Biyoinformatik ve Genetik Bölümü Koleksiyonu

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Citation - WoS: 22
Citation - Scopus: 25
Absolute Configuration and Biological Profile of Pyrazoline Enantiomers as Mao Inhibitory Activity
(Wiley, 2019) Goksen, Umut Salgin; Sarıgül, Sevgi; Bultinck, Patrick; Herrebout, Wouter; Doğan, İlknur; Yelekçi, Kemal; Uçar, Gülberk; Kelekçi, Nesrin Gökhan
A new racemic pyrazoline derivative was synthesized and resolved to its enantiomers using analytic and semipreparative high-pressure liquid chromatography. The absolute configuration of both fractions was established using vibrational circular dichroism. The in vitro monoamine oxidase (MAO) inhibitory profiles were evaluated for the racemate and both enantiomers separately for the two isoforms of the enzyme. The racemic compound and both enantiomers were found to inhibit hMAO-A selectively and competitively. In particular the R enantiomer was detected as an exceptionally potent and a selective MAO-A inhibitor (K-i = 0.85 x 10(-3) +/- 0.05 x 10(-3) mu M and SI: 2.35 x 10(-5)) whereas S was determined as poorer compound than R in terms of K-i and SI (0.184 +/- 0.007 and 0.001). The selectivity of the enantiomers was explained by molecular modeling docking studies based on the PDB enzymatic models of MAO isoforms.
The Association of Gvhd With Hla Dr Alleles, Ifn-Gamma, Tgf-Beta, and Mbl2 Gene Polymorphism
(Wiley, 2019) Oğuz, Rusdu; Çiftçi, Hayriye Şentürk; Gökçe, Muge; Öğret, Yeliz; Karadeniz, Sedat Tanju; Pehlivan, Sacide; Aydın, Filiz
[Abstract Not Available]
Citation - WoS: 12
Citation - Scopus: 12
Blind Dockings of Benzothiazoles To Multiple Receptor Conformations of Triosephosphate Isomerase From Trypanosoma Cruzi and Human
(Wiley-VCH Verlag GmbH, 2011) Kurkcuoglu, Zeynep; Ural, Gulgun; Akten, Ebru Demet; Doruker, Pemra
We aim to uncover the binding modes of benzothiazoles which have been reported as specific inhibitors of triosephosphate isomerase from the parasite Trypanosoma cruzi (TcTIM) by performing blind dockings on both TcTIM and human TIM (hTIM). Detailed analysis of binding sites and specific interactions are carried out based on ensemble dockings to multiple receptor conformers obtained from molecular dynamics simulations. In TcTIM dimer dockings the inhibitors preferentially bind to the tunnel-shaped cavity formed at the interface of the subunits whereas non-inhibitors mostly choose other sites. In contrast TcTIM monomer binding interface and hTIM dimer interface do not present a specific binding site for the inhibitors. These findings point to the importance of the tunnel and of the dimeric form for inhibition of TcTIM. Specific interactions of the inhibitors and their sulfonate-free derivatives with the receptor residues indicate the significance of sulfonate group for binding affinity and positioning on the TcTIM dimer interface. One of the inhibitors also binds to the active site which may explain its relatively higher inhibition effect on hTIM.
Citation - WoS: 18
Citation - Scopus: 19
Carboxylic Acid Derivatives Display Potential Selectivity for Human Histone Deacetylase 6: Structure-Based Virtual Screening Molecular Docking and Dynamics Simulation Studies
(Elsevier Science, 2018) Uba, Abdullahi Ibrahim; Yelekçi, Kemal
Human histone deacetylase 6 (HDAC6) has been shown to play a major role in oncogenic cell transformation via deacetylation of alpha-tubulin making it a viable target of anticancer drug design and development. The crystal structure of HDAC6 catalytic domain 2 has been recently made available providing avenues for structure-based drug design campaign. Here in our continuous effort to identify potentially selective HDAC6 inhibitors structure-based virtual screening of similar to 72 461 compounds was carried out using Autodock Vina. The top 100 compounds with calculated Delta G < -10 kcal/mol were manually inspected for binding mode orientation. Furthermore the top 20 compounds with reasonable binding modes were evaluated for selectivity by further docking against HDAC6 and HDAC7 using Autodock4. Four compounds with a carboxylic fragment displayed potential selectivity for HDAC6 over HDAC7 and were found to have good druglike and ADMET properties. Their docking complexes were then submitted to 10 ns-molecular dynamics (MD) simulation using nanoscale MD (NAMD) software to examine the stability of ligand binding modes. These predicted inhibitors remained bound to HDAC6 in the presence of water and ions and the root-mean-square deviation (RMSD) radius of gyration (Rg) and nonbond distance (protein-ligand) profiles suggested that they might be stable over time of the simulation. This study may provide scaffolds for further lead optimization towards the design of HDAC6 inhibitors with improved selectivity. (C) 2018 Elsevier Ltd. All rights reserved.
Citation - WoS: 5
Citation - Scopus: 7
Computational Analysis of a Zn-Bound Tris(imidazolyl) Calix[6]arene Aqua Complex: Toward Incorporating Second-Coordination Sphere Effects Into Carbonic Anhydrase Biomimetics
(Amer Chemical Soc, 2013) Koziol, Lucas; Eşsiz, Şebnem; Wong, Sergio E.; Lau, Edmond Y.; Valdez, Carlos A.; Satcher, Joe H. Jr.; Aines, Roger D.; Lightstone, Felice C.
Molecular dynamics simulations and quantum-mechanical calculations were performed to characterize a supra-molecular tris(imidazolyl) calix[6]arene Zn2+ aqua complex as a biomimetic model for the catalyzed hydration of carbon dioxide to bicarbonate H2O + CO2 -> H+ + HCO3-. On the basis of potential-of-mean-force (PMF) calculations stable conformations had distorted 3-fold symmetry and supported either one or zero encapsulated water molecules. The conformation with an encapsulated water molecule is calculated to be lower in free energy than the conformation with an empty cavity (Delta G = 1.2 kcal/mol) and is the calculated free-energy minimum in solution. CO2 molecule partitioning into the cavity is shown to be very facile proceeding with a barrier of 1.6 kcal/mol from a weak encounter complex which stabilizes the species by about 1.0 kcal/mol. The stabilization energy of CO2 is calculated to be larger than that of H2O (Delta Delta G = 1.4 kcal/mol) suggesting that the complex will preferentially encapsulate CO2 in solution. In contrast the PMF for a bicarbonate anion entering the cavity is calculated to be repulsive in all nonbonding regions of the cavity due to the diameter of the calix[6]arene walls. Geometry optimization of the Zn-bound hydroxide complex with an encapsulated CO2 molecule showed that multiple noncovalent interactions direct the reactants into optimal position for nucleophilic addition to occur. The calixarene complex is a structural mimic of the hydrophilic/hydrophobic divide in the enzyme providing a functional effect for CO2 addition in the catalytic cycle. The results show that Zn-binding calix[6]arene scaffolds can be potential synthetic biomimetics for CO2 hydration catalysis both in terms of preferentially encapsulating CO2 from solution and by spatially fixing the reactive species inside the cavity.
Citation - WoS: 8
Citation - Scopus: 10
Controlling the Growth of Particle Size and Size Distribution of Silica Nanoparticles by the Thin Film Structure
(Springer, 2012) Uysal, Bengü Özuğur; Tepehan, Fatma Zehra
Nanostructured silicondioxide thin films were prepared by sol-gel spin coating technique. The SiO2 films were made using a conventional mixture of tetraethoxysilane (TEOS) deionized water and ethanol with various NH3/TEOS ratios. The nanostructured silica films were made using a mixture of the SiO2 sol and regular SiO2 sol to control the enlargement of the particles inside the films. The structural morphological and optical characterizations of the as-deposited and annealed films were carried out using X-ray diffraction (XRD) atomic force microscopy scanning electron microscopy NKD spectrophotometer and ultraviolet-visible (UV-vis) spectroscopy. The transmittance data of the infrared spectra of the films were recorded using an FT-IR Spectrometer. The XRD studies showed that as-deposited films were amorphous and the formation of the alfa-cristobalite phase of the silica film was investigated at annealing temperature close to 1100 A degrees C. Optical properties of the transmittance spectra in the s and p-polarization modes were collected. Refractive indices and extinction coefficients were determined with respect to the NH3/TEOS ratios in the compositions of the films. Optical cut-off wavelength values were investigated from the extrapolation of the absorbance spectra which was estimated from the UV-vis spectroscopy measurements. A red shift in the absorption threshold indicated that the size of silica nanoparticles was increased by an increase in the NH3/TEOS volume ratio from 1:64 to 1:8.
Citation - WoS: 6
Citation - Scopus: 8
Critical Phenomenon During Photoinitiated Gelation at Different Temperatures: a Photo-Dsc Study
(Elsevier Science, 2011) Dogruyol, Zekeriya; Arsu, Nergis; Dogruyol, Sevnur Keskin; Pekcan, Önder
The behaviour of photoinitiated radical polymerization of an 80 wt% epoxy diacrylate (EA) and 20 wt% tripropyleneglycoldiacrylate (TPGDA) mixture with 2-mercaptothioxanthone (TX-SH) photoinitiator was studied at different temperatures by using photo-differential scanning calorimetric (Photo-DSC) technique. All photopolymerization reactions were carried out under the same conditions. It was observed that all conversion curves during gelation at different temperatures present nice sigmoidal behaviour which suggests the application of the percolation model. Observations around the critical time called the glass transition point (t(g)) taken to reach the maximum rate of polymerization (Rp(max)) show that the gel fraction exponent (beta) obeyed the percolation model. The produced beta values were found to be around 0.50 predicting that the system under consideration belongs to the same universality class. However. Rp(max) and the final conversion (C(s)) values were found to increase when the temperature was increased up to a certain value. On the other hand t(g) values decreased and became saturated as the temperature was increased. (C) 2011 Elsevier B.V. All rights reserved.
Citation - WoS: 51
Citation - Scopus: 55
Crossover From Vibrational To Rotational Collectivity in Heavy Nuclei in the Shell-Model Monte Carlo Approach
(Amer Physical Soc., 2013) Özen, Cem; Alhassid, Yoram; Nakada, Hitoshi
Heavy nuclei exhibit a crossover from vibrational to rotational collectivity as the number of neutrons or protons increases from shell closure towards midshell but the microscopic description of this crossover has been a major challenge. We apply the shell model Monte Carlo approach to families of even-even samarium and neodymium isotopes and identify a microscopic signature of the crossover from vibrational to rotational collectivity in the low-temperature behavior of < J(2)>(T) where J is the total spin and T is the temperature. This signature agrees well with its values extracted from experimental data. We also calculate the state densities of these nuclei and find them to be in very good agreement with experimental data. Finally we define a collective enhancement factor from the ratio of the total state density to the intrinsic state density as calculated in the finite-temperature Hartree-Fock-Bogoliubov approximation. The decay of this enhancement factor with excitation energy is found to correlate with the pairing and shape phase transitions in these nuclei. DOI: 10.1103/PhysRevLett.110.042502
Citation - WoS: 5
Citation - Scopus: 5
Discovery of High Affinity Ligands for Beta(2)-Adrenergic Receptor Through Pharmacophore-Based High-Throughput Virtual Screening and Docking
(Elsevier Science Inc, 2014) Yakar, Rüya; Akten, Ebru Demet
Novel high affinity compounds for human beta(2)-adrenergic receptor (beta(2)-AR) were searched among the clean drug-like subset of ZINC database consisting of 9928465 molecules that satisfy the Lipinski's rule of five. The screening protocol consisted of a high-throughput pharmacophore screening followed by an extensive amount of docking and rescoring. The pharmacophore model was composed of key features shared by all five inactive states of beta(2)-AR in complex with inverse agonists and antagonists. To test the discriminatory power of the pharmacophore model a small-scale screening was initially performed on a database consisting of 117 compounds of which 53 antagonists were taken as active inhibitors and 64 agonists as inactive inhibitors. Accordingly 7.3% of the ZINC database subset (729413 compounds) satisfied the pharmacophore requirements along with 44 antagonists and 17 agonists. Afterwards all these hit compounds were docked to the inactive apo form of the receptor using various docking and scoring protocols. Following each docking experiment the best pose was further evaluated based on the existence of key residues for antagonist binding in its vicinity. After final evaluations based on the human intestinal absorption (HIA) and the blood brain barrier (BBB) penetration properties 62 hit compounds have been clustered based on their structural similarity and as a result four scaffolds were revealed. Two of these scaffolds were also observed in three high affinity compounds with experimentally known K-i values. Moreover novel chemical compounds with distinct structures have been determined as potential beta(2)-AR drug candidates. (C) 2014 Elsevier Inc. All rights reserved.
Citation - Scopus: 16
Discovery of New Azoles With Potent Activity Against Candida Spp. and Candida Albicans Biofilms Through Virtual Screening
(Elsevier, 2020) Karakurt, Arzu; Kart, Didem; Öztürk, Naile; Kaynak, F. Betül; Gencel, Melis; Taşkor, Gülce; Karakurt, Arzu; Saraç, Selma; Eşsiz, Şebnem; Dalkara, Sevim
Systemic candidiasis is a rampant bloodstream infection ofCandidaspp. andC. albicansis the majorpathogen isolated from infected humans. Azoles, the most common class of antifungals which sufferfrom increasing resistance, and especially intrinsically resistant non-albicans Candida(NAC) species, actby inhibiting fungal lanosterol 14a-demethylase (CYP51). In this study we identified a number of azolecompounds in 1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethanol/ethanone oxime ester structurethrough virtual screening using consensus scoring approach, synthesized and tested them for theirantifungal properties. We reached several hits with potent activity against azole-susceptible and azole-resistantCandidaspp. as well as biofilms ofC. albicans.5i's minimum inhibitor concentration (MIC) was0.125mg/ml againstC. albicans, 0.5mg/ml againstC. kruseiand 1mg/ml against azole-resistantC. tropicalisisolate. Considering the MIC values offluconazole against these fungi (0.5, 32 and 512mg/ml, respec-tively),5iemerged as a highly potent derivative. The minimum biofilm inhibitor concentration (MBIC) of5c,5j, and5pwere 0.5mg/ml (and5iwas 2mg/ml) againstC. albicansbiofilms, lower than that ofamphotericin B (4mg/ml), afirst-line antifungal with antibiofilm activity. In addition, the active com-pounds showed neglectable toxicity to human monocytic cell line. We further analyzed the dockingposes of the active compounds inC. albicansCYP51 (CACYP51) homology model catalytic site andidentified molecular interactions in agreement with those of known azoles with fungal CYP51s andmutagenesis studies of CACYP51. We observed the stability of CACYP51 in complex with5iin moleculardynamics simulations.©2019 Elsevier Masson SAS. All rights reserved.1. IntroductionSystemic candidiasis is a major public health issue, especiallywith immune-suppressed cases reaching high mortality rates. Themembers of the genusCandidaare the most frequently recoveredfrom human fungal infection andCandida albicans, so far, is theleading pathogen identified in nosocomial candidiasis [1]. Inaddition to increasing drug-resistant strains ofC. albicans, emer-gence of non-albicans Candidaspp. (NAC) complicate the treatmentof mycoses [2].C. tropicalisis among the NACs that show reducedsusceptibility tofirst-line antifungals reportedly leading to break-through fungemia among high-risk patients [3,4]. Also,C. kruseiisknown to be intrinsically resistant to a number of azoles includingfluconazole [5]. One of the several mechanisms of therapy-resistance is formation of biofilms, which are complex microor-ganism colonies enclosed in an exopolysaccharide matrix on bioticand non-biotic surfaces. Persistent biofilms make fungi much lesssusceptible to antifungal drugs compared to their planktonic formsfor a number of reasons [6e8]. Therefore it is essential to design*Corresponding author. Hacettepe University Faculty of Pharmacy, Departmentof Pharmaceutical Chemistry, 06100, Sihhiye, Ankara, Turkey.E-mail addresses:[email protected],[email protected](S. Sari).Contents lists available atScienceDirectEuropean Journal of Medicinal Chemistryjournal homepage:http://www.elsevier.com/locate/ejmechhttps://doi.org/10.1016/j.ejmech.2019.06.0830223-5234/©2019 Elsevier Masson SAS. All rights reserved.European Journal of Medicinal Chemistry 179 (2019) 634e648
Citation - WoS: 6
Citation - Scopus: 6
The Effect of Surfaces on The Orientational Properties and Phase Transitions Peculiarities of a Nonpolar Smectogen
(World Scientific Publ Co Pte Ltd, 2010) Yıldız, Sevtap; Zayim, Esra Ozkan; Pekcan, Önder; Özbek, Haluk
The effect of thin films on the orientational and optical properties of nonpolar monolayer smectogen 4-butoxyphenyl-4'-decyloxybenzoate ((10) over barO (4) over bar) liquid crystal has been studied by polarizing microscopy and high-resolution photon transmission method. The uniform planar textures of (10) over barO (4) over bar on the surfaces coated with WO3 VO2 and WO3-VO2 mixture thin films have been obtained. No significant shifts in the phase transition temperatures to lower values under the influence of the surfaces have been observed. We have also presented the new experimental data on the critical behavior of the layer compression modulus B near the nematic-smectic A transition. It was observed that the data in the vicinity of the transition can be described by a power law expression after the introduction of a first-order correction-to-scaling term within the limit of experimental error. The resulting critical exponent was found to be 0.34 -/+ 0.01 which is good agreement with the previously reported values for other investigated compounds in literature.
Citation - WoS: 85
Citation - Scopus: 89
Electrical and Optical Percolations of Polystyrene Latex-Multiwalled Carbon Nanotube Composites
(Academic Press Inc Elsevier Science, 2010) Kara, Selim; Arda, Ertan; Dolastir, Fahrettin; Pekcan, Önder
Electrical conductivity and optical transmittance properties of polystyrene (PS)-multiwalled carbon nanotube (MWCNT) composite films were investigated. Composite films were prepared by mixing of various mass fractions of MWCNT in PS-water dispersions. After water evaporates powder composite films were annealed at 175 degrees C above the glass transition of PS for 20 min. Photon transmission and two point probe resistivity techniques were employed to determine the variations of the optical and the electrical properties of composites. Transmitted light intensity I(tr) and surface resistivity R(s) were monitored as a function of MWCNT mass fraction (M). It was observed that both the surface resistivity and the optical transparency were decreased by increasing the amount of MWCNT added to the polymeric system. Conductivity and optical results were interpreted according to the classical and site percolation theory respectively. The electrical (sigma) and the optical (op) percolation threshold values and critical exponents were calculated as M(sigma) = 1.8 wt.% M(op) = 0-0.13 wt.% and beta(sigma) = 2.25 beta(op) = 0.32 respectively. (C) 2010 Elsevier Inc. All rights reserved.
Citation - WoS: 8
Citation - Scopus: 8
The Electrochromic Performances of Single Phase Vo2 Nanoparticled Films
(Elsevier Science SA, 2016) Akkaya Arier, Ümit Özlem; Uysal, Bengü Özuğur
In the present work pure phase vanadium oxide VO2 nanoparticled films were synthesized using acetate based sol-gel precursors. The effect of the water: Vanadyl acetylacetonate ratio on electrochemical and structural properties of nanostructured vanadium oxide films was examined. The X-ray diffraction studies indicated that very strong crystallization of the VO2 monoclinic phase occurred for the as-deposited films at the annealing temperature of 500 degrees C. According to the atomic force microscopy and scanning electron microscopy measurements the size and morphology of the granular structured film depend on the water: Vanadyl acetylacetonate ratio. I-V curve spectra were used to compute several characteristics of the films coated on indium tin oxide substrates such as the optical density color efficiency and diffusion coefficient. Even though water: Vanadyl acetylacetonate ratio of 0.1 is expected to give the highest color efficiency value (33 cm(2)/C) higher diffusion coefficient (3.15 x 10(-12) cm(2)/s) is observed in the ratio of 0.01. As a result the correlation between the ratios and electrochromic properties of the films was established. (C) 2016 Elsevier B.V. All rights reserved.
Epitope Based Hla Matching by Using Antibody Reactivity With High Resolution Allele Typing and Hlamatchmaker Algorithm Based Software
(Wiley, 2017) Karadeniz, Sedat Tanju; Akgül, Sebahat Usta; Çiftçi, Hayriye Şentürk; Öğret, Yeliz; Oğuz, Fatma; Yelekçi, Kemal; Aydın, Filiz
[Abstract Not Available]
Citation - WoS: 11
Citation - Scopus: 20
Evaluation of Selective Human Mao Inhibitory Activities of Some Novel Pyrazoline Derivatives
(SPRINGER WIEN, 2013) Salgin-Goksen, Umut; Yabanoglu-Ciftci, Samiye; Ercan, Ayse; Yelekçi, Kemal; Ucar, Gulberk; Gokhan-Kelekçi, Nesrin
A series of 1-[2-((5-methyl/chloro)-2-benzoxazolinone-3-yl)acetyl]-35-diaryl-45-dihydro-1H-pyrazole derivatives were prepared by reacting 2-((5-methyl/chloro)-2-benzoxazolinone-3-yl)acetylhydrazine with appropriate chalcones. The chemical structures of all compounds were confirmed by elemental analyses IR H-1 NMR and ESI-MS. All the compounds were investigated for their ability to selectively inhibit monoamine oxidase (MAO) by in vitro tests. MAO activities of the compounds were compared with moclobemide and selegiline and all the compounds were found to inhibit human MAO-A selectively. The inhibition profile was found to be competitive and reversible for all compounds by in vitro tests. Among the compounds examined compounds 5ae 5af and 5ag were more selective than moclobemide with respect to the K (i) values experimentally found. In addition the compound 5bg showed MAO-A inhibitor activity as well as moclobemide. A series of experimentally tested compounds (5ae-5ch) were docked computationally to the active site of the MAO-A and MAO-B isoenzyme. The AUTODOCK 4.01 program was employed to perform automated molecular docking.
Citation - WoS: 4
Citation - Scopus: 5
Fluorescence Quenching Method for Monitoring Oxygen Diffusion Into Ps/Cnt Composite Films
(Elsevier Science SA, 2013) Yargı, Önder; Uğur, Şaziye; Pekcan, Önder
Oxygen permeabilities of nanocomposite films consisting of multi wall carbon nanotubes (MWNT) and polystyrene (PS) were determined to investigate the oxygen diffusion depending on MWNT and temperature. A method which is based on quenching of an excited phosphorescent by oxygen was applied for the measurements. The composite films were prepared from mixtures of (MWNT) and surfactant-free pyrene (P)-labeled (PS) latexes of various compositions at room temperature. These films were then annealed at 170 degrees C which is well above the glass transition (T-g) temperature of polystyrene for 10 min. Diffusion experiments were performed for eight films with different MWNT content (0 1.5 3 5 10 15 25 and 40 wt%) to evaluate the effect of MWNT content on oxygen diffusion. Diffusion coefficients were found to increase from 1.1 x 10(-12) to 41 x 10(-12) cm(2) s(-1) with increasing MWNT content. On the other hand to examine the effect of temperature on oxygen diffusion diffusion measurements were performed over a temperature range of 24-70 degrees C for three different MWNT contents (3 15 and 40 wt%) within the films. The results indicated that the values of the diffusion coefficient D are strongly dependent on both temperature and MWNT content in the film. It was also observed that the diffusion coefficients obey Arrhenius behavior from which diffusion energies were determined which increased with increase of MWNT content and temperature. (C) 2013 Elsevier B.V. All rights reserved.
Citation - WoS: 1
Citation - Scopus: 1
Fluorescence Study of Film Formation From Ps/Al2o3 Nanocomposites
(Elsevier Science, 2014) Pekcan, Önder; Uğur, Şaziye; Sunay, M. Selin
Steady state fluorescence (SSF) and UV-vis (UVV) techniques were used to study the film formation behavior of pyrene (P) labeled polystyrene (PS) latex and Al2O3 (PS/Al2O3) composites depending on PS particles size and Al2O3 content. The close-packed arrays of PS spheres (SmPS: 203 nm ; LgPS: 382 nm) templates on clean glass substrates were covered with various layers of Al2O3 by dip-coating method. Two different film series (SmPS/Al2O3 and LgPS/Al2O3) were prepared in various Al2O3 layer content. The film formation behavior of these composites were studied by annealing them at a temperature range of 100-250 degrees C and monitoring the scattered light intensity (I-sc) fluorescence intensity (I-p) from P and transmitted light intensity (I-tr) through the films after each annealing step. Optical results indicate that classical latex film formation was occurred for all Al2O3 content films and film formation process was unaffected by the Al2O3 content for both film series. Extraction of PS template produced highly ordered porous structures for high Al2O3 content in both film series. SEM images showed that the pore size and porosity could be easily tailored by varying the PS particle size and the Al2O3 content. (C) 2014 Elsevier B.V. All rights reserved.
Citation - WoS: 3
Citation - Scopus: 3
Fractal Dimension and Phase Transition of Graphene Oxide (go) Doped Polyacrylamide
(ELSEVIER SCI LTD, 2020) Evingür, Gülşen Akın; Pekcan, Önder
Graphene Oxide (GO)- Polyacrylamide composites prepared between 5 and 50 mu l GO were performed by Fluorescence Spectroscopy. The phase transition performed on the composites was measured by calculating the critical exponents, beta and gamma, respectively. In addition, fractal analysis of the composites was calculated by a fluorescence intensity of 427 nm. The geometrical distribution of GO in the composites was calculated based on the power law exponent values using scaling models. While the gelation proceeded GO plates first organized themselves into a 3D percolation cluster with the fractal dimension (D-f) of the composite, D-f = 2.63, then After it goes to diffusion limited clusters with D-f = 1.4, its dimension lines up to a Von Koch curve with a random interval of D-f = 1.14.
Citation - WoS: 20
Citation - Scopus: 20
Gelation Mechanisms
(World Scientific Publ Co Pte Ltd, 2012) Pekcan, Önder; Kara, Selim
In this paper, we survey the gelation mechanisms for various polymeric systems which are classified by the type and the strength of the cross-linkages. These are the "irreversible" gels that are cross-linked chemically by covalent bonds and the "reversible" gels that are cross-linked physically by hydrogen or ionic bonds and by the physical entanglement of polymer chains. Some of the natural polymer gels fall into the class of physical gels, among which the red algae that has attracted attention for various applications is discussed in detail. Various composite gels, formed from mixture of physical and chemical gels are also discussed in the last section of the article. Theoretical models describe the gelation as a process of random linking of subunits to larger and larger molecules by formation of an infinite network, where no matter what type of objects are linked, there is always a critical "gel point" at which the system behaves neither as a liquid nor as a solid on any length scale. The Flory-Stockmayer theory and percolation theory provide bases for modeling this sol-gel phase transition. The experimental techniques for measuring the critical exponents for sol-gel phase transitions in different polymeric systems are introduced and the validation of various theoretical predictions are surveyed.
Citation - WoS: 2
Citation - Scopus: 3
Gelation of Paam-Pvp Composites: a Fluorescence Study
(World Scientific, 2014) Evingür, Gülşen Akin; Kaygusuz, Hakan; Erim, F. Bedia; Pekcan, Önder
Hybrid hydrogels are a new class of composite materials. Polyacrylamide (PAAm) hydrogels are mainly produced by free radical crosslinking copolymerization (FCC) of AAm in the presence of N N'-methylene bis (acrylamide) (BIS) as the crosslinker. Pyranine doped PAAm-poly (N-vinyl pyrrolidone) (PVP) composite were prepared with different amounts of PVP varying in the range between 0.0015 and 0.1 gr. It was observed that pyranine molecules as a fluoroprobe bind to AAm and PVP chains upon the initiation of the polymerization causing the fluorescence spectra of the bonded pyranines shift to the shorter wavelengths. The sol-gel phase transition and its universality were monitored and tested as a function of PVP contents. Observations around the critical point show that the gel fraction exponent beta agreed with the percolation result for below 0.025 gr PVP contents. However classical result was observed above 0.0125 gr PVP content.

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