Araştırma Çıktıları | TR-Dizin | WoS | Scopus | PubMed

Permanent URI for this communityhttps://hdl.handle.net/20.500.12573/393

Browse

Now showing 1 - 20 of 413

Citation - WoS: 6
Citation - Scopus: 6
3-Sulfopropyl Methacrylate Based Cryogels as Potential Tissue Engineering Scaffolds
(Taylor & Francis Ltd, 2020) Durukan, Adile Yuruk; Isoglu, Ismail Alper; 01. Abdullah Gül University; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. Biyomühendislik
In this study, we developed cryogels containing 3-sulfopropyl methacrylate (SPMA) and 4-vinyl pyridine (4-VP) as a potential scaffold for tissue engineering applications. Cryogels with varying monomer ratios were synthesised by chemical cross-linking under cryogelation conditions. Effect of initiators and cross-linker amount (0.025-0.15 g MBA; 0.012-0.05 g APS; 2.5-12.5 mu l TEMED) and also freezing temperature (-20 and -80oC) were investigated, and the conditions were optimised according to the morphological structures examined by SEM. The functional groups of the materials were characterised by FT-IR. Compression test and swelling were applied to investigate mechanical properties and water absorption ability, respectively. As a preliminary study, selected materials were tested for cell cytotoxicity with MTT. According to our results, the ionic and biocompatible cryogels prepared in this study possessing a highly porous and interconnective structure with good mechanical characteristics and swelling properties can be suitable as tissue scaffolds for many applications.
3Mont: A Multi-Omics Integrative Tool for Breast Cancer Subtype Stratification
(Public Library Science, 2025) Unlu Yazici, Miray; Marron, J. S.; Bakir-Gungor, Burcu; Zou, Fei; Yousef, Malik; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi; 04. Yaşam ve Doğa Bilimleri Fakültesi; 04.01. Biyomühendislik
Breast Cancer (BRCA) is a heterogeneous disease, and it is one of the most prevalent cancer types among women. Developing effective treatment strategies that address diverse types of BRCA is crucial. Notably, among different BRCA molecular sub-types, Hormone Receptor negative (HR-) BRCA cases, especially Basal-like BRCA sub-types, lack estrogen and progesterone hormone receptors and they exhibit a higher tumor growth rate compared to HR+ cases. Improving survival time and predicting prognosis for distinct molecular profiles is substantial. In this study, we propose a novel approach called 3-Multi-Omics Network and Integration Tool (3Mont), which integrates various -omics data by applying a grouping function, detecting pro-groups, and assigning scores to each pro-group using Feature importance scoring (FIS) component. Following that, machine learning (ML) models are constructed based on the prominent pro-groups, which enable the extraction of promising biomarkers for distinguishing BRCA sub-types. Our tool allows users to analyze the collective behavior of features in each pro-group (biological groups) utilizing ML algorithms. In addition, by constructing the pro-groups and equalizing the feature numbers in each pro-group using the FIS component, this process achieves a significant 20% speedup over the 3Mint tool. Contrary to conventional methods, 3Mont generates networks that illustrate the interplay of the prominent biomarkers of different -omics data. Accordingly, exploring the concerted actions of features in pro-groups facilitates understanding the dynamics of the biomarkers within the generated networks and developing effective strategies for better cancer sub-type stratification. The 3Mont tool, along with all supporting materials, can be found at https://github.com/malikyousef/3Mont.git.
Citation - WoS: 12
Citation - Scopus: 14
4D-QSAR Investigation and Pharmacophore Identification of Pyrrolo[2,1-C][1,4]Benzodiazepines Using Electron Conformational-Genetic Algorithm Method
(Taylor & Francis Ltd, 2016) Ozalp, A.; Yavuz, S. C.; Sabanci, N.; Copur, F.; Kokbudak, Z.; Saripinar, E.; 01. Abdullah Gül University
In this paper, we present the results of pharmacophore identification and bioactivity prediction for pyrrolo[2,1-c][1,4]benzodiazepine derivatives using the electron conformational-genetic algorithm (EC-GA) method as 4D-QSAR analysis. Using the data obtained from quantum chemical calculations at PM3/HF level, the electron conformational matrices of congruity (ECMC) were constructed by EMRE software. The ECMC of the lowest energy conformer of the compound with the highest activity was chosen as the template and compared with the ECMCs of the lowest energy conformer of the other compounds within given tolerances to reveal the electron conformational submatrix of activity (ECSA, i.e. pharmacophore) by ECSP software. A descriptor pool was generated taking into account the obtained pharmacophore. To predict the theoretical activity and select the best subset of variables affecting bioactivities, the nonlinear least square regression method and genetic algorithm were performed. For four types of activity including the GI(50), TGI, LC50 and IC50 of the pyrrolo[2,1-c][1,4] benzodiazepine series, the r(train)(2), r(test)(2) and q(2) values were 0.858, 0.810, 0.771; 0.853, 0.848, 0.787; 0.703, 0.787, 0.600; and 0.776, 0.722, 0.687, respectively.
Citation - WoS: 3
Citation - Scopus: 3
Ab Initio Simulation of Amorphous BC3
(Elsevier, 2020) Durandurdu, Murat; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik Fakültesi
We report the structural and electrical properties of an amorphous BC3 model based on ab initio molecular dynamics simulations. The amorphous network is achieved from the melt and has a layer-like structure consisting of mainly hexagonal (six membered) rings as in the crystal. However, the distribution of boron atoms in the noncrystalline configuration appears to differ significantly from that of boron atoms in the crystal. The network is a solid solution and has randomly distributed nanosized graphene-like domains at each layer. Boron atoms have a tendency to form more overcoordinated defects involving with boron-boron homopolar bond(s). The mean coordination of boron and carbon atoms is 3.2 and 3.0, respectively. Interestingly the amorphous configuration is found to have a slightly higher density and bulk modulus than the crystal, which are attributed to the existence of overcoordinated units in the amorphous state. Based on the localization of the band tail states, noncrystalline BC3 is speculated to be a semiconducting material.
Citation - WoS: 1
Citation - Scopus: 2
Accelerated Artificial Bee Colony Optimization for Cost-Sensitive Neural Networks in Multi-Class Problems
(Wiley, 2025) Hacilar, Hilal; Dedeturk, Bilge Kagan; Ozmen, Mihrimah; Celik, Mehlika Eraslan; Gungor, Vehbi Cagri; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi
Metaheuristics are advanced problem-solving techniques that develop efficient algorithms to address complex challenges, while neural networks are algorithms inspired by the structure and function of the human brain. Combining these approaches enables the resolution of complex optimization problems that traditional methods struggle to solve. This study presents a novel approach integrating the ABC algorithm with ANNs for weight optimization. The method is further enhanced by vectorization and parallelization techniques on both CPU and GPU to improve computational efficiency. Additionally, this study introduces a cost-sensitive fitness function tailored for multi-class classification to optimize results by considering relationships between target class levels. It validates these advancements in two critical applications: network intrusion detection and earthquake damage estimation. Notably, this study makes a significant contribution to earthquake damage assessment by leveraging machine learning algorithms and metaheuristics to enhance predictive models and decision-making in disaster response. By addressing the dynamic nature of earthquake damage, this research fills a critical gap in existing models and broadens the understanding of how machine learning and metaheuristics can improve disaster response strategies. In both domains, the ABC-ANN implementation yields promising results, particularly in earthquake damage estimation, where the cost-sensitive approach demonstrates satisfactory outcomes in macro-F1 and accuracy. The best results for macro-F1, weighted-F1, and overall accuracy provides best results with the UNSW-NB15 and earthquake datasets, showing values of 64%, 72%, 68%, and 60%, 80%, and 79%, respectively. Comparative performance evaluations reveal that the proposed parallel ABC-ANN model, incorporating the novel cost-sensitive fitness function and enhanced by vectorization and parallelization techniques, significantly reduces training time and outperforms state-of-the-art methods in terms of macro-F1 and accuracy in both network intrusion detection and earthquake damage estimation.
Achieving High Optical Absorption in Thin Film Photovoltaic Devices via Nanopillar Arrays and Metal Nanoparticles
(Wiley-VCH Verlag GmbH, 2025) Tut, Turgut; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik Fakültesi
In this study, crystalline silicon nanopillars has been employed as a hexagonal array photonic crystal structure with low optical reflection, augmented by silver metallic nanoparticles ranging from 10 to 50 nm in diameter in order to achieve high absorption in thin silicon films, a critical factor for applications in photovoltaic devices. Initially, it has been begun with an optimized structure in terms of pillar filling ratio, pillar height, and diameter, as established in the previous study. This allows to obtain a hexagonal array of nanopillars with a surface characterized by low optical reflection. To enhance the optical absorption within the bulk of the silicon thin film, the optical scattering properties of silver (Ag) metallic nanoparticles (MNPs) has been harnessed. The integration of silver metal nanoparticles into the photonic crystal hexagonal nanopillar array involved introducing a cavity into the silicon pillar. Placing Ag MNPs near the bottom of the cavity prevented the degradation of the photonic crystal's ability to maintain low reflection within the desired optical spectrum (between 400-1100 nm). Comparison between the nanopillar hexagonal array structure with Ag MNPs and the bare silicon substrate revealed a remarkable 104.76 percent increase in optical absorption for a 1-micron thick silicon bulk material. This triple hybrid structure exhibits tremendous potential in photovoltaic device applications, including solar cells and photodetectors, with the capacity to significantly enhance conversion efficiency.
Citation - Scopus: 49
Activation of Methane by Os+: Guided-Ion and Theoretical Studies
(2013) Armentrout, Peter B.; Parke, Laura G.; Hinton, Christopher S.; Citir, Murat; 01. Abdullah Gül University
Activation of methane by the third-row transition-metal cation Os + is studied experimentally by examining the kinetic energy dependence of reactions of Os+ with CH4 and CD4 using guided-ion-beam tandem mass spectrometry. A flow tube ion source produces Os+ in its electronic ground state and primarily in the ground spin-orbit level. Dehydrogenation to form [Os,C,2 H]++H2 is exothermic, efficient, and the only process observed at low energies for reaction of Os+ with methane, whereas OsH+ dominates the product spectrum at higher energies. The kinetic energy dependences of the cross sections for several endothermic reactions are analyzed to give 0K bond dissociation energies (in eV) of D0(Os+-C)=6.20±0. 21, D0(Os+-CH)=6.77±0.15, and D0(Os +-CH3)=3.00±0.17. Because it is formed exothermically, D0(Os+-CH2) must be greater than 4.71eV, and a speculative interpretation suggests the exothermicity exceeds 0.6eV. Quantum chemical calculations at the B3LYP/def2-TZVPP level show reasonable agreement with the experimental bond energies and with previous theoretical values available. Theory also provides the electronic structures of the product species as well as intermediates and transition states along the reactive potential energy surfaces. Notably, the structure of the dehydrogenation product is predicted to be HOsCH+, rather than OsCH2+, in contrast to previous work. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. © 2013 Elsevier B.V., All rights reserved.
Citation - WoS: 5
Citation - Scopus: 4
Active Subnetwork Ga: A Two Stage Genetic Algorithm Approach to Active Subnetwork Search
(Bentham Science Publ Ltd, 2017) Ozisik, Ozan; Bakir-Gungor, Burcu; Diri, Banu; Sezerman, Osman Ugur; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi
Background: A group of interconnected genes in a protein-protein interaction network that contains most of the disease associated genes is called an active subnetwork. Active subnetwork search is an NP-hard problem. In the last decade, simulated annealing, greedy search, color coding, genetic algorithm, and mathematical programming based methods are proposed for this problem. Method: In this study, we employed a novel genetic algorithm method for active subnetwork search problem. We used active node list chromosome representation, branch swapping crossover operator, multicombination of branches in crossover, mutation on duplicate individuals, pruning, and two stage genetic algorithm approach. The proposed method is tested on simulated datasets and Wellcome Trust Case Control Consortium rheumatoid arthritis genome-wide association study dataset. Our results are compared with the results of a simple genetic algorithm implementation and the results of the simulated annealing method that is proposed by Ideker et al. in their seminal paper. Results and Conclusion: The comparative study demonstrates that our genetic algorithm approach outperforms the simple genetic algorithm implementation in all datasets and simulated annealing in all but one datasets in terms of obtained scores, although our method is slower. Functional enrichment results show that the presented approach can successfully extract high scoring subnetworks in simulated datasets and identify significant rheumatoid arthritis associated subnetworks in the real dataset. This method can be easily used on the datasets of other complex diseases to detect disease-related active subnetworks. Our implementation is freely available at https://www.ce.yildiz.edu.tr/personal/ozanoz/file/6611/ActSubGA.
Citation - WoS: 1
Citation - Scopus: 1
Addressing the Modern Regimes of Urban Spectacle: Revisiting the Ottoman General Exhibition of 1863 in Istanbul
(Sage Publications inc, 2024) Tozoglu, Ahmet Erdem; 01. Abdullah Gül University
One of the most spectacular events of the Ottoman experience of modernity was the inauguration of the Ottoman General Exposition in Istanbul in 1863. The ancient Hippodrome, which is one of the most prominent venues of the city and the setting of memorable celebrations and festivals for centuries, hosted the event and provided the visitors with the opportunity to become part of the modern regimes of gaze and spectacle. This article posits three observer roles to reveal the multilayered structure of urban spectacle in mid-century Istanbul, namely the sultanic gaze, spectacle of the ordinary citizens, and the mediated experience of the foreigner. To understand the particularities of each position, I utilize several visual and textual documents about the exhibition event. Though just a single case in Ottoman urban history, the exposition enables us to understand how the new manner of modern urban spectacle emerged during a spectacular public event in Istanbul.
Citation - WoS: 12
Citation - Scopus: 13
Advanced Tunability of Optical Properties of CdS/ZnSe Multi-Shell Quantum Dot by the Band Edge Engineering
(Elsevier, 2023) Koc, Fatih; Kavruk, Ahmet Emre; Sahin, Mehmet; 01. Abdullah Gül University; 02.02. Endüstri Mühendisliği; 02. Mühendislik Fakültesi
In this study, the advanced manipulability of wave functions in a type-II multi-shell hetero-nanostructure (MS-HNS) and the tunability of radiative exciton lifetime over a wide range with and/or without changing in transition energies has been demonstrated by the band edge engineering. For this purpose, the electronic and optical properties of exciton (X) and biexciton (XX) in a spherical CdS/ZnSe/ZnTe/CdSe HNS have been explored in detail. In the calculations, effects of all Coulombic interactions between the charges have been taken into account on the wave functions. Moreover, in the case of XX, the exchange-correlation potential between the same charged particles has also been considered. The results have been presented as a function of CdS core radius and ZnSe shell thickness and the probable physical reasons have been discussed in detail.
Citation - Scopus: 3
Aguhyper: a Hyperledger-Based Electronic Health Record Management Framework
(PeerJ Inc., 2024) Dedeturk, Beyhan Adanur; Bakir-Güngör, Burcu; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi
The increasing importance of healthcare records, particularly given the emergence of new diseases, emphasizes the need for secure electronic storage and dissemination. With these records dispersed across diverse healthcare entities, their physical maintenance proves to be excessively time-consuming. The prevalent management of electronic healthcare records (EHRs) presents inherent security vulnerabilities, including susceptibility to attacks and potential breaches orchestrated by malicious actors. To tackle these challenges, this article introduces AguHyper, a secure storage and sharing solution for EHRs built on a permissioned blockchain framework. AguHyper utilizes Hyperledger Fabric and the InterPlanetary Distributed File System (IPFS). Hyperledger Fabric establishes the blockchain network, while IPFS manages the off-chain storage of encrypted data, with hash values securely stored within the blockchain. Focusing on security, privacy, scalability, and data integrity, AguHyper’s decentralized architecture eliminates single points of failure and ensures transparency for all network participants. The study develops a prototype to address gaps identified in prior research, providing insights into blockchain technology applications in healthcare. Detailed analyses of system architecture, AguHyper’s implementation configurations, and performance assessments with diverse datasets are provided. The experimental setup incorporates CouchDB and the Raft consensus mechanism, enabling a thorough comparison of system performance against existing studies in terms of throughput and latency. This contributes significantly to a comprehensive evaluation of the proposed solution and offers a unique perspective on existing literature in the field. © 2024 Elsevier B.V., All rights reserved.
Aguhyper: A Hyperledger-Based Electronic Health Record Management Framework
(PeerJ Inc, 2024) Dedeturk, Beyhan Adanur; Bakir-Gungor, Burcu; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi
The increasing importance of healthcare records, particularly given the emergence of new diseases, emphasizes the need for secure electronic storage and dissemination. With these records dispersed across diverse healthcare entities, their physical maintenance proves to be excessively time-consuming. The prevalent management of electronic healthcare records (EHRs) presents inherent security vulnerabilities, including susceptibility to attacks and potential breaches orchestrated by malicious actors. To tackle these challenges, this article introduces AguHyper, a secure storage and sharing solution for EHRs built on a permissioned blockchain framework. AguHyper utilizes Hyperledger Fabric and the InterPlanetary Distributed File System (IPFS). Hyperledger Fabric establishes the blockchain network, while IPFS manages the off -chain storage of encrypted data, with hash values securely stored within the blockchain. Focusing on security, privacy, scalability, and data integrity, AguHyper ' s decentralized architecture eliminates single points of failure and ensures transparency for all network participants. The study develops a prototype to address gaps identi fi ed in prior research, providing insights into blockchain technology applications in healthcare. Detailed analyses of system architecture, AguHyper ' s implementation con fi gurations, and performance assessments with diverse datasets are provided. The experimental setup incorporates CouchDB and the Raft consensus mechanism, enabling a thorough comparison of system performance against existing studies in terms of throughput and latency. This contributes signi fi cantly to a comprehensive evaluation of the proposed solution and offers a unique perspective on existing literature in the fi eld.
Citation - WoS: 2
Citation - Scopus: 1
Ambipolar Small Molecular Semiconductor-Based Heterojunction Diode
(Elsevier Science SA, 2016) Ocaya, R. O.; Ozdemir, Mehmet; Ozdemir, Resul; Al-Ghamdi, Ahmed; Usta, Hakan; Farooq, W. A.; Yakuphanoglu, F.; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik Fakültesi
A heterojunction diode based on an ambipolar organic semiconductor 2,8-bis(5-(2-octyldodecyl)thien-2-yl)indeno[1,2-b]fluorene-6,12-dione (20D-TIFDKT) was fabricated on p-Si using a drop-casting technique. The current-voltage and capacitance-voltage characteristics of Al/20D-TIFDKT/p-Si/Al devices with aluminized contacts were investigated under dark and 100 mW/cm(2) illumination intensity. The result is a novel interface-state controlled diode device that is shown to be rectifying. In the forward, bias it has a current that depends on the illumination intensity at constant bias, showing potential application in low-power solar cell application. In the reverse bias, it has a response that depends on the illumination intensity regardless of the applied reverse bias. This suggests a potential use as a sensor in photoconductive applications. Between 0 and 0.7 V forward bias, the ideality factor, series resistance and barrier height average at 2.35, 67.6 k Omega and 0.842 eV, respectively, regardless of illumination. (C) 2016 Elsevier B.V. All rights reserved.
Citation - Scopus: 3
Amelioration Potential of Synthetic Oxime Chemical Cores Against Multiple Sclerosis and Alzheimer's Diseases: Evaluation in Aspects of in Silico and in Vitro Experiments
(Elsevier B.V., 2024) Yilmaz, Anil; Koca, Murat; Ercan, Selami; Acar, Özden Ozgun; Boǧa, Mehmet; Sen, Alaattin; Kurt, Adnan; 01. Abdullah Gül University
Alzheimer disease (AD) and multiple sclerosis (MS) are inflammatory neurological disorders. The main symptom of AD is dementia, and the main symptoms of MS are vertigo, sexual dysfunction, cognitive problems, and fatigue. Today, millions of people are affected by AD and MS, and the number is growing day by day. However, there are not any accurate remedies for both disorders. For this reason, discovering novel drug molecules against neurological disorders such as AD and MS is essential and precious. Oximes and benzofurans exhibit many pharmacological effects including anti-inflammatory and neurological activities. Thus, several novel compounds bearing oxime and benzofuran chemical cores were designed and synthesized, and their in vitro anticholinesterase activities were investigated in our previous study. A number of the synthesized molecules showed excellent anticholinesterase activity against both AChE and BChE enzymes. The mentioned study constituted a background for this study. In this study, we picked different chemical skeletons among all the synthesized molecules to conduct further in silico and in vitro experiments. In order to support our in vitro anticholinesterase findings, we also examined in silico anti-Alzheimer activity of the selected molecules. In addition, in silico and in vitro activities against MS disease of the synthesized molecules were investigated. Molecule 4 extraordinarily showed outstanding activity against AD disease both in silico and in vitro, as well as in silico activity against MS disease. This feature makes molecule 4 a possible drug lead molecule which is very limited in the market. On the other hand, molecule 1, a less substituted oxime skeleton, demonstrated the strongest in vitro activity against MS disease through in vitro anti-inflammatory effect. As an observation, molecule 4 was determined to be the most promising molecule to focus on in the further steps. © 2024 Elsevier B.V., All rights reserved.
Amorphous Boron Carbide From Ab Initio Simulations
(Elsevier, 2023) Yildiz, Tevhide Ayca; Durandurdu, Murat; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik Fakültesi
Citation - WoS: 5
Citation - Scopus: 5
Amorphous Boron Carbide From Ab Initio Simulations
(Elsevier, 2020) Yildiz, Tevhide Ayca; Durandurdu, Murat; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik Fakültesi
An amorphous boron carbide (a-B4C) model is generated by means of ab-initio molecular dynamics calculations within a generalized gradient approximation and its structural, mechanical and electrical features are discussed in details. The mean coordination number of B and C atoms is estimated to be 5.29 and 4.17, respectively. The pentagonal pyramid-like motifs for B atoms, having sixfold coordination, are the main building units in a-B4C and some of which involve with the development of B-12 icosahedra. On the other hand, the fourfold-coordinated units are the leading configurations for C atoms. Surprisingly the formation of C-C bonds is found to be less favorable in the noncrystalline network, compared to the crystal. a-B4C is a semiconducting material having an energy band gap considerably less than that of the crystal. A noticeably decrease in the mechanical properties of B4C is observed by amorphization. Nonetheless a-B4C is categorized as a hard material due to its high Vickers hardness of about 24 GPa.
Amorphous GaN: Polyamorphism and Crystallization at High Pressure
(Elsevier, 2024) Durandurdu, Murat; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik Fakültesi
Employing constant pressure ab initio simulations, we have shed light on the previously unknown high-pressure behavior of amorphous gallium nitride. Our findings reveal a two-step transformation sequence under pressure. The initial transition involves a polyamorphic transformation from a low-density amorphous (LDA) phase to a high-density amorphous (HDA) phase with an average coordination number of 5.4. Upon pressure release, the HDA state partially reverts to a denser amorphous network with a higher coordination number (4.34) compared to the original LDA phase. Further pressurization triggers the crystallization of the HDA state into a rocksalt structure. Remarkably, the electronic structure of the amorphous forms of GaN exhibits insignificant sensitivity to changes in coordination number, maintaining a band gap of approximately 1.7-2.0 eV across all phases.
Amorphous Silicon Nanoparticles and Silicon Nanoglasses From Ab Initio Simulations
(Springer, 2024) Bolat, Suleyman; Durandurdu, Murat; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik Fakültesi
The structural and electrical characteristics of spherical amorphous silicon nanoparticles (Si-NPs) with radii ranging from 9 to 15 & Aring;, and silicon nanoglasses (Si-NGs) formed by compressing identical-sized Si-NPs, are being investigated for the first-time using ab initio simulations. Analysis reveals predominantly fourfold coordination within Si-NPs, accompanied by noticeable coordination defects. The prevalence of fourfold coordination increases with increasing Si-NP size. Si-NGs, while exhibiting similar dominant fourfold coordination, possess a small fraction of coordination defects (5-8%) primarily concentrated at the interfaces of compressed Si-NPs. Si-NGs are found to have a more open structure compared to amorphous Si. This structural variation, along with observed distortions within Si-NGs, is hypothesized to contribute to a significant narrowing of their band gaps relative to amorphous Si.
Citation - WoS: 1
Citation - Scopus: 1
Amorphous Zircon at High Pressure
(Pergamon-Elsevier Science Ltd, 2021) Bolat, Suleyman; Durandurdu, Murat; 01. Abdullah Gül University; 02.07. Malzeme Bilimi ve Nanoteknoloji Mühendisliği; 02. Mühendislik Fakültesi
The high-pressure behavior of a very low-density amorphous zircon model having Zr (Si) coordination of 5.6 (4.02) is explored by ab initio simulations. Two consecutive pressure-induced phase modifications are proposed for this material. The first transition is from a very low-density amorphous state to a dense amorphous state having Zr (Si) coordination of 7.3 (4.5). The second one is from the dense phase to a high-density amorphous structure with Zr and Si coordination numbers of about 8 and 5.5, correspondingly. Both phase changes proceed progressively. The first phase transformation is irreversible whist the second one is reversible. The Voronoi polyhedron analysis reveals the presence of polyhedron of the zircon crystal (<0,4,4,0>), the zirconia baddaliyette phase (<1,3,3,0>) and the zirconia cotunnite state (<0,3,6,0>) around Zr atoms in the amorphous states formed on both compression and decompression, meaning that the amorphous configurations consist of a mixed state of them.
Citation - WoS: 8
Citation - Scopus: 12
AMP-GSM: Prediction of Antimicrobial Peptides via a Grouping-Scoring Approach
(MDPI, 2023) Soylemez, Ummu Gulsum; Yousef, Malik; Bakir-Gungor, Burcu; 01. Abdullah Gül University; 02. 04. Bilgisayar Mühendisliği; 02. Mühendislik Fakültesi
Due to the increasing resistance of bacteria to antibiotics, scientists began seeking new solutions against this problem. One of the most promising solutions in this field are antimicrobial peptides (AMP). To identify antimicrobial peptides, and to aid the design and production of novel antimicrobial peptides, there is a growing interest in the development of computational prediction approaches, in parallel with the studies performing wet-lab experiments. The computational approaches aim to understand what controls antimicrobial activity from the perspective of machine learning, and to uncover the biological properties that define antimicrobial activity. Throughout this study, we aim to develop a novel prediction approach that can identify peptides with high antimicrobial activity against selected target bacteria. Along this line, we propose a novel method called AMP-GSM (antimicrobial peptide-grouping-scoring-modeling). AMP-GSM includes three main components: grouping, scoring, and modeling. The grouping component creates sub-datasets via placing the physicochemical, linguistic, sequence, and structure-based features into different groups. The scoring component gives a score for each group according to their ability to distinguish whether it is an antimicrobial peptide or not. As the final part of our method, the model built using the top-ranked groups is evaluated (modeling component). The method was tested for three AMP prediction datasets, and the prediction performance of AMP-GSM was comparatively evaluated with several feature selection methods and several classifiers. When we used 10 features (which are members of the physicochemical group), we obtained the highest area under curve (AUC) value for both the Gram-negative (99%) and Gram-positive (98%) datasets. AMP-GSM investigates the most significant feature groups that improve AMP prediction. A number of physico-chemical features from the AMP-GSM's final selection demonstrate how important these variables are in terms of defining peptide characteristics and how they should be taken into account when creating models to predict peptide activity.

Browse

Browsing Araştırma Çıktıları | TR-Dizin | WoS | Scopus | PubMed by WoS Q "Q2"