Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
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Conference Object Citation - WoS: 1Citation - Scopus: 1A Mixed-Integer Dynamic and Stochastic Algae Process Optimization(Elsevier, 2024) Kivanc, Sercan; Deliismail, Özgün; Şıldır, HasanWith increased energy demand as it gets scarcer, a great deal of research is being carried out into alternatives to non - renewable energy resources. One of the promising studies is the biofuel production from micro algae. Microalgae are photosynthetic organisms and capture carbon dioxide, reducing emissions and providing valuable products (fuel, fertilizer, etc.). Thus, efficiency in the design and optimization of process related units are important. In this study, the optimal experimental conditions for Nannochloropsis Oculata were calculated under the constraints of the model equations and other process related constraints through simultaneous optimization approach. The economic evaluation of the process is also handled by introducing the uncertainty in the economic measures sampled from normal distribution to maximize the average profit. Unlike traditional approaches, the MINLP formulation, which is solved stochastically, dynamically, and simultaneously, provides more robust and reliable results, flexibility, improved decision making, reduced risks to be taken and a better understanding of risk factors. Copyright (C) 2024 The Authors. This is an open access article under the CC BY-NC-ND license (https://creativecommons.org/licenses/by-nc-nd/4.0/)Article Citation - WoS: 13Citation - Scopus: 11Bottom-Up Synthesis of Platinum Dual-Atom Catalysts on Cerium Oxide(American Chemical Society, 2024) Mekkering, Martijn J.; Laan, Petrus C. M.; Troglia, Alessandro; Bliem, Roland; Kızılkaya, Ali Can; Rothenberg, Gadi; Yan, NingWe present here the synthesis and performance of dual-atom catalysts (DACs), analogous to well-known single-atom catalysts (SACs). DACs feature sites containing pairs of metal atoms and can outperform SACs due to their additional binding possibilities. Yet quantifying the improved catalytic activity in terms of proximity effects remains difficult, as it requires both high-resolution kinetic data and an understanding of the reaction pathways. Here, we use an automated bubble counter setup for comparing the catalytic performance of ceria-supported platinum SACs and DACs in ammonia borane hydrolysis. The catalysts were synthesized by wet impregnation and characterized using SEM, HAADF-STEM, XRD, XPS, and CO-DRIFTS. High-precision kinetic studies of ammonia borane hydrolysis in the presence of SACs show two temperature-dependent regions, with a transition point at 43 degrees C. Conversely, the DACs show only one regime. We show that this is because DACs preorganize both ammonia borane and water at the dual-atom active site. The additional proximal Pt atom improves the reaction rate 3-fold and enables faster reactions at lower temperatures. We suggest that the DACs enable the activation of the water-O-H bond as well as increase the hydrogen spillover effect due to the adjacent Pt site. Interestingly, using ammonia borane hydrolysis as a benchmark reaction gives further insight into hydrogen spillover mechanisms, above what is known from the CO oxidation studies.Article Citation - WoS: 14Citation - Scopus: 163D Bioprinting of mouse pre-osteoblasts and human MSCs using bioinks consisting of gelatin and decellularized bone particles(Iop Publishing Ltd, 2024) Kara, Aylin; Distler, Thomas; Akkineni, Ashwini Rahul; Tihminlioglu, Funda; Gelinsky, Michael; Boccaccini, Aldo R.One of the key challenges in biofabrication applications is to obtain bioinks that provide a balance between printability, shape fidelity, cell viability, and tissue maturation. Decellularization methods allow the extraction of natural extracellular matrix, preserving tissue-specific matrix proteins. However, the critical challenge in bone decellularization is to preserve both organic (collagen, proteoglycans) and inorganic components (hydroxyapatite) to maintain the natural composition and functionality of bone. Besides, there is a need to investigate the effects of decellularized bone (DB) particles as a tissue-based additive in bioink formulation to develop functional bioinks. Here we evaluated the effect of incorporating DB particles of different sizes (<= 45 and <= 100 mu m) and concentrations (1%, 5%, 10% (wt %)) into bioink formulations containing gelatin (GEL) and pre-osteoblasts (MC3T3-E1) or human mesenchymal stem cells (hTERT-MSCs). In addition, we propose a minimalistic bioink formulation using GEL, DB particles and cells with an easy preparation process resulting in a high cell viability. The printability properties of the inks were evaluated. Additionally, rheological properties were determined with shear thinning and thixotropy tests. The bioprinted constructs were cultured for 28 days. The viability, proliferation, and osteogenic differentiation capacity of cells were evaluated using biochemical assays and fluorescence microscopy. The incorporation of DB particles enhanced cell proliferation and osteogenic differentiation capacity which might be due to the natural collagen and hydroxyapatite content of DB particles. Alkaline phosphatase activity is increased significantly by using DB particles, notably, without an osteogenic induction of the cells. Moreover, fluorescence images display pronounced cell-material interaction and cell attachment inside the constructs. With these promising results, the present minimalistic bioink formulation is envisioned as a potential candidate for bone tissue engineering as a clinically translatable material with straightforward preparation and high cell activity.Article Citation - WoS: 4Citation - Scopus: 3Atomic-Scale Insights Into Carbon Dioxide Hydrogenation Over Bimetallic Iron-Cobalt Catalysts: a Density Functional Theory Study(MDPI, 2023) Tuncer, Dilan; Kızılkaya, Ali CanThe conversion of carbon dioxide to fuels and chemicals is a promising long-term approach for mitigating CO2 emissions. Despite extensive experimental efforts, a fundamental understanding of the bimetallic catalytic structures that selectively produce the desired products is still lacking. Here, we report on a computational surface science approach into the effect of the Fe doping of Co(111) surfaces in relation to CO2 hydrogenation to C1 products. Our results indicate that Fe doping increases the binding strength of surface species but slightly decreases the overall catalytic activity due to an increase in the rate-limiting step of CO dissociation. FeCo(111) surfaces hinder hydrogenation reactions due to lower H coverages and higher activation energies. These effects are linked to the Lewis basic character of the Fe atoms in FeCo(111), leading to an increased charge on the adsorbates. The main effect of Fe doping is identified as the inhibition of oxygen removal from cobalt surfaces, which can be expected to lead to the formation of oxidic phases on bimetallic FeCo catalysts. Overall, our study provides comprehensive mechanistic insights related to the effect of Fe doping on the catalytic behavior and structural evolution of FeCo bimetallic catalysts, which can contribute to the rational design of bimetallic catalysts.Review Citation - WoS: 30Citation - Scopus: 33Molecular Separation by Using Active and Passive Microfluidic Chip Designs: a Comprehensive Review(Wiley, 2023) Ebrahimi, Aliakbar; Didarian, Reza; Shih, Chih-Hsin; Nasseri, Behzad; Ethan Li, Yi-Chen; Shih, Steven; İçöz, Kutay; Tarım, Ergün Alperay; Akpek, Ali; Çeçen, Berivan; Bal Öztürk, Ayça; Güleç, Kadri; Tarım, Burcu Sırma; Tekin, Hüseyin CumhurSeparation and identification of molecules and biomolecules such as nucleic acids, proteins, and polysaccharides from complex fluids are known to be important due to unmet needs in various applications. Generally, many different separation techniques, including chromatography, electrophoresis, and magnetophoresis, have been developed to identify the target molecules precisely. However, these techniques are expensive and time consuming. “Lab-on-a-chip” systems with low cost per device, quick analysis capabilities, and minimal sample consumption seem to be ideal candidates for separating particles, cells, blood samples, and molecules. From this perspective, different microfluidic-based techniques have been extensively developed in the past two decades to separate samples with different origins. In this review, “lab-on-a-chip” methods by passive, active, and hybrid approaches for the separation of biomolecules developed in the past decade are comprehensively discussed. Due to the wide variety in the field, it will be impossible to cover every facet of the subject. Therefore, this review paper covers passive and active methods generally used for biomolecule separation. Then, an investigation of the combined sophisticated methods is highlighted. The spotlight also will be shined on the elegance of separation successes in recent years, and the remainder of the article explores how these permit the development of novel techniques. © 2023 The Authors. Advanced Materials Interfaces published by Wiley-VCH GmbH.Article Citation - Scopus: 2A Comparative Assessment for Efficient Oleuropein Extraction From Olive Leaf (olea Europaea L. Folium)(Murat Yakar, 2023) Recepoğlu, Yaşar Kemal; Gümüşbulut, Gülin; Yüksel Özşen, AslıSince oleuropein has long been known in the health sector and is abundant directly in our country as the fourth largest olive producer, oleuropein, the predominant phenolic ingredient in olive leaves, was recovered in this study using Soxhlet extraction. The effects of different solvent types (acetonitrile, ethanol, methanol, and water), extraction period (4 cycles, 4 h, and 8 h), particle size (250-500 µm and 900-2000 µm), and pretreatment of olive leaves on the yield of oleuropein were examined to determine the maximum yield. A greater oleuropein yield was obtained when the particle size of olive leaves utilized for extraction was lowered. Furthermore, aqueous solvents revealed a higher yield of oleuropein than pure solvents and prolonging the extraction duration resulted in a significant increase in the amount of oleuropein extracted. On the other hand, pretreatment of olive leaves resulted in a reduction in oleuropein output. As a result, with 36% extraction efficiency in terms of olive leaf conversion, the highest oleuropein extraction yield was obtained as 13.35 mg g-1 dry leaf for 8 h of extraction time using olive leaves with a particle size of 250-500 µm and an 80% methanol solution as solvent. © Author(s) 2023.Article Citation - WoS: 2Citation - Scopus: 2Further Developments of the Extended Quadrature Method of Moments To Solve Population Balance Equations(Cell Press, 2023) Turan, Meltem; Dutta, AbhishekDeveloping numerical methods to solve polydispersed flows using a Population Balance Equation (PBE) is an active research topic with wide engineering applications. The Extended Quadrature Method of Moments (EQMOM) approximates the number density as a positive mixture of Kernel Density Functions (KDFs) that allows physical source terms in the PBEs to compute continuous or point-wise form according to the moments. The moment-inversion procedure used in EQMOM has limitations such as the inability to calculate certain roots even if it is defined, absence of consistent result when multiple roots exist or when the roots are nearly equal. To address these limitations, the study proposes a modification of the moment-inversion procedure to solve the PBE based on the proposed Halley-Ridder (H-R) method. Although there is no significant improvement in the extent of variability relative to the mean of the tested shape parameter cr values, an increase in the number of floating point operations (FLOPS) is observed which the proposed algorithm responds in limitations mentioned above. The total number of FLOPS for all the kernels used for the approximation increased by around 30%. This is an improvement towards the development of a more reliable and robust moment-inversion procedure.Review Citation - WoS: 39Citation - Scopus: 37Engineered Liposomes in Interventional Theranostics of Solid Tumors(American Chemical Society, 2023) Kommineni, Nagavendra; Chaudhari, Ruchita; Conde, Joao; Cecen, Berivan; Chandra, Pranjal; Prasad, Rajendra; Tamburacı, SedefEngineered liposomal nanoparticles have unique characteristicsas cargo carriers in cancer care and therapeutics. Liposomal theranosticshave shown significant progress in preclinical and clinical cancermodels in the past few years. Liposomal hybrid systems have not onlybeen approved by the FDA but have also reached the market level. Nanosizedliposomes are clinically proven systems for delivering multiple therapeuticas well as imaging agents to the target sites in (i) cancer theranosticsof solid tumors, (ii) image-guided therapeutics, and (iii) combinationtherapeutic applications. The choice of diagnostics and therapeuticscan intervene in the theranostics property of the engineered system.However, integrating imaging and therapeutics probes within lipidself-assembly liposome may compromise their overalltheranostics performance. On the other hand, liposomal systems sufferfrom their fragile nature, site-selective tumor targeting, specificbiodistribution and premature leakage of loaded cargo molecules beforereaching the target site. Various engineering approaches, viz., grafting,conjugation, encapsulations, etc., have been investigated to overcomethe aforementioned issues. It has been studied that surface-engineeredliposomes demonstrate better tumor selectivity and improved therapeuticactivity and retention in cells/or solid tumors. It should be notedthat several other parameters like reproducibility, stability, smoothcirculation, toxicity of vital organs, patient compliance, etc. mustbe addressed before using liposomal theranostics agents in solid tumorsor clinical models. Herein, we have reviewed the importance and challengesof liposomal medicines in targeted cancer theranostics with theirpreclinical and clinical progress and a translational overview.Article Citation - WoS: 17Citation - Scopus: 16Development of Cissus Quadrangularis-Loaded Poss-Reinforced Chitosan-Based Bilayer Sponges for Wound Healing Applications: Drug Release and in Vitro Bioactivity(American Chemical Society, 2023) Değer Aker, Sibel; Tamburacı, Sedef; Tıhmınlıoğlu, FundaNowadays, antibiotic-loaded biomaterials have been widelyusedin wound healing applications. However, the use of natural extractshas come into prominence as an alternative to these antimicrobialagents in the recent period. Among natural sources, Cissus quadrangularis (CQ) herbal extract is usedfor treatment of bone and skin diseases in ayurvedic medicine dueto its antibacterial and anti-inflammatory effects. In this study,chitosan-based bilayer wound dressings were fabricated with electrospinningand freeze-drying techniques. CQ extract-loaded chitosan nanofiberswere coated on chitosan/POSS nanocomposite sponges using an electrospinningmethod. The bilayer sponge is designed to treat exudate wounds whilemimicking the layered structure of skin tissue. Bilayer wound dressingswere investigated with regard to the morphology and physical and mechanicalproperties. In addition, CQ release from bilayer wound dressings and in vitro bioactivity studies were performed to determinethe effect of POSS nanoparticles and CQ extract loading on NIH/3T3and HS2 cells. The morphology of nanofibers was investigated withSEM analysis. Physical characteristics of bilayer wound dressingswere determined with FT-IR analysis, swelling study, open porositydetermination, and mechanical test. The antimicrobial activity ofCQ extract released from bilayer sponges was investigated with a discdiffusion method. Bilayer wound dressings' in vitro bioactivity was examined using cytotoxicity determination, woundhealing assay, proliferation, and the secretion of biomarkers forskin tissue regeneration. The nanofiber layer diameter was obtainedin the range of 77.9-97.4 nm. The water vapor permeabilityof the bilayer dressing was obtained as 4021 to 4609 g/m(2)day, as it is in the ideal range for wound repair. The release ofthe CQ extract over 4 days reached 78-80% cumulative release.The release media were found to be antibacterial against Gram-negativeand Gram-positive bacteria. In vitro studies showedthat both CQ extract and POSS incorporation induced cell proliferationas well as wound healing activity and collagen deposition. As a result,CQ-loaded bilayer CHI-POSS nanocomposites were found as a potentialcandidate for wound healing applications.Article Citation - WoS: 15Citation - Scopus: 19Immobilization of Esterase From Bacillus Subtilis on Halloysite Nanotubes and Applications on Dibutyl Phthalate Degradation(Elsevier, 2023) Rosales, Emilio; Pazos, Marta; Sanroman, Maria Angeles; Balcı, Esin; Sofuoğlu, AysunDibutyl phthalate (DBP) is one of the listed phthalic acid esters (PAEs) known as the priority toxicants which exhibit carcinogenic and teratogenic properties and is responsible for endocrine disruption. Therefore, its removal has become a matter to tackle with. In this work, the feasibility of DBP degradation by esterase and lipase enzymes obtained from various microorganisms and the immobilization of the most effective in a clayey material were investigated. Esterase from Bacillus subtilis exhibited the highest degradation efficiency reaching a complete degradation. Its immobilization onto halloysite nanotubes (HNTs) by adsorption method was studied by response surface methodology using a central composite design face-centered. The four selected factors that affect the HNT-enzyme composite generation were: pH, adsorption time, enzyme/HNT (E/H) ratio, and adsorption temperature, and the optimal conditions were determined (pH 7, time 360 min, E/H ratio 0.2, temperature 30oC). Consequently, the activity did not significantly decrease by immobilization, and the adsorption efficiency and relative activity were determined to be 73.15% and 82.7%, respectively. Besides, the immobilization enhanced thermal and storage stability. As for enzyme reusability, after 7 continuous cycles, the composite maintained almost 75% of its initial activity. Both the free enzyme (1 mg/mL) and the composite degraded 100 mg/L DBP with 100% efficiency and several byproducts were detected. Moreover, the composite could be reused for 7 cycles keeping a remarkable catalytic activity. Overall, this study indicated that the HNT-enzyme composite may be used as an effective candidate for remediation of the environmental media contaminated with DBP and other PAEs.(c) 2023 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).