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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 Metallodielectric photonic crystals resonators(Society of Photo-optical Instrumentation Engineers (SPIE), 2003) Department of Physics; Serpengüzel, Ali; Faculty Member; Department of Physics; College of Sciences; 27855K-u band Fabry-Perot type resonances have been observed in the stop band of a metallodielectric photonic crystal by transmission measurements at microwave frequencies. The metallodielectric photonic crystal has a face centered cubic Bravais lattice structure with a lattice constant of 15 mm. Metallic spheres with 6.35 mm diameter are placed at the lattice sites. The metallodielectric photonic crystal displayed a directional bandgap with a lower band edge of 13.0 GHz, an upper band edge of 21.5 GHz, and a center frequency of 17.25 GHz, corresponding to a stop bandwidth center frequency ratio of 50%. The maximum rejection at the band center is 35 dB, corresponding to a 7 dB per unit cell rejection ratio. The Fabry-Perot type resonance in the k(u) band has a quality factor of 200, with a maximum transmission peak of -5 dB.Publication Open Access Protocol for structure determination of SARS-CoV-2 main protease at near-physiological-temperature by serial femtosecond crystallography(Cell Press, 2022) Dao, E. Han; Su, Zhen; Poitevin, Frederic; Yoon, Chun Hong; Kupitz, Christopher; Hayes, Brandon; Liang, Mengning; Hunter, Mark S.; Batyuk, Alexander; Sierra, Raymond G.; Ketawala, Gihan; Botha, Sabine; Department of Molecular Biology and Genetics; Ertem, Fatma Betül; Güven, Ömür; Büyükdağ, Cengizhan; Göcenler, Oktay; Ayan, Esra; Yüksel, Büşra; Gül, Mehmet; Karakadıoğlu, Gözde Usta; Çakılkaya, Barış; Johnson, Jerome Austin; Demirci, Hasan; Dağ, Çağdaş; Undergraduate Student; PhD Student; Master Student; Faculty Member; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; Koç Üniversitesi İş Bankası Enfeksiyon Hastalıkları Uygulama ve Araştırma Merkezi (EHAM) / Koç University İşbank Center for Infectious Diseases (KU-IS CID); Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; 307350The SARS-CoV-2 main protease of (Mpro) is an important target for SARS-CoV-2 related drug repurposing and development studies. Here, we describe the steps for structural characterization of SARS-CoV-2 Mpro, starting from plasmid preparation and protein purification. We detail the steps for crystallization using the sitting drop, microbatch (under oil) approach. Finally, we cover data collection and structure determination using serial femtosecond crystallography.Publication Open Access Refractive index-enhanced vortex lattices(Society of Photo-optical Instrumentation Engineers (SPIE), 2005) Oktel, Mehmet Özgür; Department of Physics; Müstecaplıoğlu, Özgür Esat; Faculty Member; Department of Physics; College of Sciences; 1674Light propagation through vortex matter in atomic Bose-Einstein condensates is examined. It is shown that vortex matter can be used as a photonic crystal by a refractive index enhancement scheme. Band structure of the vortex lattice is numerically calculated. Index enhanced vortex matter is shown to exhibit large refractive index contrast with the dilute thermal gas background in the vortex core. Depending on the depth of the index contrast full or directional photonic band gaps are found in the band structure. Experimental parameters required to generate band gaps in the visible region of the electromagnetic spectrum are calculated.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 Syntheses, crystal structures, magnetic properties and vibrational spectra of nitridoborate-halide compounds Sr-2[BN2]Br and Eu-2[BN2]X (X = Br, I) with isolated [BN2](3-) units(Oldenbourg Verlag, 2011) Aydemir, Umut; Prots, Yurii; Schnelle, Walter; Akselrud, Lev; Hoehn, Peter; Department of Chemistry; Kokal, İlkin; Somer, Mehmet Suat; Master Student; Faculty Member; Department of Chemistry; College of Sciences; N/A; 178882The title compounds Sr-2[BN2]Br (1), Eu-2[BN2]Br (2) and Eu-2[BN2]I (3) were obtained from reactions of mixtures of Sr-3[BN2](2) and SrBr2 (1) and the binaries EuN, h-BN and EuX2 (X = Br, I) (2, 3), respectively. The crystal structure of Sr-2[BN2]Br was solved from X-ray powder diffraction data and those of the europium compounds from X-ray single crystal data. Sr-2[BN2]Br and Eu-2[BN2]Br are isotypic crystallizing in the rhombohedral space group R (3) over barm (No. 166, Pearson code: hR18; Z = 3; a = 4.11692(2) angstrom, c = 26.4611(2) angstrom (1); a = 4.0728(3) angstrom, c = 26.589(3) angstrom (2)). The crystal structures are built up by layers of condensed edge-sharing [B-N-B]@Eu-6 and [Br]@Eu-6 trigonal antiprisms, which are alternately stacked along [001] Eu-2[BN2]I - isotypic to Sr-2[BN2]I - crystallizes in the monoclinic space group P2(1)/m (No. 11, Pearson code: mP24; Z = 4; a = 10.2548(6) angstrom, b = 4.1587(3) angstrom, c = 13.1234(9) angstrom, beta = 91.215(4)degrees). The crystal structure is characterized by slightly puckered layers formed by condensed edge-sharing I@Eu-6 octahedra which are separated by isolated [BN2](3-) units. The bond lengths for the strictly linear [BN2](3-) anions in (1) and (2) are d(B-N) = 1.351(4) angstrom and 1.356(8) angstrom, respectively. In Eu-2[BN2]I two crystallograhically distinct [BN2](3-) anions are present with d(B1-N) = 1.32(4) angstrom, 1.37(4)angstrom and d(B2-N) = 1.30(4) angstrom, 1.34(4) angstrom, respectively. Their bond angles vary slightly: angle(N-B1-N) = 179(3)degrees and angle(N-B2-N) = 177(3)degrees. The magnetic susceptibility data of the europium compounds (2) and (3) indicate that the Eu ions are divalent with 4f(7) configuration. Vibrational spectra were measured and interpreted based on the D infinity(h) symmetry of the discrete linear [N-B-N](3-) moieties, considering the site symmetry reduction and the presence of two distinct [BN2](3-) groups in (3).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.