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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 photonic Carnot engine powered by a spin-star network(European Physical Society (EPS), 2017) Türkpençe, Deniz; Paternostro, Mauro; Department of Physics; Altıntaş, Ferdi; Müstecaplıoğlu, Özgür Esat; Researcher; Faculty Member; Department of Physics; College of Sciences; N/A; 1674We propose a spin-star network, where a central spin-(1/2), acting as a quantum fuel, is coupled to N outer spin-(1/2) particles. If the network is in thermal equilibrium with a heat bath, the central spin can have an effective temperature, higher than that of the bath, scaling nonlinearly with N. Such temperature can be tuned with the anisotropy parameter of the coupling. Using a beam of such central spins to pump a micromaser cavity, we determine the dynamics of the cavity field using a coarse-grained master equation. We find that the central-spin beam effectively acts as a hot reservoir to the cavity field and brings it to a thermal steady state whose temperature benefits from the same nonlinear enhancement with N and results in a highly efficient photonic Carnot engine. The validity of our conclusions is tested against the presence of atomic and cavity damping using a microscopic master equation method for typical microwave cavity-QED parameters. The role played by quantum coherence and correlations on the scaling effect is pointed out. An alternative scheme where the spin-(1/2) is coupled to a macroscopic spin-(N/2) particle is also discussed. Copyright (C) EPLA, 2017
Publication Metadata only Adsorption, folding, and packing of an amphiphilic peptide at the air/water interface(amer Chemical Soc, 2012) 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; 109820Peptide oligomers play an essential role as model compounds for identifying key motifs in protein structure formation and protein aggregation. Here, we present our results, based on extensive molecular dynamics simulations, on adsorption, folding, and packing within a surface monolayer of an amphiphilic peptide at the air/water interface. Experimental results suggest that these molecules spontaneously form ordered monolayers at the interface, Adopting a beta-hairpin-like structure within the surface layer. Our results reveal that the beta-hairpin structure can be observed both in bulk and at the air/water interface. However, the presence of an interface leads to ideal partitioning of the hydrophobic and hydrophilic residues, and therefore reduces the conformational space for the molecule and increases the stability of the hairpin structure. We obtained the adsorption free energy of a single beta-hairpin at the air/water interface, and analyzed the enthalpic and entropic contributions. the adsorption process is favored by two main factors: (1) Free-energy reduction due to desolvation of the hydrophobic side chains of the peptide and release of the water molecules which form a cage around these hydrophobic groups in bulk water. (2) Reduction of the total air/water contact area at the interface upon adsorption of the peptide amphiphile. By performing mutations on the original molecule, we demonstrated the relative role of key design features of the peptide. Finally, by analyzing the potential of mean force among two peptides at the interface, we investigated possible packing mechanisms for these molecules within the surface monolayer.Publication Open Access Analysis of push-type epidemic data dissemination in fully connected networks(Elsevier, 2014) Sezer, Ali Devin; Department of Mathematics; Çağlar, Mine; Faculty Member; Department of Mathematics; College of Sciences; 105131Consider a fully connected network of nodes, some of which have a piece of data to be disseminated to the whole network. We analyze the following push-type epidemic algorithm: in each push round, every node that has the data, i.e., every infected node, randomly chooses c E Z. other nodes in the network and transmits, i.e., pushes, the data to them. We write this round as a random walk whose each step corresponds to a random selection of one of the infected nodes; this gives recursive formulas for the distribution and the moments of the number of newly infected nodes in a push round. We use the formula for the distribution to compute the expected number of rounds so that a given percentage of the network is infected and continue a numerical comparison of the push algorithm and the pull algorithm (where the susceptible nodes randomly choose peers) initiated in an earlier work. We then derive the fluid and diffusion limits of the random walk as the network size goes to infinity and deduce a number of properties of the push algorithm: (1) the number of newly infected nodes in a push round, and the number of random selections needed so that a given percent of the network is infected, are both asymptotically normal, (2) for large networks, starting with a nonzero proportion of infected nodes, a pull round infects slightly more nodes on average, (3) the number of rounds until a given proportion lambda of the network is infected converges to a constant for almost all lambda is an element of (0, 1). Numerical examples for theoretical results are provided.Publication Open Access Averaged vs. quenched large deviations and entropy for random walk in a dynamic random environment(University of Washington Press, 2017) Rassoul-Agha, Firas; Seppalainen, Timo; Department of Mathematics; Yılmaz, Atilla; Faculty Member; Department of Mathematics; College of Sciences; 26605We consider random walk with bounded jumps on a hypercubic lattice of arbitrary dimension in a dynamic random environment. The environment is temporally independent and spatially translation invariant. We study the rate functions of the level-3 averaged and quenched large deviation principles from the point of view of the particle. In the averaged case the rate function is a specific relative entropy, while in the quenched case it is a Donsker-Varadhan type relative entropy for Markov processes. We relate these entropies to each other and seek to identify the minimizers of the level-3 to level-1 contractions in both settings. Motivation for this work comes from variational descriptions of the quenched free energy of directed polymer models where the same Markov process entropy appears.Publication Open Access Collisional relaxation kinetics for ortho and para NH2- under photodetachment in cold ion traps(Royal Society of Chemistry (RSC), 2018) Gianturco, Francesco A.; Lakhmanskaya, Olga Y.; Vera, Mario Hernandez; Wester, Roland; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129The collisional cooling of the internal rotational states of the nonlinear anion NH2- ((1)A(1)), occurring at the low temperature of a cold ion trap under helium buffer gas cooling, is examined via quantum dynamics calculations and ion decay rate measurements. The calculations employ a novel ab initio potential energy surface that describes the interaction anisotropy and range of action between the molecular anions and the neutral He atoms. The state changing integral cross sections are employed to obtain the state-to-state rate coefficients, separately for the ortho- and the para-NH2- ions. These rates are in turn used to compute the state population evolution in the trap for both species, once photodetachment by a laser is initiated in the trap. The present work shows results for the combined losses of both species after the photodetachment laser is switched on and analyzes the differences of loss kinetics between the two hyperfine isomers.Publication Open Access Content-aware scalability-type selection for rate adaptation of scalable video(Springer, 2007) Akyol, Emrah; Civanlar, M. Reha; (TBD); Tekalp, Ahmet Murat; Faculty Member; (TBD); College of Engineering; 26207Scalable video coders provide different scaling options, such as temporal, spatial, and SNR scalabilities, where rate reduction by discarding enhancement layers of different scalability-type results in different kinds and/or levels of visual distortion depend on the content and bitrate. This dependency between scalability type, video content, and bitrate is not well investigated in the literature. To this effect, we first propose an objective function that quantifies flatness, blockiness, blurriness, and temporal jerkiness artifacts caused by rate reduction by spatial size, frame rate, and quantization parameter scaling. Next, the weights of this objective function are determined for different content (shot) types and different bitrates using a training procedure with subjective evaluation. Finally, a method is proposed for choosing the best scaling type for each temporal segment that results in minimum visual distortion according to this objective function given the content type of temporal segments. Two subjective tests have been performed to validate the proposed procedure for content-aware selection of the best scalability type on soccer videos. Soccer videos scaled from 600 kbps to 100 kbps by the proposed content- aware selection of scalability type have been found visually superior to those that are scaled using a single scalability option over the whole sequence.Publication Open Access Data reduction methods for ektacytometry in clinical hemorheology(IOS Press, 2013) Meiselman, Herbert J.; Başkurt, Oğuz Kerim; Faculty Member; School of Medicine; 2389Laser-diffraction ektacytometry is a generally accepted technique for measuring RBC deformability induced by fluid shear stress (SS) and yields paired elongation index-SS data at several levels of stress. Unfortunately, comparison of results is hindered by the lack of simple indices that accurately characterize these data. Several mathematical models have been proposed, including those developed for analysis of enzyme kinetics (Lineweaver-Burk, Eadie-Hofstee) and curve fitting (Streekstra-Bronkhorst). All of these analytical approaches provide a value for cell deformation at infinite stress (EImax) and the shear stress required to achieve one-half of this deformation (SS1/2); the use of non-linear regression is essential when calculating these parameters. While the current models provide equivalent results for normal RBC if used with non-linear regression, EImax and SS1/2 are not always concordant for cells with abnormal mechanical behavior. This technical note examines such differences for three conditions: glutaraldehyde treatment, mechanical stress and non-isotonic media. It was found that none of the models yield completely satisfactory values for EImax and SS1/2, especially if there are large changes of EImax. However, the ratio of SS1/2 to EImax (SS1/2/EImax) is much less affected by these problems, has similar power (i.e., standardized difference) as SS1/2 and EImax and is more robust in reflecting alterations of deformability. We thus conclude that the SS1/2/EImax ratio can be used when reporting and comparing various populations of RBC or cells obtained from subjects having different clinical states.Publication Metadata only Discretionary bonuses and turnover(Elsevier, 2019) Department of Economics; Ekinci, Emre; Faculty Member; Department of Economics; College of Administrative Sciences and Economics; 309364This paper develops a signaling model to investigate the effects of discretionary bonuses and wage increases on turnover. When the worker's output is not contractible and the firm privately learns about the match quality between the firm and the worker, bonus payments and wage increases can convey the firm's private information to the worker. If the firm credibly communicates favorable information about the match quality to a worker, the worker develops higher expectations concerning her career outcomes at the firm (such as future wage increases and promotions) and, consequently, becomes less likely to separate. The analysis demonstrates that although a wage increase and a bonus reflect the same information regarding the match quality, each serves a distinctly different role in terms of the worker's turnover decision. Specifically, the firm pays bonuses to signal a good match while using wages to respond to competing offers the worker receives. The model yields testable predictions that concern how bonuses are related to wage increases and promotions and how bonuses and wage increases are related to turnover. The empirical analysis based on the data constructed from the personnel records of a large firm in the financial services industry provides support for the model's implications.Publication Open Access Distributed patterns of brain activity that lead to forgetting(Frontiers, 2011) Badre, David; Department of Psychology; Öztekin, İlke; PhD Student; Department of Psychology; College of Social Sciences and HumanitiesProactive interference (PI), in which irrelevant information from prior learning disrupts memory performance, is widely viewed as a major cause of forgetting. However, the hypothesized spontaneous recovery (i.e., automatic retrieval) of interfering information presumed to be at the base of PI remains to be demonstrated directly. Moreover, it remains unclear at what point during learning and/or retrieval interference impacts memory performance. In order to resolve these open questions, we employed a machine-learning algorithm to identify distributed patterns of brain activity associated with retrieval of interfering information that engenders PI and causes forgetting. Participants were scanned using functional magnetic resonance imaging during an item recognition task. We induced PI by constructing sets of three consecutive study lists from the same semantic category. The classifier quantified the magnitude of category-related activity at encoding and retrieval. Category-specific activity during retrieval increased across lists, consistent with the category information becoming increasingly available and producing interference. Critically, this increase was correlated with individual differences in forgetting and the deployment of frontal lobe mechanisms that resolve interference. Collectively, these findings suggest that distributed patterns of brain activity pertaining to the interfering information during retrieval contribute to forgetting. The prefrontal cortex mediates the relationship between the spontaneous recovery of interfering information at retrieval and individual differences in memory performance.