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Simulations of the organic-molecular ordering on the solid surfaces using pair potentials
Antoš, Jakub ; Kocán, Pavel (advisor) ; Matvija, Peter (referee)
Organic molecules on a flat, unreactive, periodical surface self-assemble to ordered superstructures. The superstructures can be used to selectively tune the properties of the surface. This problem can be studied using quantum mechanical models, such as Density functional theory (DFT). The use of those models for problems with hundreds of atoms and thousand of iterations is, however, due to their complexity, computationally impractical. In this thesis we extend and test an existing algorithm developed by the advisor of this thesis. The algorithm sacrifices accuracy for a quicker simulation time by using the method of paired potentials. This method simplifies the quantum mechanical description of an atom by considering a point source of change and replaces the complex interaction between atoms with pair parametrized forces. This method is incorporated into a Monte Carlo simulation which, from a given superstructure obtained from exper- imental data, predicts the position and deformation of the molecules that minimize the total potential energy. We test the algorithm on two real-world problem sets. The algo- rithm gives results comparable to that of DFT when tested on already studied problems, yet converges to the solution much faster. It can be used as a standalone program or as an initialization to the DFT...
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Interaction of simple organic molecules with cerium oxide surfaces
Ormoš, Martin ; Matvija, Peter (advisor) ; Sobotík, Pavel (referee)
In this work we prepare well defined thin epitaxy layers of cerium oxide (CeO2) and cerium oxide with nanoparticles of platinum (CeO2/Pt) on the Cu(111) substrate. The surface was characterized before exposition by ethanol molecules, after exposition, after annealing at 725 K in UHV and after annealing in O2 atmosphere at pressure p = 5×10−7 mbar at 725 K by LEED (low-electron energy diffraction), XPS (x-ray photoelectron di- ffraction) and STM (scanning tunnelling microscopy). Layer of CeO2/Pt was also exposed to 2 mbar of methane and 2, 5 mbar of methane and oxygen mixture in a ratio 1:1. This layer was observed by NAP-STM in higher pressures. In this work we have discovered that a disordered layer is formed on the CeO2 surface after exposure to the mixture of air and ethanol. Interaction of adsorbed molecules and ceria is increased during annealing in UHV, when carbon desorbs from the surface and cerium is reduced. After annealing in oxygen cerium is reoxidized. However, even after reoxidation, the surface contains a large number of defects of various types. Significant increase in brightness was observed in the proximity of domain interfaces of cerium oxide layers during scanning at higher pressures of oxygen. This effect will be studied more closely in our future experiments. 1
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Study of the Growth of Iron Oxide on the Surface of Cerium Oxide
Pchálek, František ; Matvija, Peter (advisor) ; Kocán, Pavel (referee)
Cerium oxide (ceria) is widely used catalytic material known for its oxygen storage capacity. Iron-modified ceria-based catalysts find applications in various reactions, such as the oxidation of CO or NO. However, the existing knowledge about these catalysts is limited to relatively undefined powder samples. The aim of this Bachelor's thesis is to create well-defined model surfaces of iron oxide on ceria and characterize these surfaces using various methods such as Scanning Tunneling Microscopy (STM), Atomic Force Microscopy (AFM), X-ray Photoelectron Spectroscopy (XPS), and Low-Energy Electron Diffraction (LEED). In our work we found the following procedure for preparing the FeO(111)/ CeO2(111) surface on the Cu(111) substrate: Initially, metallic Fe is deposited onto the surface of CeO2(111) at room temperature, followed by annealing in ultra-high vacuum (UHV) up to 700 K. At room temperature, iron tends to form clusters con- sisting of both neutral Fe0 and ionic Fe3+ or Fe2+ states. After annealing in UHV up to 700 K, iron gets fully oxidized, resulting in the formation of a 2D FeO layer. This process gives rise to a moiré pattern observed in STM and LEED due to the overlay of the FeO and CeO2 lattices. By measuring the parameters of the moiré pattern, the periodicity and orientation of the deposited FeO...
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Covalently linked molecular networks on metal-passivated surfaces
Slezák, Peter ; Kocán, Pavel (advisor) ; Matvija, Peter (referee)
The creation of electronic devices only from atoms or molecules could be the next step in the creation of more advanced nanotechnologies. Initial experiments have already taken place and we know that it is possible on some surfaces. In this work, we tried to create similar simple molecular structures on surfaces with a silicon substrate. We initially modified the substrate by depositing Bismuth, Indium and a combination of both. We optimized the methods of formation of these surfaces and subsequently created simple structures with the help of deposited Dithienyl- dithiopyrolopyrrole molecules, while we successfully managed to create the intended structures on several surfaces and arranged groupings of molecules on the surfaces Si(111)/In √3 x√7, Si(111)/Bi(√3 x√3) and on Si(111)/Bi-In(√7 x√7). We subsequently created a model of interaction molecules inthis structures on substrate
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Studium interakce adsorbátu s pasivovanými povrchy Si pomocí STM
Matvija, Peter ; Kocán, Pavel (advisor) ; Švec, Martin (referee)
The scanning tunneling microscopy is used to study the morphology of Tl adlayer in various stages of Tl desorption from the Si(111) surface and to study behaviour of various adsorbates on the Si(111)/Tl-(1 × 1). The utilization of thallium layer for passivation of the Si(111) was examined closely for various adsorbates. Manganese, aluminium, indium and tin layers which were directly deposited onto the Si(111)-(7 × 7) were compared with the layers prepared by deposition of adsorbate onto the passivating layer after the subsequent thermal desorption of Tl (after annealing at ≈ 400◦ C). Examined adsorbates exhibited signs of extremely high diffusivity and weak bond with the surface Si(111)/Tl- (1 × 1). The passivating layer was stable against the adsorbates.The application of thallium in the role of surfactant caused lowering of temperature and coverage needed for the preparation of reconstructions which were observed on the surfaces prepared by the direct deposition of adsorbate. 1
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Interaction of metal atoms with metastable reconstructions of the Si(111) surface studied by STM
Matvija, Peter ; Kocán, Pavel (advisor) ; Ošťádal, Ivan (referee)
Process of reconstruction of Si(111) surface after vapor deposition of thallium and subsequent desorption is studied by STM. Dependency of surface coverage on temperature is determined and this dependency is afterwards used for determination of ideal conditions for creation of surface with the biggest possible part with metastable reconstructions (mostly (5x5) and (9x9)). This surface is then covered by vapor deposition by different amounts of Al and possibility of creation of magic clusters and other interesting structures is investigated. Structural models for magic clusters on (5x5) are proposed. The work includes description of experimental devices used in measurements as well as description of procedures and physical principles connected with functioning of STM.
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STM study of adsorption and mobility of phtalocyanine molecules on passivated silicon surfaces at lower temperatures
Szabo, Michal ; Ošťádal, Ivan (advisor) ; Matvija, Peter (referee)
The thesis deals with an experiment for studying adsorption of phthalocyanin molecules on silicon surface passivated by a tin reconstruction. The main technique used for imaging surface is scanning tunneling microscopy (STM). The work contains a brief introduction to the studied problem. It deals with the STM method and STM construction. The used ultra-vacuum experimental system is characterized together with particular steps at sample preparation for STM measurements. During the sample preparation all necessary operations were tested on the newly modified system and calibration measurements of sample annealing and tin deposition were performed. A structure of the prepared surface Si(111) 7×7 was investigated by STM and conditions for the preparation in the new system were specified. STM images were used for an evaluation of results at optimizing preparation of the passivated surface. Obtained results are important for further experiments in frame of a research focused on growing molecular structures on silicon surfaces.
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Influence of Si surface passivation on growth and ordering of nanostructures
Matvija, Peter ; Kocán, Pavel (advisor) ; Rezek, Bohuslav (referee) ; de la Torre, Bruno (referee)
Silicon is currently the most widely used semiconductor material with applications ranging from solar cells and sensors to electronic devices. Surface functionalization of silicon with molecular monolayers can be used to tune properties of the material toward a desired application. However, site-specific adsorption of molecules or molecular patterning on silicon surfaces is a difficult task due to the high reactivity of silicon. In this work, we use scanning tunneling microscopy, ab-initio calculations and kinetic Monte Carlo simulations to study adsorption of organic molecules on a bare and thallium-passivated Si(111) surface. We show that the polarity of molecules has a large impact on bonding of the molecules with the bare surface. We demonstrate that, in comparison with the bare surface, molecules or single-atom adsorbates deposited on the Tl-passivated surface have significantly higher mobility. The increased mobility induces formation of 2D gases on the surface and enables formation of self-assembled molecular structures. We propose a novel method to directly visualize the 2D surface gases and we show that a phase of surface gases containing molecule-bound dipoles can be controlled by a non-homogeneous electric field. 1
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Interaction of adsorbates with passivated Si surfaces studied by STM
Matvija, Peter ; Kocán, Pavel (advisor)
The scanning tunneling microscopy is used to study the morphology of Tl adlayer in various stages of Tl desorption from the Si(111) surface and to study behaviour of various adsorbates on the Si(111)/Tl-(1 × 1). The utilization of thallium layer for passivation of the Si(111) was examined closely for various adsorbates. Manganese, aluminium, indium and tin layers which were directly deposited onto the Si(111)-(7 × 7) were compared with the layers prepared by deposition of adsorbate onto the passivating layer after the subsequent thermal desorption of Tl (after annealing at ≈ 400◦ C). Examined adsorbates exhibited signs of extremely high diffusivity and weak bond with the surface Si(111)/Tl- (1 × 1). The passivating layer was stable against the adsorbates.The application of thallium in the role of surfactant caused lowering of temperature and coverage needed for the preparation of reconstructions which were observed on the surfaces prepared by the direct deposition of adsorbate. 1
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Study of metal surfaces in operando conditions by means of near-ambient-pressure scanning tunneling microscopy
Dlabaja, Petr ; Matvija, Peter (advisor) ; Kocán, Pavel (referee)
Title: Study of metal surfaces in operando conditions by means of near-ambient- pressure scanning tunneling microscopy Author: Petr Dlabaja Department: Department of Surface and Plasma Science Supervisor: RNDr. Peter Matvija, Ph.D., Department of Surface and Plasma Science Abstract: The thesis covers investigation of monocrystalline surfaces of metals Cu(111) and Pt(111) in high pressures. These surfaces were exposed to oxygen and carbon monoxide gasses of pressures between 1 × 10−10 mbar and 5 mbar. Changes in the structure of the surfaces was monitored using scanning tunneling microscopy, low-energy electron diffraction and X-ray photoelectron spectroscopy. Acquired results showed that reactive gasses at pressures ≈ 5 mbar affect the structure of the surfaces more prominently than the same gasses of lower pres- sures. The surface of Cu(111) at room temperature and 5 mbar pressure of O2 strongly oxidized. The surface of Pt(111) at pressure 5 mbar of gass O2 oxidized only locally, under the influence of the STM tip. Increased pressure of carbon mo- noxide induces creation of nanometric clusters on the surface of Cu(111), which agglomerate into small islands. These islands are distributed evenly on the whole surface of Cu(111). In contrast increased pressure of carbon monoxide mainly changes the shapes of...
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