Title: Molecular simulations of ice nucleation Author: Eva Pluhařová Department: Department of Physical and Macromolecular Chemistry Faculty of Science UK Advisor: doc. Mgr. Pavel Jungwirth, DSc., IOCB AS CR, v.v.i. Advisor's e-mail address: pavel.jungwirth@uochb.cas.cz Abstract: By means of molecular dynamics simulations we have systematically investigated homogeneous ice nucleation in neat and surface contaminated water. As models of the adsorbates we have assumed pentanol and pentanoic acid. In neat water nucleation preferentially starts in the subsurface region, which accommodates better than the bulk the volume increase associated with freezing. Homogeneous ice nucleation is affected more by alcohol than by acid. Water slabs covered by a disordered layer of pentanol exhibit negligible preference for subsurface nucleation and longer nucleation times in comparison with neat water, while nucleation times are almost unaffected by the presence of pentanoic acid and the subsurface preference is only slightly decreased. We tried to rationalize the differences between the effects of different compounds by their ability to orient water molecules and to change their mobility. The fact that adsorbates differ in the influence on homogeneous ice nucleation has important implications for the microphysics of...

Texture of igneous rocks, which includes size, shape and spatial distribution of grains, represents the final record of kinetic and mechanical processes operating during ascent and final emplacement of a magma. However, traditional geochemical approaches cannot assess and verify the physical processes of magma solidification, in particular, crystal nucleation and growth, textural coarsening, or mechanical crystal-melt interactions. In this work, I apply stereological methods to quantitatively characterize the textures and to interpret the crystallization history of granitic rocks in the Western Krušné hory/Erzgebirge and Vogtland. The Western Krušné hory/Erzgebirge granites consist of three suites: biotite granites (Kirchberg), muscovite-biotite microgranites (Walfischkopf), and topaz-zinnwaldite alkali- feldspar granites (Eibenstock), which consist of eight intrusive units and two aplite dyke sets. The entire granite sequence exhibits an extreme and nearly continuous differentiation range, but in detail the evolutionary trends of each suite are independent, and individual intrusive units are also clearly compositionally separated. The granites consist of 29-43 vol.% quartz, 20-30 vol. % plagioclase, 22-31 vol. % K-feldspar, 2-9 vol. % biotite, <2 vol. % muscovite, and minor topaz and apatite. All...

Variability of magmatic textures records a wide array of physicochemical and mechanical processes that have operated in a magma chamber during its crystallization. Here I investigate how the final textural record can quantitatively be used to decipher the magma crystallization history and internal dynamics of magma chambers. The thesis is based on a formulation of numerical models of texture formation under the activity of various crystallization processes. Numerical results are then compared to the new quantitative textural datasets derived from four distinct magmatic systems in the Bohemian Massif: (i) Fichtelgebirge-Smrčiny granite batholith; (ii) Krkonoše-Jizera plutonic complex; (iii) Kdyně mafic intrusion; (iv) České středohoří volcanic complex. Combination of the field textural studies with their interpretation via numerical crystallization models provides new implications regarding magmatic crystallization and internal dynamics of magma chamber. The most important results of this Ph.D. thesis are as follows: (i) a new method has been developed that allows the rates of nucleation and growth of crystals to be derived from quantitative textural data. The method requires using the crystallinity evolution in time as an independent constraint in order to provide unique solution. In case of the...

Title: Nucleation in complex systems Author: Jan Kulveit Institute: Institute of Physics of the Czech Academy of Sciences Supervisor: prof. Pavel Demo, Institute of Physics of the Czech Academy ofSciences, Department of Optical Materials Abstract: We studied nucleation in progressively more abstract contexts and systems, starting from classical nucleation theory and ending with nucleation in complex networks. The cases studied include impurity nucleation in a solid matrix on several alkali halide crystals, where we determined formation energies for clusters, treated as defects, starting from single impurity-vacancy dipole and small aggregates to possible configurations of larger clusters. In the next part, we turn to the study of heterogeneous nucleation. While in the usual treatment of heterogeneous nucleation the surface energy is assumed to be homogenous, we ask the question what happens if we consider the surface energy to be heteroge- neous.Utilizing umbrella sampling computer simulations we find the nucleation barrier can be significantly lowered in the presence of surface heterogeneity, even if the average surface energy is kept constant. In the last part we study influence of clustering coefficient on phase transitions in scale-free networks, using forward flux sampling (FFS). Keywords: nucleation,...

Microtubules (MTs) are highly dynamic structures essential for the spatio-temporal intracellular organization and transport, signal propagation, cell differentiation, motility and division. To perform these roles, MTs create arrangements capable of fast and precise adaptation to various signals. MTs are under the control of many factors regulating MT nucleation, stability and dynamics. Bone marrow-derived mast cells (BMMCs) are important immune system cells, which can cause serious diseases if their functions are deregulated. Although MT reorganization during BMMC activation is well established, the molecular mechanisms that control their remodelling are largely unknown. In the presented thesis we functionally characterised GIT1/βPIX signalling proteins, PAK1 kinase, and Ca2+ signalling in the regulation of MT nucleation in BMMCs and other cell types. We also elucidated the function of miltefosine (hexadecylphosphocholine), a promising candidate for the treatment of mast cell-driven diseases. We found that GIT1/βPIX signalling proteins are γ-tubulin-interacting proteins associating with centrosomes in BMMCs. MT nucleation is positively regulated by GIT1 and Ca2+ , whereas βPIX is a negative regulator of MT nucleation in BMMCs. Cytosolic Ca2+ affects γ-tubulin properties and stimulates the...

The spatio-temporal organization and dynamic behavior of microtubules accurately react to cellular needs during intracellular transport, signal transduction, growth, division, and differentiation. The cell generates centrosomal microtubules de novo with the help of γ-tubulin complexes (γTuRCs). The post-translational modifications fine-tune microtubule nucleation by targeting the proteins, interacting with γTuRCs. However, the exact signaling pathways, regulating centrosomal microtubule nucleation, remain mostly unknown. In the presented thesis, we functionally characterized protein tyrosine phosphatase SHP-1 and E3 UFM-protein ligase 1 (UFL1) with its interacting protein CDK5RAP3 (C53) in the regulation of centrosomal microtubule nucleation. We also elucidated the role of actin regulatory protein profilin 1 in this process. We found that SHP-1 formed complexes with γTuRC proteins and negatively regulated microtubule nucleation by modulating the amount of γ-tubulin/γTuRC at the centrosomes in bone marrow-derived mast cells (BMMCs). We suggested a novel mechanism with centrosomal tyrosine-phosphorylated Syk kinase, targeted by SHP-1 during Ag-induced BMMCs activation, regulating microtubules. We showed for the first time that UFL1/C53 protein complex is involved in the regulation of microtubule...

1 ABSTRACT: This study is dedicated to the study of nucleation of sulphuric acid and water, which presents the key process associated with secondary aerosol formation via gas to particle conversion. We investigated the nucleation rates, new aerosol particles formation and growth dynamics of newly nucleated particles. These processes were explored in both laboratory and field experiments. In the laboratory measurements, we explored the H2SO4 - H2O nucleation rates and growth rates of newly formed particles under well-defined conditions and we also investigated the effect of experimental conditions on particle growth dynamics. Furthermore, we proposed a model, which predicts the particle growth and accounts for condensation of H2SO4, H2O and NH3. The comparison of experimental growth rates with atmospheric ones was made and resulting implications of the chemical nature of compounds involved in the early growth of nucleated particles is also presented. To investigate the atmospheric H2SO4 - H2O nucleation and new particle formation, we analysed a two-year long dataset of particle number size distributions, obtained from a urban background station in Prague Suchdol. A special attention was given to a recently reported special feature of particle growth dynamics - a particle shrinkage following previous new...

Magmatic processes are major agents responsible for the formation and differentiation of the Earth's crust. In contrast to extensive efforts to improve understanding and utility of igneous geochemistry, physical processes of magma differentiation and solidification remain largely unclear. Large variability of igneous textures provides record of these processes and intensive parameters governing the crystallization. In this thesis, we develop quantitative methods, which allow us to better interpret igneous textures in the framework of physics of solidification. We have developed a new three-dimensional model of crystallization from one- component melt driven by homogeneous and heterogeneous nucleation and crystal growth. The predicted textures are quantitatively characterized by crystal size distributions, spatial distribution functions and parameters representing grain contact relationships. The model employs high resolution in a large volume simulation domain in order to produce statistically stable results. Our simulations, performed for various functional forms of nucleation and growth rates with respect to time, imply that (i) crystals are ordered (anti-clustered) on short length scales. This reflects that other crystals already have a finite size at the time of nucleation of younger crystal,...

The thesis deals with the processes that occur in the course of the manufacturing of rigid polyurethane-polyisocyanurate (PU-PIR) foams, their properties and technology. It deals above all with principles of foam nucleation and stability. The purpose of understanding these principles is their possible use for improving thermo-insulating properties of the material. The experimental part of the thesis studies the influence of additives and ultrasound on the PU-PIR foam properties. It has been found that low molecular weight compounds with perfluorinated chain leads to decreasing foam cell size and its lower thermal conductivity. The additives mentioned act probably on the surfactants principle by facilitating nucleation and stabilizing growing centres of bubbles. They probably form also part of blowing agents mixture inside the foam cells which cause lowering of thermal conductivity as well. Compounds with similar chemical structure have unique influence on the properties of rigid PU-PIR foams. Further research ought to be focused on cheaper modes of producing perfluorinated compounds.

MT nucleation from γ-tubulin complexes, located at centrosome, is an essential step in the formation of MT cytoskeleton. In mammalian cells, -tubulin is encoded by two genes. We functionally characterized two γ-tubulin proteins and have found that both are functionally equivalent. γ-Tubulin 2 is able to substitute for γ-tubulin 1 in MT nucleation. However, we revealed that unlike TUBG1, TUBG2 expression is downregulated in mouse preimplantation development. Mast cells represent effectors of the allergy reaction. Their activation by antigen induces number of cellular processes such as degranulation, proliferation and cytoskeleton rearrangements. The regulatory mechanisms of MT reorganization during mast cell activation are unknown. We identified new signaling proteins, GIT1 and PIX that interact with - tubulin. Depletion of GIT1 or PIX leads to changes in MT nucleation. GIT1 is phosphorylated on tyrosine and associates with γ-tubulin in a Ca2+ -dependent manner. Our data suggested a novel signaling pathway for MT rearrangement in mast cells where tyrosine kinase-activated GIT1 and βPIX work in concert with Ca2+ signaling to regulate MT nucleation. We tested the capability of GIT1 and PIX to influence -tubulin function in more cell types. We found out that GIT1/βPIX signaling proteins together...