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Informetrics study the information flow as a pure information phenomenon. However what are the practical applications of this problem? Information flow can be understood, investigated and managed from different points of view. The most practical one is management approach combined with intuitive analogy. Water flow parallel appears suitable. A conceptual model can be propounded upon this foundation and then used for better illustration of information flow function and key parts. Finally, a good amount of instruments and management methods can be used to manage information flows. So in chosen organization the current state of information flows and contemporary methods of its management are investigated in order to compare the theory and the practice. Concrete suggestions and statements about information flow management are deduced afterwards This paper illustrate possibilities of usage of information flow management in practice. Keywords information flow management - methods of information flow management - information flow model - practical aplications - case study - analogy - induction - Regional research library in Liberec

In the first half, the work is about human society information systems. It tries to find an origin of the information in the society, describes forms of the information and tries to explain causes for communication. Later it describes main attributes of the system itself. From mentioned facts the work then figures out an idea about new division of information systems based on the purpouse of a system. The next part concerns information structures present in the body of plants and plant neurobilology. Then the work question the relationship between the information science and the cognitive science. Later the woork tries to work out some global charakteristics of plant information structures. In the last part work discuss the basic funcions of the human brain and late discoveries in glia cells field. Conclussion of the whole work follows. Keywords *information system *information communication *living organisms *plant neurobiology *consciousness *glia *analogies

In this work I present a study dedicated to the penetration of whistler- mode waves to the ionosphere. An algorithm of automatic detection of whist- lers in spectrograms computed from the data measured on the DEMETER sa- tellite is described. A method of causative lightning detected by the EUCLID lightning detection network assignment to a detected whistlers is described. Results of statistical study dedicated to relationship between the detected whistlers and assigned causative lightning. Based on the proccessing of data from 364 passes of the DEMETER satellite over monitored area is shown, that mean whistler amplitude decreases with distance between the causative lightning, increses with causative lightning current and in the evening is ap- proximately three times higher than in the morning. A study dedicated to subprotonospheric whistlers is presented. We found, that subprotonospheric whistler causative lightnings currents are very high compared to that of usual 0+ whistlers.

This thesis is focused on theoretical study of influence of the silanol nest defects on the hydrolysis of zeolite Chabazite under harsh steaming conditions. The motivation of the thesis was a recent experiment proving that the silanol nest defect enhances the hydrolysis of a zeolite. The harsh steaming conditions have been chosen as some important technological processes involving zeolites require high temperatures and have water vapour present. The study was performed by using density functional theory calculations. To investigate the influence of the defect two models were used a reference pristine model and a defected model containing the silanol nest defect. The two models were pure siliceous Chabazite periodical models with supercell containing 36 and 35 Si tetrahedra respectively. A multi-step hydrolysis leading to detachment of a Si(OH)4 cluster from the zeolite, known as total desilication, was calculated for the two models. Multiple possible paths of the hydrolysis were discovered, compared and discussed on both models. Both the most favourable hydrolysis paths of the two model as well as their arithmetic means were compared. The experimentally set expectations that a silanol nest defect enhances the hydrolysis of the zeolite have been met.

The thesis is focused on theoretical study of hydrolysis and isotopic oxygen exchange in zeolite chabazite under steaming conditions. The theoretical study was performed by the methods of computational chemistry, namely density functional theory. Reactions of water with zeolites were investigated within the periodic model with chabazite supercell consisting of 36 Si/Al tetrahedra. Reactivity was investigated for one or two water molecules corresponding to the conditions relevant to high-temperature steaming. Relevant mechanisms of isotopic oxygen exchange were found and their competitiveness with hydrolysis was discussed.

Zeolites have been widely used in many different fields including catalysis, adsorption and separation, ion exchange, or gas storage. Conventional zeolites have three- dimensional (3D) structures with microporous channel system; typical pore sizes are well below 1 nanometer, therefore, diffusion limitation plays important role in many process and bulkier reactants (or products) cannot enter (or leave) the zeolite channel system. Two-dimensional (2D) zeolites prepared in last years can lift all diffusion limitation and they thus offer a very attractive alternative to conventional 3D zeolites. 2D zeolites attracted considerable attention on the experimental side; however, understanding of 2D zeolites based on computational investigation or on a combination of experimental and computational investigation is limited. A motivation for the computational work presented here is to improve our understanding of properties of 2D zeolites based on computational investigation. The originality of the research presented herein is in the strategy: we carried out systematic investigation of properties of corresponding 2D and 3D zeolites and we focus on the identification of similarities and differences. The most important zeolite properties, i.e., presence of Brønsted and Lewis acid sites, are investigated. A number of...

Title: Computer modeling of ion protein interactions: Allosteric effects of phenolic ligands and ions on insulin hexamer structure Author: Vladimír Palivec Department: Department of Physical and Macromolecular Chemistry Faculty of Science UK Advisor: prof. RNDr. Pavel Jungwirth, DSc., IOCB AS CR, v.v.i. Advisor's email address: pavel.jungwirth@uochb.cas.cz Abstract: Insulin hexamer is an allosteric protein capable of undergoing conformational changes between three states: T6, T3R3, and R6. Transitions between them, as well as the formation of insulin hexamers, are mediated through binding of phenolic ligands or ions. This thesis presents a molecular dynamics study of allosteric behavior of insulin using empirical force fields. Two effects are closely inspected - cation (Zn2+ , Ca2+ , K+ , and Na+ ) binding to the insulin hexamers and a possible binding of two neurotransmitters - dopamine and serotonin to the phenolic pocket. The results show that high charge density cations (Zn2+ and Ca2+ ) are mostly localized in the B13 glutamate cavity, slow- down diffusion, while preventing other cations from entering. In contrast, low charge density cations (Na+ and K+ ) do not have this effect. Concerning neurotransmitters, dopamine does not bind to the phenolic pocket whereas serotonin binds in a similar way like...

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

This thesis deals with the process of molecular ions formation in interstellar space, which played an important role in the early Universe. A large part of the work focuses on the theoretical study of quantum dynamics of the process of radiative association pre- dominantly induced by dipole transitions. The effect of quadrupole transitions on the radiative association have also been taken into account, which has been studied for the first time. Furthermore, spectroscopic characteristics of rovibronic transitions of selected di- atomic ions for the study of cosmological variability of fundamental constants were determined. The main outcomes of the thesis include the characterization of depopulation of metastable levels He (23S) and He (21S) due to radiative collisions with hydrogen, helium and lithium ions, i. e. He + A+ → HeA+ + hν. Within the study quantum dynamics calculations were carried out using a fully quan- tal approach. Studied spontaneous and stimulated processes on a specific spin manifold were characterized by energy-dependent cross sections and temperature-dependent rate coefficients. Compared to previous published works by other authors highly excited electronic states are considered. The results showed that a) the spontaneous radiative association contributes significantly to the...

Known and proposed helium chemistry embraces a large variety of small-size cationic species. Even though some of these species can be studied experimentally in the gas phase, the vast majority of contemporary studies are backed up or done entirely using high-level of theory calculations. The aim of this thesis is to present a theoretical introduction to ab initio computational chemistry from the basics (definition of the electronic problem, Born-Oppenheimer approximation, Hartree- Fock method) to the Brillouin-Wigner and Mukherjee Hilbert-space state-specific multireference coupled-cluster (MRCC) methods and their explicitly correlated versions. The thesis also contains a study of HeN2+ 2 using the mentioned MRCC methods. An important result has been, that Mukherjee's state-specific multireference coupled-cluster method with perturbative triexcitations Mk CCSD(Tu) gives results in very good agreement to conventional calculations (CASPT2 and MRCI) using a much smaller active space and smaller basis sets.

e van der Waals (vdW) interactions, or dispersion forces, are crucial in many chem- ical, physical and biological processes and received much attention from developers of density functional theory (DFT) methods. e most popular non-empirical DFT method for treating vdW interactions is the vdW density functional by Dion et al. (vdW-DF). Despite its success, vdW-DF is not accurate enough for many chemical applications. Here, we investigate two possible ways how to improve its accuracy. First, we reoptimize the only weakly speci ed parameter of vdW-DF for several semi-local functionals. On the S benchmark database set, we nd that revPBE is the best performer, decreasing the error from . % to . %. Second, a system-speci c but very accurate (∼ . kcal/mol) DFT correction scheme is proposed for precise calcula- tions of adsorbent−adsorbate interactions by combining vdW-DF and the empirical DFT/CC correction scheme. e new approach is applied to small molecules (CH , CO , H , H O, N ) interacting with a quartz surface and a lamella of UTL zeolite. e very high accuracy of the new scheme and its relatively easy use and numerical stability compared to the earlier DFT/CC scheme o er a straightforward solution for obtaining reliable predictions of adsorption energies.

Firstly, we have developed a Tensor Contraction Engine-based implementation of the BW-MRCCSD approach. The scalability tests have been performed across thousand of cores. We have further developed a novel two-level parallel algorithm for Hilbert-space MRCC methods which uses the processor groups. In this approach, references are distributed among processor groups (reference-level parallelism) and tasks of each reference are distributed inside of a given processor group (task-level parallelism). We have shown that our implementation scales across 24000 cores. The usability of our code was demonstrated on larger systems (dodecane, polycarbenes and naphthyne isomers). Finally, we present novel universal state- selective (USS) corrections to the state-specific MRCC methods. The USS-corrected MRCC results were compared with the full configuration interaction (FCI) results.

The multireference (MR) generalization of coupled cluster (CC) theory aims to describe both the static and the dynamic correlation accurately, as the standard CC method (at lower truncation levels) generally does not perform well when quasidegenerate boundary orbitals are encountered. The most promising among the MR Hilbert-space methods seems to be the state-specific MR Mukherjee's CC (MkCC) method, formulated by Mukherjee et al. [J. Chem. Phys. 110, 6171 (1999)], due to its rigorous size-extensivity and insensitivity to the intruder state problem. The main goal of this work was to include connected triples in the MkCC method. As the cost of the iterative triples limits its application, the main focus was on including triples non-iteratively. Two perturbative triples methods, namely MkCCSD(Tn) and MkCCSD(Tu) have thus been developed. For studying their accuracy, iterative triples methods (MkCCSDT and MkCCSDT-n) were also developed using the "linked" formulation. All these methods and an uncoupled version of MkCC (uMkCC) were implemented in the ACES II program. The assessment of these methods was performed on the O2, cyclobutadiene, methylene diradical, twisted ethylene, F2, BeH2 and tetramethyleneethane (TME) molecules. All these studies show that the inclusion of triexcitations improves the...

The structure and stability of Agn+ 3 clusters (n = 1, 2, 3) in zeolite Y and their photochemical properties are investigated. Silver-exchanged zeolites have potential technological applications as UV-to-visible light converters. The structure and stability of silver clusters were examined using the periodic den- sity functional theory (DFT), and employing a developed and programmed geometry optimization driver. Non-reduced silver cations are preferably lo- cated in 6-member rings, far from each other. Upon a partial reduction, trigonal clusters are formed in the sodalite cages. The photochemical prop- erties are examined by various methods including the EOM-CCSD, MRPT2 and TD-DFT. No charge transfer transitions from ligands to silver clusters are found. Instead, transitions involving d and s electrons on silver clusters fall in the visible spectral range. Our results contradict the previous sugges- tion proposing existence of linear silver clusters through a double-6-member ring unit. Both parts of our investigations (structural and photochemical) disprove this previous proposition. A new interpretation of experimental spectra is proposed-the reduced trigonal silver cluster is responsible for photoactivity of Ag-doped zeolites with a low silver loading. Theoretical in- vestigation reported in this...

In the present work the energy gap between low-lying singlet and triplet electronic states are studied using Brillouin-Wigner and Mukherjee multireference coupled cluster methods. The calculated energy gaps and vibration states are compared with experimen- tal data of photoelectron spectra reported recently in [1]. 1

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Charles University in Prague Faculty of Science Department of Modeling of Chemical Properties of Bio- and Nanostructures A novel approach for description of non-covalent intermolecular interactions Dissertation Thesis Abstract Mgr. Miroslav Rubeš Supervisor: RNDr. Ota Bludský, CSc. Institute of Organic Chemistry and Biochemistry AS CR Center for Biomolecules and Complex Molecular Systems Prague 2010 Introduction Non-covalent interactions play a major role in many important physical, chemical, and biological processes that include, for instance, inter-molecular interactions between biomolecules, adsorption and separation, self-assembly in supra-molecular chemistry, and catalytic activity. To gain a deeper understanding of such processes at the atomistic level it is often necessary to investigate these systems theoretically. Due to the complex character of relevant systems, realistic models include hundreds of atoms and, thus, the computational investigation must rely on rather approximate methods. An accurate description of these systems still represents a major challenge for theoretical chemists. Methods based on density functionals (density functional theory, DFT) are currently among the most popular approaches for computational treatment of large systems. Unfortunately, the non-covalent interactions...

Charles University in Prague Faculty of Science Department of Physical and Macromolecular Chemistry Interaction of heteroboranes with biomolecules: Accurate quantum chemical study Doctoral Thesis Abstract RNDr. Jindřich Fanfrlík Advisor: Prof. Ing. Pavel Hobza, DrSc. Institute of Organic Chemistry and Biochemistry, AS CR Center for Biomolecules and Complex Molecular Systems Prague 2008 Univerzita Karlova v Praze Přírodovĕdecká Fakulta Katedra fyzikální a makromolekulární chemie Interakce heteroboranů s biomolekulami: kvantovĕ chemická studie Autoreferát disertační práce RNDr. Jindřich Fanfrlík Školitel: Prof. Ing. Pavel Hobza, DrSc. Ústav organické chemie and biochemie, AV ČR Centrum biomolekul a komplexních molekulových systémů Praha 2008 Introduction The world wide epidemic of AIDS is caused by two species of the human immunodeficiency virus (HIV-1 and HIV-2). Its 9200-bases-long RNA genome contains three main genes: gag, pol and env. The enzymes located within the pol gene (protease PR and reverse transcriptase RT) have become major targets for drug discovery, e.g. RT inhibitor Tenofovir disoproxil fumarate (DF) discovered by A. Holy at UOCHB in Prague and manufactured by Gilead Sciences and also already ten HIV-1 PR inhibitors (PIs) have been approved for use in the clinics: The evolution of drug...

7 Concluding Remarks The aim of the presented thesis was to investigate the interactions of aromatic groups and their role in the processes of chemical and biological recognition. In particular, the role of aromatic residues in the protein hydrophobic core for the stability of the protein native fold was investigated using highJevel quantum chemical calculations. We showed that the interactions of aromatic residues not only with other aromatic and aliphatic sidechains but also with the peptide bond portion of the protein backbone can provide a substantial contribution to the protein stabilisation. Two more specific examples ofthe aromatic interactions, the interaction ofaromatic residue with proline and the aromatic-peptide bond interaction were both examined in more detail. The chapter on the IEM focused on aromatic interactions from the perspective ofall the pairwise residue interactions in protein. The aromatic residues were shown to play a key rolě in the stabilisation of the Trp-cage model protein. It was also shown that the IEM can be used as a reliable method for the identification ofthese key residues. Several computational methods were tested and it was shown that when used with the Amber parm94 foréefie|d and GB solvent model, the IEM gives satisfactory results while being computationally feasible...