Thesis starts with brief overview of the present role of pneumatic actuators. Further research is carried out in modelling and control of pneumatic actuators. A basic overview of thermodynamic laws is presented. These laws are used to assemble a mathematical model of the pneumatic drive. Subsequently the identification of model parameters is shown. A controller is propřed using fuzzy PID algorithms. Results are compared with the conventional PID controller.

We study behavior of incompressible non-Newtonian fluids with a relation be- tween the shear stress and the shear rate given by a non-monotone S-shaped curve. These fluids are described with a special class of implicit constitutive relations that may be derived in a thermodynamically consistent manner us- ing the entropy production maximization principle or gradient dynamics. In the latter approach, the constitutive relation is given as the derivative of a non-convex dissipation potential. The concept of dissipation potential allows us to discuss stability of the constitutive relation and explain the experimen- tally observed response discontinuities. We are also concerned with hydrody- namic stability of flows of implicitly constituted fluids. Finally, we propose a numerical scheme for simulation of transient flows of fluids with a specific non-monotone constitutive relation. We employ the numerical scheme in a simulation of two-dimensional Taylor-Couette flow and the numerical results confirm our theoretical observations concerning the admissible flow states.

This diploma thesis deals with the study of adsorption of low-molecular components of organic substances produced by phytoplankton - AOM (Algal Organic Matter) on AC (Activated Carbon) during drinking water treatment. For the experimental purpose in this thesis, there were used selected amino acids as low molecular substances of AOM that are difficult to remove by conventional water treatment process by coagulation. As adsorbent, there was used a detailed characterized of granulated activated carbon (GAC) - Filtrasorb TL 830 (FTL830) which is intended directly for the purpose of water treatment. There were realizing the equilibrium batch adsorption experiments with three different model amino acids - arginine (Arg), phenylalanine (Phe) and aspartic acid (Asp). There was investigated the efficiency of removing amino acid depending on the solution temperature and pH. Results of the adsorption experiments have shown that the temperature affects the adsorption efficiency. Adsorption is essentially described as an exothermic process but the adsorption of Arg and Phe from an aqueous solution to GAC occurs more efficiently at higher temperatures. It means that the adsorption is the endothermic process. In the case of Arg adsorption, the temperature was found to influence adsorption efficiency less than...

This dissertation thesis is concerned with developing a mesoscopic model for sin- gle crystalline shape-memory alloys including thermo-dynamically consistent thermo- mechanical coupling - here the term "mesoscopic" refers to the ability of the model to capture fine spatial oscillations of the deformation gradient by means of gradient Young measures. Existence of solutions to the devised model is proved in a "phase-field-like approach" by a scale transition from a microscopic model that features a term related to the interfacial energy; this scale transition from a physically relevant model justifies the mesoscopic relaxation. Further, existence of solutions is also proved by backward- Euler time discretization which forms a conceptual numerical algorithm. Based on this conceptual algorithm a computer implementation of the model has been developed and further optimized in the rate-independent isothermal setting; some calculations using this implementation are also presented. Finally, refinements s of the analysis in the convex case as well as a limit of the phase-field-like approach in this case are exposed, too.

Title: Stochastic dynamics and energetics of biomolecular systems Author: Artem Ryabov Department: Department of Macromolecular Physics Supervisor: prof. RNDr. Petr Chvosta, CSc., Department of Macromolecular Physics Abstract: The thesis comprises exactly solvable models from non-equilibrium statistical physics. First, we focus on a single-file diffusion, the diffusion of particles in narrow channel where particles cannot pass each other. After a brief review, we discuss open single-file systems with absorbing boundaries. Emphasis is put on an interplay of absorption process at the boundaries and inter-particle entropic repulsion and how these two aspects affect the dynam- ics of a given tagged particle. A starting point of the discussions is the exact distribution for the particle displacement derived by order-statistics argu- ments. The second part of the thesis is devoted to stochastic thermodynam- ics. In particular, we present an exactly solvable model, which describes a Brownian particle diffusing in a time-dependent anharmonic potential. The potential has a harmonic component with a time-dependent force constant and a time-independent repulsive logarithmic barrier at the origin. For a particular choice of the driving protocol, the exact work characteristic func- tion is obtained. An asymptotic analysis of...

While the formalism of isolated horizons is known for some time, only quite recently the near horizon solution of Einstein's equations has been found in the Bondi-like coordinates by Krishnan in 2012. In this framework, the space-time is regarded as the characteristic initial value problem with the initial data given on the horizon and another null hypersurface. It is not clear, however, what ini- tial data reproduce the simplest physically relevant black hole solution, namely that of Kerr-Newman which describes stationary, axisymmetric black hole with charge. Moreover, Krishnan's construction employs the non-twisting null geodesic congruence and the tetrad which is parallelly propagated along this congruence. While the existence of such tetrad can be easily established in general, its explicit form can be very difficult to find and, in fact it has not been provided for the Kerr-Newman metric. The goal of this thesis was to fill this gap and provide a full description of the Kerr-Newman metric in the framework of isolated horizons. In the theoretical part of the thesis we review the spinor and Newman-Penrose formalism, basic geometry of isolated horizons and then present our results. Thesis is complemented by several appendices.

We study nonlinear stability of steady state solutions of partial differential equations governing the thermomechanical evolution of viscoelastic fluids; materials that exhibit both viscous as well as elastic response when undergoing deformation. It is well-known that thermodynamical concepts can be gainfully exploited in the construction of Lya- punov functionals for nonlinear stability analysis of spatially homogeneous equilibrium rest states in thermodynamically closed systems. We show that the thermodynamically oriented approach can be utilized in the nonlinear stability analysis of spatially inhomo- geneous non-equilibrium steady states in thermodynamically open systems as well. The thesis consists of two parts. In the first part, we revisit the classical construction of Lyapunov functionals in thermodynamically closed systems and we apply the nonlinear stability theory to compressible heat-conducting viscoelastic fluids modeled by a multi- scale, as well as a purely macroscopic approach. In the second part, we focus on two special instances of thermodynamically open systems. First, we show that the spatially inhomogeneous non-equilibrium steady state of an incompressible heat-conducting vis- coelastic fluid, which occupies a mechanically isolated vessel with walls kept at spatially non-uniform...

Sequence-specific interactions between proteins and nucleic acids play an essential role in the cell biology. While several molecular mechanisms contributing to the binding speci- ficity have been identified empirically, no general protein-DNA recognition code has been described to date. In this thesis, I explore selected characteristics of protein-DNA inter- actions using computational methods. First, the pairwise interactions between the basic biomolecular building blocks-amino acids and nucleotides-are investigated. It is shown that several statistically enriched, biologically relevant interaction motifs correspond to the most energetically favorable configurations of the respective binding partners. In ad- dition, a relationship between the physico-chemical properties of the amino acid residues found at the protein-DNA interface and the local geometric features of the DNA helix is presented. Next, the applicability of molecular dynamics-based setups to the description of binding equilibria in protein-DNA systems is investigated. Discrepancies are observed between the description offered by the computer simulations and experimental results, as well as between the results obtained using two molecular mechanical force fields. Finally, the more general evolutionary aspects of protein organization...

The main result of the thesis is the derivation of quantum phenomenological gravi- tational dynamics from the thermodynamics of local causal diamonds. By taking into account logarithmic corrections to entropy implied by quantum gravity effects, we derive new gravitational equations of motion which incorporate quantum corrections. The re- sulting theory appears to be a direct generalisation of the classical unimodular gravity instead of the general relativity. Upon obtaining the equations, we discuss their prop- erties and possible implications. As by-products, we also present a novel derivation of the Einstein equations from the thermodynamics of causal diamonds and a derivation of the logarithmic corrections to black hole entropy from the existence of minimal re- solvable area. Apart from the new results, we also provide an extensive review of the thermodynamics of local causal horizons. 1

Touto prácou chcem uvažovať a vytvoriť svet, kde Energia - základná a univerzálna sila - determinuje celkovú infraštruktúru globálnych aktivít a vzťahov. Dielo predkladá dokufiktívny príbeh budúcnosti postavenej na premise, že planetárny ekosystém tvorí jednu energetickú entitu, ktorá podlieha termodynamickým zákonom, nezničiteľnosti energie a jej transformácie z mechanickej na tepelnú. Taktiež ustanovuje, že všetci aktéri, ľudskí i neľudskí, majú na tento systém energetický dopad. V spoločenskom kontexte je každému garantovaný základný energetický príjem - 10000kJ na deň - a všetky ich aktivity sú cenené na základe ich energetického prínosu a nie ich monetárnej prestíže. Vizuálny jazyk diela je postavený na juxtapozícií obrazu spoločnosti Energetickej Spravodlivosti a špekulatívneho archeologického výskum prevedeného na území súčasnej komunálnej záhrady z pohľadu utopického status quo budúcnosti. Práve toto napätie medzi realitov a fikciou vyjednáva a navrhuje možnosti nastolenia takejto budúcnosti. Mojím zámerom je predostrieť sugestívny obraz globálneho poriadku, ktorý nie je len utopický ale i inšpiratívny a v zásade dosiahnuteľný a úsiliahodný.