Humic acids and humates are principal components of humic substances major organic constituents of soil, peat, coal and water around the world. I was involved in research into molecular dynamics simulations of interactions of quartz surfaces with aqueous solutions of ions and small organic molecules representing basic building blocks of larger biomolecules and functional groups of organic matter. We studied interactions of molecules with surfaces for a set of surface charge densities corresponding to the experimentally or environmentally relevant ranges of pH values employing molecular mechanics, molecular dynamics and ab initio techniques. Simulated quartz surfaces covered the range of surface charge densities 0.00, -0.03, -0.06 and -0.12 C-m-2, approximately corresponding to pH values 4.5, 7.5, 9.5 and 11. As model molecules, benzoic acid, phenol, o-salicylic acid and their conjugated bases were chosen. My task was to prepare topologies and parametric models of selected organic matter basic building blocks organic molecules. I focused on studying interactions of these molecules in an aqueous environment with mineral surface quartz. The aim was to process simulation results and analyse conformations of the adsorption complexes and their thermodynamic properties such as interaction energies, free energies and adsorption geometries.

The thesis is devoted to study of continuum mechanics and thermodynamics and the related mathematical analysis. It consists of four self-contained chapters dealing with different aspects. The first chapter focuses on peridynamics, a non-local theory of continuum mechanics, and its relation to conventional local theory of Cauchy-Green elasticity. Similar compar- isons has been used for proving consistency and for determining some of the material coefficients in peridynamics, provided the material parameters in the local theory are known. In this chapter the formula for the non-local force-flux is computed in terms of the peridynamic interaction, relating the fundamental concepts of these two theories and establishing hence a new connection, not present in the previous works. The second and third chapters are both devoted to Rate-Independent Systems (RIS) and their applications to continuum mechanics. RIS represents a suitable approximation when the internal, viscous, and thermal effects can be neglected. RIS has been proven to be useful in modeling hysteresis, phase transitions in solids, elastoplasticity, damage, or fracture in both small and large strain regimes. In the second chapter the existence of solutions to an evolutionary rate-independ- ent model of Shape Memory Alloys (SMAs) is proven. The model...