Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

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  • Conference Object
    Microarc: Event Driven Analysis and Design Method for Microservices
    (Elsevier B.V., 2025) Yıldız, Ali; Demirors, Onur
    The rapid development of the Internet infrastructure has enabled software applications to leverage almost unlimited and scalable resources. Microservice-based architecture has emerged as a solution to harness the benefits of a distributed cloud-based infrastructure. Event-driven architecture is a powerful approach for addressing challenges in distributed systems, such as scalability, distributed data, and sharing of data at scale. In an event-driven microservice architecture, decoupled services interact by responding to events and event streams facilitate data sharing between them. Despite these advantages, there is no de facto method for the analysis and design of systems within microservice architecture. Organizations often face difficulties in developing microservice-based systems, owing to the lack of well-defined methodologies for analysis and design. In this study, we present an analysis and design method for microservice-based systems. MicroArc is a method for analyzing and designing microservice-based systems, and comprises modeling notations, guiding processes to articulate how the method is applied, and a supporting tool for modelling. The MicroArc approach enables the identification of events and microservice candidates by modeling the flow of processes in the early phase of development. © 2025 Elsevier B.V., All rights reserved.
  • Conference Object
    Dynamic Recognition of the Nucleosome Core Particle by Select Chromatin Factors
    (Elsevier B.V., 2025) Döseme, H.; Uluçay, T.; Kale, S.
    The intricate interactions between the nucleosome core particle and chromatin-binding proteins control essential biological functions templated by DNA. The nucleosome is a symmetrical and disc-shaped nucleoprotein which binds several chromatin factors in a 2:1 stoichiometry. We report computational evidence for a DNA-sequence-driven emergence of asymmetry whereby the nucleosome binding affinities of the chromatin factors are altered on each side even though the protein factors bind chemically equivalent proteinous interfaces of the nucleosome. Furthermore, none of these proteins interact directly with the nucleosomal DNA. Using atomistic molecular dynamics simulations, we surveyed five chromatin factors that are known to bind the nucleosome in a 2:1 stoichiometry. In four factors, we found that the nucleosomal gyre that binds DNA strongly is also more preferred. These factors are Sir3, PRC1, RCC1, and SAGA-DUB. However, a fifth chromatin factor, 53BP1, prefers the gyre with the weaker DNA binding with higher affinity. We argue that this tunability in nucleosome affinity could be related to the function of the chromatin interactors as 53BP1 could prefer loose DNA gyres to execute its DNA repair function. © 2025 The Authors. Published by Elsevier B.V.
  • Article
    Recent Developments in the Treatment of Leishmaniasis: Natural Compounds, Drug Targets, in Silico Molecular Docking Approaches, and Nanocarriers
    (Elsevier B.V., 2025) Gürbüz Çolak, N.
    Leishmaniasis is a common tropical disease caused by Leishmania protozoa. It affects 0.9 to 1.6 million people, causing 20,000–30,000 deaths annually. There are no effective vaccines, and current treatments have severe side effects. Drug resistance is a major obstacle in treating leishmaniasis. The necessity of drug discovery is indisputable. Natural compounds are promising candidates for drug discovery studies because of their diverse chemical structures and bioactivities. Experimental screening of compound libraries imposes high costs and is time-consuming. The molecular docking approach is beneficial for exploring new therapeutics in silico as it allows the screening of millions of drug candidates. Even if new drug candidates are discovered, delivery of the active ingredient to the target remains controversial. Nanocarriers are promising nanosystems that can address the drawbacks of drug delivery. This chapter focuses on natural compounds as drug candidates, targets, in silico drug discovery, and drug delivery for the treatment of leishmaniasis. © 2025 Elsevier Inc.
  • Conference Object
    Localizing Implicit Gradient Damage Based Modelling of Quasi-Brittle Failure With Non-Planar Crack
    (Elsevier B.V., 2024) Kaçmaz,B.; Ozdemir,I.
    Localizing implicit gradient damage (LIGD) is a gradient extended model which is equipped with a decreasing internal length scale with damage evolution, Poh and Sun (2017). The model is thermodynamically consistent and resolves the well-known problems of conventional implicit gradient damage (CIGD) model such as artificial diffusion of damage and erroneous predictions of failure initiation and propagation directions. So far, the effectiveness of the model has been demonstrated for two-dimensional quasi-brittle and three-dimensional ductile failure predictions with flat fracture surfaces. It is the aim of this contribution to assess the predictive capabilities of the model for three-dimensional quasi-brittle failures with non-planar cracks. To this end, localizing implicit gradient model is embedded within a tetrahedral element formulation and implemented in commercial finite element package Abaqus through user element (UEL) subroutine. Skew notched prismatic torsion test is modeled and capabilities of the model are assessed in terms of reaction force-displacement curves as well as the resulting crack surfaces, Brokenshire (1996), Jefferson et al. (2004). Comparison of LIGD and CIGD predictions suggest that LIGD is superior to CIGD. Furthermore, as far as capturing the experimental results is concerned, it performs as good as other alternative modeling frameworks, e.g., mixed finite element formulations. © 2024 The Author(s).
  • Article
    Citation - Scopus: 3
    Resurgent Dome and Super-Hot Enhanced Geothermal System: the Sahinkalesi Massif Within the Hasandag Stratovolcanic Province, Central Anatolia, Turkey
    (Elsevier B.V., 2024) Chandrasekharam,D.; Singh,M.; Baba,A.; Sass,I.
    The Sahinkalesi, a volcanic dome located NNE of Hasandağ, Türkiye exhibits anomalous heat flow value, geothermal gradient and the Curie point depth is located at very shallow depth in this region. Our investigation indicates presence of super-critical thermal regime (378°C) at about 4 km depth and the MT analysis indicate shallow magma chamber at about 5 km depth. The crust is relatively thin below this region with the low-velocity region located at depth of about 36 km. Thermo-Hydro-mechanical model investigation has been carried out using finite element discretization technique. For faulted zone reservoir models, 30 years of geothermal energy exploitation does not cause thermal breakthrough for mass flow rates up to 500 kg/s, however, the mean stress developed in the reservoir becomes much larger and may be unsustainable for the reservoir stability. To ensure the success of a fractured reservoir model, the use of multiple wellbores is recommended. In the case of a closed-loop geothermal system, the primary concern is the control of thermoelastic stress. This can be achieved either by increasing the wellbore depth while reducing the injection mass flow rate, or by extending the wellbore's horizontal component. The outlet temperature in both the cases maintained at 275°C. This is the first time a superhot EGS site has been identified in Türkiye. © 2024 The Author(s)
  • Conference Object
    Citation - Scopus: 2
    Crystal Plasticity Based Modelling of Shear Response of Carbon Fibre Reinforced Composites
    (Elsevier B.V., 2021) Dizman,E.A.; Özdemir,I.
    Due to their superior strength-to-weight performance, there is an increasing tendency to use carbon fibre reinforced composites (CFRP) in different engineering applications. Under transverse loading, the resulting stress-strain curve has a nonlinear character with significant hardening. As far as modelling of CFRP is concerned, the hardening behaviour is typically described by fitting curves to experimental data. Obviously, this route does not take deformation mechanisms at constituent level e.g. fibre rotation and matrix yielding, into account and leads to descriptive models rather than predictive ones. Such models yield poor predictions particularly for CFRP's with 3D microstructural architectures, which have achieved much higher ductility level and texture evolution as compared to conventional 2D architectures. In recent studies Meza et al. (2019), Tan and Liu (2020), motivated by the similarity between the shearing along slip planes and the plastic deformation of a tow, crystal plasticity is exploited to capture the evolution of the composite microstructure. This contribution focuses on the crystal plasticity inspired model of CFRP and its implementation within the commercial finite element software Abaqus through UEL subroutine. The predictions of the model are assessed by means of two example problems including combined loading scenarios. © 2021 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (https://creativecommons.org/licenses/by-nc-nd/4.0) Peer-review under responsibility of IWPDF 2021 Chair, Tuncay Yalçinkaya
  • Conference Object
    Citation - Scopus: 3
    Localizing Implicit Gradient Damage Based Treatment of Softening in Elasto-Plasticity
    (Elsevier B.V., 2021) Yasayanlar,S.; Kaçmaz,B.; Özdemir,I.
    As opposed to brittle fracture, the failure of ductile materials is preceded by severe plastic deformations. Microscopic mechanisms i.e., void growth and coalescence result in macroscopic property degradation causing softening, localization, and finally macroscopic crack. This contribution focuses on softening in elasto-plasticity and its mesh-objective description using an implicit gradient type of non-local damage mechanics framework. As reported in several studies Geers et al. (1998), Poh and Sun (2017), artificial widening of localization zone is observed when conventional implicit gradient type regularization is used. To circumvent this non-physical artifact, localizing implicit gradient damage (LIGD) formulation that is motivated by higher order continuum arguments, is adopted, Poh and Sun (2017). As opposed to previous remedies to artificial widening of the localization zone, LIGD proposes an internal length scale that decreases with deformation. A two-field (displacement-non-local equivalent plastic strain) hexahedra and a three-field (displacement-pressure-non-local equivalent plastic strain) tetrahedra element are formulated and implemented in commercial finite element software Abaqus through user element (UEL) subroutine. The effectiveness of the approach is demonstrated by solving two numerical examples. © 2021 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (https://creativecommons.org/licenses/by-nc-nd/4.0) Peer-review under responsibility of IWPDF 2021 Chair, Tuncay Yalçinkaya