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Computer modeling of interactions between hyaluronan and polylysine
Zlochová, Barbora ; Řeha,, David (referee) ; Minofar, Babak (advisor)
Hyaluronic acid is a biosaccharide naturally occurring in human tissues. As a biomaterial with a number of interesting properties, it is the subject of interest in many industrial areas such as cosmetics and medicine. It is generally known that hyaluronic acid polymers interact with peptide polymers to form complexes with various physical properties, with great potential in the field of material science. In this work, the aim was to characterize the formation of just such complexes on the case of one polymer fiber of hyaluronic acid with polylysine fibers with different numbers of lysine subunits. In the theoretical part of the work hyaluronic acid and polylysine are described in terms of their general structural properties, uses and interactions, general computational chemistry is explained, principles and parameters of molecular dynamics MD are defined, and finally the MD simulation scheme according to which the simulations in this work were built is described. In the experimental part of the work, the upcoming simulation systems PLL8, PLL10, 1HA25-8PLL10, 1HA25-10PLL10, 1HA25-12PLL10 together with the parameters and tools that were used for their construction, the work in the GROMACS environment, in which the entire construction of the simulation systems took place, was described, the preparation of the MD simulation systems itself, the start of their computational solution and analysis in the MetaCentrum was also described. In the simulated systems, the number of hydrogen bonds between the HA polymer fiber and PLL peptides of different concentrations and their interactions with the surrounding solvent were analyzed. The radius of gyration of the HA polymer fiber in the presence of PLL peptides at different concentrations was studied. The radial distribution function of the terminal residues on the PLL fibers in the vicinity of the terminal residues on the HA surface at different PLL concentrations was determined. By analyzing the data, we managed to define and determine how the interaction between HA and PLL complexes changes.
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Excitation and Detection of Plasmon Polaritons
Šustr, Libor ; Schmidt, Eduard (referee) ; Kalousek, Radek (advisor)
The diploma thesis is aimed to excitation and detection of surface plasmon polaritons by visible light. First of all, we will briefly remind some basic principles like waves, electromagnetic wave, light on the interface and optical properties of metals. By using these principles we show presence of surface plasmon polaritons states. After the explanation of their properties there will be clearly visible reasons for aplications of the special excitationand detection methods. We will describe especially the prism coupling, periodic grating coupling and SNOM. Two last sections deal with computer simulations and experiments related to these methods. This means we can exemplify some knowledge presented in previous chapters. Results of simulations are compared with the experiment where we study the excitations of surface plasmon polaritons by periodic grating on aluminium surface.
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Optimization of cooling of a family house by using a geothermal system
Buchta, Jan ; Formánek, Marian (referee) ; Šikula, Ondřej (advisor)
The master’s thesis deals with optimization of cooling system of family house using borehole heat exchanger as a single cooling source. In the experimental part of the thesis was carried out long-term mearurements. The main part of the master’s thesis is the development and verification mathematical and physical model of thermal behavior chilled room. The result are computer simulations and evaluation of individual scenarios and design requirements for a potential optimization of measurement and control system. The theoretical part generally deals with radiant cooling systems.
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Optimisation of light conditions in buildings
Vajkay, František ; Mohelníková, Jitka (advisor)
Building physics as a branch of architecture must ensure an indoor comfort of each user and inhabitant of a building object. This involves, acoustics, indoor thermal conditions and among others also daylighting and artificial lighting of buildings. Light as a particle and an electromagnetic wave, is required by the different aspects of the human organism. It allows the living beings to see, influences skin and bones, the biorhythms, etc. Therefore, it is necessary for the engineering community to predict the correct illuminance and luminance levels acting insides. The thesis deals with such issues. More precisely, it assesses the quality of design tools and methodologies, either against CIE reference cases described in CIE 171/2006 and against real measurements done over the working plane of an indoor space located in the attic of Building D of the Institute of Building Structures, Faculty of Civil Engineering, Brno University of Technology, too. The tools tested throughout the solution of the dissertation did involve three computer programs: RADIANCE, WDLS v3.1 and WDLS v4.1, and one numerographical approach, namely the Daniljuk’s innovated methodology (sometimes even combined with the theories of BRS). In addition several software’s have had been created alongside the process assessment, just to mention the “RADIANCE Script”, “RADIANCE Data Evaluation Script” or “MuuLUX“. The later was written as a communication software allowing the connection of the KONICA-MINOLTA T10 illuminance meter to a computer with the aim of data collection while long term observation. The solution did also require the establishment of a measuring element for the determination of the light reflectance values of surfaces. The solutions, results and conclusions do describe how well did the design approaches deal while predicting the resulting awaited daylight factor levels in points over the working plane.
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Modeling electroacoustic systems in COMSOL
Hanuš, Jan ; Honzík,, Petr (referee) ; Schimmel, Jiří (advisor)
The thesis aims to explore the simulation software COMSOL Multiphysics with relevance to the field of electroacoustics. The work covers general introduction to the software, including an outline of the principles of finite element method, which is the most widely used numerical method in COMSOL Multiphysics. It also includes a clear description of the individual steps required to create a simulation. Furthermore, the Acoustics Module is described, Pressure Acoustics physics interface in particular as it is used later on in the simulations. The AC/DC Module and its physical interface Electric Circuit is mentioned briefly as well. Finally, the simulations created by the author are explained in a step-by-step manner. These look at the impact of the membrane’s and waveguide’s geometries on the radiation of the speaker driver, and the shapes of the loudspeaker system’s enclosure with the edge diffraction phenomena in mind. The results of the individual simulations are presented using graphs and discussed afterwards.
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Calculation of vibrational SFG spectra from molecular dynamics simulations
MUSIL, Patrik
In this thesis, implementation of calculation vibrational Sum-Frequency Generation (SFG) spectra from classical molecular simulations of aqueous solutions in the O-H vibrations region is presented. The key part of the thesis was significant improvement of the original codes used by the group of Prof. Marie-Pierre Gaigeot to post-process ab initio molecular dynamics trajectories to predict vibrational SFG spectra and apply it to classical molecular dynamics simulations. Particular attention was paid to modifying and optimizing the code for processing much larger systems (number of molecules) and much longer trajectories (longer simulation times), allowing to take advantage of classical simulations to work on larges scales than the ab initio simulations. The code also integrates calculations of contributions from water O-H bonds and surface hydroxyls. As a new feature, calculation of cross-correlations among molecules was implemented. The performance of the resulting codes is verified and the influence of classical molecular simulation parameters, as well as parameters entering the SFG spectra calculations, on the calculated vibrational SFG spectra is studied for fluorite/water interface.
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Návrh 3D modelu reálného ustájení skotu pro potřeby počítačových simulací
MALÝ, Vítězslav
This master's thesis focuses on the creation of 3D model of real cattle housing. The model is meant to serve the needs of computer simulations in the future. The model's creation is based on a template of sample barn meant for 300 dairy cows. The drawing documentation of the barn's building serves as a basis for the creation of the model. The barn's model is made using a 3D modeling technology. For the creation of the model is used a free student version of the computer programme SolidWorks. The theoretical part of this thesis introduces the principles of animal welfare, different types of cattle housing, automatic systems in livestock farming and computer simulations. The practical part of this thesis contains the procedure of creation of individual parts of the model, their compilation and the final 3D model of the barn.
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Computer simulations of conformational behavior of block copolymers in selective solvents
Šindelka, Karel ; Limpouchová, Zuzana (advisor) ; Kuldová, Jitka (referee)
The presented bachelor thesis deals with the study of the conformational be- haviour of diblock copolymers in the selective solvent. The polymer solution was modelled using a coarse-grained model and is simulated using dissipative particle dynamics (DPD). An original C-code for DPD simulations together with a new software package for processing of simulation data was developed. Functionality of the code and software were tested for two systems. The first system corre- sponded to a linear homopolymer in a solvent and the scaling laws for homopoly- mer in dilute solution were reproduced. The second system represented diblock copolymers in selective solvents and micellar behaviour simulated with the de- veloped code agreed with simulations by Sheng et al. Then, the self-assembly of long copolymer chains in selective solvents that mimics a block copolymer of poly(methacrylic acid) and poly(ethylene oxide) in aqueous solution at pH 1 was studied for different polymer concentrations. The simulation results provided valuable insight into the studied system and serve as a good starting point for DPD simulations of this system with added surfactants and at different values of pH, where the electrostatic interactions become important.
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Korteweg fluids - modeling, analysis and computer simulations
Blaškovičová, Monika ; Málek, Josef (advisor) ; Řehoř, Martin (referee)
We present two possible thermodynamical approaches towards a derivation of a model, proposed by Korteweg at the beginning of the 20th century, that is suitable to describe phase transitions liquid-vapor with non-sharp interfaces. The first approach (Dunn, Serrin (1985)) is based on classical rational continuum thermodynamics. The second approach (Heida, Málek (2010)) stems from the principles of classical nonequilibrium continuum thermodynamics. We compare both approaches in favor of the second one. The considered constitutive equation for the Cauchy stress is nonlinear. Nonlinearity and higher order derivatives of the density makes the analysis of relevant problems for the Navier-Stokes- Korteweg (NSK) fluid more difficult in comparison to problems concerning Navier-Stokes equations. Special attention is devoted to the appropriate choice of the boundary conditions. We also investigate the influence of compressibility on the stability of bubbles by comparing numerical simulations for compressible NSK fluid and its incompressible variant. Instabilities observed for a compressible NSK fluid are due to the pressure that has a different meaning for incompressible fluid. Powered by TCPDF (www.tcpdf.org)
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