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: 3
    Citation - Scopus: 4
    Quasi-Supervised Strategies for Compound-Protein Interaction Prediction [article]
    (Wiley-VCH Verlag, 2021) Çakı, Onur; Karaçalı, Bilge
    In-silico compound-protein interaction prediction addresses prioritization of drug candidates for experimental biochemical validation because the wet-lab experiments are time-consuming, laborious and costly. Most machine learning methods proposed to that end approach this problem with supervised learning strategies in which known interactions are labeled as positive and the rest are labeled as negative. However, treating all unknown interactions as negative instances may lead to inaccuracies in real practice since some of the unknown interactions are bound to be positive interactions waiting to be identified as such. In this study, we propose to address this problem using the Quasi-Supervised Learning (QSL) algorithm. In this framework, potential interactions are predicted by estimating the overlap between a true positive dataset of compound-protein pairs with known interactions and an unknown dataset of all the remaining compound-protein pairs. The potential interactions are then identified as those in the unknown dataset that overlap with the interacting pairs in the true positive dataset in terms of the associated similarity structure. We also address the class-imbalance problem by modifying the conventional cost function of the QSL algorithm. Experimental results on GPCR and Nuclear Receptor datasets show that the proposed method can identify actual interactions from all possible combinations.
  • Article
    Citation - WoS: 4
    Citation - Scopus: 4
    Chirality Switching in Ferromagnetic Nanostructures Via Nanosecond Electric Pulses
    (Wiley-VCH Verlag, 2021) Aldulaimi, W. A. S.; Akaoğlu, C.; Şendur, Kürşat; Okatan, Mahmut Barış; Mısırlıoğlu, İbrahim Burç
    The stability of magnetism in reduced dimensions has become a major scientific agenda in the pursuit of implementing magnetic nanostructures as functional components in spintronic devices. Methods to probe and control magnetization states of such structures in a deterministic manner include use of spin polarized currents, photon absorption, and relatively recently, electric fields that tailor magnetoelectric coupling in multiferroic based structures. In theory, a short electric pulse is able to generate localized magnetic fields that can couple to the local magnetic dipoles electrodynamically. Here, using the Landau-Lifshitz-Gilbert formalism of magnetism dynamics combined with continuum Maxwell relations, the response of a ferromagnetic permalloy nanodisc to nanosecond electric field pulses is studied. The dynamics of the magnetic order of the nanodiscs during this process are examined and discussed. Ferromagnet nanodiscs, when below a critical size and in the absence of any external field, relax to a vortex phase as the ground state due to the demagnetizing field. Simulations demonstrate that the planar chirality of such a ferromagnet nanodisc can be switched via a time-wise asymmetric electric field pulse on the order of a few ns duration that generates radially varying tangential magnetic fields. These fields couple to the vortex state of the nanodisc ferromagnet electrodynamically, revealing an effective and robust method to control chirality.