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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access Emergence of near-infrared photoluminescence via ZnS shell growth on the AgBiS2 nanocrystals(American Chemical Society, 2024) Department of Chemistry; Department of Electrical and Electronics Engineering; Önal, Asım; Kaya, Tarık Safa; Metin, Önder; Nizamoğlu, Sedat; Department of Chemistry; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of EngineeringAgBiS2 nanocrystals (NCs), composed of nontoxic, earth-abundant materials and exhibiting an exceptionally high absorption coefficient from visible to near-infrared (>105 cm(-1)), hold promise for photovoltaics but have lack of photoluminescence (PL) due to intrinsic nonradiative recombination and challenging shell growth. In this study, we reported a facile wet-chemical approach for the epitaxial growth of ZnS shell on AgBiS2 NCs, which triggered the observation of PL emission in the near-infrared (764 nm). Since high quality of the core is critical for epitaxial shell growth, we first obtained rock-salt structured AgBiS2 NCs with high crystallinity, nearly spherical shape and monodisperse size distribution (<6%) via a dual-ligand approach reacting Ag-Bi oleate with elemental sulfur in oleylamine. Next, a zincblende ZnS shell with a low-lattice mismatch of 4.9% was grown on as-prepared AgBiS2 NCs via a highly reactive zinc (Zn(acac)(2)) precursor that led to a higher photoluminescence quantum yield (PLQY) of 15.3%, in comparison with a relatively low reactivity precursor (Zn(ac)(2)) resulting in reduced PLQY. The emission from AgBiS2 NCs with ultrastrong absorption, facilitated by shell growth, can open up new possibilities in lighting, display, and bioimaging.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 Large-scale computational screening of MOF membranes and MOF-based polymer membranes for H2/N2 separations(American Chemical Society (ACS), 2019) Department of Chemical and Biological Engineering; Azar, Ayda Nemati Vesali; Velioğlu, Sadiye; Keskin, Seda; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; N/A; 200650; 40548Several thousands of metal organic frameworks (MOFs) have been reported to date, but the information on H-2/N-2 separation performances of MOF membranes is currently very limited in the literature. We report the first large-scale computational screening study that combines state-of-the-art molecular simulations, grand canonical Monte Carlo (GCMC) and molecular dynamics (MD), to predict H-2 permeability and H-2/N-2 selectivity of 3765 different types of MOF membranes. Results showed that MOF membranes offer very high H-2 permeabilities, 2.5 x 10(3) to 1.7 x 10(6) Barrer, and moderate H-2/N-2 membrane selectivities up to 7. The top 20 MOF membranes that exceed the polymeric membranes' upper bound for H-2/N-2 separation were identified based on the results of initial screening performed at infinite dilution condition. Molecular simulations were then carried out considering binary H-2/N-2 and quaternary H-2/N-2/CO2/CO mixtures to evaluate the separation performance of MOF membranes under industrial operating conditions. Lower H-2 permeabilities and higher N-2 permeabilities were obtained at binary mixture conditions compared to the ones obtained at infinite dilution due to the absence of multicomponent mixture effects in the latter. Structure performance relations of MOFs were also explored to provide molecular-level insights into the development of new MOF membranes that can offer both high H-2 permeability and high H-2/N-2 selectivity. Results showed that the most promising MOF membranes generally have large pore sizes (>6 A) as well as high surface areas (>3500 m(2)/g) and high pore volumes (>1 cm(3)/g). We finally examined H-2/N-2 separation potentials of the mixed matrix membranes (MMMs) in which the best MOF materials identified from our high-throughput screening were used as fillers in various polymers. Results showed that incorporation of MOFs into polymers almost doubles H-2 permeabilities and slightly enhances H-2/N-2 selectivities of polymer membranes, which can advance the current membrane technology for efficient H-2 purification.Publication Open Access CdTe quantum dot sensitized hexaniobate nanoscrolls and their photoelectrochemical properties(Royal Society of Chemistry (RSC), 2012) Department of Chemistry; Öztuna, Feriha Eylül Saraç; Akkaya, Ceren Yılmaz; Acar, Havva Funda Yağcı; Ünal, Uğur; PhD Student; Faculty Member; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Sciences; N/A; N/A; 178902; N/AWe have constructed hybrid quantum dot-layered niobate films with an electrophoretic deposition method. The structure and photoelectrochemical behaviour were demonstrated.Publication Open Access Investigation of hydrodynamic behavior of alginate aerogel particles in a laboratory scale Wurster fluidized bed(Multidisciplinary Digital Publishing Institute (MDPI), 2019) Department of Chemical and Biological Engineering; Erkey, Can; Akgün, Işık Sena; Faculty Member; Researcher; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; 29633; N/AThe effects of design and operating parameters on the superficial velocity at the onset of circulatory motion and the residence time of alginate aerogel particles in a laboratory scale Wurster fluidized bed were investigated. Several sets of experiments were conducted by varying Wurster tube diameter, Wurster tube length, batch volume and partition gap height. The superficial velocities for Wurster tube with 10 cm diameter were lower than the tube with 8 cm diameter. Superficial velocities increased with increasing batch volume and partition gap height. Moreover, increasing batch volume and partition gap height led to a decrease in the particle residence time in the Wurster tube. The results showed that there is an upper limit for each parameter in order to obtain a circulatory motion of the particles. It was found that the partition gap height should be 2 cm for proper particle circulation. Maximum batch volume for the tube with 10 cm diameter was found as 500 mL whereas maximum batch volume was 250 mL for the tube with 8 cm diameter. The fluidization behavior of the aerogel particles investigated in this study could be described by the general fluidization diagrams in the literature.Publication Open Access Understanding the link between inflammasome and apoptosis through the response of THP-1 cells against drugs using droplet-based microfluidics(American Chemical Society (ACS), 2022) Gençtürk, E.; Kasım, M.; Ülgen, K.O.; Department of Physics; Department of Electrical and Electronics Engineering; Kiraz, Alper; Morova, Berna; Faculty Member; Researcher; Department of Physics; Department of Electrical and Electronics Engineering; College of Sciences; College of Engineering; 22542; N/ADroplet-based microfluidic devices are used to investigate monocytic THP-1 cells in response to drug administration.Consistent and reproducible droplets are created, each of which acts as a bioreactor to carry out single cell experiments withminimized contamination and live cell tracking under an invertedfluorescence microscope for more than 2 days. Here, the effects ofthree different drugs (temsirolimus, rifabutin, and BAY 11-7082) on THP-1 are examined and the results are analyzed in the contextof the inflammasome and apoptosis relationship. The ASC adaptor gene tagged with GFP is monitored as the inflammasomereporter. Thus, a systematic way is presented for deciphering cell-to-cell heterogeneity, which is an important issue in cancertreatment. The drug temsirolimus, which has effects of disrupting the mTOR pathway and triggering apoptosis in tumor cells, causesTHP-1 cells to express ASC and to be involved in apoptosis. Treatment with rifabutin, which inhibits proliferation and initiatesapoptosis in cells, affects ASC expression byfirst increasing and then decreasing it. CASP-3, which has a role in apoptosis and isdirectly related to ASC, has an increasing level in inflammasome conditioning. Thus, the cell under the effect of rifabutin might befaced with programmed cell death faster. The drug BAY 11-7082, which is responsible for NF Kappa B inhibition, shows similar results totemsirolimus with more than 60% of cells having highfluorescence intensity (ASC expression). The microfluidic platform presentedhere offers strong potential for studying newly developed small-molecule inhibitors for personalized/precision medicine.Publication Open Access Introduction to noise radar and its waveforms(Multidisciplinary Digital Publishing Institute (MDPI), 2020) De Palo, Francesco; Galati, Gaspare; Pavan, Gabriele; Wasserzier, Christoph; Department of Electrical and Electronics Engineering; Savcı, Kubilay; Department of Electrical and Electronics Engineering; Graduate School of Sciences and EngineeringIn the system-level design for both conventional radars and noise radars, a fundamental element is the use of waveforms suited to the particular application. In the military arena, low probability of intercept (LPI) and of exploitation (LPE) by the enemy are required, while in the civil context, the spectrum occupancy is a more and more important requirement, because of the growing request by non-radar applications; hence, a plurality of nearby radars may be obliged to transmit in the same band. All these requirements are satisfied by noise radar technology. After an overview of the main noise radar features and design problems, this paper summarizes recent developments in "tailoring" pseudo-random sequences plus a novel tailoring method aiming for an increase of detection performance whilst enabling to produce a (virtually) unlimited number of noise-like waveforms usable in different applications.Publication Open Access Quantum fluid dynamics in the Lagrangian representation and applications to photodissociation problems(American Institute of Physics (AIP) Publishing, 1999) Rabitz, H. A.; Department of Mathematics; Aşkar, Attila; Faculty Member; Department of Mathematics; College of Sciences; N/A; 178822This paper considers the practical utility of quantum fluid dynamics (QFD) whereby the time-dependent Schrodinger's equation is transformed to observing the dynamics of an equivalent "gas continuum." The density and velocity of this equivalent gas continuum are respectively the probability density and the gradient of the phase of the wave function. The numerical implementation of the QFD equations is carried out within the Lagrangian approach, which transforms the solution of Schrodinger's equation into following the trajectories of a set of mass points, i.e., subparticles, obtained by discretization of the continuum equations. The quantum dynamics of the subparticles which arise in the present formalism through numerical discretization are coupled by the density and the quantum potential. Numerical illustrations are performed for photodissociation of nocl and NO2 treated as two-dimensional models. The dissociation cross sections sigma(omega) are evaluated in the dramatically short CPU times of 33 s for nocl and 40 s for NO2 on a Pentium-200 mhz PC machine. The computational efficiency comes from a combination of (a) the QFD representation dealing with the near monotonic amplitude and phase as dependent variables, (b) the Lagrangian description concentrating the computation effort at all times into regions of highest probability as an optimal adaptive grid, and (c) the use of an explicit time integrator whereby the computational effort grows only linearly with the number of discrete points.Publication Open Access Electronic structure of atomically dispersed supported iridium catalyst controls iridium aggregation(American Chemical Society (ACS), 2020) Hoffman, Adam S.; Akgül, Deniz; Babucci, Melike; Aviyente, Viktorya; Gates, Bruce C.; Bare, Simon R.; Department of Chemical and Biological Engineering; Öztulum, Samira Fatma Kurtoğlu; 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); Graduate School of Sciences and Engineering; College of Engineering; N/A; 59917Supported iridium complexes, Ir(C2H4)2/support, were characterized by X-ray absorption spectroscopy during a temperature ramp to 120 °C in flowing H2. Iridium in complexes bonded to weak and moderate electron-donor supports, SiO2and ?-Al2O3, underwent aggregation, forming nanoparticles and clusters, respectively. When the support was a strong electron-donor (MgO), iridium remained site-isolated. Density functional theory calculations confirm the dependence of iridium-support bond strength on the support's electron-donor character. Coating the SiO2-supported complexes with 1- n-ethyl-3-methyl-imidazolium acetate enhanced electron density on the iridium, hindering its aggregation. These results demonstrate opportunities for stabilizing atomically dispersed supported noble metals under reducing conditions by choice of support/ionic liquid sheath combinations.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.