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Publication Open Access An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser(International Union of Crystallography, 2020) Assalauova, Dameli; Kim, Young Yong; Bobkov, Sergey; Khubbutdinov, Ruslan; Rose, Max; Alvarez, Roberto; Andreasson, Jakob; Balaur, Eugeniu; Contreras, Alice; Gelisio, Luca; Hajdu, Janos; Hunter, Mark S.; Kurta, Ruslan P.; Li, Haoyuan; McFadden, Matthew; Nazari, Reza; Schwander, Peter; Teslyuk, Anton; Walter, Peter; Xavier, P. Lourdu; Yoon, Chun Hong; Zaare, Sahba; Ilyin, Viacheslav A.; Kirian, Richard A.; Hogue, Brenda G.; Aquila, Andrew; Vartanyants, Ivan A.; Department of Molecular Biology and Genetics; Demirci, Hasan; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; 307350An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from half of the detector and a small fraction of single hits. The general SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus-structure determination step. The presented processing pipeline allowed us to determine the 3D structure of bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits.Publication Open Access Effect of methylation of ionic liquids on the gas separation performance of ionic liquid/metal-organic framework composites(Royal Society of Chemistry (RSC), 2018) Department of Chemical and Biological Engineering; Nozari, Vahid; Keskin, Seda; Uzun, Alper; Zeeshan, Muhammad; Faculty Member; PhD Student; Department of Chemical and Biological Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Graduate School of Sciences and Engineering; N/A; 40548; 59917; N/A1-N-Butyl-3-methylimidazolium hexafluorophosphate, [BMIM]ijPF6], and its methylated form, 1-N-butyl2,3-dimethylimidazolium hexafluorophosphate, [BMMIM]ijPF6], were incorporated into CuBTC to examine the effect of methylation of ionic liquids (ILs) on the gas separation performance of the corresponding IL/ metal–organic framework (MOF) composites. Spectroscopic analysis revealed that the interactions of the methylated ILs with CuBTC were weaker compared to those of its non-methylated counterpart. Gas uptake measurements illustrated that this difference in the interactions influences the gas separation performance of the composites. Accordingly, the CO2/N2: 15/85 and CH4/N2: 50/50 selectivities increased by 37% and 60% for [BMMIM]ijPF6]/CuBTC and 34% and 50% for [BMIM]ijPF6]/CuBTC, respectively, compared to the corresponding selectivities of pristine CuBTC at 1000 mbar. The results revealed another structural parameter controlling the performance of the IL/MOF composites, a novel type of material with rapidly expanding application areas.Publication Open Access Enhancing CO2/CH4 and CO2/N-2 separation performances of ZIF-8 by post-synthesis modification with [BMIM][SCN](Elsevier, 2018) Department of Chemical and Biological Engineering; Keskin, Seda; Uzun, Alper; Zeeshan, Muhammad; Faculty Member; PhD Student; Department of Chemical and Biological Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Graduate School of Sciences and Engineering; 40548; 59917; N/AIonic liquid (IL)-incorporated metal organic frameworks (MOFs) are promising materials for gas adsorption and separation processes. In this work, 1-n-butyl-3-methylimidazolium thiocyanate ([BMIM][ SCN]) was incorporated in a zeolitic imidazolate framework (ZIF-8) to examine the adsorption and separation of different gases. X-ray diffraction (XRD) and scanning electron microscopy (SEM) results confirmed that ZIF-8 retains its structural integrity in the IL-incorporated sample. The Brunauer-Emmett-Teller (BET) surface area and pore volume of the IL-incorporated sample decreased significantly indicating the IL confinement into the MOF. Results of thermogravimetric analysis (TGA) demonstrate changes in the decomposition temperatures of both bulk IL and pristine ZIF-8 when the IL was incorporated into the MOF pores. Fourier transform infrared (FTIR) spectroscopy was performed to confirm the presence of interactions and successful incorporation of IL into MOF. Gas adsorption isotherms of CO2, CH4, and N-2 were measured for pristine ZIF-8 and IL-incorporated ZIF-8. The uptake amounts for each gas decreased as compared to their values on pristine ZIF-8, however, the decrease in the CO2 uptake was less compared to CH4 and N-2. The IL-incorporated sample exhibited approximately 2.6-times higher ideal selectivity for CO2/CH4 and four-times higher ideal selectivity for CO2/N-2 at 1 mbar than their corresponding values for pristine ZIF-8. These results indicate that IL-MOF combinations offer a huge potential for gas separations.Publication Open Access MOF/COF hybrids as next generation materials for energy and biomedical applications(Royal Society of Chemistry (RSC), 2022) Eruçar, İlknur; Department of Chemical and Biological Engineering; Keskin, Seda; Altıntaş, Çiğdem; Researcher; Department of Chemical and Biological Engineering; College of Engineering; Graduate School of Sciences and Engineering; 40548; N/AThe rapid increase in the number and variety of metal organic frameworks (MOFs) and covalent organic frameworks (COFs) has led to groundbreaking applications in the field of materials science and engineering. New MOF/COF hybrids combine the outstanding features of MOF and COF structures, such as high crystallinities, large surface areas, high porosities, the ability to decorate the structures with functional groups, and improved chemical and mechanical stabilities. These new hybrid materials offer promising performances for a wide range of applications including catalysis, energy storage, gas separation, and nanomedicine. In this highlight, we discuss the recent advancements of MOF/COF hybrids as next generation materials for energy and biomedical applications with a special focus on the use of computational tools to address the opportunities and challenges of using MOF/COF hybrids for various applications.Publication Open Access Semiconductor and dielectric microspheres for optoelectronic applications(Society of Photo-optical Instrumentation Engineers (SPIE), 2005) Department of Physics; Department of Electrical and Electronics Engineering; Serpengüzel, Ali; Yılmaz, Yiğit Ozan; Kurt, Adnan; Faculty Member; Master Student; Teaching Faculty; Department of Physics; Department of Electrical and Electronics Engineering; College of Sciences; 27855; N/A; 194455Microspheres possess high quality factor morphology-dependent resonances, i.e., whispering gallery modes. These resonances have narrow linewidths necessary for applications to compact optoelectronic devices for wavelength division multiplexing. The morphology dependent resonances have high quality factors of 104 and 105 with channel spacings of 0.14 nm in glass and 0.05 nm in silicon microspheres.Publication Open Access Zero-phonon-line emission of single molecules for applications in quantum information processing(Society of Photo-optical Instrumentation Engineers (SPIE), 2005) Ehrl, M; Brauchle, C; Zumbusch, A.; Hellerer, Th.; Department of Physics; Kiraz, Alper; Müstecaplıoğlu, Özgür Esat; Faculty Member; Faculty Member; Department of Physics; College of Sciences; 22542; 1674A single photon source which generates transform limited single photons is highly desirable for applications in quantum optics. Transform limited emission guarantees the indistinguishability of the emitted single photons. This, in turn brings groundbreaking applications in linear optics quantum information processing within an experimental reach. Recently, self-assembled InAs quantum dots and trapped atoms have successfully been demonstrated as such sources for highly indistinguishable single photons. Here, we demonstrate that nearly transform limited zero-phonon-line (ZPL) emission from single molecules can be obtained by using vibronic excitation. Furthermore we report the results of coincidence detection experiments at the output of a Michelson-type interferometer. These experiments reveal Hong-Ou-Mandel correlations as a proof of the indistinguishability of the single photons emitted consecutively from a single molecule. Therefore, single molecules constitute an attractive alternative to single InAs quantum dots and trapped atoms for applications in linear optics quantum information processing. Experiments were performed with a home-built confocal microscope keeping the sample in a superfluid liquid Helium bath at 1.4K. We investigated terrylenediimide (TDI) molecules highly diluted in hexadecane (Shpol'skii matrix). A continuous wave single mode dye laser was used for excitation of vibronic transitions of individual molecules. From the integral fluorescence, the ZPL of single molecules was selected with a spectrally narrow interference filter. The ZPL emission was then sent to a scanning Fabry-Perot interferometer for linewidth measurements or a Michelson-type interferometer for coincidence detection.