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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 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 Dimerization of pyrrole(TÜBİTAK, 1998) Yurtsever, Mine; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129Accurate ab-inito quantum mechanical calculations of pyrrole dimers are reported. The thermodynamical stabilities of dimers with alpha - alpha, alpha -beta, and beta - beta type linkages are compared in order to predict the possibilities of branching in polypyrroles. Calculations employing large basis sets and including electron correlation effects predict the alpha - alpha dimers as the most stable form. However, an alpha - beta type bonding requires only 1.5-2.0 kcal/mol, and the energy necessary to introduce a beta - beta type bond is 3.6-4.0 kcal/mol. These values show that a high degree of branching is possible even at room temperatures.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.Publication Open Access Epitranscriptomics of ischemic heart disease-the IHD-EPITRAN study design and objectives(Multidisciplinary Digital Publishing Institute (MDPI), 2021) Sikorski, Vilbert; Karjalainen, Pasi; Blokhina, Daria; Oksaharju, Kati; Khan, Jahangir; Katayama, Shintaro; Rajala, Helena; Suihko, Satu; Tuohinen, Suvi; Teittinen, Kari; Nummi, Annu; Nykanen, Antti; Eskin, Arda; Stark, Christoffer; Biancari, Fausto; Kiss, Jan; Simpanen, Jarmo; Ropponen, Jussi; Lemstrom, Karl; Savinainen, Kimmo; Lalowski, Maciej; Kaarne, Markku; Jormalainen, Mikko; Elomaa, Outi; Koivisto, Pertti; Raivio, Peter; Backstrom, Pia; Dahlbacka, Sebastian; Syrjala, Simo; Vainikka, Tiina; Vahasilta, Tiina; Karelson, Mati; Mervaala, Eero; Juvonen, Tatu; Laine, Mika; Laurikka, Jari; Vento, Antti; Kankuri, Esko; Department of Chemical and Biological Engineering; Tunçbağ, Nurcan; Faculty Member; Department of Chemical and Biological Engineering; School of Medicine; College of Engineering; 245513Epitranscriptomic modifications in RNA can dramatically alter the way our genetic code is deciphered. Cells utilize these modifications not only to maintain physiological processes, but also to respond to extracellular cues and various stressors. Most often, adenosine residues in RNA are targeted, and result in modifications including methylation and deamination. Such modified residues as N-6-methyl-adenosine (m(6)A) and inosine, respectively, have been associated with cardiovascular diseases, and contribute to disease pathologies. The Ischemic Heart Disease Epitranscriptomics and Biomarkers (IHD-EPITRAN) study aims to provide a more comprehensive understanding to their nature and role in cardiovascular pathology. The study hypothesis is that pathological features of IHD are mirrored in the blood epitranscriptome. The IHD-EPITRAN study focuses on m(6)A and A-to-I modifications of RNA. Patients are recruited from four cohorts: (I) patients with IHD and myocardial infarction undergoing urgent revascularization; (II) patients with stable IHD undergoing coronary artery bypass grafting; (III) controls without coronary obstructions undergoing valve replacement due to aortic stenosis and (IV) controls with healthy coronaries verified by computed tomography. The abundance and distribution of m(6)A and A-to-I modifications in blood RNA are charted by quantitative and qualitative methods. Selected other modified nucleosides as well as IHD candidate protein and metabolic biomarkers are measured for reference. The results of the IHD-EPITRAN study can be expected to enable identification of epitranscriptomic IHD biomarker candidates and potential drug targets.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.