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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access DNA methylation profiling identifies novel markers of progression in hepatitis B-related chronic liver disease(BioMed Central, 2016) Vatansever, Sezgin; Hardy, Timothy; Sarı, Aysegül Akder; Çakalağaoğlu, Fulya; Avcı, Arzu; Zeybel, Gemma Louise; Bashton, Matthew; Mathers, John C.; Ünsal, Belkis; Mann, Jelena; N/A; Department of Molecular Biology and Genetics; Department of Molecular Biology and Genetics; Zeybel, Müjdat; Karahüseyinoğlu, Serçin; Faculty Member; Faculty Member; School of Medicine; 214694; 110772Background: Chronic hepatitis B infection is characterized by hepatic immune and inflammatory response with considerable variation in the rates of progression to cirrhosis. Genetic variants and environmental cues influence predisposition to the development of chronic liver disease; however, it remains unknown if aberrant DNA methylation is associated with fibrosis progression in chronic hepatitis B. Results: To identify epigenetic marks associated with inflammatory and fibrotic processes of the hepatitis B-induced chronic liver disease, we carried out hepatic genome-wide methylation profiling using Illumina Infinium beadarrays comparing mild and severe fibrotic disease in a discovery cohort of 29 patients. We obtained 310 differentially methylated regions and selected four loci comprising three genes from the top differentially methylated regions: hypermethylation of HOXA2 and HDAC4 along with hypomethylation of PPP1R18 were significantly linked to severe fibrosis. We replicated the prominent methylation marks in an independent cohort of 102 patients by bisulfite modification and pyrosequencing. The timing and causal relationship of epigenetic modifications with disease severity was further investigated using a cohort of patients with serial biopsies. Conclusions: Our findings suggest a linkage of widespread epigenetic dysregulation with disease progression in chronic hepatitis B infection. Cpg methylation at novel genes sheds light on new molecular pathways, which can be potentially exploited as a biomarker or targeted to attenuate inflammation and fibrosis.Publication Open Access Ultraslow optical modes in Bose-Einstein condensates(Society of Photo-optical Instrumentation Engineers (SPIE), 2007) Tarhan, Devrim; Postacıoğlu, Nazmi; Department of Physics; Department of Physics; Müstecaplıoğlu, Özgür Esat; Faculty Member; College of Sciences; 1674Light can be slowed down to ultraslow speeds via electromagnetically induced transparency in atomic Bose-Einstein condensates. This is thought to be useful for storage of quantum information for weak probe pulses. We investigate the effects of inhomogeneous density profile of-the condensate on propagation of such ultraslow pulses. We find that spatial density of an atomic condensate leads to a graded refractive index profile, for an off-resonant probe pulse when condensate parameters are suitably chosen. Within the window of negligible absorption, conditions for degenerate multiple waveguide modes are determined. Both analytical and numerical studies are presented to reveal the effects of experimentally controllable parameters, such as temperature and interatomic interaction strength on the number of modes. Group velocity dispersion and modal dispersion are discussed. The effect of waveguide dispersion, in addition to usual material dispersion, on ultraslow pulses is pointed out.Publication Open Access On the capacity of diffusion-based molecular communications with SiNW FET-based receiver(Institute of Electrical and Electronics Engineers (IEEE), 2016) Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; Kuşcu, Murat; Akan, Özgür Barış; Faculty Member; College of EngineeringMolecular communication (MC) is a bio-inspired communication method based on the exchange of molecules for information transfer among nanoscale devices. Although MC has been extensively studied from various aspects, limitations imposed by the physical design of transceiving units have been largely neglected in the literature. Recently, we have proposed a nanobioelectronic MC receiver architecture based on the nanoscale field effect transistor-based biosensor (bioFET) technology, providing noninvasive and sensitive molecular detection at nanoscale while producing electrical signals at the output. In this paper, we derive analytical closed-form expressions for the capacity and capacity-achieving input distribution for a memoryless MC channel with a silicon nanowire (SiNW) FET-based MC receiver. The resulting expressions could be used to optimize the information flow in MC systems equipped with nanobioelectronic receivers.Publication Open Access Database for CO2 separation performances of MOFs based on computational materials screening(American Chemical Society (ACS), 2018) Eruçar, İlknur; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Altıntaş, Çiğdem; Avcı, Gökay; Harman, Hilal Dağlar; Azar, Ayda Nemati Vesali; Velioğlu, Sadiye; Keskin, Seda; Researcher; Post Doctorate Student; College of Engineering; N/A; N/A; N/A; N/A; N/A; 40548Metal-organic frameworks (MOFs) are potential adsorbents for CO2 capture. Because thousands of MOFs exist, computational studies become very useful in identifying the top performing materials for target applications in a time-effective manner. In this study, molecular simulations were performed to screen the MOF database to identify the best materials for CO2 separation from flue gas (CO2/N-2) and landfill gas (CO2/CH4) under realistic operating conditions. We validated the accuracy of our computational approach by comparing the simulation results for the CO2 uptakes, CO2/N-2 and CO2/CH4 selectivities of various types of MOFs with the available experimental data. Binary CO2/N-2 and CO2/CH4 mixture adsorption data were then calculated for the entire MOF database. These data were then used to predict selectivity, working capacity, regenerability, and separation potential of MOFs. The top performing MOF adsorbents that can separate CO2/N-2 and CO2/CH4 with high performance were identified. Molecular simulations for the adsorption of a ternary CO2/N-2/CH4 mixture were performed for these top materials to provide a more realistic performance assessment of MOF adsorbents. The structure-performance analysis showed that MOFs with Delta Q(st)(0) > 30 kJ/mol, 3.8 angstrom < pore-limiting diameter < 5 angstrom, 5 angstrom < largest cavity diameter < 7.5 angstrom, 0.5 < phi < 0.75, surface area < 1000 m(2)/g, and rho > 1 g/cm(3) are the best candidates for selective separation of CO2 from flue gas and landfill gas. This information will be very useful to design novel MOFs exhibiting high CO2 separation potentials. Finally, an online, freely accessible database https://cosmoserc.ku.edu.tr was established, for the first time in the literature, which reports all of the computed adsorbent metrics of 3816 MOFs for CO2/N-2, CO2/CH4, and CO2/N-2/CH4 separations in addition to various structural properties of MOFs.Publication Open Access The variable selection problem in the Three Worlds of Welfare literature(Springer, 2019) Öker, İbrahim; Yıldırım, Kerem; Yakut-Çakar, Burcu; Department of Sociology; Department of Sociology; Yörük, Erdem; Faculty Member; College of Social Sciences and Humanities; 28982Based on a quantitative meta-analysis of empirical studies, this article points out a significant flaw in the Three Worlds of Welfare literature, the variable selection problem. Compiling, classifying, and quantitatively analysing all variables that have been employed in this literature, the article shows first that variable selection has depended more on case selection than on theory. Scholars tend to employ variables based on data availability, rather than selecting variables according to theoretical frameworks. Second, the use of welfare policy variables is mostly limited to the analysis of Organization for Economic Co-operation and Development (OECD) countries, while studies analysing non-OECD countries, where data is limited, tend to use developmental outcome variables as a proxy. This tendency harms conceptualization and operationalization of welfare regimes, as well as blur the boundary between development and welfare regimes studies. Third, the use of original Esping-Andersen variables remains very limited, undermining continuity, comparability, and reliability within the literature.Publication Open Access Improving CO2 separation performance of MIL-53(Al) by incorporating 1-N-Butyl-3-methylimidazolium methyl sulfate(Wiley, 2019) Department of Chemical and Biological Engineering; N/A; Department of Chemical and Biological Engineering; Kulak, Harun; Polat, Hüsamettin Mert; Kavak, Safiyye; Keskin, Seda; Uzun, Alper; Faculty Member; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; N/A; N/A; N/A; 40548; 599171-n-Butyl-3-methylimidazolium methyl sulfate is incorporated into MIL-53(Al). Detailed characterization is done by X-ray fluorescence, Brunauer-Emmett-Teller surface area, scanning electron microscopy, X-ray diffraction, Fourier-transform infrared spectroscopy, and thermogravimetric analysis. Results show that ionic liquid (IL) interacts directly with the framework, significantly modifying the electronic environment of MIL-53(Al). Based on the volumetric gas adsorption measurements, CO2, CH4, and N-2 adsorption capacities decreased from 112.0, 46.4, and 19.6 cc (STP) g(MIL-53(Al))(-1) to 42.2, 13.0, and 4.3 cc (STP) g(MIL-53(Al))(-1) at 5 bar, respectively, upon IL incorporation. Data show that this postsynthesis modification leads to more than two and threefold increase in the ideal selectivity for CO2 over CH4 and N-2 separations, respectively, as compared with pristine MIL-53(Al). The isosteric heat of adsorption (Qst) values show that IL incorporation increases CO2 affinity and decreases CH4 and N-2 affinities. Cycling adsorption-desorption measurements show that the composite could be regenerated with almost no decrease in the CO2 adsorption capacity for six cycles and confirm the lack of any significant IL leaching. The results offer MIL-53(Al) as an excellent platform for the development of a new class of IL/MOF composites with exceptional performance for CO2 separation.Publication Open Access Topological superfluid phases of an atomic Fermi gas with in- and out-of-plane Zeeman fields and equal Rashba-Dresselhaus spin-orbit coupling(American Physical Society (APS), 2013) Subaşı, Ahmet Levent; Department of Physics; Department of Physics; Işkın, Menderes; Faculty Member; College of Sciences; 29659We analyze the effects of in-and out-of-plane Zeeman fields on the BCS-Bose-Einstein condensation (BEC) evolution of a Fermi gas with equal Rashba-Dresselhaus (ERD) spin-orbit coupling (SOC). We show that the ground state of the system involves gapless superfluid phases that can be distinguished with respect to the topology of the momentum-space regions with zero excitation energy. For the BCS-like uniform superfluid phases with zero center-of-mass momentum, the zeros may correspond to one or two doubly degenerate spheres, two or four spheres, two or four concave spheroids, or one or two doubly degenerate circles, depending on the combination of Zeeman fields and SOC. Such changes in the topology signal a quantum phase transition between distinct superfluid phases and leave their signatures on some thermodynamic quantities. We also analyze the possibility of Fulde-Ferrell-Larkin-Ovchinnikov (FFLO)-like nonuniform superfluid phases with finite center-of-mass momentum and obtain an even richer phase diagram.Publication Open Access Stickelberger elements and Kolyvagin systems(Duke University Press (DUP), 2011) Department of Mathematics; Department of Mathematics; Büyükboduk, Kazım; Faculty Member; College of SciencesIn this paper, we construct (many) Kolyvagin systems out of Stickelberger elements utilizing ideas borrowed from our previous work on Kolyvagin systems of Rubin-Stark elements. The applications of our approach are twofold. First, assuming Brumer’s conjecture, we prove results on the odd parts of the ideal class groups of CM fields which are abelian over a totally real field, and we deduce Iwasawa’s main conjecture for totally real fields (for totally odd characters). Although this portion of our results has already been established by Wiles unconditionally (and refined by Kurihara using an Euler system argument, when Wiles’s work is assumed), the approach here fits well in the general framework the author has developed elsewhere to understand Euler/Kolyvagin system machinery when the core Selmer rank is r >1 (in the sense of Mazur and Rubin). As our second application, we establish a rather curious link between the Stickelberger elements and Rubin-Stark elements by using the main constructions of this article hand in hand with the “rigidity” of the collection of Kolyvagin systems proved by Mazur, Rubin, and the author.Publication Open Access Silicon photonics with microspheres(Society of Photo-optical Instrumentation Engineers (SPIE), 2006) Department of Physics; N/A; Department of Physics; Serpengüzel, Ali; Akatlar, Onur; Kurt, Adnan; Faculty Member; Teaching Faculty; College of Sciences; College of Engineering; 27855; N/A; 194455Silicon microspheres coupled to optical fibers have been used for optical channel dropping in the near-IR. The observed morphology dependent resonances had quality factors of 100000. These optical resonances provide the necessary narrow linewidths, that are needed for high resolution optical filtering applications in the near-IR. In addition to filtering, detection, and switching applications of this photonic system is studied in the near-IR as well as far-IR. The silicon microsphere shows promise as a building block for silicon photonics in the near-IR as well as, mid-IR, and far-IR.Publication Open Access Analysis of correlations between energy and residue fluctuations in native proteins and determination of specific sites for binding(American Physical Society (APS), 2009) Haliloğlu, Turkan; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; College of Engineering; 179997The Gaussian network model is used to derive the correlations between energy and residue fluctuations in native proteins. Residues are identified that respond strongly to energy fluctuations and that display correlations with the remaining residues of the protein at the highest modes. We postulate that these residues are located at specific sites for drug binding. We test the validity of this postulate on a data set of 33 structurally distinct proteins in the unbound state. Detailed results are presented for drug binding to the HIV protease.