WoS İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394

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Citation - WoS: 1
Citation - Scopus: 1
3-State Protein Secondary Structure Prediction Based on Scope Classes
(Inst Tecnologia Parana, 2021) Atasever, Sema; Azginoglu, Nuh; Erbay, Hasan; Aydin, Zafer
Improving the accuracy of protein secondary structure prediction has been an important task in bioinformatics since it is not only the starting point in obtaining tertiary structure in hierarchical modeling but also enhances sequence analysis and sequence-structure threading to help determine structure and function. Herein we present a model based on DSPRED classifier, a hybrid method composed of dynamic Bayesian networks and a support vector machine to predict 3-state secondary structure information of proteins. We used the SCOPe (Structural Classification of Proteins-extended) database to train and test the model. The results show that DSPRED reached a Q(3) accuracy rate of 82.36% when trained and tested using proteins from all SCOPe classes. We compared our method with the popular PSI PRED on the SCOPe test datasets and found that our method outperformed PSI PRED.
A Comprehensive Review on the Extraction and Recovery of Lithium from Primary and Secondary Sources: Advances Toward Battery-Grade Materials
(Wiley, 2025) Top, Soner; Kursunoglu, Sait; Altiner, Mahmut
Lithium-ion battery (LIB) technologies have become indispensable to modern energy systems, driving global demand for high-purity lithium compounds. This review focuses on lithium recovery and purification strategies for battery-grade lithium carbonate (Li2CO3) and lithium hydroxide (LiOH), addressing both primary sources (brines and minerals) and secondary sources (waste materials). Industrially established processes, such as evaporation-based brine treatment and conventional metallurgical methods, are discussed alongside emerging techniques, including membrane separation, solvent extraction, and CO2-assisted precipitation. Particular attention is given to lithium precipitation mechanisms, the behaviour of co-existing ions during extraction, and the specific quality requirements for cathode material synthesis. By evaluating process scalability, environmental impact, and product purity, this review provides a comprehensive understanding of current practices and future directions. Additionally, it highlights the growing importance of lithium in the context of accelerating electric vehicle (EV) adoption, underscoring the bright and expanding future of the lithium industry.
A Potential Hemostatic Chitosan/Gelatin Cryogel Impregnated with Verbascum Thapsus Leaf Extract for Noncompressible Hemorrhage Management
(IOP Publishing Ltd, 2025) Uzuner, Hacernur; Yuruk, Adile; Isoglu, Ismail Alper
In this study, we prepared a series of chitosan/gelatin (CS/GEL) cryogels containing Verbascum thapsus (V. thapsus) leaf extract and identified a lead formulation for noncompressible hemorrhage (NCH). Cryogels with average pore diameters ranging from 225 to 478 mu m were fabricated through cryogelation at various CS/GEL ratios. C15 was chosen as the base scaffold due to its homogeneous pore distribution, with a pore size coefficient of variation (CV) of approximately 0.22. Extract loading was 1%, 5%, 10%, and 20% w/v. Functional porosity was reported by the relative accessible void index (RAVI). In PBS, the values relative to neat C15 were 1.00, 0.27, 0.20, 0.13, and 0.09 for concentrations of 0%, 1%, 5%, 10%, and 20% w/v, respectively. In citrated blood, the series was 1.00, 0.29, 0.12, 0.14, and 0.09. After loading, equilibrium swelling decreased and the compressive modulus increased, consistent with partial pore filling in a fixed network. The cryogels maintained an interconnected macroporous network and showed swelling from 300% to 3600% in blood and PBS. Antibacterial activity reached 89% inhibition, and cell viability remained above 80%. Hemolysis was low and within acceptance limits. Clotting improved in whole blood as the blood clotting index decreased from 11.9 to 6.5, and the clotting time was approximately 6 min. The 5% w/v group provided the optimal balance of clotting, antibacterial effects, and biocompatibility. This study presents a novel hemostatic CS/GEL cryogel containing V. thapsus leaf extract that holds strong potential for future applications in NCH management.
Citation - WoS: 3
Citation - Scopus: 3
Ab Initio Simulation of Amorphous BC3
(Elsevier, 2020) Durandurdu, Murat
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: 3
Citation - Scopus: 2
Ab Initio Study of Boron-Rich Amorphous Boron Carbides
(Wiley, 2023) Yildiz, Tevhide Ayca; Durandurdu, Murat
Amorphous boron carbide compositions having high B contents (BxC1-x, 0.50 <= x <= 0.95) are systematically created by way of ab initio molecular dynamics calculations, and their structural, electrical, and mechanical characteristics are inclusively investigated. The coordination number of both B and C atoms increases progressively with increasing B/C ratio and more close-packed materials having pentagonal pyramid motifs form. An amorphous diamond-like local arrangement is found to be dominant up to 65% B content, and beyond this content, a mixed state of amorphous diamond- and B-like structures is perceived in the models because sp(3) hybridization around C atoms is still leading one for all compositions. The pentagonal pyramid motifs around C atoms are anticipated to appear beyond 65% content. The intericosahedral linear C-B-C chains do not form in any model. All amorphous boron carbides are semiconducting materials. The mechanical properties gradually increase with increasing B concentration, and some amorphous compositions are proposed to be hard materials on the basis of their Vickers hardness estimation.
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
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.
Adult Zebrafish Brain as a Demyelination Model and Role of WNF Signaling in Remyelination
(Wiley, 2024) Bora, U.; Demirbasoglu, E. S.; Turhanlar-Sahin, E.; Guner, H.; Ozhan, G.
Citation - WoS: 35
Citation - Scopus: 39
Advances in Micelle-Based Drug Delivery: Cross-Linked Systems
(Bentham Science Publ Ltd, 2017) Isoglu, Ismail Alper; Ozsoy, Yildiz; Isoglu, Sevil Dincer
There are several barriers that drug molecules encounter in body beginning from kidney filtration and reticulo-endothelial system (RES) clearance to cellular trafficking. Multifunctional nanocarriers have a great potential for the delivery of drugs by enhancing therapeutic activity of existing methodologies. A variety of nanocarriers are constructed by different material types, which have unique physicochemical properties for drug delivery applications. Micelles formed by amphiphilic polymers are one of the most important drug/nanocarrier formulation products, in which the core part is suitable for encapsulation of hydrophobic agent whereas the outer shell can be utilized for targeting the drug to the disease area. Micelles as self-assembled nanostructures may encounter difficulties in biodistribution of encapsulated drugs because they have a tendency to be dissociated in dilution or high ionic strength. Therefore, therapeutic efficiency is decreased and it requires high amount of drug to be administered to achieve more efficient result. To overcome this problem, covalently stabilized structures produced by cross-linking in core or shell part, which can prevent the micelle dissociation and regulate drug release, have been proposed. These systems can be designed as responsive systems in which cross-links are degradable or hydrolysable under specific conditions such as low pH or reductive environment. These are enhancing characteristics in drug delivery because their cleavage allows the release of bioactive agent encapsulated in the carrier at a certain site or time. This review describes the chemical methodologies for the preparation of cross-linked micelles, and reports an update of latest studies in literature.
Advances in Natural Building and Construction Materials
(MDPI, 2025) Strzalkowski, Pawel; Sousa, Luis; Koken, Ekin
Citation - WoS: 3
Citation - Scopus: 3
Alantolactone Ameliorates Graft Versus Host Disease in Mice
(Elsevier, 2024) Odabas, Gul Pelin; Aslan, Kubra; Suna, Pinar Alisan; Kendirli, Perihan Kader; Erdem, Serife; Cakir, Mustafa; Unal, Ekrem
The anti-inflammatory and immunosuppressive drugs which are used in the treatment of Graft-versus-Host Disease (GVHD) have limited effects in controlling the severity of the disease. In this study, we aimed to investigate the prophylactic effect of Alantolactone (ALT) in a murine model of experimental GVHD. The study included 4 BALB/c groups as hosts: Naive (n = 7), Control GVHD (n = 16), ALT-GVHD (n = 16), and Syngeneic transplantation (n = 10). Busulfan (20 mg/kg/day) for 4 days followed by cyclophosphamide (100 mg/kg/day) were administered for conditioning. Allogeneic transplantation was performed with cells collected from mismatched female C57BL/6, and GVHD development was monitored by histological and flow cytometric assays. Additionally, liver biopsies were taken from GVHD patient volunteers between ages 2-18 (n = 4) and non-GVHD patients between ages 2-50 (n = 5) and cultured ex vivo with ALT, and the supernatants were used for ELISA. ALT significantly ameliorated histopathological scores of the GVHD and improved GVHD clinical scores. CD8+ T cells were shown to be reduced after ALT treatment. More importantly, ALT treatment skewed T cells to a more naive phenotype (CD62L+ CD44-). ALT did not alter Treg cell number or frequency. ALT treatment appears to suppress myeloid cell lineage (CD11c+). Consistent with reduced myeloid lineage, liver and small intestine levels of GM-CSF were reduced in ALT-treated mice. IL-6 gene expression was significantly reduced in the intestinal tissue. Ex vivo ALT-treated liver biopsy samples from GVHD patients showed a trend of decrease in proinflammatory cytokines but there was no statistical significance. Collectively, the data indicated that ALT may have immunomodulatory actions in a preclinical murine GVHD model.
Citation - WoS: 4
Citation - Scopus: 4
All-Polymer Ultrasonic Transducer Design for an Intravascular Ultrasonography Application
(Tubitak Scientific & Technological Research Council Turkey, 2019) Hah, Dooyoung
Intravascular ultrasonography (IVUS), a medical imaging modality, is used to obtain cross-sectional views of blood vessels from inside. In IVUS, transducers are brought to the proximity of the imaging targets so that high-resolution images can be obtained at high frequency without much concern of signal attenuation. To eliminate mechanical rotation rendered in conventional IVUS, it is proposed to manufacture a transducer array on a flexible substrate and wrap it around a cylindrical frame. The transducer of consideration is a capacitive micromachined ultrasonic transducer (CMUT). The whole device needs to be made out of polymers to be able to endure a high degree of bending (radius: 1 mm) Bending of the devices leads to considerable changes in the device characteristics, including resonant frequency and pull-in voltage due to geometrical dimension changes and stress induced. The main purpose of this work is to understand the effect of bending on the device characteristics by means of finite element analysis. Another objective of the work is to understand the relationships between such an effect and the device geometries. It is learned that the bending-induced stress depends strongly on anchor width, membrane thickness, and substrate thickness. It is also learned that resonant frequency and pull-in voltage become lower in most cases because of using a flexible substrate in comparison to those of the device on a rigid substrate. Bending-induced stress increases the spring constant and hence increases resonant frequency and pull-in voltage, although this effect is relatively weaker. For most of the device geometries, pull-in voltage is too high for the polymer material to endure. This is the main drawback of the all-polymer CMUT. In order to meet the design goal of 20 MHz resonant frequency, the membrane radius has to be smaller than 7.7 mu m for a thickness of 3 mu m.
Citation - WoS: 6
Citation - Scopus: 6
Amorphous BC5 From First Principles Calculations
(Elsevier, 2022) Durandurdu, Murat
A boron-substituted amorphous graphite (BC5) network is generated using a first principles molecular dynamics simulation and its atomic structure and electrical and mechanical properties are discussed in details. The network has a layered structure with primarily hexagonal (six membered) rings and its average coordination is about 3.0. The material is a solid solution having a minor amount of B-B homopolar bonds. It is structurally different from the BC5 crystal or monolayers proposed in the literature. The model is a semimetal material based on a generalized gradient approximation with the Hubbard correction (GGA+U) calculation. When its mechanical properties are concerned, they are comparable with those of graphite or amorphous graphite.
Citation - WoS: 3
Citation - Scopus: 3
Amorphous Boron Arsenide
(Elsevier, 2019) Durandurdu, Murat
The short-range order and electrical properties of amorphous boron arsenide (BAs) are evaluated by means of ab initio molecular dynamics simulations. The amorphous model is obtained from the fast solidification of the BAs melt and consists of B-rich and As-rich domains. The average coordination number of B- and As-atoms are found as 4.97 and 3.34, respectively. B-atoms have a tendency to form pentagonal pyramidal-like configurations as commonly seen in boron or boron rich materials. Yet B-12 molecules do not develop in the system but the formation of a B-10 cluster is perceived in the network. On the other hand, As-atoms have a trend to structure chain-like motifs and four-membered rings. Amorphization yield about 31% volume expansion in the amorphous network. All these findings reveal that the model shows strong chemical disorder and its short-range order is considerably different than that of the crystal. Amorphization-induced metallization is proposed for BAs.
Citation - WoS: 6
Citation - Scopus: 5
Amorphous Boron Carbide From Ab Initio Simulations
(Elsevier, 2020) Yildiz, Tevhide Ayca; Durandurdu, Murat
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 Boron Carbide From Ab Initio Simulations
(Elsevier, 2023) Yildiz, Tevhide Ayca; Durandurdu, Murat
Citation - WoS: 2
Citation - Scopus: 2
Amorphous Boron Carbonitride (BC4N) From Ab Initio Simulations
(Elsevier, 2024) Durandurdu, Murat
This study utilizes ab initio molecular dynamics simulations to explore the structure and properties of amorphous boron carbonitride (a-BC4N). A 432-atom model, generated via a conventional melt-and-quench technique, exhibits a graphite-like structure with all elements possessing an average coordination number of about 3.0. C atoms dominate within individual layers, interspersed with distinct BN domains. This atomic arrangement deviates considerably from that proposed for crystalline BC4N structures. Despite this structural variation, the aBC4N model is likely a narrow band gap semiconductor (0.15 eV), similar to its crystalline counterparts. In terms of mechanical properties, a-BC4N demonstrates similarities with various layered materials while exhibiting a notably larger bulk modulus.
Citation - WoS: 2
Citation - Scopus: 2
Amorphous Boron Phosphide: An Ab Initio Investigation
(Elsevier, 2021) Bolat, Suleyman; Durandurdu, Murat
We generate a structural model of amorphous boron phosphide (BP) by quenching the melt via ab initio molecular dynamics calculations and compare it structurally and electrically with the crystal. We find that both phases of BP have a significantly different short-range order. Namely, the amorphous network presents strong chemical disorder and structural defects. P-atoms form only undercoordinated defects while B atoms present both undercoordinated and overcoordinated defects. The mean coordination number of B and P atoms is 4.17 and 3.69, correspondingly. Some of overcoordinated B atoms with chemical disorder yield the formation of pentagonal-pyramid-like motifs and a cage-like B10 cluster in the amorphous network. About 13 % volume expansion is observed by amorphization, probably due to the low-coordinated structural defects. The amorphous configuration is semiconductor as in the crystal but has a smaller energy band gap.
Citation - WoS: 4
Citation - Scopus: 4
Amorphous Boron Suboxide
(Wiley, 2019) Durandurdu, Murat
We study the atomic structure and the electronic and mechanical properties of amorphous boron suboxide (B6O) using an ab initio molecular dynamic technique. The amorphous network is attained from the rapid solidification of the melt and found to consist of boron and oxygen-rich regions. In the boron-rich regions, boron atoms form mostly perfect or imperfect pentagonal pyramid-like configurations that normally yield the construction of ideal and incomplete B-12 molecules in the model. In addition to the B-12 molecules, we also observe the development of a pentagonal bipyramid (B-7) molecule in the noncrystalline structure. In the oxygen-rich regions, on the other hand, boron and oxygen atoms form threefold and twofold coordinated motifs, respectively. The boron-rich and oxygen-rich regions indeed represent structurally the characteristic of amorphous boron and boron trioxide (B2O3). The amorphous phase possesses a small band gap energy with respect to the crystal. On the bases of the localization of the tail states, we suggest that the p-type doping might be more convenient than the n-type doping in amorphous B6O. Bulk modulus and Vickers hardness of the noncrystalline configuration is estimated are be 106 and 13-18 GPa, respectively, which are noticeably less than those of the crystalline structure. Such a noticeable decrease in the mechanical properties is attributed to the presence of open structured B2O3 glassy domains in the amorphous model.
Citation - WoS: 3
Citation - Scopus: 3
Amorphous Carbon Nitride (C3N4)
(Elsevier, 2024) Durandurdu, Murat
This detailed investigation employs an ab initio approach to explore the atomic structure and electronic properties of an amorphous carbon nitride (C3N4) model. The model, designed with an exact 3:4 ratio, is based on an amorphous boron nitride configuration. The study reveals crucial insights into the mean coordination number for C and N atoms within the amorphous structure. With values of 2.95 for C atoms and 2.21 for N atoms, these coordination numbers closely resemble those observed in graphite -like crystals. The local structure of the amorphous network exhibits similarities to the triazine-based graphitic C3N4 crystal and is notably devoid of homopolar bonds. The estimated band gap for the amorphous C3N4 model is 1.2 eV, representing a significant reduction compared to the crystal structure, which exhibits a band gap of about 2.93 eV as determined through GGA+U calculations.
Citation - WoS: 1
Citation - Scopus: 1
Amorphous GaN: Polyamorphism and Crystallization at High Pressure
(Elsevier, 2024) Durandurdu, Murat
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.

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