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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 A challenge for peptide coarse graining: transferability of fragment-based models(Wiley-V C H Verlag Gmbh, 2011) Villa, Alessandra; Peter, Christine; N/A; Department of Mechanical Engineering; Engin, Özge; Sayar, Mehmet; Master Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 109820Peptides are highly promising building blocks for design and development of novel materials with potential application areas ranging from drug design to biotechnology. The necessity to understand the structural and thermodynamic properties of these complex materials has led to a dramatic increase in the development of computational techniques geared specifically towards peptide-based systems. Both all-atom (AA) and coarse-grained (CG) simulations of such materials have become extremely important, where the latter is an indispensable tool for reaching the time and length scales relevant to the experiments. Here, we review different approaches and discuss the challenges in the development of CG models for peptides. In particular, we concentrate on the transferability of fragment-based CG models. We analyze the transferability of a solvent-free CG model developed to model hydrophobic phenylalanine dipeptides (FF) in water. Here, we employ the same CG strategy-with non-bonded potentials based on peptide fragments-to two other hydrophobic dipeptides, valine-phenylalanine (VF) and isoleucine-phenylalanine (IF). In line with the previously developed model, the dipeptides are described by seven beads and the potentials developed for FF (bonded and non-bonded) are directly applied to describe the phenylalanine and backbone atoms, while new potentials are developed to account for the valine and isoleucine sidechains. By comparing AA and CG intra and intermolecular samplings, we show the ability of the CG model to reproduce the conformational behavior and thermodynamic association properties of the corresponding atomistic systems.Publication Metadata only A LES/PDF simulator on block-structured meshes(Taylor & Francis Ltd, 2019) Pope, Stephen B.; N/A; Department of Mechanical Engineering; Türkeri, Hasret; Muradoğlu, Metin; PhD Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 46561A block-structured mesh large-eddy simulation (LES)/probability density function (PDF) simulator is developed within the OpenFOAM framework for computational modelling of complex turbulent reacting flows. The LES/PDF solver is a hybrid solution methodology consisting of (i) a finite-volume (FV) method for solving the filtered mass and momentum equations (LES solver), and (ii) a Lagrangian particle-based Monte Carlo algorithm (PDF solver) for solving the modelled transport equation of the filtered joint PDF of compositions. Both the LES and the PDF methods are developed and combined to form a hybrid LES/PDF simulator entirely within the OpenFOAM framework. The in situ adaptive tabulation method [S.B. Pope, Computationally efficient implementation of combustion chemistry using in situ adaptive tabulation, Combust. Theory Model. 1 (1997), pp. 41-63; L. Lu, S.R. Lantz, Z. Ren, and B.S. Pope, Computationally efficient implementation of combustion chemistry in parallel PDF calculations, J. Comput. Phys. 228 (2009), pp. 5490-5525] is incorporated into the new LES/PDF solver for efficient computations of combustion chemistry with detailed reaction kinetics. The method is designed to utilise a block-structured mesh and can readily be extended to unstructured grids. The three-stage velocity interpolation method of Zhang and Haworth [A general mass consistency algorithm for hybrid particle/finite-volume PDF methods, J. Comput. Phys. 194 (2004), pp. 156-193] is adapted to interpolate the LES velocity field onto particle locations accurately and to enforce the consistency between LES and PDF fields at the numerical solution level. The hybrid algorithm is fully parallelised using the conventional domain decomposition approach. A detailed examination of the effects of each stage and the overall performance of the velocity interpolation algorithm is performed. Accurate coupling of the LES and PDF solvers is demonstrated using the one-way coupling methodology. Then the fully two-way coupled LES/PDF solver is successfully applied to simulate the Sandia Flame-D, and a turbulent non-swirling premixed flame and a turbulent swirling stratified flame from the Cambridge turbulent stratified flame series [M.S. Sweeney, S. Hochgreb, M.J. Dunn, and R.S. Barlow, The structure of turbulent stratified and premixed methane/air flames I: Non-swirling flows, Combust. Flame 159 (2012), pp. 2896-2911; M.S. Sweeney, S. Hochgreb, M.J. Dunn, and R.S. Barlow, The structure of turbulent stratified and premixed methane/air flames II: Swirling flows, Combust. Flame 159 (2012), pp. 2912-2929]. It is found that the LES/PDF method is very robust and the results are in good agreement with the experimental data for both flames.Publication Metadata only A microstructure-sensitive model for simulating the impact response of a high-manganese austenitic steel(Asme, 2016) N/A; N/A; Department of Mechanical Engineering; Mirzajanzadeh, Morad; Canadinç, Demircan; PhD Student; Faculty Member; Department of Mechanical Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; College of Engineering; N/A; 23433Microstructurally informed macroscopic impact response of a high-manganese austenitic steel was modeled through incorporation of the viscoplastic self-consistent (VPSC) crystal plasticity model into the ANSYS LS-DYNA nonlinear explicit finite-element (FE) frame. Voce hardening flow rule, capable of modeling plastic anisotropy in microstructures, was utilized in the VPSC crystal plasticity model to predict the micromechanical response of the material, which was calibrated based on experimentally measured quasi-static uniaxial tensile deformation response and initially measured textures. Specifically, hiring calibrated Voce parameters in VPSC, a modified material response was predicted employing local velocity gradient tensors obtained from the initial FE analyses as a new boundary condition for loading state. The updated micromechanical response of the material was then integrated into the macroscale material model by calibrating the Johnson-Cook (JC) constitutive relationship and the corresponding damage parameters. Consequently, we demonstrate the role of geometrically necessary multi-axial stress state for proper modeling of the impact response of polycrystalline metals and validate the presented approach by experimentally and numerically analyzing the deformation response of the Hadfield steel (HS) under impact loading.Publication Metadata only A novel tactile sensor for detecting lumps in breast tissue(Springer-Verlag Berlin, 2010) Güçlü, Burak; Yıldız, Mustafa Z.; N/A; Department of Mechanical Engineering; Ayyıldız, Mehmet; Başdoğan, Çağatay; Master Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 125489We developed a compact tactile sensor in order to guide the clinician or the self-user for non-invasive detection of lumps. The new design has an advantage over the existing discrete tactile sensors and detection methods by efficiently sensing force distribution over an area without any side effects. The sensor consists of 10x10 infrared emitter-detector pairs, a silicon-rubber elastic pad, and a contoured tactile interface (25x21 moving pins) for palpating three-dimensional objects. To demonstrate the practical use of the sensor, first a cylindrical tissue-like silicon phantom was prepared, then a 13 mm diameter rigid spherical object was placed at varying depths of 0-20 mm to simulate cancerous lumps in breast tissue, and finally the tactile sensor was systematically pressed on the phantom to successfully detect the lumps for compression depths of I 024 mm. The location and the estimated radius of each lump were calculated from the recorded tactile images.Publication Metadata only A short-term in vivo evaluation of the Istanbul heart left ventricular assist device in a pig model(Middle East Society for Organ Transplantation, 2019) Küçükaksu, Deniz Süha; Bakuy, Vedat; Arat, Nurcan; Erkasap, Pelin Çelikbilek; Aksoy, Emin; Department of Mechanical Engineering; N/A; N/A; N/A; N/A; N/A; Lazoğlu, İsmail; Öztürk, Çağlar; Aka, İbrahim Başar; Yalçın, Özlem; Uğurel, Elif; Ruacan, Ahmet Şevket; Faculty Member; PhD Student; PhD Student; Faculty Member; Researcher; Faculty Member; Department of Mechanical Engineering; Manufacturing and Automation Research Center (MARC); College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; School of Medicine; School of Medicine; School of Medicine; 179391; N/A; N/A; 218440; N/A; N/AObjectives: a continuous-flow centrifugal blood pump system has been recently developed as an implantable left ventricular assist device for patients with endstage heart failure. The objective of this study was to evaluate the initial in vivo performance of a newly developed left ventricular assist device (iHeart or Istanbul heart; Manufacturing and Automation Research Center, Koc University, Istanbul, Turkey) in an acute setting using a pig model. Materials and Methods: three pigs (77, 83, 92 kg) received implants via a median sternotomy, with animals supported for up to 6 hours. An outflow cannula was anastomosed to the ascending aorta. Anticoagulation was applied by intravenous heparin administration. During the support period, pump performance was evaluated under several flow and operating conditions. All pigs were humanely sacrificied after the experiments, and organs were examined macroscopically and histopathologically. Results: flow rate ranged between 1.5 and 3.6 L/min with pump speeds of 1500 to 2800 revolutions/min and motor current of 0.6 to 1.3 A. Initial findings confirmed thatthe iHeart ventricular assist device had sufficient hydraulic performance to support the circulation. During the experimental period, plasma free hemoglobin levels were found to be within normalranges. Thrombus formation was not observed inside the pump in all experiments. Conclusions: the iHeart ventricular assist device demonstrated encouraging hemodynamic performance and good biocompatibility in the pig model for use as an implantable left ventricular assist device. Further acute in vivo studies will evaluate the short-term pump performance prior to chronic studies for long-term evaluation.Publication Metadata only A variable elastance-based mock circulation model for replicating human cardiovascular system(Wichtig Editore, 2011) Küçükaksu, S.; Şahin, Tuğcan; Department of Mechanical Engineering; Lazoğlu, İsmail; Faculty Member; Department of Mechanical Engineering; College of Engineering; 179391N/APublication 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 Development of a finite element model of the human cervical spine(Turkish Neurosurgery Society, 2014) N/A; N/A; Department of Mechanical Engineering; N/A; Zafarparandeh, Iman; Erbulut, Deniz Ufuk; Lazoğlu, İsmail; Özer, Ali Fahir; PhD Student; Researcher; Faculty Member; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; School of Medicine; College of Engineering; School of Medicine; N/A; 37661; 179391; 1022The finite element model has been used as an effective tool in human spine biomechanics. Biomechanical finite element models have provided basic insights into the workings of the cervical spine system. Advancements in numerical methods during the last decade have enabled researchers to propose more accurate models of the cervical spine. The new finite element model of the cervical spine considers the accurate representation of each tissue regarding the geometry and material. The aim of this paper is to address the new advancements in the finite element model of the human cervical spine. The procedures for creating a finite element model are introduced, including geometric construction, material-property assignment, boundary conditions and validation. The most recent and published finite element models of the cervical spine are reviewed. / Sonlu eleman yöntemi efektif bir araç olarak omurga biyomekaniğinde yaygın kullanılmaktadır. Servikal omurga içerisinde meydana gelebilecek biyomekanik değişimlerin incelenmesine fırsat verebilmektedir. Geçtiğimiz on yıl içerisinde, geliştirilmiş olan nümerik metodlar sayesinde, daha gerçekçi omurga modellerinin çıkarılması sağlanmıştır. Günümüzde, servikal omurga modellerinde kullanılan geometri ve malzeme özellikleri olabildiğince gerçeğe yakın oluşturulabilmektedir. Bu makalenin amacı, sonlu eleman yöntemi kullanılarak insan servikal modellinin oluşturulmasını örneklerle açıklamaktır. Servikal omurga modelinin sonlu eleman yöntemi ile oluşturulmasının her bir adımı detaylı ele alınmıştır. Literatürde en son yayınlanan servikal omurga sonlu eleman modelleri incelenmiş ve karşılaştırılmıştır.Publication Metadata only Development of a novel shrouded impeller pediatric blood pump(Springer Japan Kk, 2018) N/A; N/A; N/A; Department of Mechanical Engineering; N/A; Khan, Talha Irfan; Zad, Haris Sheh; Lazoğlu, İsmail; Yalçın, Özlem; PhD Student; PhD Student; Faculty Member; Faculty Member; Department of Mechanical Engineering; Manufacturing and Automation Research Center (MARC); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; N/A; N/A; 179391; 218440The aim of this work was to analyze a shrouded impeller pediatric ventricular assist device (SIP-VAD). This device has distinctive design characteristics and parameter optimizations for minimization of recirculation flow and reduction in high-stress regions that cause blood damage. Computational Fluid Dynamics (CFD) simulations were performed to analyze the optimized design. The bench-top prototype of SIP-VAD was manufactured with biocompatible stainless steel. A study on the hydrodynamic and hemodynamic performance of the SIP-VAD was conducted with predictions from CFD and actual experimentation values, and these results were compared. The CFD analysis yielded a pressure range of 29-90 mmHg corresponding to flow rates of 0.5-3 L/min over 9000-11000 rpm. The predicted value of the normalized index of hemolysis (NIH) was 0.0048 g/100 L. The experimental results with the bench-top prototype showed a pressure rise of 30-105 mmHg for the flow speed of 8000-12000 rpm and flow rate of 0.5-3.5 L/min. The maximum difference between CFD and experimental results was 4 mmHg pressure. In addition, the blood test showed the average NIH level of 0.00674 g/100 L. The results show the feasibility of shrouded impeller design of axial-flow pump for manufacturing the prototype for further animal trials.
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