Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 4Citation - Scopus: 6Rational Design of Thermophilic Cyp119 for Progesterone Hydroxylation by in Silico Mutagenesis and Docking Screening(Elsevier, 2023) Kestevur Doğru, Ekin; Güralp, Gülce; Uyar, Arzu; Sürmeli, Nur BaşakSteroid-based chemicals can affect the metabolism, immune functions, and development of sexual characteristics. Because of these effects, steroid derivatives are widely used in the pharmaceutical industry. Progesterone is a steroid-based hormone that mainly controls the ovulation period of women but is also a precursor molecule for the synthesis of important hormones like testosterone and cortisone. Cytochrome P450 (CYP) enzymes are important for the production of hydroxyprogesterones in the industry since they can catalyze regio- and enantioselective hydroxylation reactions. Although human CYP enzymes can catalyze hydroxyprogesterone synthesis with high selectivity, these enzymes are membrane bound, which limits their application for industrial production. CYP119 is a soluble and thermophilic enzyme from the archaea Sulfolobus acidocaldarius. Even though the native substrate of the enzyme is not known, CYP119 can catalyze styrene epoxidation, lauric acid hydroxylation, and Amplex®Red peroxidation. In this work, an in silico mutagenesis approach was used to design CYP119 mutants with high progesterone affinity. Energy scores of progesterone docking simulations were used for the design and elimination of single, double, and triple mutants of CYP119. Among designed 674 mutants, five of them match the criteria for progesterone hydroxylation. The most common mutation of these five mutants, L69G mutant was analyzed using independent molecular dynamics (MD) simulations in comparison with the wild-type (WT) enzyme. L69G CYP119, was expressed and isolated from Escherichia coli; it showed 800-fold higher affinity for progesterone compared to WT CYP119. L69G CYP119 also catalyzed progesterone hydroxylation. The novel designed enzyme L69G CYP119 is a potential versatile biocatalyst for progesterone hydroxylation that is expected to be stable under industrial production conditions.Article Citation - WoS: 17Citation - Scopus: 18Electric Field Controlled Heat Transfer Through Silicon and Nano-Confined Water(Taylor & Francis, 2019) Yenigün, Onur; Barışık, MuratNanoscale heat transfer between two parallel silicon slabs filled with deionized water was studied under varying electric field in heat transfer direction. Two oppositely charged electrodes were embedded into the silicon walls to create a uniform electric field perpendicular to the surface, similar to electrowetting-on-dielectric technologies. Through the electrostatic interactions, (i) surface charge altered the silicon/water interface energy and (ii) electric field created orientation polarization of water by aligning dipoles to the direction of the electric field. We found that the first mechanism can manipulate the interface thermal resistance and the later can change the thermal conductivity of water. By increasing electric field, Kapitza length substantially decreased to 1/5 of its original value due to enhanced water layering, but also the water thermal conductivity lessened slightly since water dynamics were restricted; in this range of electric field, heat transfer was doubled. With a further increase of the electric field, electro-freezing (EF) developed as the aligned water dipoles formed a crystalline structure. During EF (0.53 V/nm), water thermal conductivity increased to 1.5 times of its thermodynamic value while Kapitza did not change; but once the EF is formed, both Kapitza and conductivity remained constant with increasing electric field. Overall, the heat transfer rate increased 2.25 times at 0.53 V/nm after which it remains constant with further increase of the electric field.Article Citation - WoS: 18Citation - Scopus: 17Wetting of Single Crystalline and Amorphous Silicon Surfaces: Effective Range of Intermolecular Forces for Wetting(Taylor and Francis Ltd., 2020) Özçelik, Hüseyin Gökberk; Özdemir, Abdullah Cihan; Kim, Bohung; Barışık, MuratWetting at nanoscale is a property of a three-dimensional region with a finite length into the solid domain from the surface. Understanding the extent of the solid region effective on wetting is important for recent coating applications as well as for both crystalline and amorphous solids of different atomic ordering. For such a case, we studied the wetting behaviour of silicon surfaces at various crystalline and amorphous states. Molecular distributions of amorphous systems were varied by changing the amorphisation conditions of silicon. Semi-cylindrical water droplets were formed on the surfaces to be large enough to remain independent of line tension and Tolman length effects. Contact angles showed up to 38% variation by the change in the atomic orientation of silicon. Instead of a homogeneous solid density definition, we calculated different solid densities for a given surface measured inside different extents from the interface. We correlated the observed wetting variation with each of these different solid densities to determine which extent governs the wetting variation. We observed that the variation of solid density measured inside a 0.13 nm extent from the surface reflected the variation of wetting angle better for both single crystalline and amorphous silicon surfaces.Article Citation - WoS: 44Citation - Scopus: 47Electric Field Controlled Transport of Water in Graphene Nano-Channels(American Institute of Physics, 2017) Çelebi, Alper Tunga; Barışık, Murat; Beşkök, AliMotivated by electrowetting-based flow control in nano-systems, water transport in graphene nano-channels is investigated as a function of the applied electric field. Molecular dynamics simulations are performed for deionized water confined in graphene nano-channels subjected to opposing surface charges, creating an electric field across the channel. Water molecules respond to the electric field by reorientation of their dipoles. Oxygen and hydrogen atoms in water face the anode and cathode, respectively, and hydrogen atoms get closer to the cathode compared to the oxygen atoms near the anode. These effects create asymmetric density distributions that increase with the applied electric field. Force-driven water flows under electric fields exhibit asymmetric velocity profiles and unequal slip lengths. Apparent viscosity of water increases and the slip length decreases with increased electric field, reducing the flow rate. Increasing the electric field above a threshold value freezes water at room temperature.Article Citation - WoS: 24Citation - Scopus: 26Role of Surface Oxidation on the Size Dependent Mechanical Properties of Nickel Nanowires: a Reaxff Molecular Dynamics Study(Royal Society of Chemistry, 2017) Aral, Gürcan; Islam, Md Mahbubul; Van Duin, Adri C. T.Highly reactive metallic nickel (Ni) is readily oxidized by oxygen (O2) molecules even at low temperatures. The presence of the naturally resulting pre-oxide shell layer on metallic Ni nano materials such as Ni nanowires (NW) is responsible for degrading the deformation mechanisms and related mechanical properties. However, the role of the pre-oxide shell layer on the metallic Ni NW coupled with the complicated mechanical deformation mechanism and related properties have not yet been fully and independently understood. For this reason, the ReaxFF reactive force field for Ni/O interactions was used to investigate the effect of surface oxide layers and the size-dependent mechanical properties of Ni NWs under precisely controlled tensile loading conditions. To directly quantify the size dependent surface oxidation effect on the tensile mechanical deformation behaviour and related properties for Ni NWs, first, ReaxFF-molecular dynamics (MD) simulations were carried out to study the oxidation kinetics on the free surface of Ni NWs in a molecular O2 environment as a function of various diameters (D = 5.0, 6.5, and 8.0 nm) of the NWs, but at the same length. Single crystalline, pure metallic Ni NWs were also studied as a reference. The results of the oxidation simulations indicate that a surface oxide shell layer with limiting thickness of ∼1.0 nm was formed on the free surface of the bare Ni NW, typically via dissociation of the O-O bonds and the subsequent formation of Ni-O bonds. Furthermore, we investigated the evolution of the size-dependent intrinsic mechanical elastic properties of the core-oxide shell (Ni/NixOy) NWs by comparing them with their un-oxidized counterparts under constant uniaxial tensile loading. We found that the oxide shell layer significantly decreases the mechanical properties of metallic Ni NW as well as facilitates the initiation of plastic deformation as a function of decreasing diameter. The disordered oxide shell layer on the Ni NW's surface remarkably reduces the yield stress and Young's modulus, due to the increased softening effects with the decreasing NW diameter, compared to un-oxidized counterparts. Moreover, the onset of plastic deformation occurs at a relatively low yielding strain and stress level for the smaller diameter of oxide-coated Ni NWs in comparison to their pure counterparts. Furthermore, for pure Ni NWs, Young's modulus, the yielding stress and strain slightly decrease with the decrease in the diameter size of Ni NWs.Article Citation - WoS: 130Citation - Scopus: 135Thermal Transport Properties of Mos2 and Mose2 Monolayers(IOP Publishing Ltd., 2016) Kandemir, Ali; Yapıcıoğlu, Haluk; Kınacı, Alper; Çalın, Tahir; Sevik, CemThe isolation of single- to few-layer transition metal dichalcogenides opens new directions in the application of two-dimensional materials to nanoelectronics. The characterization of thermal transport in these new low-dimensional materials is needed for their efficient implementation, either for general overheating issues or specific applications in thermoelectric devices. In this study, the lattice thermal conductivities of single-layer MoS2 and MoSe2 are evaluated using classical molecular dynamics methods. The interactions between atoms are defined by Stillinger-Weber-type empirical potentials that are developed to represent the structural, mechanical, and vibrational properties of the given materials. In the parameterization of the potentials, a stochastic optimization algorithm, namely particle swarm optimization, is utilized. The final parameter sets produce quite consistent results with density functional theory in terms of lattice parameters, bond distances, elastic constants, and vibrational properties of both single-layer MoS2 and MoSe2. The predicted thermal properties of both materials are in very good agreement with earlier first-principles calculations. The discrepancies between the calculations and experimental measurements are most probably caused by the pristine nature of the structures in our simulations.Article Citation - WoS: 33Citation - Scopus: 39Molecular Free Paths in Nanoscale Gas Flows(Springer Verlag, 2015) Barışık, Murat; Beşkök, AliAverage distance traveled by gas molecules between intermolecular collisions, known as the mean free path (MFP), is a key parameter for characterizing gas flows in the entire Knudsen regime. Recent literature presents variations in MFP as a function of the surface confinement, which is in disagreement with the kinetic theory and leads to wrong physical interpretations of nanoscale gas flows. This controversy occurs due to erroneous definition and calculation practices, such as consideration of gas wall collisions, using local bins smaller than a MFP, and utilizing time frames shorter than a mean collision time in the MFP calculations. This study reports proper molecular MFP calculations in nanoscale confinements by using realistic molecular surfaces. We utilize molecular dynamics (MD) simulations to calculate gas MFP in three-dimensional periodic systems of various sizes and for force-driven gas flows confined in nano-channels. Studies performed in the transition flow regime in various size nano-channels and under a range of gas–surface interaction strengths have shown isotropic mean travelled distance and MFP values in agreement with the kinetic theory regardless of the surface forces and surface adsorption effects. Comparison of the velocity profiles obtained in MD simulations with the linearized Boltzmann solutions at predicted Knudsen values shows good agreement in the bulk of the channels, while deviations in the near wall region due to the influence of surface forces are reported.Article Citation - WoS: 13Citation - Scopus: 16Thermochromism in Oligothiophenes: the Role of the Internal Rotation(American Chemical Society, 2002) Elmacı, Nuran; Yurtsever, ErsinThe relation between thermochromism in polythiophenes and the internal rotation is studied by density-functional theory (DFT). For head-to-tail methyl-substituted thiophenes, rotational potential maps of dimer and trimer are calculated. With time-dependent-DFT methodology the absorption spectra of these oligomers in UV-vis region are calculated as functions of the torsional angles. Theoretical temperature-dependent UV-vis spectra are generated from the distribution of torsional angles. The results show that the internal rotation alone is not sufficient to explain the mechanism of thermochromism.