in English Ondřej Kincl 21 May 2020 Rolling turbine is a small hydraulic turbine invented by Doc. Ing. Miroslav Sedláček CSc. in 1998. This turbine is bladeless, exhibits various interesting behaviour and operates on the basis of a yet unknown hydraulic principle. This thesis attempts to find an explanation using incompressible Navier- Stokes equations. We will introduce the concept of drag inversion - the idea that fluid force in rolling turbines is a positive feedback to the motion itself. This is explained in a simplified model using analytical methods. These results are then verified in a numerical simulation.

Environmental and energy issues have stimulated renewed interest in utilizing both water and methanol as reagents and reaction mediums. Our current interest is to evaluate the scope of group nine organometallics and establish thermodynamic parameters for their reactivity in aqueous solvent. A comprehensive thermodynamic database for a wide scope of organo-rhodium transformations in a range of reaction media including benzene, water, and methanol has been well established by our group. Aqueous solutions of rhodium porphyrin have been determined to manifest an exceptional range of substrate reactions with carbon monoxide, dihydrogen, olefins, methanol and aldehydes. This study will focus on expansion of the thermodynamic database to all the group nine metals, particularly the iridium porphyrin systems in both water and methanol. Substrate reactivity and development of new mechanistic strategies for the conversion of carbon monoxide, alkanes, and alkenes to organic oxygenates are central objectives. Water/Methanol soluble porphyrin iridium complexes including iridium tetrakis(p-sulfonatophenyl)porphyrin ((TSPP)Ir) and iridium tetrakis(3,5-sulfonatomesityl)porphyrin ((TMPS)Ir) derivatives can be prepared by sulfonation of tetra phenyl porphyrin (H2TPP) and tetra mesityl porphyrin (H2TMP). The reactivity of dihydrogen with aqueous solutions of iridium(III) tetrakis(p-sulfonatophenyl)porphyrin ((TSPP)Ir(III)) complexes produce equilibrium distributions between six iridium species including iridium hydride ([(TSPP)Ir-D(D2O)]-4), iridium(I) ([(TSPP)IrI(D2O)]-5), and iridium (II) dimer ([(TSPP)IrII(D2O)]2-8) complexes. Each of these types of iridium porphyrin species including Ir(I), Ir(II), Ir(III), Ir-H, and Ir-OH function as precursors for a range of organometallic substrate reactions. A primary objective is to define the quantitative relationships pertaining to the distribution of species in aqueous solution as a function of the dihydrogen and hydrogen ion concentrations through direct measurement of five equilibrium constants along with free energy changes of coordinated water and free energy changes of reactions of dihydrogen in water. Reactivity, kinetics and evaluation of equilibrium thermodynamics, including the reactions of iridium hydroxide and methoxide with olefins to produce beta-hydroxyalkyl and beta-methoxyalkyl complexes, reactions of iridium hydride and olefins to produce iridium alkyl complexes, and reactions of iridium hydride with carbon monoxide to produce iridium formyl [Ir-CHO] complexes are also objectives of this research. Another research goal is the design and synthesis of diporphyrin ligands that form dimetal complexes capable of preorganizing transition states for substrate reactions that involve two metal centers. Dirhodium dimetalloradical complexes are observed to manifest large rate increases over mono-metalloradical activation reactions of hydrogen, methane, and other small molecule substrates. In this study, synthesis of diporphyrin (bisporphyrin) ligands and other ligands which will permit dimetallo complexes like anti-aromatic [14]annulene and low steric porphine ligands will be also be examined. / Chemistry

We have explored correlations between the measured efficiency of the RNAi process and several computed signatures that characterize equilibrium secondary structure of the participating mRNA, siRNA, and their complexes. A previously published data set of 609 experimental points was used for the analysis. While virtually no correlation with the computed structural signatures are observed for individual data points, several clear trends emerge when the data is averaged over 10 bins of N ~ 60 data points per bin. The strongest trend is a positive linear (r² = 0.87) correlation between ln(remaining mRNA) and ΔG_ms, the combined free energy cost of unraveling the siRNA and creating the break in the mRNA secondary structure at the complementary target strand region. At the same time, the free energy change ΔG_total of the entire process mRNA + siRNA → (mRNA – siRNA)_complex is not correlated with RNAi efficiency, even after averaging. These general findings appear to be robust to details of the computational protocols. The correlation between computed ΔG_ms and experimentally observed RNAi efficiency can be used to enhance the ability of a machine learning algorithm based on a support vector machine (SVM) to predict effective siRNA sequences for a given target mRNA. Specifically, we observe modest, 3 to 7%, but consistent improvement in the positive predictive value (PPV) when the SVM training set is pre- or post-filtered according to a ΔG_ms threshold. / Master of Science

In this research, a first-principles, non-equilibrium thermodynamic-ensemble approach applicable across all temporal and spatial scales is developed based on steepest-entropy-ascent quantum thermodynamics (SEAQT). The SEAQT framework provides an equation of motion consisting of both reversible mechanical dynamics and irreversible relaxation dynamics, which is able to describe the evolution of any state of any system, equilibrium or non-equilibrium. Its key feature is that the irreversible dynamics is based on a gradient dynamics in system state space instead of the microscopic mechanics of more traditional approaches. System energy eigenstructure and density operator (or ensemble probability distribution) describe the system and system thermodynamic state, respectively. Extensive properties (i.e., energy, entropy, and particle number) play a key role in formulating the equation of motion and in describing non-equilibrium state evolutions. All the concepts involved in this framework (i.e., eigentstructure, density operator, and extensive properties) are well defined at all temporal and spatial scales leading to the extremely broad applicability of SEAQT. The focus of the present research is that of developing non-equilibrium thermodynamic models based specifically on the irreversible part of the equation of motion of SEAQT and applying these to the study of pure relaxation processes of systems in non-equilibrium states undergoing chemical reactions and heat and mass diffusion. As part of the theoretical investigation, the new concept of hypo-equilibrium state is introduced and developed. It is able to describe any non-equilibrium state going through a pure relaxation process and is a generalization of the concept of stable equilibrium of equilibrium thermodynamics to the non-equilibrium realm. Using the concept of hypo-equilibrium state, it is shown that non-equilibrium intensive properties can be fundamentally defined throughout the relaxation process. The definition of non-equilibrium intensive properties also relies on various ensemble descriptions of system state. In this research, three SEAQT ensemble descriptions, i.e., the canonical, grand canonical, and isothermal-isobaric, are derived corresponding, respectively, to the definition of temperature, chemical potential, and pressure. To computationally and not just theoretically permit the application of the SEAQT framework across all scales, a density of states method is developed, which is applicable to solving the SEAQT equation of motion for all types of non-equilibrium relaxation processes. In addition, a heterogeneous multiscale method (HMM) algorithm is also applied to extend the application of the SEAQT framework to multiscale modeling. Applications of this framework are given for systems involving chemical kinetics, the heat and mass diffusion of indistinguishable particles, power cycles, and the complex, coupled reaction-diffusion pathways of a solid oxide fuel cell (SOFC) cathode. / Ph. D.

Intrinsic quantum Thermodynamics (IQT) is a theory that unifies thermodynamics and quantum mechanics into a single theory. Its mathematical framework, steepest-entropy-ascent quantum thermodynamics (SEAQT), can be used to model and describe the non-equilibrium phenomenon of diffusion based on the principle of steepest-entropy ascent. The research presented in this dissertation demonstrates the capability of this framework to model and describe diffusion at atomistic levels and is used here to develop a non-equilibrium-based model for an isolated system in which He3 diffuses in He4. The model developed is able to predict the non-equilibrium and equilibrium characteristics of diffusion as well as capture the differences in behavior of fermions (He3) and bosons (He4). The SEAQT framework is also used to develop the transient and steady-state model for an open system in which oxygen diffuses through a tin anode. The two forms of the SEAQT equation of motion are used. The first, which only involves a dissipation term, is applied to the state evolution of the isolated system as its state relaxes from some initial non-equilibrium state to stable equilibrium. The second form, the so-called extended SEAQT equation of motion, is applied to the transient state evolution of an open system undergoing a dissipative process as well mass-interactions with two mass reservoirs. In this case, the state of the system relaxes from some initial transient state to steady state. Model predictions show that the non-equilibrium thermodynamic path that the isolated system takes significantly alters the diffusion data from that of the equilibrium-based models for isolated atomistic-level systems found in literature. Nonetheless, the SEAQT equilibrium predications for He3 and He4 capture the same trends as those found in the literature providing a point of validation for the SEAQT framework. As to the SEAQT results for the open system, there is no data in the literature with which to compare since the results presented here are completely original to this work. / Ph. D.

Thermodynamic analysis of solid oxide cells Petr Vágner The thesis deals with continuum thermodynamic modeling and analysis of phe- nomena in solid oxide electrochemical cells. A general description of the evo- lution of charged mixtures using partial mass densities, momentum density, entropy density, electric induction, magnetic field, polarization, and magnetiza- tion based on the GENERIC framework is formulated. The formulation is used to recover the Landau-Lifshitz magnetization relaxation model, the Single Re- laxation Time model for dielectrics, and the generalized Poisson-Nernst-Planck model. The latter model is consequently linked to the second part, where a novel double layer model of an yttria-stabilized zirconia interface is formulated within non-equilibrium thermodynamics. The model is solved for numerically in the time domain, and cyclic voltammetry of the system is analyzed. The last part of the thesis demonstrates the limits of Exergy Analysis on a simple solid oxide hydrogen fuel cell model with non-isothermal boundary. It is demon- strated that the minimization of entropy production does not necessarily lead to the maximization of the electric power for certain optimization scenarios. The thesis consists of a compilation of published and unpublished results of the author.

A theoretical model describing the motion of a small, fast rare gas atom as it passes over a liquid surface is developed and discussed in detail. A key feature of the model is its reliance on coarse-grained capillary wave and local mode descriptions of the liquid surface. Mathematically, the model is constructed with several concepts from probability and stochastic analysis. The model makes predictions that are quantitative agreement with neon-liquid surface scattering data collected by other research groups. These predictions include the dominance of single, rather than multiple, neon-liquid surface collision dynamics, an average of 60 % energy transfer from a neon atom upon colliding with a non-metallic surface, and an average of 25 % energy transfer upon colliding with a metallic surface. In addition to this work, two other investigations into the gas-liquid interface are discussed. The results of an experimental investigation into the thermodynamics of a gas flux through an aqueous surface are presented, and it is shown that a nitrous oxide flux is mostly due to the presence of a temperature gradient in the gas-liquid interface. Evidence for a reaction between a carbon dioxide flux and an ammonia monolayer on an aqueous surface to produce ammonium carbamate is also found. The second of these is an investigation into the mechanism of bromine production from deliquesced sodium bromide aerosol in the presence of ozone, and involves a sensitivity and uncertainty analysis of the computer aerosol kinetics model MAGIC. It is shown that under dark, non-photolytic conditions, bromine production can be accounted for almost exclusively by a reaction between gas-phase ozone and surface-bound bromide ions. Under photolytic conditions, bromine production instead involves a complicated interplay between various gas-phase and aqueous-phase reactions.

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.

La démarche de conception et de sûreté du réacteur ASTRID, démonstrateur de Réacteur à Neutrons Rapides refroidi au Sodium, implique la modélisation de scénarios d’accidents graves qui font intervenir une fusion du cœur du réacteur. L’objectif de la thèse, en soutien à cette modélisation, est de contribuer à l’identification des processus susceptibles de faire bifurquer un scénario d’accident grave. Deux phases d’un scénario sont traitées pour cela. Tout d’abord, le début d’une séquence de perte de débit primaire non protégée est analysé à l’aide d’un critère analytique développé pendant la thèse, visant à prédire la bifurcation de la décroissance du débit vers un état stabilisé ou bien vers un état instable, menant à la dégradation du cœur. Ce nouveau critère, qui présente l’intérêt de tenir compte de l’effet de l’évolution de la puissance sur la stabilité du débit, est vérifié à l’aide d’un outil de calcul dédié aux accidents de perte de débit non protégés. Dans un second temps, les processus prépondérants impliqués dans une vaporisation de combustible liquide suivie d’une détente de sa vapeur, consécutives à une excursion de puissance accidentelle, sont identifiés via une analyse dimensionnelle. En reprenant les résultats de cette analyse, un outil de calcul est par la suite développé, dont l’objet est de déterminer l’énergie mécanique transmise à la cuve du réacteur lors de la détente. La question du transfert thermique entre la vapeur de combustible se détendant et le caloporteur est particulièrement étudiée. Cet outil est validé via une comparaison à des résultats expérimentaux et à des résultats de calculs issus d’un autre code. Des études paramétriques permettent enfin de quantifier la variabilité des résultats due au choix de modélisation et aux incertitudes sur les données physiques employées. / Severe accidents’ modeling is required for the design and safety analysis of ASTRID, a Generation IV Sodium-cooled Fast Reactor under development in France. This thesis aims at contributing to identify the driving processes of ASTRID’s severe accidents scenarios. First, a stability criterion is developed to analyze the beginning of an unprotected loss of flow accident. This stability criterion assesses whether the decreasing flow is stable or unstable, leading to the core disassembly. This criterion also considers power variations during the loss of flow, which former stability criteria do not take into account. Then, the driving processes of a transient involving a fuel vaporisation followed by its vapor expansion are identified using a dimensional analysis. The simplifications justified by this dimensional analysis are considered further to develop a numerical tool that computes the mechanical energy transmitted to the core vessel in case of fuel vaporisation. The thermal exchange between the expanding fuel vapor and the sodium coolant is especially analyzed. The tool is validated by comparing its results to experimental measures and to another tool’s computations. In the end, parametric studies are done in order to assess the tool computations’ variability induced by physical uncertainties or modeling options.

There is a continuing interest in the subject of arene carbonylation, especially in strong acids and environmentally-benign alternatives are sought to HF/BF3 and to AlCl3 as conversion agents. Ionic liquids offer a powerful solvent for useful conversion agents such as aluminum chloride. The ILs permit AlCl3 to be used at lower HCl partial pressures than with other solvents. The superior reactivity demonstrated by acidic, chloroaluminate ILs is probably due to their enhanced solvation power for HCl and CO. Addition of HCl gas increased reactivity of the system by forming Brnsted acids, and toluene carbonylation is a Brnsted demanding reaction. It was found that reaction is stoichiometric in Al species and only intrinsically acidic ILs are active for toluene carbonylation, therefore it was possible to correlate observed conversion with predicted amounts of Lewis + Brnsted acids. Molecular modeling provided information about the different species present in these ILs and predicted 1H NMR, and 27Al NMR spectrum. Predictions suggested that three types of HCl species are present; and these predictions were confirmed using data of 13C-labeled acetone and its 13C-NMR spectra. These data showed that only one of the three types of HCl in the IL were super acidic. Reactivity towards arene formylation can be tuned by adjusting the ligands R and R in the organic cation and by changing the anion. This reactivity tuning can be exploited in a process where high acidity is required for the conversion of substrate but where separation of product from IL is facilitated by low acidity.