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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access Enhanced sinterability, thermal conductivity and dielectric constant of glass-ceramics with PVA and BN additions(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Akkasoğlu, Ufuk; Çiçek, Buğra; N/A; Department of Chemistry; Arıbuğa, Dilara; Balcı, Özge; Researcher; Department of Chemistry; Koç University AKKİM Boron-Based Materials _ High-technology Chemicals Research _ Application Center (KABAM) / Koç Üniversitesi AKKİM Bor Tabanlı Malzemeler ve İleri Teknoloji Kimyasallar Uygulama ve Araştırma Merkezi (KABAM); Graduate School of Sciences and Engineering; College of Sciences; N/A; 295531With the rapid development of the microelectronics industry, many efforts have been made to improve glass-ceramics' sinterability, thermal conductivity, and dielectric properties, which are essential components of electronic materials. In this study, low-alkali borosilicate glass-ceramics with PVA addition and glass-BN composites were prepared and successfully sintered at 770 degrees C. The phase composition, density, microstructure, thermal conductivity, and dielectric constant were investigated. It was shown that PVA addition contributes to the densification process of glass-ceramics (~88% relative density, with closed/open pores in the microstructure) and improves the thermal conductivity of glass material from 1.489 to 2.453 W/K.m. On the other hand, increasing BN addition improves microstructures by decreasing porosities and thus increasing relative densities. A glass-12 wt. % BN composite sample exhibited almost full densification after sintering and presented apparent and open pores of 2.6 and 0.08%, respectively. A high thermal conductivity value of 3.955 W/K.m and a low dielectric constant of 3.00 (at 5 MHz) were observed in this material. Overall, the resulting glass-ceramic samples showed dielectric constants in the range of 2.40-4.43, providing a potential candidate for various electronic applications.Publication Open Access Optimum folding pathways of proteins: their determination and properties(American Institute of Physics (AIP) Publishing, 2006) Department of Chemical and Biological Engineering; Güner, Pınar Tatar; Arkun, Yaman; Erman, Burak; Teaching Faculty; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 188227; 108526; 179997We develop a dynamic optimization technique for determining optimum folding pathways of proteins starting from different initial configurations. A coarse-grained Go model is used. Forces acting on each bead are (i) the friction force, (ii) forces from bond length constraints, (iii) excluded volume constraints, and (iv) attractive forces between residue pairs that are in contact in the native state. An objective function is defined as the total attractive energy between nonbonded residues, which are neighbors in the native state. The objective function is minimized over all feasible paths, satisfying bond length and excluded volume constraints. The optimization problem is nonconvex and contains a large number of constraints. An augmented Lagrangian method with a penalty barrier function was used to solve the problem. The method is applied to a 36-residue protein, chicken villin headpiece. Sequences of events during folding of the protein are determined for various pathways and analyzed. The relative time scales are compared and scaled according to experimentally measured events. Formation times of the helices, turn, and the loop agree with experimental data. We obtain the overall folding time of the protein in the range of 600 ns-1.2 mu s that is smaller than the experimental result of 4-5 mu s, showing that the optimal folding times that we obtain may be possible lower bounds. Time dependent variables during folding and energies associated with short- and long-range interactions between secondary structures are analyzed in modal space using Karhunen-Loeve expansion.Publication Open Access Adaptive Q control for tapping-mode nanoscanning using a piezoactuated bimorph probe(American Institute of Physics (AIP) Publishing, 2007) Department of Mechanical Engineering; Günev, İhsan; Varol, Aydın; Karaman, Sertaç; Başdoğan, Çağatay; Master Student; Faculty Member; Department of Mechanical Engineering; College of Engineering; N/A; N/A; N/A; 125489A new approach, called adaptive Q control, for tapping-mode atomic force microscopy (AFM) is introduced and implemented on a homemade AFM setup utilizing a laser Doppler vibrometer and a piezoactuated bimorph probe. In standard Q control, the effective Q factor of the scanning probe is adjusted prior to the scanning depending on the application. However, there is a trade-off in setting the effective Q factor of an AFM probe. The Q factor is either increased to reduce the tapping forces or decreased to increase the maximum achievable scan speed. Realizing these two benefits simultaneously using standard Q control is not possible. In adaptive Q control, the Q factor of the probe is set to an initial value as in standard Q control, but then modified on the fly during scanning when necessary to achieve this goal. In this article, we present the basic theory behind adaptive Q control, the electronics enabling the online modification of the probe's effective Q factor, and the results of the experiments comparing three different methods: scanning (a) without Q control, (b) with standard Q control, and (c) with adaptive Q control. The results show that the performance of adaptive Q control is superior to the other two methods.Publication Open Access Solvation of carbonaceous molecules by para-H2 and ortho-D2clusters. II. Fullerenes(American Institute of Physics (AIP) Publishing, 2016) Calvo, F.; Department of Chemistry; Yurtsever, İsmail Ersin; Doctor; Department of Chemistry; College of Sciences; 7129The coating of various fullerenes by para-hydrogen and ortho-deuterium molecules has been computationally studied as a function of the solvent amount. Rotationally averaged interaction potentials for structureless hydrogen molecules are employed to model their interaction with neutral or charged carbonaceous dopants containing between 20 and 240 atoms, occasionally comparing different fullerenes having the same size but different shapes. The solvation energy and the size of the first solvation shell obtained from path-integral molecular dynamics simulations at 2 K show only minor influence on the dopant charge and on the possible deuteration of the solvent, although the shell size is largest for ortho-D-2 coating cationic fullerenes. Nontrivial finite size effects have been found with the shell size varying non-monotonically close to its completion limit. For fullerenes embedded in large hydrogen clusters, the shell size and solvation energy both follow linear scaling with the fullerene size. The shell sizes obtained for C-60(+) and C-70(+) are close to 49 and 51, respectively, and agree with mass spectrometry experiments.Publication Open Access Solvation of carbonaceous molecules by para-H-2 and ortho-D-2 clusters. I. Polycyclic aromatic hydrocarbons(American Institute of Physics (AIP) Publishing, 2016) Calvo, F.; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129This work theoretically examines the progressive coating of planar polycyclic aromatic hydrocarbon (PAH) molecules ranging from benzene to circumcoronene (C54H18) by para-hydrogen and ortho-deuterium. The coarse-grained Silvera-Goldman potential has been extended to model the interactions between hydrogen molecules and individual atoms of the PAH and parametrized against quantum chemical calculations for benzene-H-2. Path-integral molecular dynamics simulations at 2 K were performed for increasingly large amounts of hydrogen coating the PAH up to the first solvation shell and beyond. From the simulations, various properties were determined such as the size of the first shell and its thickness as well as the solvation energy. The degree of delocalization was notably quantified from an energy landscape perspective, by monitoring the fluctuations among inherent structures sampled by the trajectories. Our results generally demonstrate a high degree of localization owing to relatively strong interactions between hydrogen and the PAH, and qualitatively minor isotopic effects. In the limit of large hydrogen amounts, the shell size and solvation energy both follow approximate linear relations with the numbers of carbon and hydrogen in the PAH.Publication Open Access State feedback control for adjusting the dynamic behavior of a piezoactuated bimorph atomic force microscopy probe(American Institute of Physics (AIP) Publishing, 2009) Güvenç, Levent; Department of Mechanical Engineering; Örün, Bilal; Necipoğlu, Serkan; Başdoğan, Çağatay; Master Student; Faculty Member; Department of Mechanical Engineering; College of Engineering; N/A; N/A; 125489We adjust the transient dynamics of a piezoactuated bimorph atomic force microscopy (AFM) probe using a state feedback controller. This approach enables us to adjust the quality factor and the resonance frequency of the probe simultaneously. First, we first investigate the effect of feedback gains on dynamic response of the probe and then show that the time constant of the probe can be reduced by reducing its quality factor and/or increasing its resonance frequency to reduce the scan error in tapping mode AFM.Publication Open Access Time-resolved local strain tracking microscopy for cell mechanics(American Institute of Physics (AIP) Publishing, 2016) Aydın, O.; Aksoy, B.; Akalın, O. B.; Department of Chemistry; Department of Mechanical Engineering; Bayraktar, Halil; Alaca, Burhanettin Erdem; Faculty Member; Department of Chemistry; Department of Mechanical Engineering; College of Sciences; College of EngineeringA uniaxial cell stretching technique to measure time-resolved local substrate strain while simultaneously imaging adherent cells is presented. The experimental setup comprises a uniaxial stretcher platform compatible with inverted microscopy and transparent elastomer samples with embedded fluorescent beads. This integration enables the acquisition of real-time spatiotemporal data, which is then processed using a single-particle tracking algorithm to track the positions of fluorescent beads for the subsequent computation of local strain. The present local strain tracking method is demonstrated using polydimethylsiloxane (PDMS) samples of rectangular and dogbone geometries. The comparison of experimental results and finite element simulations for the two sample geometries illustrates the capability of the present system to accurately quantify local deformation even when the strain distribution is non-uniform over the sample. For a regular dogbone sample, the experimentally obtained value of local strain at the center of the sample is 77%, while the average strain calculated using the applied cross-head displacement is 48%. This observation indicates that considerable errors may arise when cross-head measurement is utilized to estimate strain in the case of non-uniform sample geometry. Finally, the compatibility of the proposed platform with biological samples is tested using a unibody PDMS sample with a well to contain cells and culture media. HeLa S3 cells are plated on collagen-coated samples and cell adhesion and proliferation are observed. Samples with adherent cells are then stretched to demonstrate simultaneous cell imaging and tracking of embedded fluorescent beads.Publication Open Access Glioma-on-a-chip models(Multidisciplinary Digital Publishing Institute (MDPI), 2021) İlçi, İrem Sultan; Department of Mechanical Engineering; N/A; N/A; Önder, Tuğba Bağcı; Taşoğlu, Savaş; Üstün, Merve; Dabbagh, Sajjad Rahmani; Faculty Member; Department of Mechanical Engineering; KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Social Sciences and Humanities; 184359; 291971; N/A; N/AGlioma, as an aggressive type of cancer, accounts for virtually 80% of malignant brain tumors. Despite advances in therapeutic approaches, the long-term survival of glioma patients is poor (it is usually fatal within 12-14 months). Glioma-on-chip platforms, with continuous perfusion, mimic in vivo metabolic functions of cancer cells for analytical purposes. This offers an unprecedented opportunity for understanding the underlying reasons that arise glioma, determining the most effective radiotherapy approach, testing different drug combinations, and screening conceivable side effects of drugs on other organs. Glioma-on-chip technologies can ultimately enhance the efficacy of treatments, promote the survival rate of patients, and pave a path for personalized medicine. In this perspective paper, we briefly review the latest developments of glioma-on-chip technologies, such as therapy applications, drug screening, and cell behavior studies, and discuss the current challenges as well as future research directions in this field.Publication Open Access 3D printed microneedles for point of care biosensing applications(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Department of Mechanical Engineering; Sarabi, Misagh Rezapour; Nakhjavani, Sattar Akbar; Taşoğlu, Savaş; Faculty Member; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); Koç Üniversitesi İş Bankası Yapay Zeka Uygulama ve Araştırma Merkezi (KUIS AI)/ Koç University İş Bank Artificial Intelligence Center (KUIS AI); Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 291971Microneedles (MNs) are an emerging technology for user-friendly and minimally invasive injection, offering less pain and lower tissue damage in comparison to conventional needles. With their ability to extract body fluids, MNs are among the convenient candidates for developing biosensing setups, where target molecules/biomarkers are detected by the biosensor using the sample collected with the MNs. Herein, we discuss the 3D printing of microneedle arrays (MNAs) toward enabling point-of-care (POC) biosensing applications.Publication Open Access Statistical thermodynamics of residue fluctuations in native proteins(American Institute of Physics (AIP) Publishing, 2009) Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Yoğurtçu, Osman Nuri; Gür, Mert; Erman, Burak; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; College of Engineering; N/A; N/A; 179997Statistical thermodynamics of residue fluctuations of native proteins in a temperature, pressure, and force reservoir is formulated. The general theory is discussed in terms of harmonic and anharmonic fluctuations of residues. The two elastic network models based on the harmonic approximation, the anisotropic network and the Gaussian network models are discussed as the limiting cases of the general theory. The heat capacity and the correlations between the energy fluctuations and residue fluctuations are obtained for the harmonic approximation. The formulation is extended to large fluctuations of residues in order to account for effects of anharmonicity. The fluctuation probability function is constructed for this purpose as a tensorial Hermite series expansion with higher order moments of fluctuations as coefficients. Evaluation of the higher order moments using the proposed statistical thermodynamics model is explained. The formulation is applied to a hexapeptide and the fluctuations of residues obtained by molecular dynamics simulations are characterized in the framework of the model developed. In particular, coupling of two different modes in the nonlinear model is discussed in detail.