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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 Metadata only Aerothermal load and drag force analysis of the electromagnetically launched projectiles under rarefied gas conditions(IEEE-Inst Electrical Electronics Engineers Inc, 2015) Şengil, Nevsan; Department of Physics; Şengil, Uluç; Master Student; Department of Physics; Graduate School of Social Sciences and Humanities; N/AElectromagnetically launched projectiles fly with hypersonic speeds in different regions of the Earth's atmosphere. Because of their hypersonic speeds, these projectiles are designed to withstand extreme thermal loads. Drag forces should also be considered to maximize the operational range. To reduce the thermal loads and drag forces, the geometric shape of these projectiles should be carefully designed. We can utilize either experimental or numerical methods to calculate these heating effects and drag forces. Numerical methods are more economic in terms of monetary cost and time. However, we cannot use the same numerical method in different regions of the Earth's atmosphere. In this paper, we used direct simulation Monte Carlo method to calculate thermal loads and drag forces of four different projectile geometries in the rarefied part of the atmosphere. Simulation results show that thermal loads and drag forces vary considerably depending on the projectile geometry.Publication Metadata only Analysis of internal design parameters to minimize geometrical losses in free-space optical communication link(Polish Acad Sciences Inst Physics, 2018) Mushtaq, M. T.; Yasir, S. M.; Khan, M. S.; Wahid, A.; N/A; PhD Student; Graduate School of Sciences and Engineering; N/ADuring the last two decades, free-space optical links got considerable importance due to their benefits of higher data rates, license free-spectrum, easy and rapid deployment and mobility. Free-space optical links use carrier frequency in the range of 20 THz to 375 THz (in near infrared (IR) region and visible band in wavelengths) to establish a communication link for terrestrial communication, inter-satellite links, deep space links, ground-to-satellite and satellite-to-ground links. Free-space optical links are also useful for different military applications, disaster recovery and last mile access. However, despite of having all these advantages the performance of free-space optical links depends upon the atmospheric conditions and parameters of system design. Geometrical losses of free-space optical links are directly related to parameters of system design or internal parameters. In this paper we analyzed different parameters of system design to minimize the geometrical losses. We presented the analysis of internal design parameters like divergence angle, diameter of receiver aperture, diameter of transmitter aperture, link distance and suggested the suitable parameters of system design.Publication Metadata only Canonical transformations in three-dimensional phase-space(2009) Hakioğlu, Tuğrul; Department of Physics; Department of Physics; Dereli, Tekin; Faculty Member; Other; Department of Physics; College of Sciences; College of Sciences; 201358; N/ACanonical transformation in a three-dimensional phase-space endowed with Nambu bracket is discussed in a general framework. Definition of the canonical transformations is constructed based on canonoid transformations. It is shown that generating functions, transformed Hamilton functions and the transformation itself for given generating functions can be determined by solving Pfaffian differential equations corresponding to that quantities. Types of the generating functions are introduced and all of them are listed. Infinitesimal canonical transformations are also discussed. Finally, we show that the decomposition of canonical transformations is also possible in three-dimensional phase space as in the usual two-dimensional one.Publication Metadata only D=3 anisotropic and d=2 tj models: phase diagrams, thermodynamic properties, and chemical potential shift(Springer, 2006) Hinczewski, M.; Department of Physics; Berker, Ahmet Nihat; Faculty Member; Department of Physics; College of Sciences; 179795The anisotropic d=3 tJ model is studied by renormalization-group theory, yielding the evolution of the system as interplane coupling is varied from the isotropic three-dimensional to quasi-two-dimensional regimes. Finite-temperature phase diagrams, chemical potential shifts, and in-plane and interplane kinetic energies and antiferromagnetic correlations are calculated for the entire range of electron densities. We find that the novel tau phase, seen in earlier studies of the isotropic d=3 tJ model, persists even for strong anisotropy. While the tau phase appears at low temperatures at 30-35% hole doping away from [n(i)]=1, at smaller hole dopings we see a complex lamellar structure of antiferromagnetic and disordered regions, with a suppressed chemical potential shift, a possible marker of incommensurate ordering in the form of microscopic stripes. An investigation of the renormalization-group flows for the isotropic two-dimensional tJ model also shows a clear pre-signature of the tau phase, which in fact appears with finite transition temperatures upon addition of the smallest interplane coupling.Publication Open Access Deagglomeration of nanoparticle clusters in a "cavitation on chip" device(American Institute of Physics (AIP) Publishing, 2020) Gevari, M.T.; Niazi, S.; Şendur, K.; Mengüç, M. P.; Ghorbani, M.; Koşar, A.; Department of Mechanical Engineering; Karimzadehkhouei, Mehrdad; Researcher; Department of Mechanical Engineering; Graduate School of Sciences and EngineeringDue to the potential of significant energy release in cavitating flows, early cavitation inception and intensification of cavitating flows are of great importance. To use this potential, we investigated the deagglomeration of nanoparticle clusters with the implementation of hydrodynamic cavitation in a microfluidic device. For this purpose, a microfluidic device with a micro-orifice geometry was designed and fabricated using standard microfabrication processes. The system was tested with distilled water in the assembled experimental setup. The flow patterns were characterized using the cavitation number and inlet pressure. Titania nanoparticles were utilized to prepare nanoparticle suspensions. The suspensions were heated to allow agglomeration of nanoparticles. The system was operated with the new working fluid (nanoparticle clusters) at different inlet pressures. After characterizing flow patterns, the flow patterns were compared with those of pure water. The deagglomeration effects of hydrodynamic cavitation on nanoparticle clusters showed the possibility to apply this method for the stabilization of nanoparticles, which paves way to the implementation of nanoparticle suspensions to thermal fluid systems for increased energy efficiency as well as to drug delivery. Our results also indicate that the presence of nanoparticles in the working fluid enhanced cavitation intensity due to the increase in the number of heterogeneous nucleation sites.Publication Metadata only Dispersive propagation of ultras low pulses in an atomic Bose-Einstein condensate(Polish Acad Sciences Inst Physics, 2011) Tarhan, Devrim; Sefi, Seçkin; Department of Physics; Müstecaplıoğlu, Özgür Esat; Faculty Member; Department of Physics; College of Sciences; 1674One-dimensional propagation of ultraslow optical pulses in an atomic Bose-Einstein condensate taking into account the dispersion and the spatial inhomogeneity is investigated. Analytical and semi-analytical solutions of the dispersive inhomogeneous wave equation modeling the ultraslow pulse propagation are developed and compared against the standard wave equation solvers based upon Cranck-Nicholson and pseudo-spectral methods. The role of curvature of the trapping potential of the condensate on the amount of dispersion of the ultraslow pulse is pointed out.Publication Metadata only Enhancing capacity of coherent optical information storage and transfer in a Bose-Einstein condensate(2007) N/A; Department of Physics; Department of Physics; Müstecaplıoğlu, Özgür Esat; Tarhan, Devrim; Faculty Member; Other; Department of Physics; College of Sciences; College of Sciences; 1674; N/AThe coherent optical information storage capacity of an atomic Bose-Einstein condensate is examined. The theory of slow light propagation in atomic clouds is generalized to the short-pulse regime by taking into account group velocity dispersion. It is shown that the number of stored pulses in the condensate can be optimized for a particular coupling laser power, temperature, and interatomic interaction strength. Analytical results are derived for a semi-ideal model of the condensate using the effective uniform density zone approximation. Detailed numerical simulations are also performed. It is found that the axial density profile of the condensate protects the pulse against group velocity dispersion. Furthermore, taking into account the finite radial size of the condensate, multimode light propagation in an atomic Bose-Einstein condensate is investigated. The number of modes that can be supported by a condensate is found. The single-mode condition is determined as a function of experimentally accessible parameters including trap size, temperature, condensate number density, and scattering length. Quantum coherent atom-light interaction schemes are proposed for enhancing multimode light propagation effects.Publication Open Access Estimation of pulsatile energy dissipation in intersecting pipe junctions using inflow pulsatility indices(American Institute of Physics (AIP) Publishing, 2021) Dur, Onur; Department of Mechanical Engineering; Pekkan, Kerem; Rasooli, Reza; Faculty Member; Researcher; Department of Mechanical Engineering; Graduate School of Health Sciences; College of Engineering; 161845; N/AThis study aims to characterize the effect of inflow pulsatility on the hydrodynamic power loss inside intersecting double-inlet, double-outlet pipe intersection (DIPI) with cross-flow mixing. An extensive set of computational fluid dynamics (CFD) simulations was performed in order to identify the individual effects of flow pulsatility parameters, i.e., amplitude, frequency, and relative phase shift between the inflow waveform oscillations, on power loss. An experimentally validated second order accurate solver is employed in this study. To predict the pulsatile flow performance of any given arbitrary inflow waveforms, we proposed three easy-to-calculate pulsatility indices. The frequency-coupled quasi-steady flow theory is incorporated to identify the functional form of pulsatile power loss as a function of these indices. Our results indicated that the power loss within the inflow branch sections, lumped outflow-junction section, and the whole conduit correlates strongly with the pulsatility of each inflow waveform, the total inflow pulsatility, and inflow frequency content, respectively. The complete CFD simulation matrix provided a unified analytical expression that predicts pulsatile power loss inside a one-degree offset DIPI geometry. The predictive accuracy of this expression is evaluated in comparison to the CFD evaluation of arbitrary multi-harmonic inflow waveforms. These results have important implications on hydrodynamic pipe networks that employ complex junctions as well as in the patient-to-patient comparison of surgically created vascular connections. Coupling the present analytical pulsatile power loss expression with non-dimensional steady power loss formulation provided a valuable predictive tool to estimate the pulsatile energy dissipation for any arbitrary junction geometry with minimum use of the costly CFD computations.Publication Metadata only Exactly solvable pairing model using an extension of the Richardson-Gaudin approach(World Scientific Publ Co Pte Ltd, 2005) Balantekin, AB; Pehlivan, Y; Department of Physics; Dereli, Tekin; Faculty Member; Department of Physics; College of Sciences; 201358We introduce a new class of exactly solvable boson pairing models using the technique of Richardson and Gaudin. Analytical expressions for all energy eigenvalues and the first few energy eigenstates are given. In addition, another solution to Gaudin's equation is also mentioned. A relation with the Calogero-Sutherland model is suggested.