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Publication Open Access 3D engineered neural co-culture model and neurovascular effects of marine fungi-derived citreohybridonol(American Institute of Physics (AIP) Publishing, 2022) Polat, İrem; Özkaya, Ferhat Can; El-Neketi, Mona; Ebrahim, Weaam; Şengül, Gülgün; Department of Mechanical Engineering; Sokullu, Emel; Sarabi, Misagh Rezapour; Taşoğlu, Savaş; Faculty Member; Faculty Member; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Koç Üniversitesi İş Bankası Yapay Zeka Uygulama ve Araştırma Merkezi (KUIS AI)/ Koç University İş Bank Artificial Intelligence Center (KUIS AI); KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); School of Medicine; Graduate School of Sciences and Engineering; College of Engineering; 163024; N/A; 291971Marine-based biomolecules are emerging metabolites that have gained attention for developing novel biomaterials, drugs, and pharmaceutical in vitro platforms. Here, we developed a 3D engineered neural co-culture model via a 3D prototyped sliding frame-platform for multi-step UV lithography and investigated the neurovascular potential of citreohybridonol in neuroblastoma treatment. Citreohybridonol was isolated from a sponge-derived fungus Penicillium atrovenetum. The model was characterized by Fourier-transform infrared spectroscopy and scanning electron microscopy analysis. Human umbilical cord vein endothelial cells (HUVECs) and neuroblastoma (SH-SY5Y) cell lines were encapsulated in gelatin methacrylate (GelMA) with and without citreohybridonol. The effect of citreohybridonol on the proliferation capacity of cells was assessed via cell viability and immunostaining assays. GelMA and 3D culture characterization indicated that the cells were successfully encapsulated as axenic and mixed with/without citreohybridonol. The cytotoxic test confirmed that the 3D microenvironment was non-toxic for cultural experiments, and it showed the inhibitory effects of citreohybridonol on SH-SY5Y cells and induced the proliferation of HUVECs. Finally, immunohistochemical staining demonstrated that citreohybridonol suppressed SH-SY5Y cells and induced vascularization of HUVECs in mixed 3D cell culture.Publication Open Access 3D printing of elastomeric bioinspired complex adhesive microstructures(Wiley, 2021) Dayan, Cem Balda; Chun, Sungwoo; Krishna Subbaiah, Nagaraj; Drotlef, Dirk Michael; Akolpoğlu, Mükrime Birgül; Department of Mechanical Engineering; Sitti, Metin; Faculty Member; Department of Mechanical Engineering; College of Engineering; School of Medicine; 297104Bioinspired elastomeric structural adhesives can provide reversible and controllable adhesion on dry/wet and synthetic/biological surfaces for a broad range of commercial applications. Shape complexity and performance of the existing structural adhesives are limited by the used specific fabrication technique, such as molding. To overcome these limitations by proposing complex 3D microstructured adhesive designs, a 3D elastomeric microstructure fabrication approach is implemented using two-photon-polymerization-based 3D printing. A custom aliphatic urethane-acrylate-based elastomer is used as the 3D printing material. Two designs are demonstrated with two combined biological inspirations to show the advanced capabilities enabled by the proposed fabrication approach and custom elastomer. The first design focuses on springtail- and gecko-inspired hybrid microfiber adhesive, which has the multifunctionalities of side-surface liquid super-repellency, top-surface liquid super-repellency, and strong reversible adhesion features in a single fiber array. The second design primarily centers on octopus- and gecko-inspired hybrid adhesive, which exhibits the benefits of both octopus- and gecko-inspired microstructured adhesives for strong reversible adhesion on both wet and dry surfaces, such as skin. This fabrication approach could be used to produce many other 3D complex elastomeric structural adhesives for future real-world applications.Publication Open Access A broken gauge approach to gravitational mass and charge(Springer, 2002) Tucker, R. W.; Department of Physics; Dereli, Tekin; Faculty Member; Department of Physics; College of Sciences; 201358We argue that a spontaneous breakdown of local Weyl invariance offers a mechanism in which gravitational interactions contribute to the generation of particle masses and their electric charge. The theory is formulated in terms of a spacetime geometry whose natural connection has both dynamic torsion and non-metricity. Its structure illuminates the role of dynamic scales used to determine measurable aspects of particle interactions and it predicts an additional neutral vector boson with electroweak properties. © SISSA/ISAS 2002.Publication Open Access A comparative study on GaSb epilayers grown on nominal and vicinal Si(100) substrates by molecular beam epitaxy(Institute of Physics (IOP) Publishing, 2020) Arpapay, Burcu; Suyolcu, Y. Eren; van Aken, Peter A.; Gülgün, Mehmet Ali; Serincan, Uğur; Çorapçıoğlu, Gülcan; n2STAR-Koç University Nanofabrication and Nanocharacterization Center for Scientifc and Technological Advanced ResearchThe direct growth of GaSb buffer layers on Si substrates is attracting considerable interest in the integration of group III-Sb based device structures on lower-cost Si substrates. Here, we present the effect of various growth steps on the defect types and defect density that are crucial for advancing high crystal quality GaSb buffer layer on nominal/vicinal Si substrate. As a growth step, the applied thermal annealing at an intermediate step provided a decrease in the threading dislocation (TD) density down to 1.72 x 10(8) cm(-2), indicating a more effective method compared to post-growth annealing. Additionally, the importance of period number and position of GaSb/AlSb superlattice layers inserted in GaSb epilayers is demonstrated. In the case of the GaSb epilayers grown on vicinal substrates, the APB density as low as 0.06 mu m(-1) and TD density of 1.98 x 10(8) cm(-2) were obtained for the sample grown on 4 degrees miscut Si(100) substrate.Publication Open Access A computational study of two-phase viscoelastic systems in a capillary tube with a sudden contraction/expansion(American Institute of Physics (AIP) Publishing, 2016) Department of Mechanical Engineering; Izbassarov, Daulet; Muradoğlu, Metin; PhD Student; Faculty Member; Department of Mechanical Engineering; College of Engineering; N/A; 46561Two-phase viscoelastic systems are computationally studied in a pressure-driven flow with a sudden contraction and expansion using a finite-difference/front-tracking method. The effects of viscoelasticity in drop and bulk fluids are investigated including high Weissenberg and Reynolds number cases up to Wi = 100 and Re = 100. The Finitely Extensible Non-linear Elastic-Chilcott and Rallison (FENE-CR) model is used to account for the fluid viscoelasticity. Extensive computations are performed to examine drop dynamics for a wide range of parameters. It is found that viscoelasticity interacts with drop interface in a non-monotonic and complicated way, and the two-phase viscoelastic systems exhibit very rich dynamics especially in the expansion region. At high Re, the drop undergoes large deformation in the contraction region followed by strong shape oscillations in the downstream of the expansion. For a highly viscous drop, a re-entrant cavity develops in the contraction region at the trailing edge which, in certain cases, grows and eventually causes encapsulation of ambient fluid. The re-entrant cavity formation is initiated at the entrance of the contraction and is highly influenced by the viscoelasticity. Compared to the corresponding straight channel case, the effects of viscoelasticity are reversed in the constricted channel: Viscoelasticity in drop/continuous phase hinders/enhances formation of the re-entrant cavity and entrainment of ambient fluid into main drop. Encapsulation of ambient fluid into main droplet may be another route to produce a compound droplet in microfluidic applications. (C) 2016 AIP Publishing LLC.Publication Open Access A critical approach to the biocompatibility testing of NiTi orthodontic archwires(Vibgyor Online Publishers, 2016) Şahbazoğlu, D.; Toker, S. M.; Saher, D.; Department of Mechanical Engineering; Canadinç, Demircan; Gümüş, Berkay; Uzer, Benay; Yıldırım, Cansu; Polat-Altıntaş, Sevgi; Faculty Member; Department of Mechanical Engineering; College of Engineering; 23433; N/A; N/A; N/A; N/AThe biocompatibility of Nickel-Titanium (NiTi) archwires was investigated by simulating actual contact state of archwires around brackets, which enabled incorporation of realistic mechanical conditions into ex situ experiments. Specifically, archwires (undeformed, and bound to brackets on acrylic dental molds) were statically immersed in artificial saliva (AS) for 31 days. Following the immersion, the archwires and the immersion solutions were analyzed with the aid of variouselectron-optical techniques, and it was observed that carbon-rich corrosion products formed on both archwire sets upon immersion. The corrosion products preferentially formed at the archwire–bracket contact zones, which is promoted by the high energy of these regions and the micro-cracks brought about by stress assisted corrosion. Moreover, it is suggested that these corrosion products prevented significant Ni or Ti ion release by blocking the micro-cracks, which, otherwise, would have led to enhanced ion release during immersion. The current findings demonstrate the need for incorporating both realistic chemical and mechanical conditions into the ex situ biocompatibility experiments of orthodontic archwires, including the archwire-bracket contact.Publication Open Access A divergence-free parametrization for dynamical dark energy(Institute of Physics (IOP) Publishing, 2015) Vazquez, J. Alberto; Department of Physics; Dereli, Tekin; Akarsu, Özgür; Faculty Member; Department of Physics; College of Sciences; 201358; N/AWe introduce a new parametrization for the dark energy, led by the same idea to the linear expansion of the equation of state in scale factor a and in redshift z, which diverges neither in the past nor future and contains the same number of degrees of freedom with the former two. We present constraints of the cosmological parameters using the most updated baryon acoustic oscillation (BAO) measurements along with cosmic microwave background (CMB) data and a recent reanalysis of Type Ia supernova (SN) data. This new parametrization allowed us to carry out successive observational analyses by decreasing its degrees of freedom systematically until ending up with a dynamical dark energy model that has the same number of parameters with ACDM. We found that the dark energy source with a dynamical equation of state parameter equal 2/3 at the early universe and -1 today fits the data slightly better than A.Publication Open Access A diversity combination model incorporating an inward bias for interaural time-level difference cue integration in sound lateralization(Multidisciplinary Digital Publishing Institute (MDPI), 2020) N/A; Department of Computer Engineering; Mojtahedi, Sina; Erzin, Engin; Ungan, Pekcan; Faculty Member; Faculty Member; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; N/A; 34503; N/AA sound source with non-zero azimuth leads to interaural time level differences (ITD and ILD). Studies on hearing system imply that these cues are encoded in different parts of the brain, but combined to produce a single lateralization percept as evidenced by experiments indicating trading between them. According to the duplex theory of sound lateralization, ITD and ILD play a more significant role in low-frequency and high-frequency stimulations, respectively. In this study, ITD and ILD, which were extracted from a generic head-related transfer functions, were imposed on a complex sound consisting of two low- and seven high-frequency tones. Two-alternative forced-choice behavioral tests were employed to assess the accuracy in identifying a change in lateralization. Based on a diversity combination model and using the error rate data obtained from the tests, the weights of the ITD and ILD cues in their integration were determined by incorporating a bias observed for inward shifts. The weights of the two cues were found to change with the azimuth of the sound source. While the ILD appears to be the optimal cue for the azimuths near the midline, the ITD and ILD weights turn to be balanced for the azimuths far from the midline.Publication Open Access A hybrid broadband metalens operating at ultraviolet frequencies(Nature Publishing Group (NPG), 2021) Department of Physics; Ali, Farhan; Ramazanoğlu, Serap Aksu; Faculty Member; Department of Physics; Graduate School of Sciences and Engineering; College of Sciences; N/A; 243745The investigation on metalenses have been rapidly developing, aiming to bring compact optical devices with superior properties to the market. Realizing miniature optics at the UV frequency range in particular has been challenging as the available transparent materials have limited range of dielectric constants. In this work we introduce a low absorption loss and low refractive index dielectric material magnesium oxide, MgO, as an ideal candidate for metalenses operating at UV frequencies. We theoretically investigate metalens designs capable of efficient focusing over a broad UV frequency range (200–400 nm). The presented metalenses are composed of sub-wavelength MgO nanoblocks, and characterized according to the geometric Pancharatnam–Berry phase method using FDTD method. The presented broadband metalenses can focus the incident UV light on tight focal spots (182 nm) with high numerical aperture (NA ≈ 0.8). The polarization conversion efficiency of the metalens unit cell and focusing efficiency of the total metalens are calculated to be as high as 94%, the best value reported in UV range so far. In addition, the metalens unit cell can be hybridized to enable lensing at multiple polarization states. The presented highly efficient MgO metalenses can play a vital role in the development of UV nanophotonic systems and could pave the way towards the world of miniaturization.Publication Open Access A multi-state coarse grained modeling approach for an intrinsically disordered peptide(American Institute of Physics (AIP) Publishing, 2017) Department of Chemical and Biological Engineering; N/A; Sayar, Mehmet; Dalgıçdır, Cahit; Ramezanghorbani, Farhad; Faculty Member; PhD Student; Department of Chemical and Biological Engineering; College of Engineering; Graduate School of Sciences and Engineering; 109820; N/A; N/AMany proteins display a marginally stable tertiary structure, which can be altered via external stimuli. Since a majority of coarse grained (CG) models are aimed at structure prediction, their success for an intrinsically disordered peptide's conformational space with marginal stability and sensitivity to external stimuli cannot be taken for granted. In this study, by using the LK alpha 14 peptide as a test system, we demonstrate a bottom-up approach for constructing a multi-state CG model, which can capture the conformational behavior of this peptide in three distinct environments with a unique set of interaction parameters. LK alpha 14 is disordered in dilute solutions; however, it strictly adopts the alpha-helix conformation upon aggregation or when in contact with a hydrophobic/hydrophilic interface. Our bottom-up approach combines a generic base model, that is unbiased for any particular secondary structure, with nonbonded interactions which represent hydrogen bonds, electrostatics, and hydrophobic forces. We demonstrate that by using carefully designed all atom potential of mean force calculations from all three states of interest, one can get a balanced representation of the nonbonded interactions. Our CG model behaves intrinsically disordered in bulk water, folds into an alpha-helix in the presence of an interface or a neighboring peptide, and is stable as a tetrameric unit, successfully reproducing the all atom molecular dynamics simulations and experimental results.