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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access Synchronous and asynchronous response in dynamically perturbed proteins(American Chemical Society (ACS), 2021) Erkip, Albert; Erman, Batu; Department of Chemical and Biological Engineering; Hacısüleyman, Aysima; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 179997We present a dynamic perturbation-response model of proteins based on the Gaussian Network Model, where a residue is perturbed periodically, and the dynamic response of other residues is determined. The model shows that periodic perturbation causes a synchronous response in phase with the perturbation and an asynchronous response that is out of phase. The asynchronous component results from the viscous effects of the solvent and other dispersive factors in the system. The model is based on the solution of the Langevin equation in the presence of solvent, noise, and perturbation. We introduce several novel ideas: The concept of storage and loss compliance of the protein and their dependence on structure and frequency; the amount of work lost and the residues that contribute significantly to the lost work; new dynamic correlations that result from perturbation; causality, that is, the response of j when i is perturbed is not equal to the response of i when j is perturbed. As examples, we study two systems, namely, bovine rhodopsin and the class of nanobodies. The general results obtained are (i) synchronous and asynchronous correlations depend strongly on the frequency of perturbation, their magnitude decreases with increasing frequency, (ii) time-delayed mean-squared fluctuations of residues have only synchronous components. Asynchronicity is present only in cross correlations, that is, correlations between different residues, (iii) perturbation of loop residues leads to a large dissipation of work, (iv) correlations satisfy the hypothesis of pre-existing pathways according to which information transfer by perturbation rides on already existing equilibrium correlations in the system, (v) dynamic perturbation can introduce a selective response in the system, where the perturbation of each residue excites different sets of responding residues, and (vi) it is possible to identify nondissipative residues whose perturbation does not lead to dissipation in the protein. Despite its simplicity, the model explains several features of allosteric manipulation.Publication Open Access Distinguishing genuine Imperial Qing Dynasty porcelain from ancient replicas by on-site non-invasive XRF and Raman spectroscopy(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Colomban, P.; Gironda, M.; d'Abrigeon, P.; Franci, Gülsu Şimşek; Researcher; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM)The combined use of non-invasive on-site portable techniques, Raman microscopy, and X-ray fluorescence spectroscopy on seven imperial bowls and two decorated dishes, attributed to the reigns of the Kangxi, Yongzheng, Qianlong, and Daoguang emperors (Qing Dynasty), allows the identification of the coloring agents/opacifiers and composition types of the glazes and painted enamels. Particular attention is paid to the analysis of the elements used in the (blue) marks and those found in the blue, yellow, red, and honey/gilded backgrounds on which, or in reserve, a floral motif is principally drawn. The honey-colored background is made with gold nanoparticles associated with a lead- and arsenic-based flux. One of the red backgrounds is also based on gold nanoparticles, the second containing copper nanoparticles, both in lead-based silicate enamels like the blue and yellow backgrounds. Tin and arsenic are observed, but cassiterite (SnO2) is clearly observed in one of the painted decors (dish) and in A676 yellow, whereas lead (calcium/potassium) arsenate is identified in most of the enamels. Yellow color is achieved with Pb-Sn-Sb pyrochlore (Naples yellow) with various Sb contents, although green color is mainly based on lead-tin oxide mixed with blue enamel. The technical solutions appear very different from one object to another, which leads one to think that each bowl is really a unique object and not an item produced in small series. The visual examination of some marks shows that they were made in overglaze (A608, A616, A630, A672). It is obvious that different types of cobalt sources were used for the imprinting of the marks: cobalt rich in manganese for bowl A615 (Yongzheng reign), cobalt rich in arsenic for bowl A613 (but not the blue mark), cobalt with copper (A616), and cobalt rich in arsenic and copper (A672). Thus, we have a variety of cobalt sources/mixtures. The high purity of cobalt used for A677 bowl indicates a production after similar to 1830-1850.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 Impact of rehabilitation on fatigue in post-Covid-19 patients: a systematic review and meta-analysis(Multidisciplinary Digital Publishing Institute (MDPI), 2022) de Sire, Alessandro; Moggio, Lucrezia; Marotta, Nicola; Agostini, Francesco; Tasselli, Anna; Ferrante, Vera Drago; Curci, Claudio; Calafiore, Dario; Ferraro, Francesco; Bernetti, Andrea; Ammendolia, Antonio; Taşkıran, Özden Özyemişçi; Faculty Member; School of Medicine; 133091The post-COVID-19 syndrome may affect patients after the COVID-19 post-acute phase. In particular, the 69% of patients reported persistent fatigue at the discharge. To date, no clear data are available regarding the most effective rehabilitative approaches for the treatment of this condition. Thus, this systematic review aimed to evaluate the rehabilitation treatment's efficacy on fatigue in post-COVID-19 patients. We systematically searched PubMed, Scopus, and Web of Science databases to find longitudinal study designs presenting: post-COVID-19 patients as participants; a rehabilitative approach aimed to reduce post-COVID-19 syndrome as intervention; and fatigue intensity assessed through an evaluation tool that quantified the perceived exertion (i.e., fatigue severity scale, FSS; Borg Scale (BS); Borg Category Ratio 10, CR10; Checklist Individual Strength (CIS) fatigue scale; FACIT (Functional Assessment of Chronic Illness Therapy) fatigue scale). The present systematic review protocol was registered on PROSPERO (registration number CRD42021284058). Out of 704 articles, 6 studies were included. Nearly all patients showed COVID-19-related fatigue, and after the rehabilitation treatment, only 17% of subjects reported the persistency of symptoms. The overall effect size reported a -1.40 decrease in Borg Category Ratio 10 with a SE of 0.05 and a 95% CI between -1.50 and -1.30 (p < 0.001). The present systematic review and meta-analysis underlines the rehabilitation role in the fatigue reduction in patients affected by post-COVID-19 syndrome.Publication Open Access Synthesis and characterization of mesoporous zirconium oxide thin films(Institute of Physics (IOP) Publishing, 2010) Department of Chemistry; Miko, Annamaria; Demirel, Adem Levent; Somer, Mehmet Suat; Teaching Faculty; Faculty Member; Faculty Member; Department of Chemistry; College of Sciences; N/A; 6568; 178882Zirconium oxide (ZrO2) has generated wide interest because of its potential in applications such as solid oxide fuel cells, catalysts and optical devices. In these applications, it is important to control the grain size of the material and increase the surface area by introducing porosity with tailored pore size. This paper presents a synthesis route for the preparation of mesoporous zirconia using spin-coating method combined with block copolymer templating evaporation induced self assembly (EISA). The hybrid mesophase was formed by zirconium oxychloride precursor ZrOCl2 center dot 8H(2)O and Brij 700 poly-ethylene oxide based block copolymer template C18H37(OCH2CH2). FT-IR and Raman measurements of the hybrid mesophase provided information on the possible intermolecular interactions between the precursor and the copolymer template. The results indicate a weak ion-dipole interaction between the inorganic precursor and the organic template after the solvent evaporation, possibly directly between the zirconium and the oxygen of the poly-ethylene oxide chain. The removal of the organic block copolymer by heat treatment resulted in mesoporous zirconia with pore size of similar to 4-8 nm and crystalline grain size of similar to 10-17 nm. The morphology in thin films depended significantly on the solvent quality and the block copolymer concentration. Tailoring the surface morphology and the grain size resulted in super-hydrophilic mesoporous zirconia thin films in contrast to water contact angle of 50 degrees on conventional tetragonal zirconium oxide.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 Mechanochemical synthesis and consolidation of nanostructured cerium hexaboride(University of Novi Sad, 2019) Ağaoğulları, Duygu; Akçamlı, Nazlı; Suryanarayana, Challapalli; Duman, İsmail; Öveçoğlu, Mustafa Lütfi; Department of Chemistry; Balcı, Özge; Researcher; Department of Chemistry; College of Sciences; 295531This study reports on the mechanochemical synthesis (MCS) and consolidation of nanostructured CeB6 powders of high purity. CeB6 powders were prepared via MCS by milling CeO2, B2O3 and Mg powders in a high-energy ball mill for different milling times. The effects of milling time on the formation, microstructure and thermal behaviour of the synthesized powders were investigated and the optimum MCS duration was determined. Purified powders were obtained after HCl leaching by removing MgO by-product. The prepared powders were characterized by a number of techniques including X-ray diffraction, stereomicroscopy, scanning and transmission electron microscopy coupled with energy dispersive spectrometry, differential scanning calorimetry, atomic absorption spectrometry, particle size analysis, surface area analysis and vibrating sample magnetometry. The high-purity CeB6 powders having an average particle size of 86 nm were consolidated by cold-pressing followed by pressureless sintering at 1700 degrees C for 5 h. The bulk CeB6 specimen was investigated for its microstructure, density, electrical resistivity, surface roughness and some mechanical properties (microhardness and wear behaviour). The relative density, electrical resistivity, microhardness and wear rate of the bulk CeB6 were determined as 95.2% TD, 57.50 mu W.cm, 11.65 GPa and 1.46 x 10(-4) mm(3)/N.m, respectively.Publication Open Access Emerging applications of electrochemical impedance spectroscopy in tear film analysis(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Department of Mechanical Engineering; Taşoğlu, Savaş; Özdalgıç, Berin; Gül, Münire; Atçeken, Nazente; Uygun, Zihni Onur; Faculty Member; PhD Student; Other; 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); College of Engineering; 291971; 323683; N/A; N/A; N/AHuman tear film, with a flow rate of 1–3 µL/min, is a rich bodily fluid that transmits a variety of metabolites and hormones containing proteins, lipids and electrolytes that provide clues about ocular and systemic diseases. Analysis of disease biomarkers such as proteins, mRNA, enzymes and cytokines in the tear film, collected by noninvasive methods, can provide significant results for sustaining a predictive, preventive and personalized medicine regarding various diseases such as glaucoma, diabetic retinopathy, keratoconus, dry eye, cancer, Alzheimer’s disease, Parkinson’s disease and COVID-19. Electrochemical impedance spectroscopy (EIS) offers a powerful technique for analyzing these biomarkers. EIS detects electrical equivalent circuit parameters related to biorecognition of receptor–analyte interactions on the electrode surface. This method is advantageous as it performs a label-free detection and allows the detection of non-electroactive compounds that cannot be detected by direct electron transfer, such as hormones and some proteins. Here, we review the opportunities regarding the integration of EIS into tear fluid sampling approaches.Publication Open Access A near-infrared benzothiazole-based chemodosimeter for rapid and selective detection of hydrogen sulfide(Turkish Chemical Society / Türkiye Kimya Derneği, 2021) Department of Chemistry; Kölemen, Safacan; Faculty Member; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Boron and Advanced Materials Application and Research Center (KUBAM) / Koç Üniversitesi Bor ve İleri Malzemeler Uygulama ve Araştırma Merkezi (KUBAM); College of Sciences; 272051Hydrogen sulfide (H2S) is a biologically relevant gaseous molecule, which involves in a wide variety of physiological and pathological processes. Thus, detection of H2S is highly valuable in order to clarify its complex roles. In this study, a new benzothiazole-based donor-acceptor type H 2S selective chemodosimeter (HP-1) was synthesized and its H2S detection capabilities were investigated in aqueous solutions. HP-1 exhibited a red-shifted absorption signal at 530 nm and a near-infrared (NIR) fluorescence peak at 680 nm as a result of enhanced intramolecular charge transfer (ICT) in the presence of H2S, which enabled a selective and very rapid ratiometric fluorescent detection. HP-1 was also showed to be highly sensitive toward H2S with a very low limit of detection value.Publication Open Access Computational insights into efficient CO2 and H2S capture through zirconium MOFs(Elsevier, 2022) Department of Chemical and Biological Engineering; Keskin, Seda; Demir, Hakan; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40548; N/ASeparation of CO2 involving mixtures is relevant to the various industrial settings and preserving environment for which different classes of materials including metal-organic frameworks (MOFs) have been researched. Herein, CO2/CO, CO2/H-2, CO2/N-2, and H2S/CO2 separation properties of the zirconium MOFs are computationally investigated mimicking vacuum swing adsorption (VSA) process. Structure-performance relationships are established and the best performing adsorbent materials are determined considering three performance metrics: adsorption selectivity, working capacity, and regenerability. For CO2/CO separation in dry conditions, PCN-59, BUT-10, and PCN-58 are identified to be the top three materials with CO2/CO selectivities of 219.8, 47.2, and 28.6, CO2 working capacities of 6.9, 5.3, and 4.0 mol/kg, CO2 regenerabilities of 63.3, 82.1, and 87.2 %, successively. In humid conditions, UiO-66-OH and MOF-805 appear promising for CO2/CO separation. Regarding CO2/H-2 separation in dry conditions, PCN-59, BUT-10, and LIFM-94 are ranked as the top three MOFs exhibiting CO2/H-2 selectivities of 1445.6, 378.1, and 411.3, CO2 working capacities of 3.6, 2.4, and 2.2 mol/kg, and CO2 regenerabilities of 56.6, 84.9, and 83.9 %, successively. These three materials are also found to be the top three materials for CO2/N-2 separation in dry conditions with CO2/N-2 selectivities of 346.0, 53.3, and 54.9, CO2 working capacities of 3.6, 2.3, and 2.2 mol/kg, and CO2 regenerabilities of 56.3, 84.1, and 83.9 %, successively. For CO2/H-2 and CO2/N-2 separation in humid conditions, UiO-66-NH2 is potentially useful. Considering H2S/CO2 separation in dry conditions, NU-1101, PCN-58, and LMOF-1 are identified to be the best three MOFs attaining H2S/CO2 selectivities of 109.7, 30.9, and 90.7, H2S working capacities of 1.6, 2.3, and 1.2 mol/kg, and H2S regenerabilities of 43.0, 56.4, and 43.7 %, respectively. All top materials for H2S/CO2 separation show relatively large water affinities (PCN-57 having the smallest affinity) which might render them inefficient for H2S/CO2 separation in humid conditions. Adsorbate density profiles are generated for the top 3 materials to elucidate the adsorption mechanisms for each gas separation. A comparison of predictions based on PACMOF and EQeq charges demonstrates drastic differences in material rankings, and separation performance metrics.
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