Statistical mechanics of protein complexed and condensed DNA

In this thesis I treat various biophysical questions arising in the context of complexed / ”protein-packed” DNA and DNA in confined geometries (like in viruses or toroidal DNA condensates). Using diverse theoretical methods I consider the statistical mechanics as well as the dynamics of DNA under these conditions. In the first part of the thesis (chapter 2) I derive for the first time the single molecule ”equation of state”, i.e. the force-extension relation of a looped DNA (Eq. 2.94) by using the path integral formalism. Generalizing these results I show that the presence of elastic substructures like loops or deflections caused by anchoring boundary conditions (e.g. at the AFM tip or the mica substrate) gives rise to a significant renormalization of the apparent persistence length as extracted from single molecule experiments (Eqs. 2.39 and 2.98). As I show the experimentally observed apparent persistence length reduction by a factor of 10 or more is naturally explained by this theory. In chapter 3 I theoretically consider the thermal motion of nucleosomes along a DNA template. After an extensive analysis of available experimental data and theoretical modelling of two possible mechanisms I conclude that the ”corkscrew-motion” mechanism most consistently explains this biologically important process. In chapter 4 I demonstrate that DNA-spools (architectures in which DNA circumferentially winds on a cylindrical surface, or onto itself) show a remarkable ”kinetic inertness” that protects them from tension-induced disruption on experimentally and biologically relevant timescales (cf. Fig. 4.1 and Eq. 4.18). I show that the underlying model establishes a connection between the seemingly unrelated and previously unexplained force peaks in single molecule nucleosome and DNA-toroid stretching experiments. Finally in chapter 5 I show that toroidally confined DNA (found in viruses, DNAcondensates or sperm chromatin) undergoes a transition to a twisted, highly entangled state provided that the aspect ratio of the underlying torus crosses a certain critical value (cf. Eq. 5.6 and the phase diagram in Fig. 5.4). The presented mechanism could rationalize several experimental mysteries, ranging from entangled and supercoiled toroids released from virus capsids to the unexpectedly short cholesteric pitch in the (toroidaly wound) sperm chromatin. I propose that the ”topological encapsulation” resulting from our model may have some practical implications for the gene-therapeutic DNA delivery process.

Travelling emblems of power: the Ghanaian ‘Seat of State’ /// Arbeitspapiere / Institut für Ethnologie und Afrikastudien ; 94

This paper presents a case study of the self-confident and creative fusion of European and African political symbols and rituals that is characteristic of Ghanaian statehood and nation-making. It explores the aesthetic and historical genealogy of the Ghanaian ‘Seat of State’, a throne-like stool on which the President sits when attending Parliament on important state occasions. The Seat was crafted in the early 1960s by Kofi Antubam, one of the chief ‘state artists’ during the Nkrumah regime, and incorporates symbols of Asante royal authority, European aristocratic imagery as well as Ghanaian neo-traditional emblems such as the Black Star. The discussion of the Seat of State’s political meaning is followed by some more general observations on the history of party politics and parliamentary procedure in Ghana as examples of travelling political paradigms.

Thermodynamic and mechanical properties of polymer-solvent systems

This work presents the results of theoretical and experimental characterization of thermodynamic, mechanical and transport properties in polymer solvent systems. The polymer solvent pairs considered ranged to those in which the polymer is rubbery, to those in which the initially glassy polymeric matrix is plasticized by the action of the low molecular weight species. Advanced Equation of State models have been adopted for thermodynamic modeling,along with a rigorous procedure that enables to extend their applicability to the non equilibrium, glassy region. Mass sorption kinetics had been modeled with phenomenological models and with advanced kinetic models.

Ab initio quantum mechanical investigation of structural and chemical-physical properties of selected minerals for minero-petrological, structural ceramic and biomaterial applications

The purpose of this thesis is the atomic-scale simulation of the crystal-chemical and physical (phonon, energetic) properties of some strategically important minerals for structural ceramics, biomedical and petrological applications. These properties affect the thermodynamic stability and rule the mineral-environment interface phenomena, with important economical, (bio)technological, petrological and environmental implications. The minerals of interest belong to the family of phyllosilicates (talc, pyrophyllite and muscovite) and apatite (OHAp), chosen for their importance in industrial and biomedical applications (structural ceramics) and petrophysics. In this thesis work we have applicated quantum mechanics methods, formulas and knowledge to the resolution of mineralogical problems ("Quantum Mineralogy”). The chosen theoretical approach is the Density Functional Theory (DFT), along with periodic boundary conditions to limit the portion of the mineral in analysis to the crystallographic cell and the hybrid functional B3LYP. The crystalline orbitals were simulated by linear combination of Gaussian functions (GTO). The dispersive forces, which are important for the structural determination of phyllosilicates and not properly con-sidered in pure DFT method, have been included by means of a semi-empirical correction. The phonon and the mechanical properties were also calculated. The equation of state, both in athermal conditions and in a wide temperature range, has been obtained by means of variations in the volume of the cell and quasi-harmonic approximation. Some thermo-chemical properties of the minerals (isochoric and isobaric thermal capacity) were calculated, because of their considerable applicative importance. For the first time three-dimensional charts related to these properties at different pressures and temperatures were provided. The hydroxylapatite has been studied from the standpoint of structural and phonon properties for its biotechnological role. In fact, biological apatite represents the inorganic phase of vertebrate hard tissues. Numerous carbonated (hydroxyl)apatite structures were modelled by QM to cover the broadest spectrum of possible biological structural variations to fulfil bioceramics applications.

The Effects of Privatization of State-Owned Enterprises in Poland and East Germany

The main goal of this project was to propose appropriate methods of analysing the effects of the privatisation of state-owned enterprises, methods which were then tested on a limited sample of 16 Polish and 8 German enterprises privatised in 1992. A considerable amount of information was collected relating to the six-year period 1989-1994 relating to most aspects of the companies' activities. The effects of privatisation were taken to be those changes within the enterprises which were the result of privatisation, in such areas as production, the productivity of labour and fixed assets, investments and innovations, employment and wages, economic incentives (especially for top managers), financing (internal and external sources), bad debts and economic effects (financial analysis). A second important goal was to identify the main factors which represent methodological obstacles in surveys of the effects of privatisation during a period of fundamental transformation of the entire economic system. The list of enterprises for the research was compiled in such a way as to allow for the differentiation of ownership structures of privatised firms and to permit (at least to a certain extent) the empirical verification of some hypotheses regarding the privatisation process. The enterprises selected were divided into the following three groups representing (as far as possible) various types of ownership structures or types of control: (1) enterprises control by strategic investors (domestic or foreign), (2) enterprises controlled by employees (employee-owned companies), (3) enterprises controlled by managers. Formal methods such as econometric models with varying parameters were used to separate pure privatisation effects from other factors which influence various aspects of an enterprise's working, including policies on the productivity of labour and capital, average wages, the remuneration of top managers, etc. While the group admits that their findings and conclusions cannot be treated as representative of all privatised enterprises in Poland and Germany, they found considerable convergence with their findings and those of other surveys conducted on a wider scale. The main hypotheses that were confirmed included that privatisation (especially in companies controlled by large investors and managers) leads to a significant increase in the effectiveness of these production process, growing pay differentials between different employee groups (e.g. between executives and rank-and-file employees) and between different jobs and positions within particular professional groups. They also confirmed the growing importance in incentives to top executives of incentives linked with the company's economic effects (particularly profit-related incentives), long-term incentives and the capital market.