2) Makale

Bu koleksiyon için kalıcı URI

https://hdl.handle.net/20.500.12604/386

Listeleniyor 1 - 20 / 28

Effects of different formulation PEDOT:PSS hole transport layers on photovoltaic performance of organic solar cells
(John Wiley and Sons, August 2017) Ongul, Fatih; Yuksel, Sureyya Aydin; Kazici, Mehmet; Bozar, Sinem; Gunbatti, Anil; Gunes, Serap
In this study, the effects of the various types of PEDOT:PSS with different conductivities on the photovoltaic parameters of organic solar cells were investigated. The performances of five various commercially available PEDOT:PSS with formulations such as FET, PT2, PH1000, PH500 and PH were compared. It was observed that the device employing PH1000 as an interlayer between ITO and the active layer exhibited the highest photovoltaic performance as compared to other devices with FET, PT2, PH500 and PH.
Statistical efficiency of methods for computing free energy of hydration
(2018) Yildirim, Ahmet; A. Wassenaar, Tsjerk; van der Spoel, David
The hydration free energy (HFE) is a critical property for predicting and understanding chemical and biological processes in aqueous solution. There are a number of computational methods to derive HFE, generally classified into the equilibrium or non-equilibrium methods, based on the type of calculations used. In the present study, we compute the hydration free energies of 34 small, neutral, organic molecules with experimental HFE between +2 and -16 kcal/mol. The one-sided non-equilibrium methods Jarzynski Forward (JF) and Backward (JB), the two-sided non-equilibrium methods Jarzynski mean based on the average of JF and JB, Crooks Gaussian Intersection (CGI), and the Bennett Acceptance Ratio (BAR) are compared to the estimates from the two-sided equilibrium method Multistate Bennett Acceptance Ratio (MBAR), which is considered as the reference method for HFE calculations, and experimental data from the literature. Our results show that the estimated hydration free energies from all the methods are consistent with MBAR results, and all methods provide a mean absolute error of ∼0.8 kcal/mol and root mean square error of ∼1 kcal for the 34 organic molecules studied. In addition, the results show that one-sided methods JF and JB result in systematic deviations that cannot be corrected entirely. The statistical efficiency ε of the different methods can be expressed as the one over the simulation time times the average variance in the HFE. From such an analysis, we conclude that ε(MBAR) > ε(BAR) ≈ ε(CGI) > ε(JX), where JX is any of the Jarzynski methods. In other words, the non-equilibrium methods tested here for the prediction of HFE have lower computational efficiency than the MBAR method.
Only a Subset of Normal Modes is Sufficient to Identify Linear Correlations in Proteins.
(2018) Tekpinar, Mustafa; Yildirim, Ahmet
Identification of correlated residues in proteins is very important for many areas of protein research such as drug design, protein domain classification, signal transmission, allostery and mutational studies. Pairwise residue correlations in proteins can be obtained from experimental and theoretical ensembles. Since it is difficult to obtain proteins in various conformational states experimentally, theoretical methods such as all-atom molecular dynamics simulations and normal-mode analysis are commonly used methods to obtain protein ensembles and, therefore, pairwise residue correlations. The extent of agreement for the correlations obtained with all-atom molecular dynamics and elastic network model based normal-mode analysis is an important issue to investigate due to orders of magnitude computational advantage in terms of wall time for normal-mode based calculation. We performed multiple microsecond long equilibrium classical molecular dynamics simulations for six proteins. We calculated normalized dynamical cross-correlations and linear mutual information as pairwise residue correlations from the trajectories of these simulations. Then, we calculated the same pairwise residue correlations with two elastic network model based normal-mode analysis methods and compared our results with the former. The results show that elastic network model based normal-mode analysis can provide a fast and accurate estimation of linear correlations within proteins. Finally, we observed that only a subset of modes is sufficient to obtain linear correlations in proteins. This conclusion has crucial implications for understanding correlations within very large protein assemblies such as viral capsids.
Binding of Pollutants to Biomolecules: A Simulation Study
(2016) Yildirim, Ahmet; Zhang, Jin; Manzetti, Sergio; van der Spoel, David
A number of cases around the world have been reported where animals were found dead or dying with symptoms resembling a thiamine (vitamin B) deficiency, and for some of these, a link to pollutants has been suggested. Here, we investigate whether biomolecules involved in thiamin binding and transport could be blocked by a range of different pollutants. We used in silico docking of five compound classes (25 compounds in total) to each of five targets (prion protein, ECF-type ABC transporter, thi-box riboswitch receptor, thiamin pyrophosphokinase, and YKoF protein) and subsequently performed molecular dynamics (MD) simulations to assess the stability of the complexes. The compound classes were thiamin analogues (control), pesticides, veterinary medicines, polychlorinated biphenyls, and dioxins, all of which are prevalent in the environment to some extent. A few anthropogenic compounds were found to bind the ECF-type ABC transporter, but none binds stably to prion protein. For the riboswitch, most compounds remained in their binding pockets during 50 ns of MD simulation, indicating that RNA provides a promiscuous binding site. In both YKoF and thiamin pyrophosphokinase (TPK), most compounds remain tightly bound. However, TPK biomolecules undergo pollutant-induced conformational changes. Although most compounds are found to bind to some of these targets, a larger data set is needed along with more quantitative methods like free energy perturbation calculations before firm conclusions can be drawn. This study is in part a test bed for large-scale quantitative computational screening of interactions between biological entities and pollutant molecules.
Molecular dynamics study of the effect of active site protonation on Helicobacter pylori 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
(2015) Tekpinar, Mustafa; Yildirim, Ahmet; A. Wassenaar, Tsjerk
The protein 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) is involved in the quorum sensing of several bacterial species, including Helicobacter pylori. In particular, these bacteria depend on MTAN for synthesis of vitamin K2 homologs. The residue D198 in the active site of MTAN seems to be of crucial importance, by acting as a hydrogen-bond acceptor for the ligand. In this study, we investigated the conformation and dynamics of apo and holo H. pylori MTAN (HpMTAN), and assessed the effect of protonation of D198 by use of molecular dynamics simulations. Our results show that protonation of the active site of HpMTAN can cause a conformational transition from a closed state to an open state even in the absence of substrate, via inter-chain mechanical coupling.
Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions
(2015) M. Fischer, Nina; J. van Maaren, Paul; C. Ditz, Jonas; Yildirim, Ahmet; van der Spoel, David
In order to increase the accuracy of classical computer simulations, existing methodologies may need to be adapted. Hitherto, most force fields employ a truncated potential function to model van der Waals interactions, sometimes augmented with an analytical correction. Although such corrections are accurate for homogeneous systems with a long cutoff, they should not be used in inherently inhomogeneous systems such as biomolecular and interface systems. For such cases, a variant of the particle mesh Ewald algorithm (Lennard-Jones PME) was already proposed 20 years ago (Essmann et al. J. Chem. Phys. 1995, 103, 8577-8593), but it was implemented only recently (Wennberg et al. J. Chem. Theory Comput. 2013, 9, 3527-3537) in a major simulation code (GROMACS). The availability of this method allows surface tensions of liquids as well as bulk properties to be established, such as density and enthalpy of vaporization, without approximations due to truncation. Here, we report on simulations of ≈150 liquids (taken from a force field benchmark: Caleman et al. J. Chem. Theory Comput. 2012, 8, 61-74) using three different force fields and compare simulations with and without explicit long-range van der Waals interactions. We find that the density and enthalpy of vaporization increase for most liquids using the generalized Amber force field (GAFF, Wang et al. J. Comput. Chem. 2004, 25, 1157-1174) and the Charmm generalized force field (CGenFF, Vanommeslaeghe et al. J. Comput. Chem. 2010, 31, 671-690) but less so for OPLS/AA (Jorgensen and Tirado-Rives, Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6665-6670), which was parametrized with an analytical correction to the van der Waals potential. The surface tension increases by ≈10(-2) N/m for all force fields. These results suggest that van der Waals attractions in force fields are too strong, in particular for the GAFF and CGenFF. In addition to the simulation results, we introduce a new version of a web server, http://virtualchemistry.org, aimed at facilitating sharing and reuse of input files for molecular simulations.
Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field
(2015) Unan, Hulya; Yildirim, Ahmet; Tekpinar, Mustafa
Adenylate kinase is a widely used test case for many conformational transition studies. It performs a large conformational transition between closed and open conformations while performing its catalytic function. To understand conformational transition mechanism and impact of force field choice on E. Coli adenylate kinase, we performed all-atom explicit solvent classical molecular dynamics simulations starting from the closed conformation with four commonly used force fields, namely, Amber99, Charmm27, Gromos53a6, Opls-aa. We carried out 40 simulations, each one 200 ns. We analyzed completely 12 of them that show full conformational transition from the closed state to the open one. Our study shows that different force fields can have a bias toward different transition pathways. Transition time scales, frequency of conformational transitions, order of domain motions and free energy landscapes of each force field may also vary. In general, Amber99 and Charmm27 behave similarly while Gromos53a6 results have a resemblance to the Opls-aa force field results.
Molecular dynamics investigation of Helicobacter pylori chemotactic protein CheY1 and two mutants
(2014) Yildirim, Ahmet; Tekpinar, Mustafa; A. Wassenaar, Tsjerk
CheY is a chemotactic response regulator protein modulating the rotation direction of bacterial flagellar motors. It plays an important role in the colonization and infection of Helicobacter pylori (H. pylori), which is a common pathogen. Recently, the structure of CheY1 of H. pylori (HpCheY1) was solved, showing similarities and differences with CheY from E. coli. Here, we report 200 ns atomistic molecular dynamics (MD) simulations of HpCheY1 and two mutants. The results suggest that the surface of HpCheY1 has regions with increased affinity for Mg²⁺. In addition, wildtype HpCheY1 (WT HpCheY1) shows characteristic dynamics in helix 4, which is involved in FliM binding. This dynamics is altered in the D53A mutant and completely suppressed in the T84A mutant. The results are discussed in relation to the binding and function of HpCheY1.
Ab initio calculations of the elastic, electronic, optical, and vibrational properties of PdGa compound under pressure
(2012) Koc, Husnu; Yildirim, Ahmet; Deligoz, Engin
The structural, elastic, electronic, optical, and vibrational properties of cubic PdGa compound are investigated using the norm-conserving pseudopotentials within the local density approximation (LDA) in the framework of the density functional theory. The calculated lattice constant has been compared with the experimental value and has been found to be in good agreement with experimental data. The obtained electronic band structures show that PdGa compound has no band gap. The second-order elastic constants have been calculated, and the other related quantities such as the Young's modulus, shear modulus, Poisson's ratio, anisotropy factor, sound velocities, and Debye temperature have also been estimated. Our calculated results of elastic constants show that this compound is mechanically stable. Furthermore, the real and imaginary parts of the dielectric function and the optical constants such as the electron energy-loss function, the optical dielectric constant and the effective number of electrons per unit cell are calculated and presented in the study. The phonon dispersion curves are also derived using the direct method.
Ab initio calculation of the structural, elastic, electronic, and linear optical properties of ZrPtSi and TiPtSi ternary compounds
(2012) Koc, Husnu; Yildirim, Ahmet; Tetik, Erkan; Deligoz, Engin
The structural, elastic, electronic, and optical properties of orthorhombic ZrPtSi and TiPtSi ternary compounds are investigated using the norm-conserving pseudopotentials within the generalized gradient approximation (GGA) in the frame of density functional theory. The calculated lattice param- eters have been in agreement with the available experimental data. The second-order elastic constants have been calculated, and the other related quantities such as the Young’s modulus, shear modulus, Poisson’s ratio, anisotropy factor, sound velocities, and Debye temperature have also been estimated. The electronic structure of ZrPtSi and TiPtSi compounds are calculated by using the first principles GW and GGA approximations. The real and imaginary parts of the dielectric function and the optical constants such as the optical dielectric constant and the effective number of electrons per unit cell are also presented.
First-principles study of the structural, elastic, electronic, optical, and vibrational properties of intermetallic Pd2Ga
(2012) Yildirim, Ahmet; Koc, Husnu; Deligoz, Engin
The structural, elastic, electronic, optical, and vibrational properties of the orthorhombic Pd 2 Ga compound are investigated using the norm-conserving pseudopotentials within the local density approximation in the frame of density functional theory. The calculated lattice parameters have been compared with the experimental values and found to be in good agreement with these results. The second-order elastic constants and the other relevant quantities, such as the Young’s modulus, shear modulus, Poisson’s ratio, anisotropy factor, sound velocity, and Debye temperature, have been calculated. It is shown that this compound is mechanically stable after analysing the calculated elastic constants. Furthermore, the real and imaginary parts of the dielectric function and the optical constants, such as the optical dielectric constant and the effective number of electrons per unit cell, are calculated and presented. The phonon dispersion curves are derived using the direct method. The present results demonstrate that this compound is dynamically stable.
Investigation of anisotropic thermal conductivity of uniaxial and biaxial Gay–Berne particles with molecular dynamics simulation
(2011) Yildirim, Ahmet; Eroglu, Erol; Yilmaz, Suleyman
In this study, we investigated uniaxial and biaxial Gay– Berne (GB) particles with the help of the molecular dynamics (MD) simulation. Anisotropic thermal conductivities of the uniaxial and biaxial GB liquid crystal molecules were calculated both in the random molecular orientation and in the molecular orientations of 08, 458 and 908 using the Müller-Plathe method. In the uniaxial molecules, it was found that the thermal conductivity ratios between the parallel and perpendicular components for the smectic and nematic phases are about 2.2:1 and 2.8:1, respectively. As for biaxial molecules, these ratios between the parallel and perpendicular components of molecules for the smectic and nematic phases are about 3.9:1 and 3.8:1, respectively.
Numerical Determination of Thermal-Diffusivity Coefficients of Some Nematic Liquid Crystals in Situ
(2009) Yilmaz, Suleyman; Yildirim, Ahmet
In this study, a new experimental study has been implemented to deter- mine the thermal-diffusivity parameters of industrial nematic liquid crystals, 4-pentyl- 4 -cyanobiphenyl (5CB) and 4 -octyl-4-cyanobiphenyl (8CB), both numerically by using the finite difference method (FDM) for forward solutions and experimentally by measuring the temperature variation with time and position. The most important parts of this experimental study are the heating system and the liquid crystal cell, which were constructed in-house to determine the temperatures of the materials in situ. Four different positions for local measurements have been studied, and the opti- mum graph of this variation has been determined. The experimental and theoretical results of this study are consistent with previous measurements performed by means of a conventional thermal technique.
Optical Properties of Nematic Liquid Crystal (C 21 H 27 NO 2 S) Under AC/DC Electric Fields
(2009) Emek, Mehriban; Besli, Nurettin; Yilmaz, Suleyman; Yildirim, Ahmet
In this study, the effects of the phase transition on the optical transmittance of the nematic liquid crystal C21H27NO2S, 4′-isothiocyanatophenyl-4-pentylbicyclo[2,2,2]octane-1-carboxylate are investigated in terms of temperature variation and rotational angle of the polarizer through electro-optical methods under AC / DC electric fields. It is observed that the domain structure of the material is affected considerably by the applied electric field as the temperature changes. Under applied electric fields, the crystal-nematic (CN) phase-transition point changes and the behaviour of the liquid crystal in the phase-transition region shows some differences. The intensity of the light passing through the system under a DC electric field increases as the electric field rises. Nevertheless, the intensity of the transmitted light under an AC electric field increases at the beginning and then decreases as the electric field rises to a temperature of more than 355 K. These results can be explained through the formation of a domain structure during the phase-transition process and the light scattering caused by these structures.
Synthesis and characterization of Mn and Co codoped ZnO nanoparticles
(Superlattices and Microstructures, 2015-07-01) Abdullahi, Sabiu Said; Köseoğlu, Yüksel; Güner, Sadık; kazan, sinan; Kocaman, Bayram; Ndikilar, Chifu E.
MnxCo0.1Zn0.9-xO nanoparticles with different doping concentration (x = 0.0, 0.05, 0.1, 0.15, and 0.2) has been successfully synthesized by microwave assisted combustion synthesis method using urea as a fuel. The structural, morphological, compositional, magnetic and optical properties of these nanoparticles were investigated by X-ray diffraction (XRD), Scanning electron microscopes (FE-SEM JEOL-7001), Energy-dispersive X-ray spectroscopy (EDX), Quantum Design Physical Property Measurement System (PPMS) and UV–visible spectroscopy, respectively. The structural properties showed the formation of single phase Wurtzite structure of ZnO, with the strong diffraction peaks appear in (1 0 0), (0 0 2) and (1 0 1) respectively. The average size of the nanoparticles decreases from 32.65 to 23.69 nm as dopant concentration is increase. Scanning electron microscope (SEM) pictures showed that smaller crystallites have sizes smaller than 100 nm, no phase separation and agglomeration was observed. Moreover, Energy-dispersive X-ray spectroscopy (EDX) confirmed the synthesis results. The magnetic characterization of the samples reveals that the samples showed paramagnetic and ferromagnetic behavior, meanwhile there is no linear variation of magnetic moment with concentration of Mn ion whereby at x = 0.15 the samples show room temperature ferromagnetic behavior with coercive field and remanent magnetization of 47.70 Oe and 1.8 × 10-1 emu/g, respectively. UV–vis spectroscopy results show that the optical band gap of the nanoparticles varies between 3.24 eV and 3.02 eV.
Magnetic and structural characterization of Ni(1-x)Gex thin film
(Journal of Magnetism and Magnetic Materials, 2015-01-01) kazan, sinan; Kocaman, Bayram; parabaş, adem; yıldız, fikret; aktaş, Bekir
In this study, the growth and magnetic properties of Ni(1-x)Gex thin films on naturally oxidized Si(100) substrate by a molecular beam epitaxy (MBE) technique were investigated. The surface morphology and structural properties of the thin films were investigated by scanning electron microscopy (SEM) and X-ray diffraction techniques. The magnetic properties of the films were measured by ferromagnetic resonance (FMR) and vibrating sample magnetometer (VSM) techniques. SEM images show that the morphology of the films depends on chemical composition of the films. The analysis of FMR spectra and VSM results shows that the saturation magnetization, coercive field and effective magnetization of Ni(1-x)Gex film decrease with the increase of Ge content up to a certain value (atomic percent of Ge at 9%) which is called critical Ge concentration. The magnetization dynamics and agglomeration of NiGe thin film with varying Ge concentration have been presented for potential application like helical magnetic properties as in FeGe.
Reduction of shunt current in buffer-free IrMn based spin-valve structures
(Journal of Magnetism and Magnetic Materials, 2018-06-15) Kocaman, Bayram; Akdoğan, Numan
The presence of thick buffer layers in magnetic sensor devices decreases sensor sensitivity due to shunt currents. With this motivation, we produced IrMn-based spin-valve multilayers without using buffer layer. We also studied the effects of post-annealing and IrMn thickness on exchange bias field (HEB) and blocking temperature (TB) of the system. Magnetization measurements indicate that both HEB and TB values are significantly enhanced with post-annealing of IrMn layer. In addition, we report that IrMn thickness of the system strongly influences the magnetization and transport characteristics of the spin-valve structures. We found that the minimum thickness of IrMn layer is 6?nm in order to achieve the lowest shunt current and high blocking temperature (>300?K). We also investigated the training of exchange bias to check the long-term durability of IrMn-based spin-valve structures for device applications.
The effect of spatial distribution of Zn vacancies in ZnS quantum dots on optical absorption spectra
(2017-04-05) Pimachev, Artem; Proshchenko, Vitaly; Horoz, Sabit; Sahin, Omer; Dahnovsky, Yuri
In this work we propose how to identify the location and spatial distribution of Zn vacancies in ZnS quantum dots (QDs). The experiments reveal a peak shift in absorption spectra towards the lower energies (about 0.1 eV) in the presence of Zn vacancies. To explain such a shift we computationally study the absorption spectra when Zn vacancies are localized in the core, on the surface, and both in the core and on the surface of a quantum dot. From the comparison with the experimental data we conclude that the most favorable configuration of the vacancies is an aggregation on a QD surface. We find that Zn vacancies localized in the core or uniformly distributed on the QD surface, do not explain the experimentally observed shift in the absorption curves.
Room temperature d0 ferromagnetism in ZnS nanocrystals
(2016-05-27) Proshchenko, Vitaly; Horoz, Sabit; Tang, Jinke; Dahnovsky, Yuri
Room temperature ferromagnetic semiconductors have a great deal of advantage because of their easy integration into semiconductor devices. ZnS nanocrystals (NCs), bulk, and surfaces exhibit d0 ferromagnetism at room temperature. The experiments reveal that NC ferromagnetism takes place at low and room temperatures only due to Zn vacancies (S vacancies do not contribute). To understand the mechanism of d0 ferromagnetism, we introduce the surface-bulk model of a nanocrystal, which includes both surface and bulk magnetizations. The calculations demonstrate that the surface has the higher than bulk magnetization. We find the mechanism of the ferromagnetism is due to sulfur s- and p-electrons in a tetrahedral crystal field. The bulk magnetic moment increases with Zn vacancy concentration at small concentrations and then goes down at larger concentrations. A surface magnetic moment behaves differently with the concentration. It is always a monotonically rising function. We find that the total NC magnetic moment increases with the size and concentration of Zn vacancies (only low concentrations). We also study the magnetization per unit cell where we find that it decreases for the surface and increases for bulk magnetism with the NC size.
Investigations of structural, optical, and photovoltaic properties of Fe-alloyed ZnS quantum dots
(2017-03-15) Horoz, Sabit; Sahin, Omer
Pure ZnS and Fe-alloyed ZnS quantum dots (QDs) prepared by wet-chemical method at room temperature using mercaptoethanol as a capping agent. The nominal concentrations of Fe were 5, 10, and 15% weight of Fe. The QDs were characterized by X-ray diffraction (XRD), scanning electron microscope (SEM), energy dispersive analysis of X-rays (EDAX), optical absorption and photoluminescence (PL) measurements. The cubic phase of pure and Fe-alloyed ZnS QDs was indicated using the XRD measurements. It was determined that the sizes of doped samples decrease as the Fe concentrations are increased. The band gaps of QDs were investigated using optical measurements. It was observed that the band gaps and the absorption windows of Fe-alloyed ZnS QDs increase with the increase in the concentrations of Fe. It was seen that as the concentration of Fe increases, both the absorption and the emission peaks of the alloyed ZnS QDs shift to shorter wavelength. The photovoltaic properties of Fe alloyed ZnS QDs have been investigated in this study for the first time. The pure ZnS and Fe-alloyed ZnS QDs were used to make quantum dots-sensitized solar cells. The performances of the solar cells, with the short circuit current density (JSC) and open circuit voltage (VOC) and incident photon to electron conversion efficiency (IPCE) of Fe-alloyed ZnS QDs increased with increasing Fe doping. Thus, Fe-alloyed ZnS QDs can be used as promising materials in solar cell technology due to fact that they have wider optical absorption spectrums.

Güncel Gönderiler