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: 21Citation - Scopus: 24Effect of Nano-Film Thickness on Thermal Resistance at Water/Silicon Interface(Elsevier Ltd., 2019) Yenigün, Onur; Barışık, MuratParallel to the developments in micro/nano manufacturing techniques, component sizes in micro/nano electro mechanical systems have been decreasing to nanometer scales. Decrease in lengths in heat transfer direction below the heat carrier phonon length scales reduces thermal conduction in semiconductors. This study shows that such altered phonon spectrums with the decrease of size also reduce the heat transfer at the solid/liquid interfaces and can be correlated with the thermal conductivity of the slab. Using Molecular Dynamics (MD), we measured heat transfer between water and silicon of different thickness between 5 nm and 60 nm. Silicon slabs exhibit a linear temperature profile through the bulk where thermal conductivities measured based on Fourier law decreased by the decreasing slab thickness. We applied a semi-theoretical formulism on variation of conductivity by slab thickness. At the interface of these slabs and water, heat passage is disturbed due to the phonon mismatch of dissimilar materials, which is mostly considered as solid/liquid couple interface properties by the earlier literature. Resistance for phonon passage characterized as Kapitza length (L-K) is measured for different slab thicknesses at different surface wetting conditions varying between hydrophilic to hydrophobic. Increasing surface wetting decreases the L-K while at a certain wetting, decreasing the slab thickness increases the L-K. Once the L-K of different size slabs normalized by its bulk value (assumed to be the L-K of the thickest slab at the corresponding wetting), L-K variation by silicon thickness shows a universal behavior independent of surface wetting. A mathematical model describing the exponential increase of L-K by decreasing thickness was developed and validated by an earlier model. We further developed a correlation between the corresponding changes of L-K and conductivity with respective to their bulk values by analytically combining two models as (L-K/L-K-(Bulk)) = exp (3.94(k(Bulk) - k)/(k x k(Bulk))), using which L-K can be predicted from available thermal conductivities of a certain material. Results are crucial for thermal management of current and future electronics. (C) 2019 Elsevier Ltd. All rights reserved.Article Citation - WoS: 15Citation - Scopus: 16Parametrizing Nonbonded Interactions Between Silica and Water From First Principles(Elsevier, 2020) Özçelik, H. Gökberk; Sözen, Yiğit; Şahin, Hasan; Barışık, MuratSilica has been used in a vast number of micro/nano-fluidic technologies where interactions of water with silica at the molecular level play a key role. In such small systems, an understanding of mass and heat transport or surface wetting relies on accurate calculations of the water-silica interface coupling through atomic interactions. Molecular dynamics (MD) is a convenient tool for such use, but force field parameters for nonbonded interactions are required as an input, which are very limited in literature. These interaction parameters can be predicted by density functional theory, but dispersion forces are not calculated in standard models for electron correlations that additional correction models have been proposed at different levels of sophistications, and still under development. Accordingly, this work employs state of the art quantum chemistry to compute the binding energies. Force field parameters for silica/water van der Waals interactions were calculated, and later tested in MD simulations of water droplet on silica surface. While the standard dispersion corrections overestimated the binding energy, Becke-Johnson model yielded interactions parameters recovering experimentally measured wetting behavior of silica with a water contact angle of approximately 12.4 degrees on the flat and clean silica surface. Results will be useful for the current molecular modelling attempts by providing transferable parameters for simple silica/water van der Waals interactions as an alternative to existing complex surface interaction models.Article Citation - WoS: 19Citation - Scopus: 22Thermal Conductivity Engineering of Bulk and One-Dimensional Si-Ge Nanoarchitectures(Taylor and Francis Ltd., 2017) Kandemir, Ali; Özden, Ayberk; Çağın, Tahir; Sevik, CemVarious theoretical and experimental methods are utilized to investigate the thermal conductivity of nanostructured materials; this is a critical parameter to increase performance of thermoelectric devices. Among these methods, equilibrium molecular dynamics (EMD) is an accurate technique to predict lattice thermal conductivity. In this study, by means of systematic EMD simulations, thermal conductivity of bulk Si-Ge structures (pristine, alloy and superlattice) and their nanostructured one dimensional forms with square and circular cross-section geometries (asymmetric and symmetric) are calculated for different crystallographic directions. A comprehensive temperature analysis is evaluated for selected structures as well. The results show that one-dimensional structures are superior candidates in terms of their low lattice thermal conductivity and thermal conductivity tunability by nanostructuring, such as by diameter modulation, interface roughness, periodicity and number of interfaces. We find that thermal conductivity decreases with smaller diameters or cross section areas. Furthermore, interface roughness decreases thermal conductivity with a profound impact. Moreover, we predicted that there is a specific periodicity that gives minimum thermal conductivity in symmetric superlattice structures. The decreasing thermal conductivity is due to the reducing phonon movement in the system due to the effect of the number of interfaces that determine regimes of ballistic and wave transport phenomena. In some nanostructures, such as nanowire superlattices, thermal conductivity of the Si/Ge system can be reduced to nearly twice that of an amorphous silicon thermal conductivity. Additionally, it is found that one crystal orientation, < 100 >, is better than the < 111 > crystal orientation in one-dimensional and bulk SiGe systems. Our results clearly point out the importance of lattice thermal conductivity engineering in bulk and nanostructures to produce high-performance thermoelectric materials.