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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access Development of highly luminescent and cytocompatible near-IR-emitting aqueous Ag2S quantum dots(Royal Society of Chemistry (RSC), 2012) Çizmeciyan, M. Natali; Erdem, Rengin; Özen, Can; Kurt, Adnan; N/A; Department of Physics; Department of Chemistry; Hocaoğlu, İbrahim; Sennaroğlu, Alphan; Acar, Havva Funda Yağcı; PhD Student; Faculty Member; Department of Physics; Department of Chemistry; Graduate School of Sciences and Engineering; College of Sciences; N/A; 23851; 178902Colloidally stable and highly luminescent near-IR emitting Ag2S quantum dots (NIRQDs) were prepared by a very simple aqueous method using 2-mercaptopropionic acid (2MPA) as a coating. Emission of Ag2S-2MPA NIRQDs can be tuned between 780 and 950 nm. These NIRQDs have photoluminescence quantum yields (PLQY) around 7–39% and exhibit excellent cytocompatibility even at 600 mg mL 1 in NIH/3T3 cells. With such improved properties, Ag2S-2MPA NIRQDs have a great potential in practical bio-applications.Publication Open Access Modification of the surface plasmon enhanced optical forces on metal nanorod pairs by axial rotation and by dielectric intralayer(Elsevier, 2014) Department of Physics; Yalçın, Aybike Ural; Güven, Kaan; Müstecaplıoğlu, Özgür Esat; Faculty Member; Faculty Member; Department of Physics; College of Sciences; N/A; 52290; 1674We investigate numerically the effect of axial rotation and the presence of a dielectric intralayer on the spectral behavior of the optical force on a gold nanorod pair. The frequency spectrum of the optical force is obtained through the Maxwell stress tensor formulation and the full vectorial solution of electromagnetic waves. The common and the relative forces, which are defined through the optical force acting on each nanorod, are computed for different axial rotations and for different permittivity and thickness of the dielectric intralayer. We found that both the misalignment and the dielectric intralayer can be utilized to tailor the magnitude and direction of the relative optical force, providing a tunable attractive or repulsive response between the nanorods. (C) 2014 Elsevier B.V. All rights reserved.Publication Open Access Optimum folding pathways of proteins: their determination and properties(American Institute of Physics (AIP) Publishing, 2006) Department of Chemical and Biological Engineering; Güner, Pınar Tatar; Arkun, Yaman; Erman, Burak; Teaching Faculty; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 188227; 108526; 179997We develop a dynamic optimization technique for determining optimum folding pathways of proteins starting from different initial configurations. A coarse-grained Go model is used. Forces acting on each bead are (i) the friction force, (ii) forces from bond length constraints, (iii) excluded volume constraints, and (iv) attractive forces between residue pairs that are in contact in the native state. An objective function is defined as the total attractive energy between nonbonded residues, which are neighbors in the native state. The objective function is minimized over all feasible paths, satisfying bond length and excluded volume constraints. The optimization problem is nonconvex and contains a large number of constraints. An augmented Lagrangian method with a penalty barrier function was used to solve the problem. The method is applied to a 36-residue protein, chicken villin headpiece. Sequences of events during folding of the protein are determined for various pathways and analyzed. The relative time scales are compared and scaled according to experimentally measured events. Formation times of the helices, turn, and the loop agree with experimental data. We obtain the overall folding time of the protein in the range of 600 ns-1.2 mu s that is smaller than the experimental result of 4-5 mu s, showing that the optimal folding times that we obtain may be possible lower bounds. Time dependent variables during folding and energies associated with short- and long-range interactions between secondary structures are analyzed in modal space using Karhunen-Loeve expansion.Publication Open Access Solvation of carbonaceous molecules by para-H2 and ortho-D2clusters. II. Fullerenes(American Institute of Physics (AIP) Publishing, 2016) Calvo, F.; Department of Chemistry; Yurtsever, İsmail Ersin; Doctor; Department of Chemistry; College of Sciences; 7129The coating of various fullerenes by para-hydrogen and ortho-deuterium molecules has been computationally studied as a function of the solvent amount. Rotationally averaged interaction potentials for structureless hydrogen molecules are employed to model their interaction with neutral or charged carbonaceous dopants containing between 20 and 240 atoms, occasionally comparing different fullerenes having the same size but different shapes. The solvation energy and the size of the first solvation shell obtained from path-integral molecular dynamics simulations at 2 K show only minor influence on the dopant charge and on the possible deuteration of the solvent, although the shell size is largest for ortho-D-2 coating cationic fullerenes. Nontrivial finite size effects have been found with the shell size varying non-monotonically close to its completion limit. For fullerenes embedded in large hydrogen clusters, the shell size and solvation energy both follow linear scaling with the fullerene size. The shell sizes obtained for C-60(+) and C-70(+) are close to 49 and 51, respectively, and agree with mass spectrometry experiments.Publication Open Access Solvation of carbonaceous molecules by para-H-2 and ortho-D-2 clusters. I. Polycyclic aromatic hydrocarbons(American Institute of Physics (AIP) Publishing, 2016) Calvo, F.; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129This work theoretically examines the progressive coating of planar polycyclic aromatic hydrocarbon (PAH) molecules ranging from benzene to circumcoronene (C54H18) by para-hydrogen and ortho-deuterium. The coarse-grained Silvera-Goldman potential has been extended to model the interactions between hydrogen molecules and individual atoms of the PAH and parametrized against quantum chemical calculations for benzene-H-2. Path-integral molecular dynamics simulations at 2 K were performed for increasingly large amounts of hydrogen coating the PAH up to the first solvation shell and beyond. From the simulations, various properties were determined such as the size of the first shell and its thickness as well as the solvation energy. The degree of delocalization was notably quantified from an energy landscape perspective, by monitoring the fluctuations among inherent structures sampled by the trajectories. Our results generally demonstrate a high degree of localization owing to relatively strong interactions between hydrogen and the PAH, and qualitatively minor isotopic effects. In the limit of large hydrogen amounts, the shell size and solvation energy both follow approximate linear relations with the numbers of carbon and hydrogen in the PAH.Publication Open Access Lubricated friction and volume dilatancy are coupled(American Institute of Physics (AIP) Publishing, 2002) Granick, S.; Demirel, Adem Levent; Faculty Member; College of Sciences; 6568Dilation (expansion of film thickness) by similar to0.1 A, which is less than one-tenth of the width of confined fluid molecules, was observed when confined films crossed from the resting state ("static friction") to sliding ("kinetic friction"). These measurements were based on using piezoelectric bimorph sensors possessing extremely high resolution for detecting position changes, during the course of sliding molecularly thin films of squalane, a model lubricant fluid, between atomically smooth single crystals of mica. Detailed inspection of energy balance shows that the dilation data and the friction forces satisfied energy conservation of identifiable energies at the slip point, from static to kinetic friction. This shows experimentally, for the first time to the best of our knowledge, a direct coupling between friction forces and decrease in the mean density of the intervening molecularly thin fluid.Publication Open Access Composites of porous materials with ionic liquids: synthesis, characterization, applications, and beyond(Elsevier, 2022) Department of Chemical and Biological Engineering; Durak, Özce; Zeeshan, Muhammad; Habib, Nitasha; Gülbalkan, Hasan Can; Alsuhile, Ala Abdulalem Abdo Moqbel; Çağlayan, Hatice Pelin; Öztulum, Samira Fatma Kurtoğlu; Zhao, Yuxin; Haşlak, Zeynep Pınar; Uzun, Alper; Keskin, Seda; PhD Student; PhD Student; 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); College of Engineering; Graduate School of Sciences and Engineering; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; 59917; 40548Modification of the physicochemical properties of porous materials by using ionic liquids (ILs) has been widely studied for various applications. The combined advantages of ILs and porous materials provide great potential in gas adsorption and separation, catalysis, liquid-phase adsorption and separation, and ionic conductivity owing to the superior performances of the hybrid composites. In this review, we aimed to provide a perspective on the evolution of IL/porous material composites as a research field by discussing several different types of porous materials, including metal organic frameworks (MOFs), covalent organic frameworks (COFs), zeolites, and carbonaceous-materials. The main challenges and opportunities in synthesis methods, characterization techniques, applications, and future opportunities of IL/porous materials are discussed in detail to create a road map for the area. Future advances of the field addressed in this review will provide in-depth insights into the design and development of these novel hybrid materials and their replacement with conventional materials.Publication Open Access Vertically oriented hexagonal mesoporous zirconia thin films by block copolymer templating(Royal Society of Chemistry (RSC), 2012) 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; 178882We report the synthesis of vertically oriented, long-range ordered hexagonal mesoporous zirconia thin ?lms. The orientation of hexagonally ordered cylindrical mesopores in thin films was effectively controlled by taking advantage of the temperature dependent hydrophobicity of the templating block copolymer PEO–PPO–PEO. Vertical orientation was obtained when temperature was 30 C or above throughout the process. Dehydration and enhanced chemical incompatibility between the PEO and PPO blocks at slightly elevated temperatures are proposed to play a key role in the vertical orientation of the mesopores. The temperature changes act on the entire ?lm rather than just at the interfaces and the process can be applied to any mesoporous inorganic ?lm.