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Aplication of explicitly correlated multi-reference coupled cluster methods
Lang, Jakub ; Pittner, Jiří (advisor) ; Fišer, Jiří (referee)
Nowdays, coupled cluster method belongs to one of the most used quantum chemical methods. However, the single-reference coupled cluster methods are not able to describe systems where the static correlation have an important role. Multireference coupled cluster methods developed in our group can describe both static and dy- namic correlation and can be used for problematic systems. Together with explicitly correlated wavefunction, which can properly describe the electronic cusp and speed up the convergence to the complete ba- sis set limit, they are able to calculate computationally demanding diradicals. Multireference CC calculations of tetramethylenethane have been perforemd and the performance of explicitly correlated version is discussed. Calculations of the isomerization of bicyclobu- tane using the multireference approach are presented as well. 1
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Ab initio study of {101-2} twinning transition in magnesium
Káňa, Tomáš ; Ostapovets, Andriy
Twinning is an important deformation mode in materials with the hexagonal close-packed (hcp) structures. The shear deformation combined with shuffling of atomic planes can lead to a transition between the Mg hcp structure and a twinned hcp structure. Studying such a transition by means of ab initio methods should bring more insight into the twinning mechanism in magnesium where the {1012} planes are the twinning planes. Comparison of ab initio results with those obtained using the semi-empirical embedded atom method is provided. It can help improve the fitted parameters of the embedded atom method.
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Web Server for Protein Structure Prediction
Votroubek, Lukáš ; Očenášek, Pavel (referee) ; Burgetová, Ivana (advisor)
This work deals with proteins, especially with their structure and kinds of tertiary, or 3D, structure prediction. Tertiary structure prediction is very important for function prediction of this vitally important substance. Bioinformatics do this prediction much more effective and faster, because classical methods of structure prediction directly from molecule are very expensive and slow. On the other hand they are much more exact. Objective of this thesis is to describe tertiary structure prediction methods, describe used tools and possibility of automatic communication with them. Next objective is describe implementation of server, that will serve to protein engineers for more effective finding of information about tertiary structure from more servers without requesting each of them separately. Results of testing will be described in this work too.
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Modelling of Chemical Processes
Al Mahmoud Alsheikh, Amer ; Bártlová,, Milada (referee) ; Urban,, Ján (referee) ; Žídek, Jan (advisor)
V této práci je prezentována studie fragmentačního procesu zvolené molekuly a jeho vztah ke složení fragmentačních produktů. Práce je zaměřená na výpočet fragmentační energie molekuly pomocí ab initio kvantově chemických metod, metodou „density functional theory (DFT)“ a také srovnáním s experimentem. Je prezentován vliv výpočetní metody, bázového setu, a geometrie molekuly na simulaci. Byla porovnána fragmentace methylfenylsilanu (MPS), dimethylfenylsilanu (DMPS), a trimetylfenylsilanu (TMPS). Fragmentace byla iniciována monochromatickým elektronovým svazkem (EII). Hmotnostní spektrometrie byla využita ke studiu složení fragmentačních produktů MPS a TMPS. Fragmentační produkty MPS a TMPS měřené v rámci této práce byly doplněny o experimentální studii DMPS, která byla prezentována v literatuře. Takto byla získána řada molekul, které jsou strukturně podobné, ale mají výrazně rozdílné chování během fragmentace. Pomocí měření účinného průřezu byly měřeny disociační energie vazeb a tyto disociační energie byly vypočteny pomocí metody DFT. Kombinací teoretického výpočtu metodou DFT a experimentálního měření jsme poukázali na společné rysy a na rozdíly ve fragmentačním schématu všech tří molekul. Navrhli jsme odštěpení dvou vodíkových atomů během plazmově indukovaného fragmentačního procesu. Vodíky mohou být odštěpeny pomocí dvou mechanismů: i. odštěpení dvou vodíků jeden po druhém a ii. odštěpení molekuly H2 v jednom kroku. Z profilů energie dokážeme určit, který mechanismus bude v tom konkrétním případě pravděpodobnější. Předpokládaný mechanismus je v korelaci s experimentálními výsledky fragmentace zjištěnými z hmotnostních spekter.
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First-principles study of stability of solid crystals
Pleskot, Ondřej ; Šesták, Petr (referee) ; Černý, Miroslav (advisor)
This work deals with a modeling of an electronic structure of solid crystals. Specifically, densities of valence electrons, and the density of states are calculated using first-principles code VASP for three crystals representing three different types of bonding. These are the metal bonding in a crystal of aluminum, the covalent bonding in a diamond crystal, and an ionic bonding in the crystal of rock salt. From calculated values of stress and crystal energy are then determined some macroscopic parameters of crystals, such as the equilibrium lattice parameter, the bulk modulus and the theoretical strength under isotropic tension.
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Strength and magnetism of Mn-Pt nanocomposites
Káňa, Tomáš ; Šob, Mojmír
Using ab initio electronic structure calculations, we have analysed Mn atoms dissolved in a platinum matrix, forming thus intermetallics MnPt3, MnPt7 and MnPt15 that can be considered as prototypes of natural Mn–Pt nanocomposites. On the whole, manganese addition makes the resulting Mn–Pt compound softer but increases its resistance to shape deformation. With increasing Mn content, both tensile and compressive theoretical strength is enhanced. In agreement with experiment, our calculations confirm the antiferromagnetic (AFM) ground state of the MnPt7 structure with spins directions altering along the [100] crystallographic direction (AFM [100]). In addition, we have proposed and studied three prototypes of linear MnPt15 nanocomposites consisting of Mn nanochains in the Pt matrix. Again, AFM [100] ordering was found in the ground state of MnPt15.
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Ab initio studie magnetismu Ni a Co podél trigonální deformační dráhy
Zelený, Martin ; Šob, Mojmír
We have calculated the total energies of nickel and cobalt as a function of volume and trigonal deformation for various magnetic phases and found the phase boundaries between the FM and NM modifications. The calculated contour plots can be used for the understanding and prediction of lattice parameters and magnetic states of Ni and Co thin films on various fcc (111) metallic substrates.
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Ab initio study of phase stability in metals
Káňa, Tomáš ; Hüger, E. ; Šob, Mojmír
We employ ab initio calculations to study the behavior of total energy along the transformation paths between the hexagonal close-packed (hcp) structure and face-centered cubic (fcc) structure in Al, Co, Ni, Cu and Pd. We found one peculiar transformation path wit h extremely low energy barrier of only 0.010 eV/atom for Al, 0.020 eV/atom for Pd, 0.030 eV/atom for Cu, 0.033 eV/atom for Ni and 0.050 eV/atom for Co.
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First principles study of polymorfy of Ni and Co thin layers
Zelený, Martin ; Šob, Mojmír
The total energy profiles of trigonal and hexagonal bulk Ni and Co are employed to advance our understanding of epitaxial growth of Ni and Co thin films on various fcc(111) substrates. For nickel films, we predict the fcc stacking in the neighbourhood of the ground state and for the distance of nearest neighbors larger than 5.18 a.u. the film should exhibit hcp layer stacking. Cobalt films behave differently. The hcp phases are energetically more favorable in whole region studied.
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