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.

Agricultural Production and Yield Estimation: Two distinctive aspects of Brazilian Agriculture and a perspective on world food problems

Brazil has been increasing its importance in agricultural markets. The reasons are well known to be the relative abundance of land, the increasing technology used in crops, and the development of the agribusiness sector which allow for a fast response to price stimuli. The elasticity of acreage response to increases in expected return is estimated for Soybeans in a dynamic (long term) error correction model. Regarding yield patterns, a large variation in the yearly rates of growth in yield is observed, climate being probably the main source of this variation which result in ‘good’ and ‘bad’ years. In South America, special attention should be given to the El Niño and La Niña phenomena, both said to have important effects on rainfalls patterns and consequently in yield. The influence on El Niño and La Niña in historical data is examined and some ways of estimating the impact of climate on yield of Soybean and Corn markets are proposed. Possible implications of climate change may apply.

Ein Beitrag zur Modellierung und Simulation von elektromechanischen Systemen

Die in dieser Arbeit durchgeführten Untersuchungen zeigen, daß es möglich ist, komplexe thermische Systeme, unter Verwendung der thermisch-, elektrischen Analogien, mit PSpice zu simulieren. Im Mittelpunkt der Untersuchungen standen hierbei Strangkühlkörper zur Kühlung von elektronischen Bauelementen. Es konnte gezeigt werden,daß alle Wärmeübertragungsarten, (Wärmeleitung, Konvektion und Wärmestrahlung) in der Simulation berücksichtigt werden können. Für die Berechnung der Konvektion wurden verschiedene Methoden hergeleitet. Diese gelten zum einen für verschiedene Kühlkörpergeometrien, wie z.B. ebene Flächen und Kühlrippenzwischenräume, andererseits unterscheiden sie sich, je nachdem, ob freie oder erzwungene Konvektion betrachtet wird. Für die Wärmestrahlung zwischen den Kühlrippen wurden verschiedenen Berechnungsmethoden entwickelt. Für die Simulation mit PSpice wurde die Berechnung der Wärmestrahlung zwischen den Kühlrippen vereinfacht. Es konnte gezeigt werden, daß die Fehler, die durch die Vereinfachung entstehen, vernachlässigbar klein sind. Für das thermische Verhalten einer zu kühlenden Wärmequelle wurde ein allgemeines Modell entworfen. Zur Bestimmung der Modellparameter wurden verschiedene Meßverfahren entwickelt. Für eine im Fachgebiet Elektromechanik entwickelte Wärmequelle zum Test von Kühlvorrichtungen wurde mit Hilfe dieser Meßverfahren eine Parameterbestimmung durchgeführt. Die Erstellung des thermischen Modells eines Kühlkörpers für die Simulation in PSpice erfordert die Analyse der Kühlkörpergeometrie. Damit diese Analyse weitestgehend automatisiert werden kann, wurden verschiedene Algorithmen unter Matlab entwickelt. Es wurde ein Algorithmus entwickelt, der es ermöglicht, den Kühlkörper in Elementarzellen zu zerlegen, die für die Erstellung des Simulationsmodells benötigt werden. Desweiteren ist es für die Simulation notwendig zu wissen, welche der Elementarzellen am Rand des Kühlkörpers liegen, welche der Elementarzellen an einem Kühlrippenzwischenraum liegen und welche Kühlkörperkanten schräg verlaufen. Auch zur Lösung dieser Aufgaben wurden verschiedene Algorithmen entwickelt. Diese Algorithmen wurden zu einem Programm zusammengefaßt, das es gestattet, unterschiedliche Strangkühlkörper zu simulieren und die Simulationsergebnisse in Form der Temperaturverteilung auf der Montagefläche des Kühlkörpers grafisch darzustellen. Es können stationäre und transiente Simulationen durchgeführt werden. Desweiteren kann der thermische Widerstand des Kühlkörpers RthK als Funktion der Verlustleistung der Wärmequelle dargestellt werden. Zur Verifikation der Simulationsergebnisse wurden Temperaturmessungen an Kühlkörpern durchgeführt und mit den Simulationsergebnissen verglichen. Diese Vergleiche zeigen, daß die Abweichungen im Bereich der Streuung der Temperaturmessung liegen. Das hier entwickelte Verfahren zur thermischen Simulation von Strangkühlkörpern kann somit als gut bewertet werden.

Studies on arbuscular mycorrhiza (AM) in the Alentejo (Portugal) using pea mutants resistant to AM fungi as a control tool for field conditions

The utilization and management of arbuscular mycorrhiza (AM) symbiosis may improve production and sustainability of the cropping system. For this purpose, native AM fungi (AMF) were sought and tested for their efficiency to increase plant growth by enhanced P uptake and by alleviation of drought stress. Pot experiments with safflower (Carthamus tinctorius) and pea (Pisum sativum) in five soils (mostly sandy loamy Luvisols) and field experiments with peas were carried out during three years at four different sites. Host plants were grown in heated soils inoculated with AMF or the respective heat sterilized inoculum. In the case of peas, mutants resistant to AMF colonization were used as non-mycorrhizal controls. The mycorrhizal impact on yields and its components, transpiration, and P and N uptake was studied in several experiments, partly under varying P and N levels and water supply. Screening of native AMF by most probable number bioassays was not very meaningful. Soil monoliths were placed in the open to simulate field conditions. Inoculation with a native AMF mix improved grain yield, shoot and leaf growth variables as compared to control. Exposed to drought, higher soil water depletion of mycorrhizal plants resulted in a haying-off effect. The growth response to this inoculum could not be significantly reproduced in a subsequent open air pot experiment at two levels of irrigation and P fertilization, however, safflower grew better at higher P and water supply by multiples. The water use efficiency concerning biomass was improved by the AMF inoculum in the two experiments. Transpiration rates were not significantly affected by AM but as a tendency were higher in non-mycorrhizal safflower. A fundamental methodological problem in mycorrhiza field research is providing an appropriate (negative) control for the experimental factor arbuscular mycorrhiza. Soil sterilization or fungicide treatment have undesirable side effects in field and greenhouse settings. Furthermore, artificial rooting, temperature and light conditions in pot experiments may interfere with the interpretation of mycorrhiza effects. Therefore, the myc- pea mutant P2 was tested as a non-mycorrhizal control in a bioassay to evaluate AMF under field conditions in comparison to the symbiotic isogenetic wild type of var. FRISSON as a new integrative approach. However, mutant P2 is also of nod- phenotype and therefore unable to fix N2. A 3-factorial experiment was carried out in a climate chamber at high NPK fertilization to examine the two isolines under non-symbiotic and symbiotic conditions. P2 achieved the same (or higher) biomass as wild type both under good and poor water supply. However, inoculation with the AMF Glomus manihot did not improve plant growth. Differences of grain and straw yields in field trials were large (up to 80 per cent) between those isogenetic pea lines mainly due to higher P uptake under P and water limited conditions. The lacking N2 fixation in mutants was compensated for by high mineral N supply as indicated by the high N status of the pea mutant plants. This finding was corroborated by the results of a major field experiment at three sites with two levels of N fertilization. The higher N rate did not affect grain or straw yields of the non-fixing mutants. Very efficient AMF were detected in a Ferric Luvisol on pasture land as revealed by yield levels of the evaluation crop and by functional vital staining of highly colonized roots. Generally, levels of grain yield were low, at between 40 and 980 kg ha-1. An additional pot trial was carried out to elucidate the strong mycorrhizal effect in the Ferric Luvisol. A triplication of the plant equivalent field P fertilization was necessary to compensate for the mycorrhizal benefit which was with five times higher grain yield very similar to that found in the field experiment. However, the yield differences between the two isolines were not always plausible as the evaluation variable because they were also found in (small) field test trials with apparently sufficient P and N supply and in a soil of almost no AMF potential. This similarly occurred for pea lines of var. SPARKLE and its non-fixing mycorrhizal (E135) and non-symbiotic (R25) isomutants, which were tested in order to exclude experimentally undesirable benefits by N2 fixation. In contrast to var. FRISSON, SPARKLE was not a suitable variety for Mediterranean field conditions. This raises suspicion putative genetic defects other than symbiotic ones may be effective under field conditions, which would conflict with the concept of an appropriate control. It was concluded that AMF resistant plants may help to overcome fundamental problems of present research on arbuscular mycorrhiza, but may create new ones.

Landschaftsperspektiven der Nutzer

Die vorliegende Arbeit macht Vorschläge zur Einbindung der Öffentlichkeit in Planungsbestrebungen vor Ort, wobei vor allem Methoden empirischer Sozialforschung und deren Anwendbarkeit in landschaftsplanerischen Vorhaben näher betrachtet werden. Hiermit finden insbesondere Wertezuweisungen durch die Bürger stärkere Berücksichtigung. Es wird angenommen, dass, um eine zukunftsweisende Landschaftsplanung zu etablieren, Planer und Fachleute lernen müssen, wie die lokale Bevölkerung ihre Umwelt wahrnimmt und empfindet und welche Ideen sie für die zukünftige Entwicklung der Landschaft haben. Als empirische Grundlage werden Fallstudien aus Bad Soden am Taunus, Hamburg-Wilhelmsburg und Kassel-Rothenditmold präsentiert und verglichen. Rothenditmold und Wilhelmsburg zeichnen sich durch hohe Einwohneranteile mit Migrationshintergrund aus, weisen relativ hohe Arbeitslosenquoten auf und sind als soziale Brennpunkte bekannt – zumindest für Außenstehende. Beide Stadtteile versuchen ihr Image aufzuwerten. In Wilhelmsburg wird dieses Vorhaben in die großräumigen Veränderungen eingebunden, die von verschiedenen Hamburger Großprojekten ausstrahlen. In Rothenditmold ist vor allem Eigeninitiative durch den Stadtteil selbst gefragt. In Bad Soden gibt es ebenfalls viele Menschen mit ausländischen Wurzeln. Sie gehören allerdings mehrheitlich der gesellschaftlichen Mittel- und Oberschicht an. Bad Soden verfügt über ein insgesamt positives Image, das aller kulturellen Veränderungen zum Trotz beibehalten werden soll. Entsprechende Initiativen gehen hier ebenfalls von der Gemeinde selbst aus. An allen Standorten hat es drastische Landschaftsveränderungen und speziell deren Erscheinung gegeben. Bad Soden und Wilhelmsburg haben dabei Teile ihres vormals ländlichen Charakters zu bewahren, während in Rothenditmold vor allem Zeugnisse aus der Zeit der Industrialisierung erhalten sind und den Ort prägen. Die Landschaften haben jeweils ihre einzigartigen Erscheinungen. Zumindest Teile der Landschaften ermöglichen eine Identifikation, sind attraktiv und liefern gute Erholungsmöglichkeiten. Um diese Qualitäten zu bewahren, müssen sie entsprechend gepflegt und weiter entwickelt werden. Dazu sind die Interessen und Wünsche der Bewohner zu ermitteln und in Planungen einzuarbeiten. Die Arbeit strebt einen Beitrag zur Lebensraumentwicklung für und mit Menschen an, die mittels ausgewählter Methoden der empirischen Sozialforschung eingebunden werden. Dabei wird gezeigt, dass die vorgestellten und erprobten Methoden sinnvoll in Projekte der Landschaftsplanung eingebunden werden können. Mit ihnen können ergänzende Erkenntnisse zum jeweiligen Landschaftsraum gewonnen werden, da sie helfen, die kollektive Wahrnehmung der Landschaft durch die Bevölkerung zu erfassen, um sie anschließend in Planungsentwürfe einbinden zu können. Mit der Untersuchung wird in den drei vorgestellten Fallstudien exemplarisch erfasst, welche Elemente der Landschaft für die Bewohner von besonderer Bedeutung sind. Darüber hinaus lernen Planer, welche Methoden zur Ermittlung emotionaler Landschaftswerte verfügbar sind und auf welcher Ebene der Landschaftsplanung sowie bei welchen Zielgruppen sie eingesetzt werden können. Durch die Verknüpfung landschaftsplanerischer Erfassungsmethoden mit Methoden der empirischen Sozialwissenschaft (Fragebogen, Interviews, „Spaziergangsinterviews“, gemeinsame Erarbeitung von Projekten bis zur Umsetzung) sowie der Möglichkeit zur Rückkoppelung landschaftsplaneri-scher Entwürfe mit der Bevölkerung wird eine Optimierung dieser Entwürfe sowohl im Sinne der Planer als auch im Sinne der Bürger erreicht. Zusätzlich wird die Wahrnehmung teilnehmender Bevölkerung für ihre Umwelt geschärft, da sie aufgefordert wird, sich mit ihrer Lebensumgebung bewusst auseinander zu setzen. Die Ergebnisse dieser Untersuchung sind Beitrag und Beleg zu der Annahme, dass ergänzende Methoden in der Landschaftsplanung zur stärkeren Interessenberücksichtigung der von Planung betroffenen Menschen benötigt werden. Zudem zeigen die Studien auf, wie man dem planungsethischen Anspruch, die Öffentlichkeit einzubeziehen, näher kommt. Resultat sind eine bessere Bewertung und Akzeptanz der Planungen und das nicht nur aus landschaftsplanerisch-fachlicher Sicht. Landschaftsplaner sollten ein Interesse daran haben, dass ihre Entwürfe ernst genommen und akzeptiert werden. Das schaffen sie, wenn sie der Bevölkerung nicht etwas aufplanen, sondern ihnen entsprechende Einflussmöglichkeiten bieten und Landschaft mit ihnen gemeinsam entwickeln.

Decision‐Making in Public Good Dilemmas: Theory and Agent‐Based Simulation

In many real world contexts individuals find themselves in situations where they have to decide between options of behaviour that serve a collective purpose or behaviours which satisfy one’s private interests, ignoring the collective. In some cases the underlying social dilemma (Dawes, 1980) is solved and we observe collective action (Olson, 1965). In others social mobilisation is unsuccessful. The central topic of social dilemma research is the identification and understanding of mechanisms which yield to the observed cooperation and therefore resolve the social dilemma. It is the purpose of this thesis to contribute this research field for the case of public good dilemmas. To do so, existing work that is relevant to this problem domain is reviewed and a set of mandatory requirements is derived which guide theory and method development of the thesis. In particular, the thesis focusses on dynamic processes of social mobilisation which can foster or inhibit collective action. The basic understanding is that success or failure of the required process of social mobilisation is determined by heterogeneous individual preferences of the members of a providing group, the social structure in which the acting individuals are contained, and the embedding of the individuals in economic, political, biophysical, or other external contexts. To account for these aspects and for the involved dynamics the methodical approach of the thesis is computer simulation, in particular agent-based modelling and simulation of social systems. Particularly conductive are agent models which ground the simulation of human behaviour in suitable psychological theories of action. The thesis develops the action theory HAPPenInGS (Heterogeneous Agents Providing Public Goods) and demonstrates its embedding into different agent-based simulations. The thesis substantiates the particular added value of the methodical approach: Starting out from a theory of individual behaviour, in simulations the emergence of collective patterns of behaviour becomes observable. In addition, the underlying collective dynamics may be scrutinised and assessed by scenario analysis. The results of such experiments reveal insights on processes of social mobilisation which go beyond classical empirical approaches and yield policy recommendations on promising intervention measures in particular.

Caimanes and the Water - Infinite Legal Struggles about a Finite Good

This report is intended to shed more light on the ongoing water struggle in Caimanes, a small urban area in the central northern area of Chile, neighbouring Latin America’s biggest tailings dam. Undoubtedly, the water in Caimanes is running out and the conflict between the opponents of the dam and its owner, a multinational copper enterprise, is getting more and more attention by the national and also international media. In the discussion a judgment of the Chilean Supreme Court from last October plays a central role, because it is said to have granted the people from Caimanes their right to water. After a short introduction with some details about Camaines and the tailings from the dam El Mauro, the key points of this judgment shall be outlined. The final part of the report is dedicated to various institutional problems of the Chilean resources law and policy that can become virulent for the water supply and the environmental well-being of many other urban areas in the industrialized north of Chile.