Research Outputs
Permanent URI for this communityhttps://hdl.handle.net/20.500.14288/2
Browse
690 results
Search Results
Publication Metadata only (Bis)phosphonic acid-functionalized poly(ethyleneimine)- poly(amido amine)s for selective in vitro transfection of osteosarcoma cells(Amer Chemical Soc, 2021) Güven, Melek Naz; Altuncu, Seçkin; Konca, Yeliz Utku; Avcı, Duygu; N/A; Department of Chemistry; Department of Chemistry; Demirci, Gözde; Acar, Havva Funda Yağcı; Master Student; Faculty Member; Graduate School of Sciences and Engineering; College of Sciences; N/A; 178902Osteosarcoma is aggressive bone cancer, whose treatment has not changed significantly for the past few decades. Although gene therapy methods have emerged as potential treatment routes, the need for efficient and nontoxic gene delivery systems targeting osteosarcoma cells remains a challenge. High-molecular-weight poly(ethyleneimine)s (PEIs) are used as universal transfection agents; however, they cause significant cytotoxicity. on the other hand, poly(amido amine)s (PAAs) are biocompatible, biodegradable polymers with promising transfection efficiency, which should be improved further. In this paper, we combined low-molecular-weight branched PEI (1800 Da) and PAA macromers functionalized with various amounts of (bis)phosphonic acid groups and pentanol (via 5-amino-1-pentanol (AP)). The (bis)phosphonic acid groups on these polymers (PAEIs) are intended to facilitate bone targeting. The molecular weights of the PAEI polymers were between 2600 and 8600 g/mol. Their cytotoxicities and green fluorescence protein (GFP) transfection efficiencies were tested on an osteosarcoma cell line (U-2 OS cells), which is challenging to transfect, and healthy muscle cells (C2C12). Both the cytotoxicity and transfection efficiency of PAEIs were affected by the phosphonic acid (via APA, 2-aminoethyl phosphonic acid) or bisphosphonic acid (via ALE, sodium alendronate) content of the polymers. PAEIs are more cytocompatible than both linear and branched 25 kDa PEI. ALE-containing PAEIs provided better transfection than APA-containing ones. The most efficient PAEI polymer, containing a 0.7:0.3 AP/ALE ratio, displayed a transfection efficiency that was five times higher than that of 25 kDa PEI with dramatically better cytocompatibility. This is comparable to FuGENE, but PAEI is more advantageous in selective transfection of the U-2 OS. This set of polymers may be promising candidates for targeted gene therapy of osteosarcoma.Publication Metadata only 3D coffee stains(Royal Soc Chemistry, 2017) N/A; N/A; Department of Electrical and Electronics Engineering; N/A; N/A; N/A; Department of Molecular Biology and Genetics; Department of Chemistry; Department of Chemistry; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Department of Chemistry; Department of Electrical and Electronics Engineering; Doğru-Yüksel, Itır Bakış; Söz, Çağla Koşak; Press, Daniel Aaron; Melikov, Rustamzhon; Begar, Efe; Çonkar, Deniz; Karalar, Elif Nur Fırat; Yılgör, Emel; Yılgör, İskender; Nizamoğlu, Sedat; PhD Student; PhD Student; Researcher; PhD Student; PhD Student; PhD Student; PhD Student; Faculty Member; Researcher; Faculty Member; Faculty Member; N/A; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); N/A; N/A; N/A; N/A; N/A; N/A; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; College of Sciences; College of Engineering; N/A; N/A; N/A; N/A; N/A; N/A; 206349; N/A; 24181; 130295When a liquid droplet (e.g., coffee, wine, etc.) is splattered on a surface, the droplet dries in a ring-shaped stain. This widely observed pattern in everyday life occurs due to the phenomenon known as a coffee stain (or coffee ring) effect. While the droplet dries, the capillary flow moves and deposits the particles toward the pinned edges, which shows a 2D ring-like structure. Here we demonstrate the transition from a 2D to a 3D coffee stain that has a well-defined and hollow sphere-like structure, when the substrate surface is switched from hydrophilic to superhydrophobic. The 3D stain formation starts with the evaporation of the pinned aqueous colloidal droplet placed on a superhydrophobic surface that facilitates the particle flow towards the liquid-air interface. This leads to spherical skin formation and a cavity in the droplet. Afterwards the water loss in the cavity due to pervaporation leads to bubble nucleation and growth, until complete evaporation of the solvent. In addition to the superhydrophobicity of the surface, the concentration of the solution also has a significant effect on 3D coffee stain formation. Advantageously, 3D coffee stain formation in a pendant droplet configuration enables the construction of all-protein lasers by integrating silk fibroin with fluorescent proteins. No tools, components and/or human intervention are needed after the construction process is initiated; therefore, 3D coffee-stains hold promise for building self-assembled and functional 3D constructs and devices from colloidal solutions.Publication Metadata only 3D printed biodegradable polyurethaneurea elastomer recapitulates skeletal muscle structure and function(American Chemical Society (ACS), 2021) Gokyer, Seyda; Berber, Emine; Vrana, Engin; Orhan, Kaan; Abou Monsef, Yanad; Guvener, Orcun; Zinnuroglu, Murat; Oto, Cagdas; Huri, Pinar Yilgor; Department of Chemistry; Department of Chemistry; Department of Chemistry; Yılgör, Emel; Yılgör, İskender; Researcher; Faculty Member; College of Sciences; College of Sciences; N/A; 24181Effective skeletal muscle tissue engineering relies on control over the scaffold architecture for providing muscle cells with the required directionality, together with a mechanical property match with the surrounding tissue. Although recent advances in 3D printing fulfill the first requirement, the available synthetic polymers either are too rigid or show unfavorable surface and degradation profiles for the latter. In addition, natural polymers that are generally used as hydrogels lack the required mechanical stability to withstand the forces exerted during muscle contraction. Therefore, one of the most important challenges in the 3D printing of soft and elastic tissues such as skeletal muscle is the limitation of the availability of elastic, durable, and biodegradable biomaterials. Herein, we have synthesized novel, biocompatible and biodegradable, elastomeric, segmented polyurethane and polyurethaneurea (TPU) copolymers which are amenable for 3D printing and show high elasticity, low modulus, controlled biodegradability, and improved wettability, compared to conventional polycaprolactone (PCL) and PCL-based TPUs. The degradation profile of the 3D printed TPU scaffold was in line with the potential tissue integration and scaffold replacement process. Even though TPU attracts macrophages in 2D configuration, its 3D printed form showed limited activated macrophage adhesion and induced muscle-like structure formation by C2C12 mouse myoblasts in vitro, while resulting in a significant increase in muscle regeneration in vivo in a tibialis anterior defect in a rat model. Effective muscle regeneration was confirmed with immunohistochemical assessment as well as evaluation of electrical activity produced by regenerated muscle by EMG analysis and its force generation via a custom-made force transducer. Micro-CT evaluation also revealed production of more muscle-like structures in the case of implantation of cell-laden 3D printed scaffolds. These results demonstrate that matching the tissue properties for a given application via use of tailor-made polymers can substantially contribute to the regenerative outcomes of 3D printed tissue engineering scaffolds.Publication Metadata only 3D printed poly(lactic acid) scaffolds modified with chitosan and hydroxyapatite for bone repair applications(Elsevier, 2020) N/A; N/A; N/A; N/A; Department of Chemistry; Department of Chemical and Biological Engineering; Department of Chemistry; Department of Chemical and Biological Engineering; Department of Chemistry; Nazeer, Muhammad Anwaar; Önder, Özgün Can; Sevgili, İlkem; Yılgör, Emel; Kavaklı, İbrahim Halil; Yılgör, İskender; PhD Student; PhD Student; PhD Student; Researcher; Faculty Member; Faculty Member; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; College of Sciences; N/A; N/A; N/A; N/A; 40319; 241813D printed poly(lactic acid) (PLA) scaffolds surface modified with chitosan (CS) and hydroxyapatite (HA) to produce a novel bioactive composite scaffold is reported. Excellent mechanical properties of PLA, the bioactivity of CS, and osteogenic characteristics of HA are combined to fabricate composite scaffolds using a simple desktop 3D printer. Scaffolds were characterized through attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy, scanning electron microscopy (SEM), energy dispersive X-ray (EDX) spectroscopy, X-ray diffraction (XRD) and water contact angle measurements before and after modification. Formic acid was used as a solvent to prepare stable CS/HA dispersions and was found to be a suitable solvent for producing PLA/CS/HA composites. Surface properties of modified scaffolds were superior in terms of hydrophilicity and bioactivity, which resulted in enhanced attachment and proliferation of human osteosarcoma cells in vitro compared to the unmodified PLA scaffolds.Publication Metadata only 3D printing of cytocompatible gelatin-cellulose-alginate blend hydrogels(Wiley-V C H Verlag Gmbh, 2020) Erkoc, Pelin; Uvak, Ileyna; Odeh, Yazan Nitham; Akdogan, Ozan; Odeh, Yazan Nitham; Akdogan, Ozan; N/A; Department of Chemistry; Department of Chemical and Biological Engineering; Department of Chemistry; Department of Chemical and Biological Engineering; Nazeer, Muhammad Anwaar; Batool, Syeda Rubab; Kızılel, Seda; PhD Student; Researcher; Faculty Member; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; N/A; N/A; 283763D bioprinting of hydrogels has gained great attention due to its potential to manufacture intricate and customized scaffolds that provide favored conditions for cell proliferation. Nevertheless, plain natural hydrogels can be easily disintegrated, and their mechanical strengths are usually insufficient for printing process. Hence, composite hydrogels are developed for 3D printing. This study aims to develop a hydrogel ink for extrusion-based 3D printing which is entirely composed of natural polymers, gelatin, alginate, and cellulose. Physicochemical interactions between the components of the intertwined gelatin-cellulose-alginate network are studied via altering copolymer ratios. The structure of the materials and porosity are assessed using infrared spectroscopy, swelling, and degradation experiments. The utility of this approach is examined with two different crosslinking strategies using glutaraldehyde or CaCl2. Multilayer cylindrical structures are successfully 3D printed, and their porous structure is confirmed by scanning electron microscopy and Brunauer-Emmett-Teller surface area analyses. Moreover, cytocompatibility of the hydrogel scaffolds is confirmed on fibroblast cells. The developed material is completely natural, biocompatible, economical, and the method is facile. Thus, this study is important for the development of advanced functional 3D hydrogels that have considerable potential for biomedical devices and artificial tissues.Publication Metadata only A coarse grained simulation study on the morphology of aba triblock copolymers(Elsevier, 2019) Onarana, Gülşah; Yurtsever, Mine; Department of Chemistry; Department of Chemistry; Yılgör, İskender; Faculty Member; College of Sciences; 24181The Dissipative Particle Dynamics (DPD) simulation technique was used to elucidate the composition-dependent equilibrium morphological behavior of three different symmetric ABA triblock copolymers, which were; poly(epsilon-caprolactone)-poly(dimethylsiloxane)-poly(epsilon-caprolactone) (PCL-PDMS-PCL), poly(epsilon-caprolactone)-poly(ethylene oxide)-poly(epsilon-caprolactone) (PCL-PEO-PCL) and poly(L-lactide)-poly(dimethylsiloxane)-poly(L-lactide) (PLLA-PDMS-PLLA). These polymers were chosen due to their biomedical and biotechnological importance. Polymeric A and B blocks were modeled as connected chain of beads with varying incompatibility. The impact of the block incompatibilities on the microphase separation as well as on the equilibrium phase behaviors were investigated at the mesoscopic scale. A detailed visual analysis of the DPD images and constructed phase diagram showed that quite different equilibrium morphologies were attainable by controlling the molecular weights of the blocks and the strength of the intermolecular interaction between them. More compatible A and B blocks underwent lamellar to cylindrical and cylindrical to spherical phase transitions at lower B block concentrations. Our results clearly showed that, Flory-Huggins interaction parameter (chi) and degree of polymerization (N) were the only control parameters, which determined the shape and size of the phase domains, as well as the extent of equilibrium nanophase separation. Our DPD simulated morphologies were compared with experimental images obtained by Atomic Force Microscopy (AFM).Publication Metadata only A comparative study on the effect of monodisperse Au and Ag nanoparticles on the performance of organic photovoltaic devices(Elsevier, 2021) Kacus, Hatice; Sevim, Melike; Biber, Mehmet; Baltakesmez, Ali; Aydogan, Sakir; Department of Chemistry; Department of Chemistry; Metin, Önder; Faculty Member; College of Sciences; 46962The monodisperse Au (similar to 5 nm) and Ag (similar to 3 nm) nanoparticles used in this study were obtained using surfactant-assistant solvothermal methods and characterized by XRD TEM and SEM. Then, these nanoparticles were embedded into the P3HT:PCBM photoactive layer at different ratios and the effects of the nanoparticles on the performance of the organic solar cells have been studied by varying the loading percent of the NPs in the range of 0.5-2 wt%. The best solar cell composition was determined to be 1 wt% for Au NPs and 0.5 wt% for Ag NPs. Optical absorption spectrum of P3HT:PCBM, P3HT:PCBM:AuNPs and P3HT:PCBM:AgNPs active layers were obtained using UV-visible spectroscopy. The J-V plots of ITO/PEDOT:PSS/P3HT:PCBM/LiF/Al solar cells having 1.10(-6) m(2) OSC area and with different Au NPs and Ag NPs loading ratios in the P3HT:PCBM were obtained under air mass (AM) 1.5G illumination. Open circuit voltage, short-circuit current density, fill factor, and power conversion efficiency of the OSC were calculated. The highest PCE values were obtained as 3.35% for Au NPs and as 3.50% for Ag NPs doped devices. This increase in PCEs was explained by a plasmonic effect that stems from the metallic NPs.Item Metadata only A comprehensive study of microstructure, mechanical behavior, biocorrosion, and cytotoxicity of RF-PVD deposited Ti1.5ZrTa0.5Nb0.5X0.5 (X: Hf, Mo, and W) refractory high-entropy alloy films on 316L(Elsevier Sci Ltd, 2023) 0000-0002-0487-5766; 0000-0002-8436-2214; 0000-0001-8311-5484; 0000-0001-5601-8814; 0000-0003-4718-1243; 0000-0001-6753-9316; N/A; N/A; N/A; Department of Chemistry; Department of Chemistry; N/A; Alamdari, Armin Asghari; Hashemkhani, Mahshid; Hendessi, Saman; Acar, Havva Funda Yağcı; Ünal, Uğur; Motallebzadeh, Amir; PhD Student; PhD Student; PhD Student; Faculty Member; Faculty Member; Researcher; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; N/A; N/A; N/A; N/A; 178902; 42079; N/AIn this study, Ti1.5ZrTa0.5Nb0.5Hf0.5, Ti1.5ZrTa0.5Nb0.5Mo0.5, and Ti1.5ZrTa0.5Nb0.5W0.5 refractory high-entropy alloys (RHEA) films were deposited on the 316L substrate using radio frequency physical vapor deposition technique (RF-PVD). The structural investigations revealed that deposited RHEA films had an amorphous structure with smooth morphology and granular features that were few to several hundred nanometers in size. The external surfaces of the deposited films were composed of constituent elements in their oxide and/or suboxide forms. The enhanced contact angle, hardness, tribological performance, adhesion and resistance to scratching, biocorrosion resistance, and low release of Ni and Cr ions demonstrated that Ti1.5ZrTa0.5Nb0.5W0.5 might be a suitable protective coating for 316L biomaterials. Additionally, the in vitro cytotoxicity assessment using C2C12 muscle myoblast cells revealed no cytotoxic response and good cell proliferation.Publication Metadata only A comprehensive study on the characteristic spectroscopic features of nitrogen doped graphene(Elsevier, 2019) Ogasawara, Hirohito; N/A; N/A; N/A; Department of Chemistry; Department of Chemistry; Solati, Navid; Mobassem, Sonia; Kahraman, Abdullah; Kaya, Sarp; PhD Student; PhD Student; PhD Student; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/A; 116541Despite significant methodical improvements in the synthesis of N-doped graphene, there are still unsolved questions regarding the control of content and the configuration of nitrogen species in graphene honeycomb network. A cross-examination of X-ray photoelectron spectroscopy and Raman spectroscopy findings indicates that the nitrogen dopant amount is graphene thicknesses dependent, but the various nitrogen dopant coordination can be obtained on both double- and few-layer graphene. Characteristic defect features (D') appearing in Raman spectra upon N-doping is sensitive to nitrogen dopant coordination, graphitic-pyridinic/nitrilic species and therefore the doping level can be identified. Pyridinic and nitrilic nitrogen as primary species turn graphene to p-type semiconductor after a mild thermal treatment.Item Metadata only A facile preparation of graphene hydrogel-supported bimetallic RuM (M: Co, Ni, Cu) nanoparticles as catalysts in the hydrogen generation from ammonia borane(Walter de Gruyter Gmbh, 2023) 0000-0003-1622-4992; 0000-0002-0601-2526; Zaier, Ibtihel; Department of Chemistry; Department of Chemistry; Metin, Önder; Eroğlu, Zafer; Faculty Member; Researcher; College of Sciences; College of Sciences; 46962; N/AThe synthesis of ultrafine well-dispersed bimetallic RuM (M: Co, Ni, Cu) nanoparticles (NPs) supported on graphene hydrogel (GH) was accomplished by a novel one-pot wet-chemical protocol that comprised the hydrothermal reduction of the mixture of graphene oxide and metal precursors by ethylene glycol (EG) in a Teflon-coated stainless-steel reactor at 180 degrees C. In this study, for the first time, we report the synthesis of bimetallic RuM NPs anchored on GH during the hydrothermal production of GH from graphene oxide (GH-RuM) and the catalysis of the yielded GH-Ru in the hydrolysis of ammonia borane (AB). As-synthesized GH-RuM (M: Co, Ni, Cu) nanocatalysts were characterized by using many advanced instrumental techniques including TEM, XRD, XPS, and ICP-MS. The bimetallic catalysts denoted as GH-Ru20Co80, GH-Ru30Ni70 and GH-Ru10Cu90 exhibited much higher catalytic activity compared to their Ru, Co, Ni and Cu monometallic counterparts in the hydrolytic dehydrogenation of AB. The catalytic performance of as-prepared NPs in terms of hydrogen generation rate (HGR) was achieved in the order of RuCo > RuNi > RuCu and the highest HGR calculated for the catalyst GH-Ru20Co80 reached 8911.5 mL H-2 g(cat)(-1) min(-1) at room temperature with an activation energy of 52.5 kJ mol(-1).