Master Degree / Yüksek Lisans Tezleri

Permanent URI for this collectionhttps://hdl.handle.net/11147/3008

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Now showing 1 - 4 of 4
  • Master Thesis
    Enhancing L-Asparaginase Catalytic Activity for Improved Antileukemic Activity: a Computational Study on Thermococcus Kodakarensis L-Asparaginase Mutations
    (2023) Ekmekci, Pelinsu; Eraltuğ, Nur Başak Sürmeli; Karataş, Deniz
    In this study, thermostable Thermococcus kodakarensis L-asparaginase (TkA) enzyme, which lacks glutaminase activity, was studied for its structural and dynamic properties. The structural and dynamic properties of TkA, was investigated in its apo state and with the L-asparagine ligand to understand how the active site and general structure of the TkA enzyme changes with ligand binding and what effect this interaction has on the general behavior of the enzyme. T11E, T55E and D86S mutants of TkA were examined by molecular docking and molecular dynamics simulations. Binding results for molecular docking indicate that the structure is largely conserved, with root mean square deviation (RMSD) scores of −5.2 to −5.7 nm for wildtype TkA and mutants. RMSD and root mean square fluctuations (RMSF) data obtained as a result of molecular dynamics studies showed that the mutants had a stability close to that of the WT TkA enzyme, between 0.15 and 0.16 nm. In general, solvent accessible surface area (SASA) and radius of gyration analysis results support this analysis, while the D86S mutant gave more effective results than other mutants with SASA value of 260.38 nm2 /ns and radius of gyration values of 2.61 nm/ns. The total interaction energy of the ligand and WT TkA was -337.98 kJ/mol, while the interaction energy for D86S mutant was larger, at -363.03 kJ/mol. In conclusion, the study showing how the structure and dynamics of the TkA enzyme are affected by thebinding of L-asparagine ligand helps to understand the stability and functional behavior of the enzyme.
  • Master Thesis
    Investigations on Nanoscale Wetting, Fluid Transport, and Droplet Evaporation at Nanostructured Surfaces by Molecular Dynamics Simulations
    (01. Izmir Institute of Technology, 2021) Şatıroğlu, Ezgi; Barışık, Murat; Özkol, Ünver
    There is a significant need to understand solid-liquid interactions at nanoscale to determine the fluid behavior in several revolutionary applications. Specifically, nanoscale surface wetting, nanoscale liquid transport, and nanoscale heat transfer are the most sought-after subjects in recent scientific and industrial applications. This thesis focuses on characterization and possible control of wetting, fluid flow, and heat transfer using nanoscale surface structures. First, wetting behavior on a nanostructured surface was studied to resolve contact angle hysteresis. The droplet was found stabilized at a metastable state with a contact angle significantly different from its equilibrium value due to contact line pinning from the surface asperities. The contact angle was found to increase linearly by increasing droplet size when the droplet is pinned. However, these pinning effects become negligible, and the contact angle reaches the equilibrium value of the corresponding surface when the surface structure size becomes negligible compared to droplet size. Second, fluid flow in nanostructured nanochannels was studied to determine the transport behavior. While the slip boundary condition on a smooth surface correlated with the wetting angle, transport in a nanostructured channel remained mostly independent from wetting condition of the corresponding surface structure. Lastly, droplet evaporation over nanopatterned surfaces was investigated. When the droplet temperature reached the Leidenfrost point, a sudden increase in the interface thermal resistance was observed, which significantly decreased the heat transfer to the droplet. Increasing the size of the surface structure pushed the Leidenfrost point to higher surface temperatures. Current results contribute to various disciplines in engineering and applied sciences.
  • Master Thesis
    Molecular Dynamics Studies on Manipulation of Surface Wetting Using Nanoscale Surface Structures
    (Izmir Institute of Technology, 2019) Özçelik, Hüseyin Gökberk; Barışık, Murat
    The discovery of the lotus effect relating to the hydrophobic nature of lotus leaves is significant to surface structures on wetting. By considering the lotus effect, efforts have been made to mimics the effect of surface stuctures to manipulate wetting and surface patterning is introduced to capture underlying mechanism of lotus effect. Later, the effect of nanosized structures on rose petals is also addressed. Interestingly, while both lotus leaf and rose petal show hydrophobic behavior, due to nanosized structures, rose petals exhibit sticky behavior in contrast to the slippery lotus leaves. Herein, to investigate the effect of nanosized surface structures on wetting, molecular dynamics studies on wetting of nanopatterned silica surfaces are performed. Before performing wetting studies on the surfaces, ab initio based calcuations and molecular dynamics studies are conducted to assure modelled surfaces capture wetting behavior of silica surfaces and it is found that ab inito based calculations overestimate the interactions between water and silica surfaces. Consequently, parametric molecular dynamics studies are performed and force field parameters capturing wetting behavior of silica surfaces are proposed. Then, two different silica surfaces are subjected to investigation and applicability of models predicting contact angle is examined. Previous models proposed in the literature fail in predicting contact angle on nanopatterned silica surfaces. Therefore, initially, averaged water density inside the cavity is considered to characterize wetting behavior but significant variation from trendline is observed. Then, non dimensional surface parameter is proposed to capture wetting on nanopatterned silica surfaces and change in the work of adhesion is correlated with non dimensional surface parameter.
  • Master Thesis
    Molecular Dynamics Simulation Study on the Interactions Between Dna and a Conjugated Polyelectrolyte (cationic Oligothiophene)
    (Izmir Institute of Technology, 2019) Nalıncı Bardak, Nehir; Elmacı Irmak, Nuran
    The absorption spectra of the cationic polythiophenes shift to the red, or the color changes in the solution are visible to the naked eye, when single-strand DNA (ssDNA) is added, so that they can be used as a tool for DNA detection, theranostic applications, and biological sensors. The red shift or color change is explained by the fact that the ssDNA leads to conformational changes in the polythiophene, but the form of structural change remains to be elusive (i.e. flattening, twisting, stacking, etc.). In this study, molecular dynamics (MD) simulations of complexes consisted by ssDNA sequences with different nucleotides and polythiophene containing cationic side group were performed to enlighten the experimental studies. For this purpose, force field parameters of polythiophene which are not present in the current databases, were generated. The interactions between them were analyzed to determine the nature of conformational changes in the polythiophene when ssDNA was added. MD simulations has been carried out with the CHARMM-compatible force field parameters obtained in the content of this work. Radius of gyration of oligomer increases with addition of ssDNA but is more affected by homopurine strand. Planarity index gets larger upon complexation with homopurine and T_rich strand, does not change with others. H-O and electrostatic interactions which are almost doubled in nonplanar complexes can be interpreted as the major sources of conformational changes in oligomer. Considering all types of interactions between atoms in duplexes, it was observed that planarity was high in structures with less interaction of oligomer side groups.