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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 Case study of high-throughput drug screening and remote data collection for SARS-CoV-2 main protease by using serial femtosecond X-ray crystallography(Multidisciplinary Digital Publishing Institute (MDPI), 2021) Botha, Sabine; Ketawala, Gihan; Su, Zhen; Hayes, Brandon; Poitevin, Frederic; Batyuk, Alexander; Yoon, Chun Hong; Kupitz, Christopher; Durdağı, Serdar; Sierra, Raymond G.; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Güven, Ömür; Gül, Mehmet; Ayan, Esra; Johnson, Jerome Austin; Çakılkaya, Barış; Karakadıoğlu, Gözde Usta; Ertem, Fatma Betül; Tokay, Nurettin; Yüksel, Büşra; Göcenler, Oktay; Büyükdağ, Cengizhan; Demirci, Hasan; PhD Student; Master Student; Undergraduate Student; Undergraduate Student; Faculty Member; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; 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; 307350Since early 2020, COVID-19 has grown to affect the lives of billions globally. A worldwide investigation has been ongoing for characterizing the virus and also for finding an effective drug and developing vaccines. As time has been of the essence, a crucial part of this research has been drug repurposing; therefore, confirmation of in silico drug screening studies have been carried out for this purpose. Here we demonstrated the possibility of screening a variety of drugs efficiently by leveraging a high data collection rate of 120 images/second with the new low-noise, high dynamic range ePix10k2M Pixel Array Detector installed at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS). The X-ray Free-Electron Laser (XFEL) is used for remote high-throughput data collection for drug repurposing of the main protease (Mpro) of SARS-CoV-2 at ambient temperature with mitigated X-ray radiation damage. We obtained multiple structures soaked with nine drug candidate molecules in two crystal forms. Although our drug binding attempts failed, we successfully established a high-throughput Serial Femtosecond X-ray crystallographic (SFX) data collection protocol.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 Fast and selective adsorption of methylene blue from water using [BMIM][PF6]-incorporated UiO-66 and NH2-UiO-66(American Chemical Society (ACS), 2020) Department of Chemical and Biological Engineering; N/A; Kulak, Harun; Keskin, Seda; Uzun, Alper; Kavak, Safiyye; Polat, Hüsamettin Mert; Faculty Member; Department of Chemical and Biological Engineering; 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; College of Engineering; N/A; 40548; 59917; N/A; N/AIncorporation of ionic liquids (ILs) into metal-organic frameworks (MOFs) offers a broad potential in various applications. However, their applications in wastewater treatment have remained unexplored. Here, we investigate their potential in wastewater treatment and demonstrate a new concept of IL incorporation in ligand-functionalized MOFs, introducing IL/FMOFs. The composites were prepared by incorporating 1-n-butyl-3-methylimidazolium hexafluorophosphate, [BMIM][PF6], into UiO-66 and NH2-UiO-66 and tested for the adsorption of methylene blue (MB) and methyl orange (MO) from aqueous solutions. Data showed that NH2-functionalization and [BMIM][PF6] incorporation improved MB removal performance of UiO-66 by 16- and 48-times, as the capacity increased from 84.8 to 144.7 mg g(-1) and 174.1 mg g(-1), respectively. When considering both modifications together, [BMIM][PF6]/NH2-UiO-66 was almost 300 times faster than that of UiO-66, and the capacity exceeded 200 mg g(-1). Data further suggested that IL incorporation almost doubled MB/MO selectivity because of the strong electrostatic interactions and hydrogen bonding between [PF6](-) and MB, and pi-pi interactions between the [BMIM](+) cation and MB molecules. These results are the first to demonstrate the prospect of combining ligand functionalization with IL incorporation for modifying MOFs, introducing IL/FMOF composites for fast and selective removal of pollutants from wastewater.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 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 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 Real- and Q-space travelling: multi-dimensional distribution maps of crystal-lattice strain (epsilon(044)) and tilt of suspended monolithic silicon nanowire structures(International Union of Crystallography, 2020) Dolabella, Simone; Frison, Ruggero; Chahine, Gilbert A.; Richter, Carsten; Schulli, Tobias U.; Taşdemir, Zuhal; Leblebici, Yusuf; Dommann, Alex; Neels, Antonia; Department of Mechanical Engineering; Alaca, Burhanettin Erdem; Faculty Member; Department of Mechanical Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Engineering; 115108Silicon nanowire-based sensors find many applications in micro- and nano-electromechanical systems, thanks to their unique characteristics of flexibility and strength that emerge at the nanoscale. This work is the first study of this class of micro- and nano-fabricated silicon-based structures adopting the scanning X-ray diffraction microscopy technique for mapping the in-plane crystalline strain (epsilon(044)) and tilt of a device which includes pillars with suspended nanowires on a substrate. It is shown how the micro- and nanostructures of this new type of nanowire system are influenced by critical steps of the fabrication process, such as electron-beam lithography and deep reactive ion etching. X-ray analysis performed on the 044 reflection shows a very low level of lattice strain (<0.00025 Delta d/d) but a significant degree of lattice tilt (up to 0.214 degrees). This work imparts new insights into the crystal structure of micro- and nanomaterial-based sensors, and their relationship with critical steps of the fabrication process.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.