Master Degree / Yüksek Lisans Tezleri

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

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Publisher: search.filters.publisher.Izmir Institute of TechnologySubject: search.filters.subject.Molecular dynamics

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  • Master Thesis
    Molecular Dynamics Studies on Wetting Behavior of Silicon Surfaces and Heat Transfer Characteristics of Electrolyte Solution Filled Silicon Nano-Channels
    (Izmir Institute of Technology, 2020) Özdemir, Abdullah Cihan; Barışık, Murat; Barışık, Murat
    Silicon has always been of interest to researchers from various fields, especially the semiconductor industry. Silicon and silicon-based materials are frequently used in integrated circuits and micro/nano-electro-mechanical systems. Interfacial phenomena between phases is important for these applications. In this study, surface wetting and heat transfer at the solid/liquid interfacial region were investigated using the Molecular Dynamics method. The control of wetting was examined by changing silicon structure at single crystal and amorphous forms and was correlated with the surface coating thickness. Contact angles on both single crystal and amorphous surfaces were calculated. To understand the molecular regions affecting the contact angle, the near interface height parameter was defined as the distance from the surface. Then, interface densities and contact angles of single crystal and amorphous structures were calculated at each height parameter. We defined an effective range of intermolecular forces for the control of wetting. Second, heat transfer characteristics at water/silicon interfaces were examined. Solid/liquid interface is important to determine heat transfer at nanoscale. We focused on the influence of ionic conditions on heat transfer for a water-NaCl solution between two silicon walls. The surface charge density showed variation by ionic condition. We calculated surface charges naturally forming at the corresponding electrolyte concentration. With the increase in salinity, the electrolyte solution density increased and thermal conductivity decreased. Results showed good agreement with the experimental measurements. Additionally, we observed a 35% increase in heat transfer due to a decrease in interfacial thermal resistance by increasing ionic concentration to the highest salinity value of standard conditions. Heat transfer at solid/liquid interface characterized by Kapitza length was correlated with the salinity.
  • 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.