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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access Mechanistic differences of activation of Rac1(P29S) and Rac1(A159V)(American Chemical Society (ACS), 2021) Jang, Hyunbum; Nussinov, Ruth; N/A; Department of Chemical and Biological Engineering; Department of Computer Engineering; Şenyüz, Simge; Keskin, Özlem; Gürsoy, Attila; Faculty Member; Department of Chemical and Biological Engineering; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 26605; 8745Rac1 is a small GTPase that plays key roles in actin reorganization, cell motility, and cell survival/growth as well as in various cancer types and neurodegenerative diseases. Similar to other Ras superfamily GTPases, Rac1 switches between active GTP-bound and inactive GDP-bound states. Switch I and II regions open and close during GDP/GTP exchange. P29S and A159V (paralogous to K-Ras(A146)) mutations are the two most common somatic mutations of Rac1. Rac1(P2)(9S)( )is a known hotspot for melanoma, whereas Rac1(A159V) most commonly occurs in head and neck cancer. To investigate how these substitutions induce the Rac1 dynamics, we used atomistic molecular dynamics simulations on the wild-type Rac1 and two mutant systems (P29S and A159V) in the GTP bound state, and on the wild-type Rac1 and P29S mutated system in the GDP bound state. Here, we show that P29S and A159V mutations activate Rac1 with different mechanisms. In Rac1(P29S)-GTP, the substitution increases the flexibility of Switch I based on RMSF and dihedral angle calculations and leads to an open conformation. We propose that the open Switch I conformation is one of the underlying reasons for rapid GDP/GTP exchange of Rac1(P29S). On the other hand, in Rac1(A159V)-GTP, some of the contacts of the guanosine ring of GTP with Rac1 are temporarily lost, enabling the guanosine ring to move toward Switch I and subsequently close the switch. Rac1(A159V)-GTP adopts a Ras state 2 like conformation, where both switch regions are in closed conformation and Thr35 forms a hydrogen bond with the nucleotide.Publication Open Access Effect of MOF database selection on the assessment of gas storage and separation potentials of MOFs(Wiley, 2021) Eruçar, İlknur; Department of Chemical and Biological Engineering; N/A; Harman, Hilal Dağlar; Gülbalkan, Hasan Can; Aksu, Gökhan Önder; Altundal, Ömer Faruk; Altıntaş, Çiğdem; Avcı, Gökay; Keskin, Seda; Researcher; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; N/A; N/A; N/A; N/A; 40548Development of computation‐ready metal–organic framework databases (MOF DBs) has accelerated high‐throughput computational screening (HTCS) of materials to identify the best candidates for gas storage and separation. These DBs were constructed using structural curations to make MOFs directly usable for molecular simulations, which caused the same MOF to be reported with different structural features in different DBs. We examined thousands of common materials of the two recently updated, very widely used MOF DBs to reveal how structural discrepancies affect simulated CH4, H2, CO2 uptakes and CH4/H2 separation performances of MOFs. Results showed that DB selection has a significant effect on the calculated gas uptakes and ideal selectivities of materials at low pressure. A detailed analysis on the curated structures was provided to isolate the critical elements of MOFs determining the gas uptakes. Identification of the top‐performing materials for gas separation was shown to strongly depend on the DB used in simulations.Publication Open Access Exciton recycling via InP quantum dot funnels for luminescent solar concentrators(Tsinghua University, 2021) Ow-Yang, Cleva W.; N/A; N/A; Department of Physics; Department of Electrical and Electronics Engineering; Jalali, Houman Bahmani; Sadeghi, Sadra; Toker, Işınsu Baylam; Han, Mertcan; Sennaroğlu, Alphan; Nizamoğlu, Sedat; PhD Student; Master Student; Faculty Member; Faculty Member; Department of Physics; Department of Electrical and Electronics Engineering; 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; N/A; N/A; N/A; 23851; 130295Luminescent solar concentrators (LSC) absorb large-area solar radiation and guide down-converted emission to solar cells for electricity production. Quantum dots (QDs) have been widely engineered at device and quantum dot levels for LSCs. Here, we demonstrate cascaded energy transfer and exciton recycling at nanoassembly level for LSCs. The graded structure composed of different sized toxic-heavy-metal-free InP/ZnS core/shell QDs incorporated on copper doped InP QDs, facilitating exciton routing toward narrow band gap QDs at a high nonradiative energy transfer efficiency of 66%. At the final stage of non-radiative energy transfer, the photogenerated holes make ultrafast electronic transitions to copper-induced mid-gap states for radiative recombination in the near-infrared. The exciton recycling facilitates a photoluminescence quantum yield increase of 34% and 61% in comparison with semi-graded and ungraded energy profiles, respectively. Thanks to the suppressed reabsorption and enhanced photoluminescence quantum yield, the graded LSC achieved an optical quantum efficiency of 22.2%. Hence, engineering at nanoassembly level combined with nonradiative energy transfer and exciton funneling offer promise for efficient solar energy harvesting.Publication Open Access Biocompatible quantum funnels for neural photostimulation(American Chemical Society (ACS), 2019) N/A; Department of Chemical and Biological Engineering; N/A; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; N/A; Jalali, Houman Bahmani; Doğru-Yüksel, Itır Bakış; Eren, Güncem Özgün; Nizamoğlu, Sedat; Karatüm, Onuralp; Melikov, Rustamzhon; Dikbaş, Uğur Meriç; Kavaklı, İbrahim Halil; Sadeghi, Sadra; Yıldız, Erdost; Ergün, Çağla; Şahin, Afsun; PhD Student; Faculty Member; PhD Student; Master Student; Faculty Member; PhD Student; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering; College of Sciences; School of Medicine; N/A; N/A; N/A; 130295; N/A; N/A; N/A; 40319; N/A; N/A; N/A; 171267Neural photostimulation has high potential to understand the working principles of complex neural networks and develop novel therapeutic methods for neurological disorders. A key issue in the light-induced cell stimulation is the efficient conversion of light to bioelectrical stimuli. In photosynthetic systems developed in millions of years by nature, the absorbed energy by the photoabsorbers is transported via nonradiative energy transfer to the reaction centers. Inspired by these systems, neural interfaces based on biocompatible quantum funnels are developed that direct the photogenerated charge carriers toward the bionanojunction for effective photostimulation. Funnels are constructed with indium-based rainbow quantum dots that are assembled in a graded energy profile. Implementation of a quantum funnel enhances the generated photoelectrochemical current 215% per unit absorbance in comparison with ungraded energy profile in a wireless and free-standing mode and facilitates optical neuromodulation of a single cell. This study indicates that the control of charge transport at nanoscale can lead to unconventional and effective neural interfaces.Publication Open Access A diversity combination model incorporating an inward bias for interaural time-level difference cue integration in sound lateralization(Multidisciplinary Digital Publishing Institute (MDPI), 2020) N/A; Department of Computer Engineering; Mojtahedi, Sina; Erzin, Engin; Ungan, Pekcan; Faculty Member; Faculty Member; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; N/A; 34503; N/AA sound source with non-zero azimuth leads to interaural time level differences (ITD and ILD). Studies on hearing system imply that these cues are encoded in different parts of the brain, but combined to produce a single lateralization percept as evidenced by experiments indicating trading between them. According to the duplex theory of sound lateralization, ITD and ILD play a more significant role in low-frequency and high-frequency stimulations, respectively. In this study, ITD and ILD, which were extracted from a generic head-related transfer functions, were imposed on a complex sound consisting of two low- and seven high-frequency tones. Two-alternative forced-choice behavioral tests were employed to assess the accuracy in identifying a change in lateralization. Based on a diversity combination model and using the error rate data obtained from the tests, the weights of the ITD and ILD cues in their integration were determined by incorporating a bias observed for inward shifts. The weights of the two cues were found to change with the azimuth of the sound source. While the ILD appears to be the optimal cue for the azimuths near the midline, the ITD and ILD weights turn to be balanced for the azimuths far from the midline.Publication Open Access A new class of porous materials for efficient CO2 separation: ionic liquid/graphene aerogel composites(Elsevier, 2021) Department of Chemical and Biological Engineering; N/A; Department of Chemistry; Zeeshan, Muhammad; Yalçın, Kaan; Keskin, Seda; Uzun, Alper; Öztuna, Feriha Eylül Saraç; Ünal, Uğur; PhD Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Chemistry; 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; College of Sciences; N/A; N/A; 40548; 59917; N/A; 42079Here, we report a new post-synthesis modification strategy for functionalizing reduced graphene aerogels (rGAs) towards an exceptional CO2 separation performance. 1-N-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) was impregnated on a rGA, prepared by reducing GA at 700 degrees C, at various ionic liquid (IL) loadings of 5, 10, 30, and 50 wt%. The resulting composites were characterized in deep detail by X-ray photoelectron spectroscopy, X-ray diffraction, N-2 physical adsorption measurements, scanning electron microscopy, Fourier transform infrared and Raman spectroscopies, and thermogravimetric analysis. Results indicated the presence of interactions between the rGA surface and the anion of the IL, potentially improving the CO2 affinity. Volumetric gas adsorption measurements using these materials showed that the deposition of [BMIM][PF6] on rGA surface at an IL loading of 50 wt% boosts the CO2/CH4 selectivity by more than 20-times, exceeding an absolute value of 120, a remarkably higher CO2/CH4 selectivity compared to that of other functionalized materials under similar operating conditions. Tunability of both the IL structure and the surface characteristics of rGA offer a tremendous degree of flexibility for the rational design of these IL/rGA composites towards high performance in gas separation applications.Publication Open Access CRISPR-Cas-Integrated LAMP(Multidisciplinary Digital Publishing Institute (MDPI), 2022) N/A; Department of Mechanical Engineering; Özdalgıç, Berin; Taşoğlu, Savaş; Yığcı, Defne; Atçeken, Nazente; PhD Student; Faculty Member; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; N/A; 291971; N/A; N/APathogen-specific point-of-care (PoC) diagnostic tests have become an important need in the fight against infectious diseases and epidemics in recent years. PoC diagnostic tests are designed with the following parameters in mind: rapidity, accuracy, sensitivity, specificity, and ease of use. Molecular techniques are the gold standard for pathogen detection due to their accuracy and specificity. There are various limitations in adapting molecular diagnostic methods to PoC diagnostic tests. Efforts to overcome limitations are focused on the development of integrated molecular diagnostics by utilizing the latest technologies available to create the most successful PoC diagnostic platforms. With this point of view, a new generation technology was developed by combining loop-mediated isothermal amplification (LAMP) technology with clustered regularly interspaced short palindromic repeat (CRISPR)-associated (CRISPR-Cas) technology. This integrated approach benefits from the properties of LAMP technology, namely its high efficiency, short turnaround time, and the lack of need for a complex device. It also makes use of the programmable function of CRISPR-Cas technology and the collateral cleavage activity of certain Cas proteins that allow for convenient reporter detection. Thus, this combined technology enables the development of PoC diagnostic tests with high sensitivity, specificity, and ease of use without the need for complicated devices. In this review, we discuss the advantages and limitations of the CRISPR/Cas combined LAMP technology. We review current limitations to convert CRISPR combined LAMP into pathogen-specific PoC platforms. Furthermore, we point out the need to design more useful PoC platforms using microfabrication technologies by developing strategies that overcome the limitations of this new technology, reduce its complexity, and reduce the risk of contamination.Publication Open Access Acetic acid conversion to ketene on Cu2O(1 0 0): reaction mechanism deduced from experimental observations and theoretical computations(Elsevier, 2021) Tissot, H.; Halldin Stenlid, J.; Wang, C.; Brinck, T.; Sassa, Y.; Johansson, F. O. L.; Weissenrieder, J.; Department of Chemistry; N/A; Kaya, Sarp; Panahi, Mohammad; Faculty Member; PhD Student; Department of Chemistry; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); College of Sciences; Graduate School of Sciences and Engineering; 116541; N/AKetene, a versatile reagent in production of fine and specialty chemicals, is produced from acetic acid. We investigate the synthesis of ketene from acetic acid over the (3,0;1,1) surface of Cu2O(1 0 0) through analysis of the adsorption and desorption characteristics of formic and acetic acids. The results allow us to establish a reaction mechanism for ketene formation. Observations from x-ray photoelectron spectroscopy (XPS), scanning tunneling microscopy, and temperature programmed desorption (TPD), supported by a comparison with formic acid results, suggest that acetic acid reacts with Cu2O through deprotonation to form acetate species coordinated to copper sites and hydroxylation of nearby surface oxygen sites. For formic acid the decomposition of adsorbed formate species results in desorption of CO2 and CO while, for acetic acid, high yields of ketene are observed at temperature >500 K. Modeling by density functional theory (DFT) confirms the strong interaction of acetic acid with the (3,0;1,1) surface and the spontaneous dissociation into adsorbed acetate and hydrogen atom species, the latter forming an OH-group. In an identified reaction intermediate ketene binds via all C and O atoms to Cu surface sites, in agreement with interpretations from XPS. In the vicinity of the adsorbate the surface experiences a local reorganization into a c(2 × 2) reconstruction. The total computed energy barrier for ketene formation is 1.81 eV in good agreement with the 1.74 eV obtained from TPD analysis. Our experimental observations and mechanistic DFT studies suggests that Cu2O can operate as an efficient catalyst for the green generation of ketene from acetic acid.Publication Open Access Nanocrystalline cobalt-nickel-boron (metal boride) catalysts for efficient hydrogen production from the hydrolysis of sodium borohydride(Elsevier, 2021) N/A; Department of Chemical and Biological Engineering; Department of Chemistry; Paksoy, Aybike; Altıntaş, Zerrin; Khoshsima, Sina; Öztulum, Samira Fatma Kurtoğlu; Dizaji, Azam Khodadadi; Uzun, Alper; Balcı, Özge; Researcher; Researcher; Faculty Member; Researcher; Department of Chemical and Biological Engineering; Department of Chemistry; Koç University AKKİM Boron-Based Materials _ High-technology Chemicals Research _ Application Center (KABAM) / Koç Üniversitesi AKKİM Bor Tabanlı Malzemeler ve İleri Teknoloji Kimyasallar Uygulama ve Araştırma Merkezi (KABAM); 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; College of Sciences; N/A; N/A; N/A; N/A; N/A; 59917; 295531Innovative metal boride nanocatalysts containing crystalline Co-Ni based binary/ternary boride phases were synthesized and used in the hydrolysis of NaBH4. All the as-prepared catalysts were in high-purity with average particle sizes ranging between similar to 51 and 94 nm and consisting of different crystalline phases (e.g. CoB, Co2B, Co5B16, NiB, Ni4B3, Ni2Co0-67B0.33). The synergetic effect of the different binary/ternary boride phases in the composite catalysts had a positive role on the catalytic performances thus, while the binary boride containing phases of unstable cobalt borides or single Ni4B3 were not showing any catalytic activity. The Co-Ni-B based catalyst containing crystalline phases of CoB-Ni4B3 exhibited the highest H-2 production rate (500.0 mL H-2 min(-1) g(cat)(-1)), with an apparent activation energy of 32.7 kJ/mol. The recyclability evaluations showed that the catalyst provides stability even after the 5th cycle. The results suggested that the composite structures demonstrate favorable catalytic properties compared to those of their single components and they can be used as alternative and stable catalysts for efficient hydrogen production from sodium borohydride.Publication Open Access MIL-53(Al) as a versatile platform for ionic-liquid/MOF composites to enhance CO2 selectivity over CH4 and N2(Wiley, 2019) N/A; Department of Chemical and Biological Engineering; Kavak, Safiyye; Polat, Hüsamettin Mert; Kulak, Harun; Keskin, Seda; Uzun, Alper; Faculty Member; 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); College of Engineering; N/A; N/A; N/A; 40548; 59917Five different imidazolium-based ionic liquids (ILs) were incorporated into a metal–organic framework (MOF), MIL-53(Al), to investigate the effect of IL incorporation on the CO2 separation performance of MIL-53(Al). CO2, CH4, and N2 adsorption isotherms of the IL/MIL-53(Al) composites and pristine MIL-53(Al) were measured to evaluate the effect of the ILs on the CO2/CH4 and CO2/N2 selectivities of the MOF. Of the composite materials that were tested, [BMIM][PF6]/MIL-53(Al) exhibited the largest increase in CO2/CH4 selectivity, 2.8-times higher than that of pristine MIL-53(Al), whilst [BMIM][MeSO4]/MIL-53(Al) exhibited the largest increase in CO2/N2 selectivity, 3.3-times higher than that of pristine MIL-53(Al). A comparison of the CO2 separation potentials of the IL/MOF composites showed that the [BMIM][BF4]- and [BMIM][PF6]-incorporated MIL-53(Al) composites both showed enhanced CO2/N2 and CO2/CH4 selectivities at pressures of 1–5 bar compared to composites of CuBTC and ZIF-8 with the same ILs. These results demonstrate that MIL-53(Al) is a versatile platform for IL/MOF composites and could help to guide the rational design of new composites for target gas-separation applications.
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