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Kinetic Monte Carlo Simulations in Physics of Thin Films: from Growth to Electronic Properties
Gabriel, Vít ; Kocán, Pavel (advisor) ; Szabelski, Paweł (referee) ; Předota, Milan (referee)
Kinetic Monte Carlo (kMC) is a stochastic method used to simulate time evolution of a system. This algorithm finds application in various scientific fields. It is also widely used in physics of thin films. In the thesis, we developed models based on the kMC method to simulate growth and electronic properties of thin film. First, we developed the model to simulate the pulsed-laser deposition (PLD) growth of multiferroic perovskite. The model was first validated with data from literature and then used to clarify some of the phenomena observed during PLD growth. We innovatively explained the inter-layer transport crucial for film morphology using natural configuration-based processes. In addition, we were able to identify the cause of the experimentally observed decrease of surface roughness with increasing laser frequency. Second, we used the kMC method to study polaron diffusion with the aim to further understand the charge transfer in doped hematite. We applied several approximations of how dopants could affect the charge transfer and found that they influence polaron diffusion globally rather than due to strong local effects. Moreover, our model suggests that the diffusion process depends on the polaron type. We also simulated the injection of hole polarons into doped hematite. Even using the general...
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Molecular simulations of water - rutil interface
Hanke, Hynek ; Předota, Milan (advisor) ; Lísal, Martin (referee)
Study of structural and particularly dynamical properties of the interface of water with graphite and rutile surfaces points towards anomalous behavior of water molecules close to solid matter. Evaluation of statistical properties like translational and rotational diffusivity, residence times and autocorrelation functions of orientation vectors indicates that the translation and rotation of water molecules can be not only hindered, but also facilitated, according to the particular local density, interactions and and geometrical structure of the surface. The newly developed methods for the measurement of statistical rotational properties near to liquid-solid boundary overcomes the difficulties that are closely related to the measurement of dynamical properties in strongly inhomogeneous environment in a way, that can be applied to other model systems of this type.
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Morphology of two-component surface structures
Babjak, Viktor ; Kotrla, Miroslav (advisor) ; Předota, Milan (referee)
In the presented thesis we investigate heteroepitaxial growth of one element (one type of adsorbate A with negative or positive misfit relative to substrate S) and static properties of two-component surface alloy, i.e. ternary system (two types of adsorbate A and B with negative and positive misfit relative to different substrat S). We use Monte Carlo simulations for an off-lattice model in (1+1) dimensions with Lennard-Jones interaction. In case of incoherent heteroepitaxial growth we investigate formation of misfit dislocations, their influence on structure of growing film and impurity-induced formation of dislocations. Two different types of formation of dislocations are found, depending on the sign and magnitude of misfit. Simulations of static properties of two-component surface alloys show that morphology is quite different for phase separation (formation of domains consist of one type of particles in direction along and vertically towards to substrate-adsorbate interface) and intermixing regime. The structures, which emerged, depend on relative misfit, interaction and concentration of individual elements.
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Development and testing of computer models of phospholipid membranes
Nencini, Ricky ; Jungwirth, Pavel (advisor) ; Předota, Milan (referee)
Molecular dynamics simulations are an important tool for the study of biological systems, such as biomembranes. The missing electronic polarization in classical non- polarizable force fields, however, produces significant inaccuracies in the interactions of membranes with charged particles, such as ions. In this work, we implement the missing electronic polarization effects into CHARMM36 force field for phospatidylcholine lipids. This implementation is done in the mean field way by using electronic continuum correction (ECC) model. We will validate the strength of ion-membrane interactions using the electrometer concept. This concept connects the response of choline order parameters of lipid molecules with the amount of charge present in the surface of the membrane. Keywords: phosphatydylcholine, calcium ions, sodium ions, electronic continuum cor- rection, electrometer concept 1
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Pairing of biologically relevant ions in aqueous solutions
Baxová, Katarína ; Jungwirth, Pavel (advisor) ; Předota, Milan (referee)
Not accounting for the electronic polarizability due to divalent ions such as Ca2+ introduces a significant artifacts to force field-based molecular dynamic simulations of biological systems. Two newly developed parameter refinements were used to compute the free energy profile of the Ca2+ -Cl- ion dissociation in aqueous solutions, to be compared with a free energy profile obtained from ab-intio molecular dynamics and to data from neutron scattering. Next, the computational evidence for the existence of a local free energy min- imum representing a guanidinium-guanidinium contact ion pair in aqueous solu- tions is provided suggesting a global preference for a contact ion pair. Finally, the passive membrane penetration mechanism of oligoarginines was investigated on a cell membrane model systems - lipid vesicles - by fluorescent spectroscopy. In this study, a mechanistic link between membrane penetration and vesicle aggregation and fusion was found. 1
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Molecular simulations of water - rutil interface
Hanke, Hynek ; Předota, Milan (advisor) ; Lísal, Martin (referee)
Study of structural and particularly dynamical properties of the interface of water with graphite and rutile surfaces points towards anomalous behavior of water molecules close to solid matter. Evaluation of statistical properties like translational and rotational diffusivity, residence times and autocorrelation functions of orientation vectors indicates that the translation and rotation of water molecules can be not only hindered, but also facilitated, according to the particular local density, interactions and and geometrical structure of the surface. The newly developed methods for the measurement of statistical rotational properties near to liquid-solid boundary overcomes the difficulties that are closely related to the measurement of dynamical properties in strongly inhomogeneous environment in a way, that can be applied to other model systems of this type.
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Morphology of two-component surface structures
Babjak, Viktor ; Kotrla, Miroslav (advisor) ; Předota, Milan (referee)
In the presented thesis we investigate heteroepitaxial growth of one element (one type of adsorbate A with negative or positive misfit relative to substrate S) and static properties of two-component surface alloy, i.e. ternary system (two types of adsorbate A and B with negative and positive misfit relative to different substrat S). We use Monte Carlo simulations for an off-lattice model in (1+1) dimensions with Lennard-Jones interaction. In case of incoherent heteroepitaxial growth we investigate formation of misfit dislocations, their influence on structure of growing film and impurity-induced formation of dislocations. Two different types of formation of dislocations are found, depending on the sign and magnitude of misfit. Simulations of static properties of two-component surface alloys show that morphology is quite different for phase separation (formation of domains consist of one type of particles in direction along and vertically towards to substrate-adsorbate interface) and intermixing regime. The structures, which emerged, depend on relative misfit, interaction and concentration of individual elements.
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