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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 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 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 Metadata only A dynamical formulation of one-dimensional scattering theory and its applications in optics(Academic Press Inc Elsevier Science, 2014) NA; Department of Mathematics; Mostafazadeh, Ali; Faculty Member; Department of Mathematics; College of Sciences; 4231We develop a dynamical formulation of one-dimensional scattering theory where the reflection and transmission amplitudes for a general, possibly complex and energy-dependent, scattering potential are given as solutions of a set of dynamical equations. By decoupling and partially integrating these equations, we reduce the scattering problem to a second order linear differential equation with universal initial conditions that is equivalent to an initial-value time-independent Schrodinger equation. We give explicit formulas for the reflection and transmission amplitudes in terms of the solution of either of these equations and employ them to outline an inverse-scattering method for constructing finite-range potentials with desirable scattering properties at any prescribed wavelength. In particular, we construct optical potentials displaying threshold lasing, antilasing, and unidirectional invisibility.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.Publication Open Access A transferable coarse-grained model for diphenylalanine: how to represent an environment driven conformational transition(American Institute of Physics (AIP) Publishing, 2013) Peter, Christine; N/A; Department of Mechanical Engineering; Dalgıçdır, Cahit; Şensoy, Özge; Sayar, Mehmet; PhD Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; N/A; N/A; 109820One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties. (C) 2013 AIP Publishing LLC.Publication Open Access A Twitter-based economic policy uncertainty index: expert opinion and financial market dynamics in an emerging market economy(Frontiers, 2022) Altuğ, Sumru; Department of Economics; Yeşiltaş, Sevcan; Şen, Anıl; Arslan, Beyza; Faculty Member; Department of Economics; College of Administrative Sciences and Economics; Graduate School of Social Sciences and Humanities; 258768; N/A; N/AIn this paper, we construct a Twitter-based high-frequency Economic Policy Uncertainty (TEPU) index built on a select set of Twitter user accounts whose tweets are considered to reflect expert opinion on the topic. We study the relationship between the TEPU index and a set of key financial indicators for tracking financial developments in Turkey over the sample period 2013–2021. Based on the results from a vector autoregressive analysis, we find evidence that changes in expert opinion described by fluctuations in the TEPU index interact with fluctuations in financial indicators such as the exchange rate and the stock market index to capture information about high frequency events during our sample period. Second, fluctuations in the TEPU index emerge as a key indicator that helps to predict the country risk premium measured by the CDS spread. We also find evidence that the conditional volatility of the different series reflects salient events that occurred over our sample period.Publication Open Access Accelerated expansion of the Universe in a higher dimensional modified gravity with Euler-Poincaré terms(Institute of Physics (IOP) Publishing, 2015) Akarsu, Özgür; Department of Physics; Dereli, Tekin; Oflaz, Neslihan; PhD Student; Department of Physics; College of Sciences; 201358; N/AA higher dimensional modified gravity theory with an action that includes dimensionally continued Euler-Poincare forms up to second order in curvatures is considered. The variational field equations are derived. Matter in the Universe at large scales is modeled by a fluid satisfying an equation of state with dimensional dichotomy. We study solutions that describe higher dimensional steady state cosmologies with constant volume for which the three dimensional external space is expanding at an accelerated rate while the (compact) internal space is contracting. We showed that the second order Euler-Poincare term in the constructions of higher dimensional steady state cosmologies could be crucial.