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Publication Metadata only Deformations of Bloch groups and Aomoto dilogarithms in characteristic p(Academic Press Inc Elsevier Science, 2011) Department of Mathematics; Ünver, Sinan; Faculty Member; Department of Mathematics; College of Sciences; 177871In this paper, we study the Bloch group B-2(F[epsilon](2)) over the ring of dual numbers of the algebraic closure of the field with p elements, for a prime p >= 5. We show that a slight modification of Kontsevich's 11/2-logarithm defines a function on B-2(F[epsilon](2)). Using this function and the characteristic p version of the additive dilogarithm function that we previously defined, we determine the structure of the infinitesimal part of B-2(Ff[epsilon](2)) completely. This enables us to define invariants on the group of deformations of Aomoto dilogarithms and determine its structure. This final result might be viewed as the analog of Hilbert's third problem in characteristic p.Publication Metadata only Effects of ligand binding upon flexibility of proteins(Wiley-Blackwell, 2015) Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997Binding of a ligand on a protein changes the flexibility of certain parts of the protein, which directly affects its function. These changes are not the same at each point, some parts become more flexible and some others become stiffer. Here, an equation is derived that gives the stiffness map for proteins. The model is based on correlations of fluctuations of pairs of points in proteins, which may be evaluated at different levels of refinement, ranging from all atom molecular dynamics to general elastic network models, including the simplest case of isotropic Gaussian Network Model. The latter is used, as an example, to evaluate the changes of stiffness upon dimerization of ACK1. Proteins 2015; 83:805-808. (c) 2015 Wiley Periodicals, Inc.Publication Metadata only Spectroscopic characterization of Tm3+:TeO2-K2O-Nb2O5 glasses for 2- μm lasing applications(Elsevier Science Bv, 2012) Kurt, Adnan; Speghini, Adolfo; Bettinelli, Marco; Department of Physics; Department of Physics; Department of Physics; Görgülü, Adil Tolga; Çankaya, Hüseyin; Sennaroğlu, Alphan; Master Student; Researcher; Faculty Member; Department of Physics; College of Sciences; College of Sciences; College of Sciences; N/A; N/A; 23851We have performed detailed experiments to investigate the spectroscopic properties of a new type of tellurite based host doped with thulium: Tm2O3:(0.70)TeO2-(0.15)K2O-(0.15)Nb2O5 having Tm2O3 concentrations of 0.125, 0.25, 0.5, and 1.0 mol%. By performing a Judd-Ofelt analysis of the absorption bands, we obtained average radiative lifetimes of 2.57 +/- 0.20 and 0.35 +/- 0.01 ms for the H-3(4) and F-3(4) levels, respectively. Furthermore, we also observed that an increase in the Tm2O3 concentration from 0.125 to 1.0 mol% results in a decrease of the measured fluorescence lifetime from 814 to 439 mu s and from 258 to 47 mu s for the H-3(4) and F-3(4) levels, respectively, due to efficient non-radiative decay. The highest quantum efficiency of 32% was obtained for the sample doped with 0.125 mol% Tm2O3 for the H-3(4) level. Results show that cross relaxation becomes important as the ion concentration is increased, leading to the quenching of the 1460-nm band and enhancement of the 1860-nm emission. The highest emission cross section of 6.85 x 10(-21) Cm-2 measured for the 1860-nm band reveals the potential of this host for the development of 2-mu m lasers in bulk glass as well as fiber media. (C) 2011 Published by Elsevier B.V.Publication Metadata only TNF-alpha inhibition prevents cognitive decline and maintains hippocampal BDNF levels in the unpredictable chronic mild stress rat model of depression(Elsevier, 2015) Şahin, Tuğce Demirtaş; Karson, Ayşe; Yazır, Yusufhan; Bayramgürler, Dilek; Utkan, Tijen; Department of Psychology; Balcı, Fuat; Faculty Member; Department of Psychology; College of Social Sciences and Humanities; 51269Previous findings have shown that patients with depression express higher levels of proinflammatory cytokines such as TNF-alpha and IL-6. We have recently found that Infliximab (a TNF-alpha inhibitor) decreased anhedonia and despair-like behavior in the rat unpredictable chronic mild stress (UCMS) model of depression suggesting that inflammation might play an important role in depression. An increasing number of studies suggest that inflammation is also associated with cognitive impairments. The current study aimed to investigate the effect of UCMS on the cognitive performance of rats and their hippocampal BDNF levels and the effect of chronic Infliximab (5 mg/kg/weekly, i.p.) treatment on these measures. Rats were subjected to different types of stressors daily for a period of 56 days to induce depression-like state. The UCMS resulted in impairments in spatial and emotional memory acquisition and retention with no effect on the level of locomotor activity. These behavioral effects of UCMS were accompanied by reduction in the level of BDNF in the CA1 and CA3 regions of the hippocampus. Chronic Infliximab treatment prevented the UCMS-induced cognitive impairments as well as the reduction in the levels of hippocampal brain-derived neurotrophic factor (BDNF). These results suggest that Infliximab improves the spatial and emotional memory impairments induced by chronic stress in rats likely through its effects on hippocampal function by modulating inflammation.Publication Metadata only Rice bodies within the neuropathic hip in a child with congenital insensitivity to pain(Springer, 2015) Özcan, Hatice Nursun; Aydıngöz, Üstün; Kara, Ateş; Ergen, Fatma Bilge; N/A; Marangoz, Salih; Faculty Member; School of Medicine; 170439N/APublication Metadata only Between Socrates and Kant. Thinking and sensus communis in Arendt's conception of the banality of evil(Edizioni Ets, 2017) Department of Philosophy; Roney, Patrick; Faculty Member; Department of Philosophy; College of Social Sciences and Humanities; N/AThe aim of this paper is to show how Hannah Arendt develops her concept of the banality of evil through a phenomenological appropriation of Kant's theory of judgment and of the principle of sensus communis in particular. Even though Arendt initially defined the banality of evil as a form of thoughtlessness grounded upon her understanding of thinking as an inner dialogue with one's 'other' self, I argue that she develops the concept much more extensively in relation to Kant's doctrine of reflective judgment and the possibility of a sensus communis as a pre-conceptual model of unforced consensus for the public space. I further argue that her reading of Kant is carried out together with both an existential-ontological re-appraisal of appearances and its relation to the transcendental imagination. Through the emphasis on the sensus communis, the banality of evil can then be re-defined as a refusal of the same.Publication Metadata only Quasi-harmonic fluctuations of two bound peptides(Wiley-Blackwell, 2012) N/A; Department of Chemical and Biological Engineering; Gür, Mert; Erman, Burak; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; 216930; 179997Binding of two short peptides of sequences ASN-ASP-MET-PHE-ARG-LEU and LEU-LEU-PHE-MET-GLN-HIS and their bound complex structures is studied. Molecular dynamic simulations of the three structures around their respective minimum energy conformations are performed and a quasi-harmonic analysis is performed over the trajectories generated. The fluctuation correlation matrix is constructed for all C-alpha-atoms of the peptides for the full trajectory. The spring constant matrix between peptide C-alpha-atoms is obtained from the correlation matrix. Statistical thermodynamics of fluctuations, the energies, entropies, and the free energies of binding are discussed in terms of the quasi-harmonic model. Sites contributing to the stability of the system and presenting high affinity for binding are determined. Contribution of hydrophobic forces to binding is discussed. Quasi-harmonic approximation identifies the essential subspace of motions, the important interactions, and binding sites, gives the energetic contribution of each individual interaction, and filters out noise observed in molecular dynamics owing to uncorrelated motions. Comparison of the molecular dynamics results with those of the quasi-harmonic model shows the importance of entropy change, resulting from water molecules being liberated from the surfaces of the two peptides upon binding.Publication Metadata only How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues(Cell Press, 2005) Haliloğlu, Türkan; Ma, Buyong; Nussinov, Ruth; Department of Chemical and Biological Engineering; Keskin, Özlem; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 26605The underlying physico-chemical principles of the interactions between domains in protein folding are similar to those between protein molecules in binding. Here we show that conserved residues and experimental hot spots at intermolecular binding interfaces overlap residues that vibrate with high frequencies. Similarly, conserved residues and hot spots are found in protein cores and are also observed to vibrate with high frequencies. In both cases, these residues contribute significantly to the stability. Hence, these observations validate the proposition that binding and folding are similar processes. In both packing plays a critical role, rationalizing the residue conservation and the experimental alanine scanning hot spots. We further show that high-frequency vibrating residues distinguish between protein binding sites and the remainder of the protein surface.Publication Metadata only Parallel computing in Asian option pricing(Elsevier Science Bv, 2007) Sak, Halis; Boduroglu, Ilkay; Department of Industrial Engineering; Özekici, Süleyman; Faculty Member; Department of Industrial Engineering; College of Engineering; 32631We discuss the use of parallel computing in Asian option pricing and evaluate the efficiency of various algorithms. We only focus on "backward-starting fixed strike" Asian options that are continuously averaged. We implement a partial differential equation (PDE) approach that involves a single state variable to price the Asian option, and implement the same methodology to price a standard European option to check for accuracy. A parabolic PDE is solved by using both explicit and Crank-Nicolson's implicit finite-difference methods. In particular, we look for algorithms designed for implementing the computations in massively parallel processors (MPP). We evaluate the performance of the algorithms by comparing the numerical results with respect to accuracy and wall-clock time of code executions. Codes are executed on a Linux PC cluster.Publication Metadata only Asymptotic behavior of the irrational factor(Springer, 2008) Ledoan, A. H.; Zaharescu, Alexandru; Department of Mathematics; Alkan, Emre; Faculty Member; Department of Mathematics; College of Sciences; 32803We study the irrational factor function I(n) introduced by Atanassov and defined by I(n) = Pi(k)(k=1)p(v)(1/alpha v), where n = Pi(k)(v=1) p(v)(alpha v) is the prime factorization of n. We show that the sequence {G(n)/n}(n >= 1), where G(n) = Pi(n)(v=1) I(v)(1/n), is covergent; this answers a question of Panaitopol. We also establish asymptotic formulas for averages of the function I(n).