Protein Folding Simulations: Confinement, External Fields and Sequence Design

The present Thesis looks at the problem of protein folding using Monte Carlo and Langevin simulations, three topics in protein folding have been studied: 1) the effect of confining potential barriers, 2) the effect of a static external field and 3) the design of amino acid sequences which fold in a short time and which have a stable native state (global minimum). Regarding the first topic, we studied the confinement of a small protein of 16 amino acids known as 1NJ0 (PDB code) which has a beta-sheet structure as a native state. The confinement of proteins occurs frequently in the cell environment. Some molecules called Chaperones, present in the cytoplasm, capture the unfolded proteins in their interior and avoid the formation of aggregates and misfolded proteins. This mechanism of confinement mediated by Chaperones is not yet well understood. In the present work we considered two kinds of potential barriers which try to mimic the confinement induced by a Chaperon molecule. The first kind of potential was a purely repulsive barrier whose only effect is to create a cavity where the protein folds up correctly. The second kind of potential was a barrier which includes both attractive and repulsive effects. We performed Wang-Landau simulations to calculate the thermodynamical properties of 1NJ0. From the free energy landscape plot we found that 1NJ0 has two intermediate states in the bulk (without confinement) which are clearly separated from the native and the unfolded states. For the case of the purely repulsive barrier we found that the intermediate states get closer to each other in the free energy landscape plot and eventually they collapse into a single intermediate state. The unfolded state is more compact, compared to that in the bulk, as the size of the barrier decreases. For an attractive barrier modifications of the states (native, unfolded and intermediates) are observed depending on the degree of attraction between the protein and the walls of the barrier. The strength of the attraction is measured by the parameter $\epsilon$. A purely repulsive barrier is obtained for $\epsilon=0$ and a purely attractive barrier for $\epsilon=1$. The states are changed slightly for magnitudes of the attraction up to $\epsilon=0.4$. The disappearance of the intermediate states of 1NJ0 is already observed for $\epsilon =0.6$. A very high attractive barrier ($\epsilon \sim 1.0$) produces a completely denatured state. In the second topic of this Thesis we dealt with the interaction of a protein with an external electric field. We demonstrated by means of computer simulations, specifically by using the Wang-Landau algorithm, that the folded, unfolded, and intermediate states can be modified by means of a field. We have found that an external field can induce several modifications in the thermodynamics of these states: for relatively low magnitudes of the field ($<2.06 \times 10^8$ V/m) no major changes in the states are observed. However, for higher magnitudes than ($6.19 \times 10^8$ V/m) one observes the appearance of a new native state which exhibits a helix-like structure. In contrast, the original native state is a $\beta$-sheet structure. In the new native state all the dipoles in the backbone structure are aligned parallel to the field. The design of amino acid sequences constitutes the third topic of the present work. We have tested the Rate of Convergence criterion proposed by D. Gridnev and M. Garcia ({\it work unpublished}). We applied it to the study of off-lattice models. The Rate of Convergence criterion is used to decide if a certain sequence will fold up correctly within a relatively short time. Before the present work, the common way to decide if a certain sequence was a good/bad folder was by performing the whole dynamics until the sequence got its native state (if it existed), or by studying the curvature of the potential energy surface. There are some difficulties in the last two approaches. In the first approach, performing the complete dynamics for hundreds of sequences is a rather challenging task because of the CPU time needed. In the second approach, calculating the curvature of the potential energy surface is possible only for very smooth surfaces. The Rate of Convergence criterion seems to avoid the previous difficulties. With this criterion one does not need to perform the complete dynamics to find the good and bad sequences. Also, the criterion does not depend on the kind of force field used and therefore it can be used even for very rugged energy surfaces.

High-Speed Semiconductor Lasers based on Low-Dimensional Active Materials for Optical Telecommunication

The scope of this work is the fundamental growth, tailoring and characterization of self-organized indium arsenide quantum dots (QDs) and their exploitation as active region for diode lasers emitting in the 1.55 µm range. This wavelength regime is especially interesting for long-haul telecommunications as optical fibers made from silica glass have the lowest optical absorption. Molecular Beam Epitaxy is utilized as fabrication technique for the quantum dots and laser structures. The results presented in this thesis depict the first experimental work for which this reactor was used at the University of Kassel. Most research in the field of self-organized quantum dots has been conducted in the InAs/GaAs material system. It can be seen as the model system of self-organized quantum dots, but is not suitable for the targeted emission wavelength. Light emission from this system at 1.55 µm is hard to accomplish. To stay as close as possible to existing processing technology, the In(AlGa)As/InP (100) material system is deployed. Depending on the epitaxial growth technique and growth parameters this system has the drawback of producing a wide range of nano species besides quantum dots. Best known are the elongated quantum dashes (QDash). Such structures are preferentially formed, if InAs is deposited on InP. This is related to the low lattice-mismatch of 3.2 %, which is less than half of the value in the InAs/GaAs system. The task of creating round-shaped and uniform QDs is rendered more complex considering exchange effects of arsenic and phosphorus as well as anisotropic effects on the surface that do not need to be dealt with in the InAs/GaAs case. While QDash structures haven been studied fundamentally as well as in laser structures, they do not represent the theoretical ideal case of a zero-dimensional material. Creating round-shaped quantum dots on the InP(100) substrate remains a challenging task. Details of the self-organization process are still unknown and the formation of the QDs is not fully understood yet. In the course of the experimental work a novel growth concept was discovered and analyzed that eases the fabrication of QDs. It is based on different crystal growth and ad-atom diffusion processes under supply of different modifications of the arsenic atmosphere in the MBE reactor. The reactor is equipped with special valved cracking effusion cells for arsenic and phosphorus. It represents an all-solid source configuration that does not rely on toxic gas supply. The cracking effusion cell are able to create different species of arsenic and phosphorus. This constitutes the basis of the growth concept. With this method round-shaped QD ensembles with superior optical properties and record-low photoluminescence linewidth were achieved. By systematically varying the growth parameters and working out a detailed analysis of the experimental data a range of parameter values, for which the formation of QDs is favored, was found. A qualitative explanation of the formation characteristics based on the surface migration of In ad-atoms is developed. Such tailored QDs are finally implemented as active region in a self-designed diode laser structure. A basic characterization of the static and temperature-dependent properties was carried out. The QD lasers exceed a reference quantum well laser in terms of inversion conditions and temperature-dependent characteristics. Pulsed output powers of several hundred milli watt were measured at room temperature. In particular, the lasers feature a high modal gain that even allowed cw-emission at room temperature of a processed ridge wave guide device as short as 340 µm with output powers of 17 mW. Modulation experiments performed at the Israel Institute of Technology (Technion) showed a complex behavior of the QDs in the laser cavity. Despite the fact that the laser structure is not fully optimized for a high-speed device, data transmission capabilities of 15 Gb/s combined with low noise were achieved. To the best of the author`s knowledge, this renders the lasers the fastest QD devices operating at 1.55 µm. The thesis starts with an introductory chapter that pronounces the advantages of optical fiber communication in general. Chapter 2 will introduce the fundamental knowledge that is necessary to understand the importance of the active region`s dimensions for the performance of a diode laser. The novel growth concept and its experimental analysis are presented in chapter 3. Chapter 4 finally contains the work on diode lasers.

Parameter identification of structural dynamic models by inverse statistical analysis

Auf dem Gebiet der Strukturdynamik sind computergestützte Modellvalidierungstechniken inzwischen weit verbreitet. Dabei werden experimentelle Modaldaten, um ein numerisches Modell für weitere Analysen zu korrigieren. Gleichwohl repräsentiert das validierte Modell nur das dynamische Verhalten der getesteten Struktur. In der Realität gibt es wiederum viele Faktoren, die zwangsläufig zu variierenden Ergebnissen von Modaltests führen werden: Sich verändernde Umgebungsbedingungen während eines Tests, leicht unterschiedliche Testaufbauten, ein Test an einer nominell gleichen aber anderen Struktur (z.B. aus der Serienfertigung), etc. Damit eine stochastische Simulation durchgeführt werden kann, muss eine Reihe von Annahmen für die verwendeten Zufallsvariablengetroffen werden. Folglich bedarf es einer inversen Methode, die es ermöglicht ein stochastisches Modell aus experimentellen Modaldaten zu identifizieren. Die Arbeit beschreibt die Entwicklung eines parameter-basierten Ansatzes, um stochastische Simulationsmodelle auf dem Gebiet der Strukturdynamik zu identifizieren. Die entwickelte Methode beruht auf Sensitivitäten erster Ordnung, mit denen Parametermittelwerte und Kovarianzen des numerischen Modells aus stochastischen experimentellen Modaldaten bestimmt werden können.

Strategische Erfolgsfaktoren für ein kosten-risiko-optimales Public Debt Management - Organisatorische und inhaltliche Parameter im internationalen Vergleich

Aus den im Rahmen dieser Forschungsarbeit empirisch gewonnenen Erkenntnissen werden Gestaltungsempfehlungen für das Public Debt Management abgeleitet. Diese zeigen, dass ein wirtschaftliches Public Debt Management nicht ein ausschließlich kostenminimierendes (sparsames), sondern ein kosten-risiko-optimales Public Debt Management mit effektiven internen und externen Überwachungsinstrumenten und wirksamer externer Finanzkontrolle sein muss.