a center-of-mass energy of 7 TeV. Leading-order QCD predictions for inclusive dijet and W/Z+jet production combined with parton-shower Monte Carlo models are found to agree overall with the data, and the agreement improves with the implementation of jet grooming methods used to distinguish merged jets of large transverse momentum from softer QCD gluon radiation. © 2013 CERN for the benefit of the CMS collaboration.Article Citation - WoS: 15Citation - Scopus: 19Campways: Constrained Alignment Framework for the Comparative Analysis of a Pair of Metabolic Pathways(Oxford University Press, 2013) Abaka, Gamze; Bıyıkoğlu, Türker; Erten, CesimMotivation: Given a pair of metabolic pathways, an alignment of the pathways corresponds to a mapping between similar substructures of the pair. Successful alignments may provide useful applications in phylogenetic tree reconstruction, drug design and overall may enhance our understanding of cellular metabolism.Results: We consider the problem of providing one-to-many alignments of reactions in a pair of metabolic pathways. We first provide a constrained alignment framework applicable to the problem. We show that the constrained alignment problem even in a primitive setting is computationally intractable, which justifies efforts for designing efficient heuristics. We present our Constrained Alignment of Metabolic Pathways (CAMPways) algorithm designed for this purpose. Through extensive experiments involving a large pathway database, we demonstrate that when compared with a state-of-the-art alternative, the CAMPways algorithm provides better alignment results on metabolic networks as far as measures based on same-pathway inclusion and biochemical significance are concerned. The execution speed of our algorithm constitutes yet another important improvement over alternative algorithms. © The Author 2013.